@article{kleczkowski_magnesium_2021,
	title = {Magnesium {Signaling} in {Plants}},
	volume = {22},
	issn = {1422-0067},
	url = {https://www.mdpi.com/1422-0067/22/3/1159},
	doi = {10/gjd692},
	abstract = {Free magnesium (Mg2+) is a signal of the adenylate (ATP+ADP+AMP) status in the cells. It results from the equilibrium of adenylate kinase (AK), which uses Mg-chelated and Mg-free adenylates as substrates in both directions of its reaction. The AK-mediated primary control of intracellular [Mg2+] is finely interwoven with the operation of membrane-bound adenylate- and Mg2+-translocators, which in a given compartment control the supply of free adenylates and Mg2+ for the AK-mediated equilibration. As a result, [Mg2+] itself varies both between and within the compartments, depending on their energetic status and environmental clues. Other key nucleotide-utilizing/producing enzymes (e.g., nucleoside diphosphate kinase) may also be involved in fine-tuning of the intracellular [Mg2+]. Changes in [Mg2+] regulate activities of myriads of Mg-utilizing/requiring enzymes, affecting metabolism under both normal and stress conditions, and impacting photosynthetic performance, respiration, phloem loading and other processes. In compartments controlled by AK equilibrium (cytosol, chloroplasts, mitochondria, nucleus), the intracellular [Mg2+] can be calculated from total adenylate contents, based on the dependence of the apparent equilibrium constant of AK on [Mg2+]. Magnesium signaling, reflecting cellular adenylate status, is likely widespread in all eukaryotic and prokaryotic organisms, due simply to the omnipresent nature of AK and to its involvement in adenylate equilibration.},
	language = {en},
	number = {3},
	urldate = {2021-06-03},
	journal = {International Journal of Molecular Sciences},
	author = {Kleczkowski, Leszek A. and Igamberdiev, Abir U.},
	month = jan,
	year = {2021},
	pages = {1159},
}

Free magnesium (Mg2+) is a signal of the adenylate (ATP+ADP+AMP) status in the cells. It results from the equilibrium of adenylate kinase (AK), which uses Mg-chelated and Mg-free adenylates as substrates in both directions of its reaction. The AK-mediated primary control of intracellular [Mg2+] is finely interwoven with the operation of membrane-bound adenylate- and Mg2+-translocators, which in a given compartment control the supply of free adenylates and Mg2+ for the AK-mediated equilibration. As a result, [Mg2+] itself varies both between and within the compartments, depending on their energetic status and environmental clues. Other key nucleotide-utilizing/producing enzymes (e.g., nucleoside diphosphate kinase) may also be involved in fine-tuning of the intracellular [Mg2+]. Changes in [Mg2+] regulate activities of myriads of Mg-utilizing/requiring enzymes, affecting metabolism under both normal and stress conditions, and impacting photosynthetic performance, respiration, phloem loading and other processes. In compartments controlled by AK equilibrium (cytosol, chloroplasts, mitochondria, nucleus), the intracellular [Mg2+] can be calculated from total adenylate contents, based on the dependence of the apparent equilibrium constant of AK on [Mg2+]. Magnesium signaling, reflecting cellular adenylate status, is likely widespread in all eukaryotic and prokaryotic organisms, due simply to the omnipresent nature of AK and to its involvement in adenylate equilibration.

@article{igamberdiev_pyrophosphate_2021,
	title = {Pyrophosphate as an alternative energy currency in plants},
	volume = {478},
	issn = {0264-6021},
	url = {https://doi.org/10.1042/BCJ20200940},
	doi = {10.1042/BCJ20200940},
	abstract = {In the conditions of [Mg2+] elevation that occur, in particular, under low oxygen stress and are the consequence of the decrease in [ATP] and increase in [ADP] and [AMP], pyrophosphate (PPi) can function as an alternative energy currency in plant cells. In addition to its production by various metabolic pathways, PPi can be synthesized in the combined reactions of pyruvate, phosphate dikinase (PPDK) and pyruvate kinase (PK) by so-called PK/PPDK substrate cycle, and in the reverse reaction of membrane-bound H+-pyrophosphatase, which uses the energy of electrochemical gradients generated on tonoplast and plasma membrane. The PPi can then be consumed in its active forms of MgPPi and Mg2PPi by PPi-utilizing enzymes, which require an elevated [Mg2+]. This ensures a continuous operation of glycolysis in the conditions of suppressed ATP synthesis, keeping metabolism energy efficient and less dependent on ATP.},
	language = {en},
	number = {8},
	urldate = {2021-06-03},
	journal = {Biochemical Journal},
	author = {Igamberdiev, Abir U. and Kleczkowski, Leszek A.},
	month = apr,
	year = {2021},
	pages = {1515--1524},
}

In the conditions of [Mg2+] elevation that occur, in particular, under low oxygen stress and are the consequence of the decrease in [ATP] and increase in [ADP] and [AMP], pyrophosphate (PPi) can function as an alternative energy currency in plant cells. In addition to its production by various metabolic pathways, PPi can be synthesized in the combined reactions of pyruvate, phosphate dikinase (PPDK) and pyruvate kinase (PK) by so-called PK/PPDK substrate cycle, and in the reverse reaction of membrane-bound H+-pyrophosphatase, which uses the energy of electrochemical gradients generated on tonoplast and plasma membrane. The PPi can then be consumed in its active forms of MgPPi and Mg2PPi by PPi-utilizing enzymes, which require an elevated [Mg2+]. This ensures a continuous operation of glycolysis in the conditions of suppressed ATP synthesis, keeping metabolism energy efficient and less dependent on ATP.

@article{kleczkowski_optimization_2020,
	title = {Optimization of nucleotide sugar supply for polysaccharide formation via thermodynamic buffering},
	volume = {477},
	issn = {0264-6021, 1470-8728},
	url = {https://portlandpress.com/biochemj/article/477/2/341/221922/Optimization-of-nucleotide-sugar-supply-for},
	doi = {10.1042/BCJ20190807},
	abstract = {Plant polysaccharides (cellulose, hemicellulose, pectin, starch) are either direct (i.e. leaf starch) or indirect products of photosynthesis, and they belong to the most abundant organic compounds in nature. Although each of these polymers is made by a specific enzymatic machinery, frequently in different cell locations, details of their synthesis share certain common features. Thus, the production of these polysaccharides is preceded by the formation of nucleotide sugars catalyzed by fully reversible reactions of various enzymes, mostly pyrophosphorylases. These ‘buffering’ enzymes are, generally, quite active and operate close to equilibrium. The nucleotide sugars are then used as substrates for irreversible reactions of various polysaccharide-synthesizing glycosyltransferases (‘engine’ enzymes), e.g. plastidial starch synthases, or plasma membrane-bound cellulose synthase and callose synthase, or ER/Golgi-located variety of glycosyltransferases forming hemicellulose and pectin backbones. Alternatively, the irreversible step might also be provided by a carrier transporting a given immediate precursor across a membrane. Here, we argue that local equilibria, established within metabolic pathways and cycles resulting in polysaccharide production, bring stability to the system via the arrangement of a flexible supply of nucleotide sugars. This metabolic system is itself under control of adenylate kinase and nucleoside-diphosphate kinase, which determine the availability of nucleotides (adenylates, uridylates, guanylates and cytidylates) and Mg2+, the latter serving as a feedback signal from the nucleotide metabolome. Under these conditions, the supply of nucleotide sugars to engine enzymes is stable and constant, and the metabolic process becomes optimized in its load and consumption, making the system steady and self-regulated.},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Biochemical Journal},
	author = {Kleczkowski, Leszek A. and Igamberdiev, Abir U.},
	month = jan,
	year = {2020},
	pages = {341--356},
}

Plant polysaccharides (cellulose, hemicellulose, pectin, starch) are either direct (i.e. leaf starch) or indirect products of photosynthesis, and they belong to the most abundant organic compounds in nature. Although each of these polymers is made by a specific enzymatic machinery, frequently in different cell locations, details of their synthesis share certain common features. Thus, the production of these polysaccharides is preceded by the formation of nucleotide sugars catalyzed by fully reversible reactions of various enzymes, mostly pyrophosphorylases. These ‘buffering’ enzymes are, generally, quite active and operate close to equilibrium. The nucleotide sugars are then used as substrates for irreversible reactions of various polysaccharide-synthesizing glycosyltransferases (‘engine’ enzymes), e.g. plastidial starch synthases, or plasma membrane-bound cellulose synthase and callose synthase, or ER/Golgi-located variety of glycosyltransferases forming hemicellulose and pectin backbones. Alternatively, the irreversible step might also be provided by a carrier transporting a given immediate precursor across a membrane. Here, we argue that local equilibria, established within metabolic pathways and cycles resulting in polysaccharide production, bring stability to the system via the arrangement of a flexible supply of nucleotide sugars. This metabolic system is itself under control of adenylate kinase and nucleoside-diphosphate kinase, which determine the availability of nucleotides (adenylates, uridylates, guanylates and cytidylates) and Mg2+, the latter serving as a feedback signal from the nucleotide metabolome. Under these conditions, the supply of nucleotide sugars to engine enzymes is stable and constant, and the metabolic process becomes optimized in its load and consumption, making the system steady and self-regulated.

@article{igamberdiev_thermodynamic_2019,
	title = {Thermodynamic buffering, stable non-equilibrium and establishment of the computable structure of plant metabolism},
	volume = {146},
	issn = {00796107},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0079610718302037},
	doi = {10.1016/j.pbiomolbio.2018.11.005},
	language = {en},
	urldate = {2021-06-07},
	journal = {Progress in Biophysics and Molecular Biology},
	author = {Igamberdiev, Abir U. and Kleczkowski, Leszek A.},
	month = sep,
	year = {2019},
	pages = {23--36},
}

@article{decker_udp-sugar_2019,
	title = {{UDP}-{Sugar} {Producing} {Pyrophosphorylases}: {Distinct} and {Essential} {Enzymes} {With} {Overlapping} {Substrate} {Specificities}, {Providing} de novo {Precursors} for {Glycosylation} {Reactions}},
	volume = {9},
	issn = {1664-462X},
	shorttitle = {{UDP}-{Sugar} {Producing} {Pyrophosphorylases}},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2018.01822/full},
	doi = {10/gjdwdm},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Decker, Daniel and Kleczkowski, Leszek A.},
	month = jan,
	year = {2019},
	pages = {1822},
}

@article{igamberdiev_glycerate_2018,
	title = {The {Glycerate} and {Phosphorylated} {Pathways} of {Serine} {Synthesis} in {Plants}: {The} {Branches} of {Plant} {Glycolysis} {Linking} {Carbon} and {Nitrogen} {Metabolism}},
	volume = {9},
	issn = {1664-462X},
	shorttitle = {The {Glycerate} and {Phosphorylated} {Pathways} of {Serine} {Synthesis} in {Plants}},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2018.00318/full},
	doi = {10.3389/fpls.2018.00318},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Igamberdiev, Abir U. and Kleczkowski, Leszek A.},
	month = mar,
	year = {2018},
	pages = {318},
}

@article{decker_structure-activity_2018,
	title = {The structure-activity relationship of the salicylimide derived inhibitors of {UDP}-sugar producing pyrophosphorylases},
	issn = {1559-2324},
	url = {https://www.tandfonline.com/doi/full/10.1080/15592324.2018.1507406},
	doi = {10/gjdv5h},
	language = {en},
	urldate = {2021-06-07},
	journal = {Plant Signaling \& Behavior},
	author = {Decker, Daniel and Öberg, Christopher and Kleczkowski, Leszek A.},
	month = aug,
	year = {2018},
	pages = {1--3},
}

@article{lesniewska_defense_2017,
	title = {Defense {Responses} in {Aspen} with {Altered} {Pectin} {Methylesterase} {Activity} {Reveal} the {Hormonal} {Inducers} of {Tyloses}},
	volume = {173},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/173/2/1409-1419/6116100},
	doi = {10.1104/pp.16.01443},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Leśniewska, Joanna and Öhman, David and Krzesłowska, Magdalena and Kushwah, Sunita and Barciszewska-Pacak, Maria and Kleczkowski, Leszek A. and Sundberg, Björn and Moritz, Thomas and Mellerowicz, Ewa J.},
	month = feb,
	year = {2017},
	pages = {1409--1419},
}

@article{decker_identification_2017,
	title = {Identification and characterization of inhibitors of {UDP}-glucose and {UDP}-sugar pyrophosphorylases for \textit{in vivo} studies},
	volume = {90},
	issn = {09607412},
	url = {http://doi.wiley.com/10.1111/tpj.13531},
	doi = {10.1111/tpj.13531},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {The Plant Journal},
	author = {Decker, Daniel and Öberg, Christopher and Kleczkowski, Leszek A.},
	month = jun,
	year = {2017},
	pages = {1093--1107},
}

@article{decker_substrate_2017,
	title = {Substrate {Specificity} and {Inhibitor} {Sensitivity} of {Plant} {UDP}-{Sugar} {Producing} {Pyrophosphorylases}},
	volume = {8},
	issn = {1664-462X},
	url = {http://journal.frontiersin.org/article/10.3389/fpls.2017.01610/full},
	doi = {10/gcjkns},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Decker, Daniel and Kleczkowski, Leszek A.},
	month = sep,
	year = {2017},
	pages = {1610},
}

@article{keech_redox_2017,
	title = {The redox control of photorespiration: from biochemical and physiological aspects to biotechnological considerations},
	volume = {40},
	issn = {0140-7791, 1365-3040},
	shorttitle = {The redox control of photorespiration},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.12713},
	doi = {10.1111/pce.12713},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Plant, Cell \& Environment},
	author = {Keech, Olivier and Gardeström, Per and Kleczkowski, Leszek A. and Rouhier, Nicolas},
	month = apr,
	year = {2017},
	pages = {553--569},
}

@article{kunz_hexokinase_2015,
	title = {Hexokinase 1 is required for glucose-induced repression of {bZIP63}, {At5g22920}, and {BT2} in {Arabidopsis}},
	volume = {6},
	issn = {1664-462X (Print) 1664-462X (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26236323},
	doi = {10/f3n6kb},
	abstract = {Simple sugars, like glucose (Glc) and sucrose (Suc), act as signals to modulate the expression of hundreds of genes in plants. Frequently, however, it remains unclear whether this regulation is induced by the sugars themselves or by their derivatives generated in the course of carbohydrate (CH) metabolism. In the present study, we tested the relevance of different CH metabolism and allocation pathways affecting expression patterns of five selected sugar-responsive genes (bZIP63, At5g22920, BT2, MGD2, and TPS9) in Arabidopsis thaliana. In general, the expression followed diurnal changes in the overall sugar availability. However, under steady growth conditions, this response was hardly impaired in the mutants for CH metabolizing/ transporting proteins (adg1, sex1, sus1-4, sus5/6, and tpt2), including also hexokinase1 (HXK1) loss- and gain-of-function plants-gin2.1 and oe3.2, respectively. In addition, transgenic plants carrying pbZIP63::GUS showed no changes in reporter-gene-expression when grown on sugar under steady-state conditions. In contrast, short-term treatments of agar-grown seedlings with 1\% Glc or Suc induced pbZIP63::GUS repression, which became even more apparent in seedlings grown in liquid media. Subsequent analyses of liquid-grown gin2.1 and oe3.2 seedlings revealed that Glc -dependent regulation of the five selected genes was not affected in gin2.1, whereas it was enhanced in oe3.2 plants for bZIP63, At5g22920, and BT2. The sugar treatments had no effect on ATP/ADP ratio, suggesting that changes in gene expression were not linked to cellular energy status. Overall, the data suggest that HXK1 does not act as Glc sensor controlling bZIP63, At5g22920, and BT2 expression, but it is nevertheless required for the production of a downstream metabolic signal regulating their expression.},
	urldate = {2021-06-07},
	journal = {Front Plant Sci},
	author = {Kunz, S. and Gardestrom, P. and Pesquet, E. and Kleczkowski, L. A.},
	month = jul,
	year = {2015},
	note = {Edition: 2015/08/04},
	keywords = {At5g22920 expression, BT2 expression, bZIP63 expression, diurnal regulation of expression, glucose sensing, hexokinase, sugar regulation of gene expression},
	pages = {525},
}

Simple sugars, like glucose (Glc) and sucrose (Suc), act as signals to modulate the expression of hundreds of genes in plants. Frequently, however, it remains unclear whether this regulation is induced by the sugars themselves or by their derivatives generated in the course of carbohydrate (CH) metabolism. In the present study, we tested the relevance of different CH metabolism and allocation pathways affecting expression patterns of five selected sugar-responsive genes (bZIP63, At5g22920, BT2, MGD2, and TPS9) in Arabidopsis thaliana. In general, the expression followed diurnal changes in the overall sugar availability. However, under steady growth conditions, this response was hardly impaired in the mutants for CH metabolizing/ transporting proteins (adg1, sex1, sus1-4, sus5/6, and tpt2), including also hexokinase1 (HXK1) loss- and gain-of-function plants-gin2.1 and oe3.2, respectively. In addition, transgenic plants carrying pbZIP63::GUS showed no changes in reporter-gene-expression when grown on sugar under steady-state conditions. In contrast, short-term treatments of agar-grown seedlings with 1% Glc or Suc induced pbZIP63::GUS repression, which became even more apparent in seedlings grown in liquid media. Subsequent analyses of liquid-grown gin2.1 and oe3.2 seedlings revealed that Glc -dependent regulation of the five selected genes was not affected in gin2.1, whereas it was enhanced in oe3.2 plants for bZIP63, At5g22920, and BT2. The sugar treatments had no effect on ATP/ADP ratio, suggesting that changes in gene expression were not linked to cellular energy status. Overall, the data suggest that HXK1 does not act as Glc sensor controlling bZIP63, At5g22920, and BT2 expression, but it is nevertheless required for the production of a downstream metabolic signal regulating their expression.

@article{igamberdiev_optimization_2015,
	title = {Optimization of {ATP} synthase function in mitochondria and chloroplasts via the adenylate kinase equilibrium},
	volume = {6},
	issn = {1664-462X (Print) 1664-462X (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25674099},
	doi = {10.3389/fpls.2015.00010},
	abstract = {The bulk of ATP synthesis in plants is performed by ATP synthase, the main bioenergetics engine of cells, operating both in mitochondria and in chloroplasts. The reaction mechanism of ATP synthase has been studied in detail for over half a century; however, its optimal performance depends also on the steady delivery of ATP synthase substrates and the removal of its products. For mitochondrial ATP synthase, we analyze here the provision of stable conditions for (i) the supply of ADP and Mg(2+), supported by adenylate kinase (AK) equilibrium in the intermembrane space, (ii) the supply of phosphate via membrane transporter in symport with H(+), and (iii) the conditions of outflow of ATP by adenylate transporter carrying out the exchange of free adenylates. We also show that, in chloroplasts, AK equilibrates adenylates and governs Mg(2+) contents in the stroma, optimizing ATP synthase and Calvin cycle operation, and affecting the import of inorganic phosphate in exchange with triose phosphates. It is argued that chemiosmosis is not the sole component of ATP synthase performance, which also depends on AK-mediated equilibrium of adenylates and Mg(2+), adenylate transport, and phosphate release and supply.},
	urldate = {2021-06-07},
	journal = {Front Plant Sci},
	author = {Igamberdiev, A. U. and Kleczkowski, L. A.},
	month = jan,
	year = {2015},
	note = {Edition: 2015/02/13},
	keywords = {ATP synthase, adenylate kinase, chemiosmosis, chloroplasts, magnesium, mitochondria},
	pages = {10},
}

The bulk of ATP synthesis in plants is performed by ATP synthase, the main bioenergetics engine of cells, operating both in mitochondria and in chloroplasts. The reaction mechanism of ATP synthase has been studied in detail for over half a century; however, its optimal performance depends also on the steady delivery of ATP synthase substrates and the removal of its products. For mitochondrial ATP synthase, we analyze here the provision of stable conditions for (i) the supply of ADP and Mg(2+), supported by adenylate kinase (AK) equilibrium in the intermembrane space, (ii) the supply of phosphate via membrane transporter in symport with H(+), and (iii) the conditions of outflow of ATP by adenylate transporter carrying out the exchange of free adenylates. We also show that, in chloroplasts, AK equilibrates adenylates and governs Mg(2+) contents in the stroma, optimizing ATP synthase and Calvin cycle operation, and affecting the import of inorganic phosphate in exchange with triose phosphates. It is argued that chemiosmosis is not the sole component of ATP synthase performance, which also depends on AK-mediated equilibrium of adenylates and Mg(2+), adenylate transport, and phosphate release and supply.

@article{kleczkowski_sugar_2015,
	title = {Sugar {Activation} for {Production} of {Nucleotide} {Sugars} as {Substrates} for {Glycosyltransferases} in {Plants}},
	volume = {62},
	issn = {1344-7882, 1880-7291},
	url = {https://www.jstage.jst.go.jp/article/jag/62/2/62_jag.JAG-2015_003/_article},
	doi = {10.5458/jag.jag.JAG-2015_003},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Journal of Applied Glycoscience},
	author = {Kleczkowski, Leszek A. and Decker, Daniel},
	year = {2015},
	pages = {25--36},
}

@article{decker_luminescence-based_2014,
	title = {A luminescence-based assay of {UDP}-sugar producing pyrophosphorylases},
	volume = {6},
	issn = {1759-9660, 1759-9679},
	url = {http://xlink.rsc.org/?DOI=C3AY41811A},
	doi = {10/f2z926},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Anal. Methods},
	author = {Decker, Daniel and Lindberg, Stina and Eriksson, Jonas and Kleczkowski, Leszek A.},
	year = {2014},
	pages = {57--61},
}

@article{kunz_functional_2014,
	title = {Functional {Dissection} of {Sugar} {Signals} {Affecting} {Gene} {Expression} in {Arabidopsis} thaliana},
	volume = {9},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0100312},
	doi = {10/f23qnk},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Kunz, Sabine and Pesquet, Edouard and Kleczkowski, Leszek A.},
	editor = {Wu, Keqiang},
	month = jun,
	year = {2014},
	pages = {e100312},
}

@article{decker_substrate_2012,
	title = {Substrate kinetics and substrate effects on the quaternary structure of barley {UDP}-glucose pyrophosphorylase},
	volume = {79},
	issn = {00319422},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0031942212001471},
	doi = {10/f2z82t},
	language = {en},
	urldate = {2021-06-08},
	journal = {Phytochemistry},
	author = {Decker, Daniel and Meng, Meng and Gornicka, Agnieszka and Hofer, Anders and Wilczynska, Malgorzata and Kleczkowski, Leszek A.},
	month = jul,
	year = {2012},
	pages = {39--45},
}

@article{kleczkowski_common_2011,
	title = {A common structural blueprint for plant {UDP}-sugar-producing pyrophosphorylases},
	volume = {439},
	issn = {0264-6021, 1470-8728},
	url = {https://portlandpress.com/biochemj/article/439/3/375/45641/A-common-structural-blueprint-for-plant},
	doi = {10/dm53gk},
	abstract = {Plant pyrophosphorylases that are capable of producing UDP-sugars, key precursors for glycosylation reactions, include UDP-glucose pyrophosphorylases (A- and B-type), UDP-sugar pyrophosphorylase and UDP-N-acetylglucosamine pyrophosphorylase. Although not sharing significant homology at the amino acid sequence level, the proteins share a common structural blueprint. Their structures are characterized by the presence of the Rossmann fold in the central (catalytic) domain linked to enzyme-specific N-terminal and C-terminal domains, which may play regulatory functions. Molecular mobility between these domains plays an important role in substrate binding and catalysis. Evolutionary relationships and the role of (de)oligomerization as a regulatory mechanism are discussed.},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Biochemical Journal},
	author = {Kleczkowski, Leszek A. and Geisler, Matt and Fitzek, Elisabeth and Wilczynska, Malgorzata},
	month = nov,
	year = {2011},
	pages = {375--381},
}

Plant pyrophosphorylases that are capable of producing UDP-sugars, key precursors for glycosylation reactions, include UDP-glucose pyrophosphorylases (A- and B-type), UDP-sugar pyrophosphorylase and UDP-N-acetylglucosamine pyrophosphorylase. Although not sharing significant homology at the amino acid sequence level, the proteins share a common structural blueprint. Their structures are characterized by the presence of the Rossmann fold in the central (catalytic) domain linked to enzyme-specific N-terminal and C-terminal domains, which may play regulatory functions. Molecular mobility between these domains plays an important role in substrate binding and catalysis. Evolutionary relationships and the role of (de)oligomerization as a regulatory mechanism are discussed.

@article{igamberdiev_magnesium_2011,
	title = {Magnesium and cell energetics in plants under anoxia},
	volume = {437},
	issn = {0264-6021, 1470-8728},
	url = {https://portlandpress.com/biochemj/article/437/3/373/45860/Magnesium-and-cell-energetics-in-plants-under},
	doi = {10/b5db7d},
	abstract = {Stress conditions (e.g. anoxia) frequently result in a decrease of [ATP] and in an increase of [ADP] and [AMP], with a concomitant increase of [Mg2+] and other cations, e.g. Ca2+. The elevation of [Mg2+] is linked to the shift in the apparent equilibrium of adenylate kinase. As a result, enzymes that use Mg2+ as a cofactor are activated, Ca2+ activates calcium-dependent signalling pathways, and PPi can serve as an alternative energy source in its active form of MgPPi or Mg2PPi. Under anoxic conditions in plants, an important source of PPi may come as a result of combined reactions of PK (pyruvate kinase) and PPDK (pyruvate, phosphate dikinase). The PPi formed in the PPDK/PK cycle ignites glycolysis in conditions of low [ATP] by involving PPi-dependent reactions. This saves ATP and makes metabolism under stress conditions more energy efficient.},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Biochemical Journal},
	author = {Igamberdiev, Abir U. and Kleczkowski, Leszek A.},
	month = aug,
	year = {2011},
	pages = {373--379},
}

Stress conditions (e.g. anoxia) frequently result in a decrease of [ATP] and in an increase of [ADP] and [AMP], with a concomitant increase of [Mg2+] and other cations, e.g. Ca2+. The elevation of [Mg2+] is linked to the shift in the apparent equilibrium of adenylate kinase. As a result, enzymes that use Mg2+ as a cofactor are activated, Ca2+ activates calcium-dependent signalling pathways, and PPi can serve as an alternative energy source in its active form of MgPPi or Mg2PPi. Under anoxic conditions in plants, an important source of PPi may come as a result of combined reactions of PK (pyruvate kinase) and PPDK (pyruvate, phosphate dikinase). The PPi formed in the PPDK/PK cycle ignites glycolysis in conditions of low [ATP] by involving PPi-dependent reactions. This saves ATP and makes metabolism under stress conditions more energy efficient.

@article{igamberdiev_optimization_2011,
	title = {Optimization of {CO2} fixation in photosynthetic cells via thermodynamic buffering},
	volume = {103},
	issn = {03032647},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0303264710001747},
	doi = {10/d9xqmp},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Biosystems},
	author = {Igamberdiev, Abir U. and Kleczkowski, Leszek A.},
	month = feb,
	year = {2011},
	pages = {224--229},
}

@article{granado-yela_temporal_2011,
	title = {Temporal matching among diurnal photosynthetic patterns within the crown of the evergreen sclerophyll {Olea} europaea {L}.: {Within}-crown photosynthetic patterns in {O}. europaea},
	volume = {34},
	issn = {01407791},
	shorttitle = {Temporal matching among diurnal photosynthetic patterns within the crown of the evergreen sclerophyll {Olea} europaea {L}.},
	url = {http://doi.wiley.com/10.1111/j.1365-3040.2011.02283.x},
	doi = {10/c233sd},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {Plant, Cell \& Environment},
	author = {Granado-Yela, C. and García-Verdugo, C. and Carrillo, K. and Rubio De Casas, R. and Kleczkowski, L. A. and Balaguer, L.},
	month = may,
	year = {2011},
	pages = {800--810},
}

@article{kleczkowski_udp-sugar_2011,
	title = {{UDP}-{Sugar} {Pyrophosphorylase}: {A} {New} {Old} {Mechanism} for {Sugar} {Activation}},
	volume = {156},
	issn = {1532-2548},
	shorttitle = {{UDP}-{Sugar} {Pyrophosphorylase}},
	url = {https://academic.oup.com/plphys/article/156/1/3/6111433},
	doi = {10/dd7jxj},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {Kleczkowski, Leszek A. and Decker, Daniel and Wilczynska, Malgorzata},
	month = may,
	year = {2011},
	pages = {3--10},
}

@article{kleczkowski_mechanisms_2010,
	title = {Mechanisms of {UDP}-{Glucose} {Synthesis} in {Plants}},
	volume = {29},
	issn = {0735-2689, 1549-7836},
	url = {https://www.tandfonline.com/doi/full/10.1080/07352689.2010.483578},
	doi = {10/fdfr4g},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Critical Reviews in Plant Sciences},
	author = {Kleczkowski, Leszek A. and Kunz, Sabine and Wilczynska, Malgorzata},
	month = jul,
	year = {2010},
	pages = {191--203},
}

@article{jimenez_deep_2009,
	title = {Deep shade alters the acclimation response to moderate water stress in {Quercus} suber {L}.},
	volume = {82},
	issn = {0015-752X, 1464-3626},
	url = {https://academic.oup.com/forestry/article-lookup/doi/10.1093/forestry/cpp008},
	doi = {10/c83j4p},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Forestry},
	author = {Jimenez, M. D. and Pardos, M. and Puertolas, J. and Kleczkowski, L. A. and Pardos, J. A.},
	month = jul,
	year = {2009},
	pages = {285--298},
}

@article{meng_domain-specific_2009,
	title = {Domain-specific determinants of catalysis/substrate binding and the oligomerization status of barley {UDP}-glucose pyrophosphorylase},
	volume = {1794},
	issn = {15709639},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1570963909002039},
	doi = {10/fjsv4f},
	language = {en},
	number = {12},
	urldate = {2021-06-08},
	journal = {Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics},
	author = {Meng, Meng and Fitzek, Elisabeth and Gajowniczek, Agnieszka and Wilczynska, Malgorzata and Kleczkowski, Leszek A.},
	month = dec,
	year = {2009},
	pages = {1734--1742},
}

@article{igamberdiev_metabolic_2009,
	title = {Metabolic systems maintain stable non-equilibrium via thermodynamic buffering},
	volume = {31},
	issn = {02659247},
	url = {http://doi.wiley.com/10.1002/bies.200900057},
	doi = {10/csrg2d},
	language = {en},
	number = {10},
	urldate = {2021-06-08},
	journal = {BioEssays},
	author = {Igamberdiev, Abir U. and Kleczkowski, Leszek A.},
	month = oct,
	year = {2009},
	pages = {1091--1099},
}

@article{meng_udp-glucose_2009,
	title = {{UDP}-{Glucose} {Pyrophosphorylase} is not {Rate} {Limiting}, but is {Essential} in {Arabidopsis}},
	volume = {50},
	issn = {0032-0781, 1471-9053},
	url = {https://academic.oup.com/pcp/article-lookup/doi/10.1093/pcp/pcp052},
	doi = {10/cwnt2d},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {Plant and Cell Physiology},
	author = {Meng, M. and Geisler, M. and Johansson, H. and Harholt, J. and Scheller, H. V. and Mellerowicz, E. J. and Kleczkowski, L. A.},
	month = may,
	year = {2009},
	pages = {998--1011},
}

@article{timm_cytosolic_2008,
	title = {A {Cytosolic} {Pathway} for the {Conversion} of {Hydroxypyruvate} to {Glycerate} during {Photorespiration} in \textit{{Arabidopsis}}},
	volume = {20},
	issn = {1532-298X},
	url = {https://academic.oup.com/plcell/article/20/10/2848/6093042},
	doi = {10/cxddm5},
	abstract = {Abstract
            Deletion of any of the core enzymes of the photorespiratory cycle, one of the major pathways of plant primary metabolism, results in severe air-sensitivity of the respective mutants. The peroxisomal enzyme hydroxypyruvate reductase (HPR1) represents the only exception to this rule. This indicates the presence of extraperoxisomal reactions of photorespiratory hydroxypyruvate metabolism. We have identified a second hydroxypyruvate reductase, HPR2, and present genetic and biochemical evidence that the enzyme provides a cytosolic bypass to the photorespiratory core cycle in Arabidopsis thaliana. Deletion of HPR2 results in elevated levels of hydroxypyruvate and other metabolites in leaves. Photosynthetic gas exchange is slightly altered, especially under long-day conditions. Otherwise, the mutant closely resembles wild-type plants. The combined deletion of both HPR1 and HPR2, however, results in distinct air-sensitivity and a dramatic reduction in photosynthetic performance. These results suggest that photorespiratory metabolism is not confined to chloroplasts, peroxisomes, and mitochondria but also extends to the cytosol. The extent to which cytosolic reactions contribute to the operation of the photorespiratory cycle in varying natural environments is not yet known, but it might be dynamically regulated by the availability of NADH in the context of peroxisomal redox homeostasis.},
	language = {en},
	number = {10},
	urldate = {2021-06-10},
	journal = {The Plant Cell},
	author = {Timm, Stefan and Nunes-Nesi, Adriano and Pärnik, Tiit and Morgenthal, Katja and Wienkoop, Stefanie and Keerberg, Olav and Weckwerth, Wolfram and Kleczkowski, Leszek A. and Fernie, Alisdair R. and Bauwe, Hermann},
	month = dec,
	year = {2008},
	pages = {2848--2859},
}

Abstract Deletion of any of the core enzymes of the photorespiratory cycle, one of the major pathways of plant primary metabolism, results in severe air-sensitivity of the respective mutants. The peroxisomal enzyme hydroxypyruvate reductase (HPR1) represents the only exception to this rule. This indicates the presence of extraperoxisomal reactions of photorespiratory hydroxypyruvate metabolism. We have identified a second hydroxypyruvate reductase, HPR2, and present genetic and biochemical evidence that the enzyme provides a cytosolic bypass to the photorespiratory core cycle in Arabidopsis thaliana. Deletion of HPR2 results in elevated levels of hydroxypyruvate and other metabolites in leaves. Photosynthetic gas exchange is slightly altered, especially under long-day conditions. Otherwise, the mutant closely resembles wild-type plants. The combined deletion of both HPR1 and HPR2, however, results in distinct air-sensitivity and a dramatic reduction in photosynthetic performance. These results suggest that photorespiratory metabolism is not confined to chloroplasts, peroxisomes, and mitochondria but also extends to the cytosol. The extent to which cytosolic reactions contribute to the operation of the photorespiratory cycle in varying natural environments is not yet known, but it might be dynamically regulated by the availability of NADH in the context of peroxisomal redox homeostasis.

@article{meng_molecular_2008,
	title = {Molecular and kinetic characterization of two {UDP}-glucose pyrophosphorylases, products of distinct genes, from {Arabidopsis}},
	volume = {1784},
	issn = {15709639},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1570963908000794},
	doi = {10/bvzvzf},
	language = {en},
	number = {6},
	urldate = {2021-06-10},
	journal = {Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics},
	author = {Meng, Meng and Wilczynska, Malgorzata and Kleczkowski, Leszek A.},
	month = jun,
	year = {2008},
	pages = {967--972},
}

@article{meng_differential_2007,
	title = {Differential tissue/organ-dependent expression of two sucrose- and cold-responsive genes for {UDP}-glucose pyrophosphorylase in {Populus}},
	volume = {389},
	issn = {03781119},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0378111906007062},
	doi = {10/fn8z4c},
	language = {en},
	number = {2},
	urldate = {2021-06-10},
	journal = {Gene},
	author = {Meng, Meng and Geisler, Matt and Johansson, Henrik and Mellerowicz, Ewa J. and Karpinski, Stanislaw and Kleczkowski, Leszek A.},
	month = mar,
	year = {2007},
	pages = {186--195},
}

@article{geisler_universal_2006,
	title = {A universal algorithm for genome-wide in silicio identification of biologically significant gene promoter putative cis-regulatory-elements; identification of new elements for reactive oxygen species and sucrose signaling in {Arabidopsis}},
	volume = {45},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-313X.2005.02634.x},
	doi = {10/dpnz4f},
	abstract = {Short motifs of many cis-regulatory elements (CREs) can be found in the promoters of most Arabidopsis genes, and this raises the question of how their presence can confer specific regulation. We developed a universal algorithm to test the biological significance of CREs by first identifying every Arabidopsis gene with a CRE and then statistically correlating the presence or absence of the element with the gene expression profile on multiple DNA microarrays. This algorithm was successfully verified for previously characterized abscisic acid, ethylene, sucrose and drought responsive CREs in Arabidopsis, showing that the presence of these elements indeed correlates with treatment-specific gene induction. Later, we used standard motif sampling methods to identify 128 putative motifs induced by excess light, reactive oxygen species and sucrose. Our algorithm was able to filter 20 out of 128 novel CREs which significantly correlated with gene induction by either heat, reactive oxygen species and/or sucrose. The position, orientation and sequence specificity of CREs was tested in silicio by analyzing the expression of genes with naturally occurring sequence variations. In three novel CREs the forward orientation correlated with sucrose induction and the reverse orientation with sucrose suppression. The functionality of the predicted novel CREs was experimentally confirmed using Arabidopsis cell-suspension cultures transformed with short promoter fragments or artificial promoters fused with the GUS reporter gene. Our genome-wide analysis opens up new possibilities for in silicio verification of the biological significance of newly discovered CREs, and allows for subsequent selection of such CREs for experimental studies.},
	language = {en},
	number = {3},
	urldate = {2021-06-11},
	journal = {The Plant Journal},
	author = {Geisler, Matt and Kleczkowski, Leszek A. and Karpinski, Stanislaw},
	year = {2006},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-313X.2005.02634.x},
	keywords = {DNA microarray analysis, cis-regulatory-element, hormonal signaling, promoter, reactive oxygen species, sucrose},
	pages = {384--398},
}

Short motifs of many cis-regulatory elements (CREs) can be found in the promoters of most Arabidopsis genes, and this raises the question of how their presence can confer specific regulation. We developed a universal algorithm to test the biological significance of CREs by first identifying every Arabidopsis gene with a CRE and then statistically correlating the presence or absence of the element with the gene expression profile on multiple DNA microarrays. This algorithm was successfully verified for previously characterized abscisic acid, ethylene, sucrose and drought responsive CREs in Arabidopsis, showing that the presence of these elements indeed correlates with treatment-specific gene induction. Later, we used standard motif sampling methods to identify 128 putative motifs induced by excess light, reactive oxygen species and sucrose. Our algorithm was able to filter 20 out of 128 novel CREs which significantly correlated with gene induction by either heat, reactive oxygen species and/or sucrose. The position, orientation and sequence specificity of CREs was tested in silicio by analyzing the expression of genes with naturally occurring sequence variations. In three novel CREs the forward orientation correlated with sucrose induction and the reverse orientation with sucrose suppression. The functionality of the predicted novel CREs was experimentally confirmed using Arabidopsis cell-suspension cultures transformed with short promoter fragments or artificial promoters fused with the GUS reporter gene. Our genome-wide analysis opens up new possibilities for in silicio verification of the biological significance of newly discovered CREs, and allows for subsequent selection of such CREs for experimental studies.

@article{igamberdiev_equilibration_2006,
	title = {Equilibration of adenylates in the mitochondrial intermembrane space maintains respiration and regulates cytosolic metabolism},
	volume = {57},
	issn = {0022-0957},
	doi = {10.1093/jxb/erl006},
	abstract = {Adenylate kinase (AK) uses one each of Mg-complexed and free adenylates as substrates in both directions of its reaction. It is very active in the mitochondrial intermembrane space (IMS), but is absent from the mitochondrial matrix where low [ADP] upon intensive respiration limits the respiratory rate. AK activity in the IMS is linked to ATP/ADP exchange across the inner mitochondrial membrane by using ATP (imported from the matrix) and AMP as substrates, the latter provided by apyrase and other AMP-generating reactions. The ADP formed by AK is exported to the matrix (in exchange for ATP), providing a mechanism for regeneration of ADP during respiration. From the AK equilibrium, and taking pH values characteristic of subcellular compartments, [Mg2+] in the IMS is calculated as 0.4-0.5 mM and in the cytosol as 0.2-0.3 mM, whereas the MgATP:MgADP ratio in the IMS and cytosol is 6-9 and 10-15, respectively. These represent optimal conditions for transport of adenylates (via the maintenance of an ATP(free):ADP(free) ratio close to 1) and mitochondrial respiratory rates (via the maintenance of submillimolar [ADP(free)] in the IMS). This, in turn, has important consequences for mitochondrial and cytosolic metabolism, including regulation of the protein phosphorylation rate (via changes in the MgATP:AMP(free) ratio) and allosteric regulation of mitochondrial and cytosolic enzymes. Metabolomic consequences are discussed in connection with the calculation of metabolic fluxes from subcompartmental distributions of total adenylates and Mg2+.},
	language = {English},
	number = {10},
	journal = {Journal of Experimental Botany},
	author = {Igamberdiev, Abir U. and Kleczkowski, Leszek A.},
	year = {2006},
	note = {Place: Oxford
Publisher: Oxford Univ Press
WOS:000239389700001},
	keywords = {activated protein-kinase, adenylate kinase, apyrase, atp synthase, dynamic compartmentation, energy-charge, free magnesium, glutamine-synthetase, intermembrane space, magnesium, metabolomics, mitochondrion, oxidative-phosphorylation, pisum-sativum, plant-cells, respiration, spinach-chloroplasts},
	pages = {2133--2141},
}

Adenylate kinase (AK) uses one each of Mg-complexed and free adenylates as substrates in both directions of its reaction. It is very active in the mitochondrial intermembrane space (IMS), but is absent from the mitochondrial matrix where low [ADP] upon intensive respiration limits the respiratory rate. AK activity in the IMS is linked to ATP/ADP exchange across the inner mitochondrial membrane by using ATP (imported from the matrix) and AMP as substrates, the latter provided by apyrase and other AMP-generating reactions. The ADP formed by AK is exported to the matrix (in exchange for ATP), providing a mechanism for regeneration of ADP during respiration. From the AK equilibrium, and taking pH values characteristic of subcellular compartments, [Mg2+] in the IMS is calculated as 0.4-0.5 mM and in the cytosol as 0.2-0.3 mM, whereas the MgATP:MgADP ratio in the IMS and cytosol is 6-9 and 10-15, respectively. These represent optimal conditions for transport of adenylates (via the maintenance of an ATP(free):ADP(free) ratio close to 1) and mitochondrial respiratory rates (via the maintenance of submillimolar [ADP(free)] in the IMS). This, in turn, has important consequences for mitochondrial and cytosolic metabolism, including regulation of the protein phosphorylation rate (via changes in the MgATP:AMP(free) ratio) and allosteric regulation of mitochondrial and cytosolic enzymes. Metabolomic consequences are discussed in connection with the calculation of metabolic fluxes from subcompartmental distributions of total adenylates and Mg2+.

@article{ciereszko_phosphate_2006,
	title = {Phosphate deficiency-dependent upregulation of {UDP}-glucose pyrophosphorylase genes is insensitive to {ABA} and ethylene status in {Arabidopsis} leaves},
	volume = {28},
	issn = {1861-1664},
	url = {https://doi.org/10.1007/BF02706620},
	doi = {10.1007/BF02706620},
	abstract = {The effects of inorganic phosphate (Pi) deficiency and ABA/ethylene status on expression of UDP-glucose pyrophosphorylase (UGPase) genes (Ugp), involved in sucrose/polysaccharide metabolism, were investigated. Both wild-type (wt), aba and abi mutants (ABA-deficient and -in-sensitive), etr, ein and eto (ethylene resistant and overproducing) grown on Pi-deficient and complete nutrient solution, as well as phol (Pi-deficient) mutants of Arabidopsis thaliana were used for experiments. Generally, Pi-deficiency conditions (including mannose feeding to decrease cytosolic Pi pool) resulted in an increase of Ugp expression in the leaves, under all experimental conditions. Mutant backgrounds reflecting differences in ABA or ethylene status/ sensitivity had no effect on the level of Ugp up-regulation by Pi-stress. Furthermore, feeding ABA to the leaves of wt and pho1 plants had no effect on Ugp expression, regardless of the sucrose status in the leaves. The data suggest that Pi deficiency leading to up-regulation of Ugp acts independently of ABA and ethylene status.},
	language = {en},
	number = {5},
	urldate = {2021-06-11},
	journal = {Acta Physiologiae Plantarum},
	author = {Ciereszko, Iwona and Kleczkowski, Leszek A.},
	month = oct,
	year = {2006},
	pages = {387--393},
}

The effects of inorganic phosphate (Pi) deficiency and ABA/ethylene status on expression of UDP-glucose pyrophosphorylase (UGPase) genes (Ugp), involved in sucrose/polysaccharide metabolism, were investigated. Both wild-type (wt), aba and abi mutants (ABA-deficient and -in-sensitive), etr, ein and eto (ethylene resistant and overproducing) grown on Pi-deficient and complete nutrient solution, as well as phol (Pi-deficient) mutants of Arabidopsis thaliana were used for experiments. Generally, Pi-deficiency conditions (including mannose feeding to decrease cytosolic Pi pool) resulted in an increase of Ugp expression in the leaves, under all experimental conditions. Mutant backgrounds reflecting differences in ABA or ethylene status/ sensitivity had no effect on the level of Ugp up-regulation by Pi-stress. Furthermore, feeding ABA to the leaves of wt and pho1 plants had no effect on Ugp expression, regardless of the sucrose status in the leaves. The data suggest that Pi deficiency leading to up-regulation of Ugp acts independently of ABA and ethylene status.

@article{geisler-lee_poplar_2006,
	title = {Poplar carbohydrate-active enzymes. {Gene} identification and expression analyses},
	volume = {140},
	issn = {0032-0889},
	doi = {10/bj9bkd},
	abstract = {Over 1,600 genes encoding carbohydrate-active enzymes (CAZymes) in the Populus trichocarpa (Torr.\&Gray) genome were identified based on sequence homology, annotated, and grouped into families of glycosyltransferases, glycoside hydrolases, carbohydrate esterases, polysaccharide lyases, and expansins. Poplar ( Populus spp.) had approximately 1.6 times more CAZyme genes than Arabidopsis ( Arabidopsis thaliana). Whereas most families were proportionally increased, xylan and pectin-related families were underrepresented and the GT1 family of secondary metabolite-glycosylating enzymes was overrepresented in poplar. CAZyme gene expression in poplar was analyzed using a collection of 100,000 expressed sequence tags from 17 different tissues and compared to microarray data for poplar and Arabidopsis. Expression of genes involved in pectin and hemicellulose metabolism was detected in all tissues, indicating a constant maintenance of transcripts encoding enzymes remodeling the cell wall matrix. The most abundant transcripts encoded sucrose synthases that were specifically expressed in wood-forming tissues along with cellulose synthase and homologs of KORRIGAN and ELP1. Woody tissues were the richest source of various other CAZyme transcripts, demonstrating the importance of this group of enzymes for xylogenesis. In contrast, there was little expression of genes related to starch metabolism during wood formation, consistent with the preferential flux of carbon to cell wall biosynthesis. Seasonally dormant meristems of poplar showed a high prevalence of transcripts related to starch metabolism and surprisingly retained transcripts of some cell wall synthesis enzymes. The data showed profound changes in CAZyme transcriptomes in different poplar tissues and pointed to some key differences in CAZyme genes and their regulation between herbaceous and woody plants.},
	language = {English},
	number = {3},
	journal = {Plant Physiology},
	author = {Geisler-Lee, J. and Geisler, M. and Coutinho, P. M. and Segerman, B. and Nishikubo, N. and Takahashi, J. and Aspeborg, H. and Djerbi, S. and Master, E. and Andersson-Gunneras, S. and Sundberg, B. and Karpinski, S. and Teeri, T. T. and Kleczkowski, L. A. and Henrissat, B. and Mellerowicz, E. J.},
	month = mar,
	year = {2006},
	note = {Place: Rockville
Publisher: Amer Soc Plant Biologists
WOS:000235868900014},
	keywords = {arabidopsis, callose synthase, cell-walls, cellulose, family, hybrid aspen, multiple sequence alignment, pectin methylesterases, populus, sucrose},
	pages = {946--962},
}

Over 1,600 genes encoding carbohydrate-active enzymes (CAZymes) in the Populus trichocarpa (Torr.&Gray) genome were identified based on sequence homology, annotated, and grouped into families of glycosyltransferases, glycoside hydrolases, carbohydrate esterases, polysaccharide lyases, and expansins. Poplar ( Populus spp.) had approximately 1.6 times more CAZyme genes than Arabidopsis ( Arabidopsis thaliana). Whereas most families were proportionally increased, xylan and pectin-related families were underrepresented and the GT1 family of secondary metabolite-glycosylating enzymes was overrepresented in poplar. CAZyme gene expression in poplar was analyzed using a collection of 100,000 expressed sequence tags from 17 different tissues and compared to microarray data for poplar and Arabidopsis. Expression of genes involved in pectin and hemicellulose metabolism was detected in all tissues, indicating a constant maintenance of transcripts encoding enzymes remodeling the cell wall matrix. The most abundant transcripts encoded sucrose synthases that were specifically expressed in wood-forming tissues along with cellulose synthase and homologs of KORRIGAN and ELP1. Woody tissues were the richest source of various other CAZyme transcripts, demonstrating the importance of this group of enzymes for xylogenesis. In contrast, there was little expression of genes related to starch metabolism during wood formation, consistent with the preferential flux of carbon to cell wall biosynthesis. Seasonally dormant meristems of poplar showed a high prevalence of transcripts related to starch metabolism and surprisingly retained transcripts of some cell wall synthesis enzymes. The data showed profound changes in CAZyme transcriptomes in different poplar tissues and pointed to some key differences in CAZyme genes and their regulation between herbaceous and woody plants.

@article{goulas_chloroplast_2006,
	title = {The chloroplast lumen and stromal proteomes of \textit{{Arabidopsis} thaliana} show differential sensitivity to short- and long-term exposure to low temperature: \textit{{Response} of the soluble chloroplast proteomes to cold acclimation}},
	volume = {47},
	issn = {09607412},
	shorttitle = {The chloroplast lumen and stromal proteomes of \textit{{Arabidopsis} thaliana} show differential sensitivity to short- and long-term exposure to low temperature},
	url = {http://doi.wiley.com/10.1111/j.1365-313X.2006.02821.x},
	doi = {10/ftpwqm},
	language = {en},
	number = {5},
	urldate = {2021-06-11},
	journal = {The Plant Journal},
	author = {Goulas, Estelle and Schubert, Maria and Kieselbach, Thomas and Kleczkowski, Leszek A. and Gardeström, Per and Schröder, Wolfgang and Hurry, Vaughan},
	month = sep,
	year = {2006},
	pages = {720--734},
}

@article{ciereszko_expression_2005,
	title = {Expression of several genes involved in sucrose/starch metabolism as affected by different strategies to induce phosphate deficiency in {Arabidopsis}},
	volume = {27},
	issn = {0137-5881},
	doi = {10.1007/s11738-005-0018-2},
	abstract = {The effects of inorganic phosphate (Pi) deficiency on expression of genes encoding ADP-glucose pyrophosphorylase small and large subunits (ApS and ApL1, ApL2, ApL3 genes), UDP-glucose pyrophosphorylase (Ugp gene), sucrose synthase (Sus]), Soluble and insoluble acid invertases (Invand Invcw) and hexokinase (Hxk1 gene), all involved in carbohydrate metabolism, were investigated in Arabidopsis thaliana (L.) Heynh. We used soil-grown pho mutants affected in Pi status, as well as wild-type (wt) plants grown under Pi deficiency conditions in liquid medium, and leaves of wt plants fed with D-mannose. Generally, ApS, ApL1, Ugp and Inv genes were upregulated, although to a varied degree, under conditions of Pi-stress. The applied conditions had differential effects on expression of other genes Studied. For instance, Susl was downregulated in phol (Pi-deficient) mutant, but was unaffected in wt plants grown in liquid medium under P-deficiency. Mannose had distinct coil contration-dependent effects on expression of genes under Study, possibly reflecting a dual role of mannose as a sink for Pi and as glucose analog. Feeding- Pi (at up to 200 mM) to the detached leaves of wt plants strongly affected the expression of ApL1, ApL2, Sus1 and Inv genes, possibly due to an osmotic effect exerted by Pi. The data Suggest that ADP-glucose and UDP-glucose pyrophosphorylases (ent, 0 zymes indirectly involved in Pi recycling) as well as invertases (sucrose hydrolysis) are transcriptionally regulated by Pi-deficiency, which may play a role in homeostatic mechanisms that acclimate the plant to the Pi-stress conditions.},
	language = {English},
	number = {2},
	journal = {Acta Physiologiae Plantarum},
	author = {Ciereszko, I. and Kleczkowski, L. A.},
	year = {2005},
	note = {Place: Heidelberg
Publisher: Springer Heidelberg
WOS:000229991800002},
	keywords = {Arabidopsis, acclimation, adp-glucose pyrophosphorylase, bean roots, carbohydrate metabolism regulation, gene expression, light, phaseolus-vulgaris l., pho   mutants, phosphate starvation, photosynthesis, small-subunit, sugars, thaliana, transduction},
	pages = {147--155},
}

The effects of inorganic phosphate (Pi) deficiency on expression of genes encoding ADP-glucose pyrophosphorylase small and large subunits (ApS and ApL1, ApL2, ApL3 genes), UDP-glucose pyrophosphorylase (Ugp gene), sucrose synthase (Sus]), Soluble and insoluble acid invertases (Invand Invcw) and hexokinase (Hxk1 gene), all involved in carbohydrate metabolism, were investigated in Arabidopsis thaliana (L.) Heynh. We used soil-grown pho mutants affected in Pi status, as well as wild-type (wt) plants grown under Pi deficiency conditions in liquid medium, and leaves of wt plants fed with D-mannose. Generally, ApS, ApL1, Ugp and Inv genes were upregulated, although to a varied degree, under conditions of Pi-stress. The applied conditions had differential effects on expression of other genes Studied. For instance, Susl was downregulated in phol (Pi-deficient) mutant, but was unaffected in wt plants grown in liquid medium under P-deficiency. Mannose had distinct coil contration-dependent effects on expression of genes under Study, possibly reflecting a dual role of mannose as a sink for Pi and as glucose analog. Feeding- Pi (at up to 200 mM) to the detached leaves of wt plants strongly affected the expression of ApL1, ApL2, Sus1 and Inv genes, possibly due to an osmotic effect exerted by Pi. The data Suggest that ADP-glucose and UDP-glucose pyrophosphorylases (ent, 0 zymes indirectly involved in Pi recycling) as well as invertases (sucrose hydrolysis) are transcriptionally regulated by Pi-deficiency, which may play a role in homeostatic mechanisms that acclimate the plant to the Pi-stress conditions.

@article{kleczkowski_factors_2005,
	title = {Factors affecting oligomerization status of {UDP}-glucose pyrophosphorylase},
	volume = {66},
	issn = {0031-9422},
	url = {https://www.sciencedirect.com/science/article/pii/S0031942205004607},
	doi = {10.1016/j.phytochem.2005.09.034},
	abstract = {UDP-glucose pyrophosphorylase (UGPase) is involved in the production of UDP-glucose, a key precursor to polysaccharide synthesis in all organisms. UGPase activity has recently been proposed to be regulated by oligomerization, with monomer as the active species. In the present study, we investigated factors affecting oligomerization status of the enzyme, using purified recombinant barley UGPase. Incubation of wild-type (wt) UGPase with phosphate or Tris buffers promoted oligomerization, whereas Mops and Hepes completely dissociated the oligomers to monomers (the active form). Similar buffer effects were observed for KK127-128LL and C99S mutants of UGPase; however, the buffers had a relatively small effect on the oligomerization status of the LIV135-137NIN mutant, impaired in deoligomerization ability and showing only 6–9\% activity of the wt. Buffer composition had no effect on UGPase activity at UGPase protein concentrations below ca. 20ng/ml. However, at higher protein concentration the activity in Tris, but not Mops nor Hepes, underestimated the amount of the enzyme. The data suggest that oligomerization status of UGPase can be controlled by subtle changes in an immediate environment (buffers) and by protein dilution. The evidence is discussed in relation to our recent model of UGPase structure/function, and with respect to earlier reports on the oligomeric integrity/activity of UGPases from eukaryotic tissues.},
	language = {en},
	number = {24},
	urldate = {2021-06-11},
	journal = {Phytochemistry},
	author = {Kleczkowski, Leszek A. and Martz, Françoise and Wilczynska, Malgorzata},
	month = dec,
	year = {2005},
	keywords = {Cellulose, Protein oligomerization, Sucrose, UDP-glucose synthesis},
	pages = {2815--2821},
}

UDP-glucose pyrophosphorylase (UGPase) is involved in the production of UDP-glucose, a key precursor to polysaccharide synthesis in all organisms. UGPase activity has recently been proposed to be regulated by oligomerization, with monomer as the active species. In the present study, we investigated factors affecting oligomerization status of the enzyme, using purified recombinant barley UGPase. Incubation of wild-type (wt) UGPase with phosphate or Tris buffers promoted oligomerization, whereas Mops and Hepes completely dissociated the oligomers to monomers (the active form). Similar buffer effects were observed for KK127-128LL and C99S mutants of UGPase; however, the buffers had a relatively small effect on the oligomerization status of the LIV135-137NIN mutant, impaired in deoligomerization ability and showing only 6–9% activity of the wt. Buffer composition had no effect on UGPase activity at UGPase protein concentrations below ca. 20ng/ml. However, at higher protein concentration the activity in Tris, but not Mops nor Hepes, underestimated the amount of the enzyme. The data suggest that oligomerization status of UGPase can be controlled by subtle changes in an immediate environment (buffers) and by protein dilution. The evidence is discussed in relation to our recent model of UGPase structure/function, and with respect to earlier reports on the oligomeric integrity/activity of UGPases from eukaryotic tissues.

@article{ciereszko_interactive_2005,
	title = {Interactive effects of phosphate deficiency, sucrose and light/dark conditions on gene expression of {UDP}-glucose pyrophosphory lase in {Arabidopsis}},
	volume = {162},
	issn = {0176-1617},
	doi = {10.1016/j.jplph.2004.08.003},
	abstract = {The effects of inorganic phosphate (Pi) status, light/dark and sucrose on expression of UDP-glucose pyrophosphorylase (UGPase) gene (Ugp), which is involved in sucrose/ polysaccharides metabolism, were investigated using Arabidopsis wild-type (wt) plants and mutants impaired in Pi and carbohydrate status. Generally, P-deficiency resulted in increased Ugp expression and enhanced UGPase activity and protein content, as found for wt plants grown on P-deficient and complete nutrient solution, as well as for pho1 (P-deficient) mutants. Ugp was highly expressed in darkened leaves of pho1, but not wt plants; daily tight exposure enhanced Ugp expression both in wt and pho mutants. The pho1 and pho2 (Pi-accumulating) mutations had Little or no effect on leaf contents of glucose and fructose, regardless of light/dark conditions, whereas pho1 plants had much higher Levels of sucrose and starch in the dark than pho2 and wt plants. The Ugp was up-regutated when leaves were fed with sucrose in wt plants, but the expression in pho2 background was much less sensitive to sucrose supply than in wt and pho1 plants. Expression of Ugp in pgm1 and sex1 mutants (impaired in starch/sugar content) was not dependent on starch content, and not tightly correlated with soluble sugar status. Okadaic acid (OKA) effectively blocked the P-starvation and sucrose -dependent expression of Ugp in excised leaves, whereas staurosporine (STA) had only a small effect on both processes (especially in -P leaves), suggesting that P-starvation and sucrose effects on Ugp are transmitted by pathways that may share similar components with respect to their (in)sensitivity to OKA and STA. The results of this study suggest that Ugp expression is modulated by an interaction of signals derived from P-deficiency status, sucrose content and dark/ light conditions, and that light/ sucrose and P-deficiency may have additive effects on Ugp expression. (c) 2004 Elsevier GmbH. All rights reserved.},
	language = {English},
	number = {3},
	journal = {Journal of Plant Physiology},
	author = {Ciereszko, I. and Johansson, H. and Kleczkowski, L. A.},
	month = mar,
	year = {2005},
	note = {Place: Jena
Publisher: Elsevier Gmbh, Urban \& Fischer Verlag
WOS:000228215900012},
	keywords = {accumulation, bean-plants, gene regulation, metabolism, okadaic acid, pho mutants, phosphate deficiency, phosphorus, photosynthesis, pi and sucrose   signaling, protein, roots, starch mutants, sucrose metabolism, thaliana},
	pages = {343--353},
}

The effects of inorganic phosphate (Pi) status, light/dark and sucrose on expression of UDP-glucose pyrophosphorylase (UGPase) gene (Ugp), which is involved in sucrose/ polysaccharides metabolism, were investigated using Arabidopsis wild-type (wt) plants and mutants impaired in Pi and carbohydrate status. Generally, P-deficiency resulted in increased Ugp expression and enhanced UGPase activity and protein content, as found for wt plants grown on P-deficient and complete nutrient solution, as well as for pho1 (P-deficient) mutants. Ugp was highly expressed in darkened leaves of pho1, but not wt plants; daily tight exposure enhanced Ugp expression both in wt and pho mutants. The pho1 and pho2 (Pi-accumulating) mutations had Little or no effect on leaf contents of glucose and fructose, regardless of light/dark conditions, whereas pho1 plants had much higher Levels of sucrose and starch in the dark than pho2 and wt plants. The Ugp was up-regutated when leaves were fed with sucrose in wt plants, but the expression in pho2 background was much less sensitive to sucrose supply than in wt and pho1 plants. Expression of Ugp in pgm1 and sex1 mutants (impaired in starch/sugar content) was not dependent on starch content, and not tightly correlated with soluble sugar status. Okadaic acid (OKA) effectively blocked the P-starvation and sucrose -dependent expression of Ugp in excised leaves, whereas staurosporine (STA) had only a small effect on both processes (especially in -P leaves), suggesting that P-starvation and sucrose effects on Ugp are transmitted by pathways that may share similar components with respect to their (in)sensitivity to OKA and STA. The results of this study suggest that Ugp expression is modulated by an interaction of signals derived from P-deficiency status, sucrose content and dark/ light conditions, and that light/ sucrose and P-deficiency may have additive effects on Ugp expression. (c) 2004 Elsevier GmbH. All rights reserved.

@article{geisler_toward_2004,
	title = {Toward a blueprint for {UDP}-glucose pyrophosphorylase structure/function properties: homology-modeling analyses},
	volume = {56},
	issn = {1573-5028},
	shorttitle = {Toward a blueprint for {UDP}-glucose pyrophosphorylase structure/function properties},
	url = {https://doi.org/10.1007/s11103-004-4953-x},
	doi = {10/dtvfpb},
	abstract = {UDP-glucose pyrophosphorylase (UGPase) is an important enzyme of synthesis of sucrose, cellulose, and several other polysaccharides in all plants. The protein is evolutionarily conserved among eukaryotes, but has little relation, aside from its catalytic reaction, to UGPases of prokaryotic origin. Using protein homology modeling strategy, 3D structures for barley, poplar, and Arabidopsis UGPases have been derived, based on recently published crystal structure of human UDP-N-acetylglucosamine pyrophosphorylase. The derived 3D structures correspond to a bowl-shaped protein with the active site at a central groove, and a C-terminal domain that includes a loop (I-loop) possibly involved in dimerization. Data on a plethora of earlier described UGPase mutants from a variety of eukaryotic organisms have been revisited, and we have, in most cases, verified the role of each mutation in enzyme catalysis/regulation/structural integrity. We have also found that one of two alternatively spliced forms of poplar UGPase has a very short I-loop, suggesting differences in oligomerization ability of the two isozymes. The derivation of the structural model for plant UGPase should serve as a useful blueprint for further function/structure studies on this protein.},
	language = {en},
	number = {5},
	urldate = {2021-06-15},
	journal = {Plant Molecular Biology},
	author = {Geisler, Matt and Wilczynska, Malgorzata and Karpinski, Stanislaw and Kleczkowski, Leszek A.},
	month = nov,
	year = {2004},
	pages = {783--794},
}

UDP-glucose pyrophosphorylase (UGPase) is an important enzyme of synthesis of sucrose, cellulose, and several other polysaccharides in all plants. The protein is evolutionarily conserved among eukaryotes, but has little relation, aside from its catalytic reaction, to UGPases of prokaryotic origin. Using protein homology modeling strategy, 3D structures for barley, poplar, and Arabidopsis UGPases have been derived, based on recently published crystal structure of human UDP-N-acetylglucosamine pyrophosphorylase. The derived 3D structures correspond to a bowl-shaped protein with the active site at a central groove, and a C-terminal domain that includes a loop (I-loop) possibly involved in dimerization. Data on a plethora of earlier described UGPase mutants from a variety of eukaryotic organisms have been revisited, and we have, in most cases, verified the role of each mutation in enzyme catalysis/regulation/structural integrity. We have also found that one of two alternatively spliced forms of poplar UGPase has a very short I-loop, suggesting differences in oligomerization ability of the two isozymes. The derivation of the structural model for plant UGPase should serve as a useful blueprint for further function/structure studies on this protein.

@article{kleczkowski_udp-glucose_2004,
	title = {{UDP}-{Glucose} {Pyrophosphorylase}. {An} {Old} {Protein} with {New} {Tricks}},
	volume = {134},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.103.036053},
	doi = {10/dwmw23},
	number = {3},
	urldate = {2021-06-15},
	journal = {Plant Physiology},
	author = {Kleczkowski, Leszek A. and Geisler, Matt and Ciereszko, Iwona and Johansson, Henrik},
	month = mar,
	year = {2004},
	pages = {912--918},
}

@article{igamberdiev_membrane_2003,
	title = {Membrane potential, adenylate levels and {Mg2}+ are interconnected via adenylate kinase equilibrium in plant cells},
	volume = {1607},
	issn = {0005-2728},
	doi = {10/b97n7t},
	abstract = {Concentrations of adenylate species and free magnesium (Mg2+) within cells are mediated by the equilibrium governed by adenylate kinase (AK), the enzyme abundant in plants in chloroplast stroma and intermembrane spaces of chloroplasts and mitochondria. Ratios of free and Mg-bound adenylates (linked to the values of [Mg2+] established under AK equilibrium) can be rationalized in terms of the overall dependence of concentrations of Mg2+ and free and Mg-bound adenylates, as well as electric potential values across the inner membranes of mitochondria and chloroplasts. The potential across the inner mitochondrial membrane, by driving adenylate translocators, equilibrates free adenylates across the inner membrane according to the Nernst equation and contributes to the ATP(total)/ADP(total) ratio in the cytosol. The ratio affects the exchange of free adenylates with chloroplasts and this, in turn, influences the value of potential across the inner chloroplast membrane. From measurements of subcellular ATP(total)/ADP(total) ratios, we suggest a method of estimating the values of potential across inner membranes of mitochondria and chloroplasts in vivo, which allows a comparison of the operation of these organelles under different physiological conditions. We discuss also how the equilibration of adenylates by AK drives adenylate transport across membranes, and establishes [Mg2+] in the cytosol and chloroplast stroma, maintaining the rates of photosynthesis and respiration. This provides a tool for metabolomic research, by which the determined concentrations of adenylate species could be used for computation of essential metabolic parameters in the cell and in subcellular compartments. (C) 2003 Elsevier B.V. All rights reserved.},
	language = {English},
	number = {2-3},
	journal = {Biochimica Et Biophysica Acta-Bioenergetics},
	author = {Igamberdiev, A. U. and Kleczkowski, L. A.},
	month = dec,
	year = {2003},
	note = {Place: Amsterdam
Publisher: Elsevier Science Bv
WOS:000187241500005},
	keywords = {adenylate kinase, adp, atp/adp ratios, barley, chloroplast, cytosol, free magnesium, hordeum-vulgare protoplasts, intermembrane space, leaf   protoplasts, membrane potential, metabolomics, mitochondrial electron-transport, mitochondrion, photosynthesis, spinach-chloroplasts},
	pages = {111--119},
}

Concentrations of adenylate species and free magnesium (Mg2+) within cells are mediated by the equilibrium governed by adenylate kinase (AK), the enzyme abundant in plants in chloroplast stroma and intermembrane spaces of chloroplasts and mitochondria. Ratios of free and Mg-bound adenylates (linked to the values of [Mg2+] established under AK equilibrium) can be rationalized in terms of the overall dependence of concentrations of Mg2+ and free and Mg-bound adenylates, as well as electric potential values across the inner membranes of mitochondria and chloroplasts. The potential across the inner mitochondrial membrane, by driving adenylate translocators, equilibrates free adenylates across the inner membrane according to the Nernst equation and contributes to the ATP(total)/ADP(total) ratio in the cytosol. The ratio affects the exchange of free adenylates with chloroplasts and this, in turn, influences the value of potential across the inner chloroplast membrane. From measurements of subcellular ATP(total)/ADP(total) ratios, we suggest a method of estimating the values of potential across inner membranes of mitochondria and chloroplasts in vivo, which allows a comparison of the operation of these organelles under different physiological conditions. We discuss also how the equilibration of adenylates by AK drives adenylate transport across membranes, and establishes [Mg2+] in the cytosol and chloroplast stroma, maintaining the rates of photosynthesis and respiration. This provides a tool for metabolomic research, by which the determined concentrations of adenylate species could be used for computation of essential metabolic parameters in the cell and in subcellular compartments. (C) 2003 Elsevier B.V. All rights reserved.

@article{siedlecka_small_2003,
	title = {The small subunit {ADP}-glucose pyrophosphorylase ({ApS}) promoter mediates okadaic acid-sensitive {uidA} expression in starch-synthesizing tissues and cells in {Arabidopsis}},
	volume = {217},
	issn = {1432-2048},
	url = {https://doi.org/10.1007/s00425-003-0982-y},
	doi = {10.1007/s00425-003-0982-y},
	abstract = {Transgenic plants of Arabidopsis thaliana Heynh., transformed with a bacterial β-glucuronidase (GUS) gene under the control of the promoter of the small subunit (ApS) of ADP-glucose pyrophosphorylase (AGPase), exhibited GUS staining in leaves (including stomata), stems, roots and flowers. Cross-sections of stems revealed GUS staining in protoxylem parenchyma, primary phloem and cortex. In young roots, the staining was found in the root tips, including the root cap, and in vascular tissue, while the older root–hypocotyl axis showed prominent staining in the secondary phloem and paratracheary parenchyma of secondary xylem. The GUS staining co-localized with ApS protein, as found by tissue printing using antibodies against ApS. Starch was found only in cell and tissue types exhibiting GUS staining and ApS labelling, but not in all of them. For example, starch was lacking in the xylem parenchyma and secondary phloem of the root–hypocotyl axis. Sucrose potently activated ApS gene expression in leaves of wild-type (wt) plants, and in transgenic seedlings grown on sucrose medium where GUS activity was quantified with 4-methylumbelliferyl-β-glucuronide as substrate. Okadaic acid, an inhibitor of protein phosphatases 1 and 2A, completely blocked expression of ApS in mature leaves of wt plants and prevented GUS staining in root tips and flowers of the transgenic plants, suggesting a similar signal transduction mechanism for ApS expression in various tissues. The data support the key role of AGPase in starch synthesis, but they also underlie the ubiquitous importance of the ApS gene for AGPase function in all organs/tissues of Arabidopsis.},
	language = {en},
	number = {2},
	urldate = {2021-10-21},
	journal = {Planta},
	author = {Siedlecka, Anna and Ciereszko, Iwona and Mellerowicz, Ewa and Martz, Françoise and Chen, Jychian and Kleczkowski, Leszek A.},
	month = jun,
	year = {2003},
	pages = {184--192},
}

Transgenic plants of Arabidopsis thaliana Heynh., transformed with a bacterial β-glucuronidase (GUS) gene under the control of the promoter of the small subunit (ApS) of ADP-glucose pyrophosphorylase (AGPase), exhibited GUS staining in leaves (including stomata), stems, roots and flowers. Cross-sections of stems revealed GUS staining in protoxylem parenchyma, primary phloem and cortex. In young roots, the staining was found in the root tips, including the root cap, and in vascular tissue, while the older root–hypocotyl axis showed prominent staining in the secondary phloem and paratracheary parenchyma of secondary xylem. The GUS staining co-localized with ApS protein, as found by tissue printing using antibodies against ApS. Starch was found only in cell and tissue types exhibiting GUS staining and ApS labelling, but not in all of them. For example, starch was lacking in the xylem parenchyma and secondary phloem of the root–hypocotyl axis. Sucrose potently activated ApS gene expression in leaves of wild-type (wt) plants, and in transgenic seedlings grown on sucrose medium where GUS activity was quantified with 4-methylumbelliferyl-β-glucuronide as substrate. Okadaic acid, an inhibitor of protein phosphatases 1 and 2A, completely blocked expression of ApS in mature leaves of wt plants and prevented GUS staining in root tips and flowers of the transgenic plants, suggesting a similar signal transduction mechanism for ApS expression in various tissues. The data support the key role of AGPase in starch synthesis, but they also underlie the ubiquitous importance of the ApS gene for AGPase function in all organs/tissues of Arabidopsis.

@article{ciereszko_effects_2002,
	title = {Effects of phosphate deficiency and sugars on expression of rab18 in {Arabidopsis}: hexokinase-dependent and okadaic acid-sensitive transduction of the sugar signal},
	volume = {1579},
	issn = {0167-4781},
	shorttitle = {Effects of phosphate deficiency and sugars on expression of rab18 in {Arabidopsis}},
	url = {https://www.sciencedirect.com/science/article/pii/S016747810200502X},
	doi = {10.1016/S0167-4781(02)00502-X},
	abstract = {The lack of phosphorus in the nutrient medium increased the expression of rab18, an abscisic acid (ABA)-responsive gene, in leaves of Arabidopsis thaliana. The expression of this gene was also upregulated after feeding the excised leaves with d-mannose and sucrose for both wild-type (wt) and aba1 (ABA-deficient) mutant plants. For aba1 mutants, both the phosphate deficiency and sugar effects on rab18 were weaker than in wt plants, suggesting possible involvement of both ABA-dependent and ABA-independent components in signalling. Transgenic Arabidopsis plants with increased hexokinase (HXK) expression had a much higher sucrose-dependent level of rab18 mRNA, implying the HXK involvement in sensing/transmitting the sugar signal. Sucrose-related induction of rab18 was completely inhibited by okadaic acid (OKA), suggesting the involvement of specific protein phosphatase(s) in transduction of the sugar signal. The results suggest that rab18 is regulated via interaction of a plethora of signals, including ABA, sugar and phosphate deficiency, and that the sugar effect is transmitted via a HXK-pathway, involving OKA-sensitive component(s). The findings prompt caution in linking the expression of rab18 solely to ABA signalling.},
	language = {en},
	number = {1},
	urldate = {2021-10-19},
	journal = {Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression},
	author = {Ciereszko, Iwona and Kleczkowski, Leszek A},
	month = nov,
	year = {2002},
	keywords = {Gene expression, Mannose, Phosphate stress, Sucrose, mutant},
	pages = {43--49},
}

The lack of phosphorus in the nutrient medium increased the expression of rab18, an abscisic acid (ABA)-responsive gene, in leaves of Arabidopsis thaliana. The expression of this gene was also upregulated after feeding the excised leaves with d-mannose and sucrose for both wild-type (wt) and aba1 (ABA-deficient) mutant plants. For aba1 mutants, both the phosphate deficiency and sugar effects on rab18 were weaker than in wt plants, suggesting possible involvement of both ABA-dependent and ABA-independent components in signalling. Transgenic Arabidopsis plants with increased hexokinase (HXK) expression had a much higher sucrose-dependent level of rab18 mRNA, implying the HXK involvement in sensing/transmitting the sugar signal. Sucrose-related induction of rab18 was completely inhibited by okadaic acid (OKA), suggesting the involvement of specific protein phosphatase(s) in transduction of the sugar signal. The results suggest that rab18 is regulated via interaction of a plethora of signals, including ABA, sugar and phosphate deficiency, and that the sugar effect is transmitted via a HXK-pathway, involving OKA-sensitive component(s). The findings prompt caution in linking the expression of rab18 solely to ABA signalling.

@article{ciereszko_expression_2002,
	title = {Expression of genes for sucrose synthase and {UDP}-glucose pyrophosphorylase under changing conditions of {Pi} and sucrose (in {Polish}) ({Zeszyty} {Problemowe} {Postepow} {Nauk} {Rolniczych} 481: 281-287)},
	volume = {481},
	shorttitle = {Expression of genes for sucrose synthase and {UDP}-glucose pyrophosphorylase under changing conditions of {Pi} and sucrose (in {Polish}) ({Zeszyty} {Problemowe} {Postepow} {Nauk} {Rolniczych} 481},
	abstract = {The effect of inorganic phosphate (Pi) level and carbohydrate/osmotic status on expression of genes encoding UDP-glucose pyrophosphorylase (Ugp) and sucrose synthase (Sus1) were investigated in Arabidopsis thaliana (L.) HEYNH. leaves. Phosphate deficiency strongly induced Ugp gene expression and had no influence on the level of Sus1 transcript in the leaves of Arabidopsis. Feeding leaves with Pi, at the concentration of 20-200 mmol-dm⁻³, increased Sus1 expression and had no significant effect on Ugp transcript level. Genes for UDP-glucose pyrophosphorylase and sucrose synthase were found to be strongly regulated by sugar and sugar/osmoticum, respectively. The increase of Ugp and Sus1 expression after feeding of sucrose to the leaves of pho1 mutant of Arabidopsis was not significantly higher than the transcripts level in wild-type plants. Sucrose, exogenously provided to the leaves of pho2 mutant had lower effect on Ugp transcript level than in wild-type plants, however Sus1 upregulation was higher in pho2 than in w-t. Sucrose-related induction of Ugp was inhibited by okadaic acid, an inhibitor of protein phosphatases; on the other hand, Sus1 expression was enhanced after okadaic acid treatment. The obtained results suggest that Ugp and Sus1 genes expression, both P- modulated and sugar/osmoticum-dependent, are regulated via distinct sensing mechanisms and distinct signaling pathways and are closely involved in homeos- tatic readjustments of plant responses to environmental stresses.},
	author = {Ciereszko, Iwona and Kleczkowski, Leszek},
	month = jan,
	year = {2002},
	pages = {281--287},
}

The effect of inorganic phosphate (Pi) level and carbohydrate/osmotic status on expression of genes encoding UDP-glucose pyrophosphorylase (Ugp) and sucrose synthase (Sus1) were investigated in Arabidopsis thaliana (L.) HEYNH. leaves. Phosphate deficiency strongly induced Ugp gene expression and had no influence on the level of Sus1 transcript in the leaves of Arabidopsis. Feeding leaves with Pi, at the concentration of 20-200 mmol-dm⁻³, increased Sus1 expression and had no significant effect on Ugp transcript level. Genes for UDP-glucose pyrophosphorylase and sucrose synthase were found to be strongly regulated by sugar and sugar/osmoticum, respectively. The increase of Ugp and Sus1 expression after feeding of sucrose to the leaves of pho1 mutant of Arabidopsis was not significantly higher than the transcripts level in wild-type plants. Sucrose, exogenously provided to the leaves of pho2 mutant had lower effect on Ugp transcript level than in wild-type plants, however Sus1 upregulation was higher in pho2 than in w-t. Sucrose-related induction of Ugp was inhibited by okadaic acid, an inhibitor of protein phosphatases; on the other hand, Sus1 expression was enhanced after okadaic acid treatment. The obtained results suggest that Ugp and Sus1 genes expression, both P- modulated and sugar/osmoticum-dependent, are regulated via distinct sensing mechanisms and distinct signaling pathways and are closely involved in homeos- tatic readjustments of plant responses to environmental stresses.

@article{ciereszko_glucose_2002,
	title = {Glucose and mannose regulate the expression of a major sucrose synthase gene in {Arabidopsis} via hexokinase-dependent mechanisms},
	volume = {40},
	issn = {0981-9428},
	url = {https://www.sciencedirect.com/science/article/pii/S0981942802014523},
	doi = {10/ct2hnm},
	abstract = {Sucrose synthase (SuSy) is an important enzyme involved in sucrose synthesis/breakdown in all plants. Sus1, a major SuSy gene in Arabidopsis thaliana, was upregulated by sucrose, glucose and D-mannose, but not 3-O-methylglucose, when those compounds were fed to excised leaves. Mannose was more effective than glucose or sucrose in the induction of Sus1, with strong effects observed at a concentration as low as 20 mM. When fed to the excised leaves, N-acetyl-glucosamine, an inhibitor of hexokinase (HXK) enzymatic activity, decreased sucrose- and glucose-dependent, but not mannose-dependent, upregulation of Sus1. The sucrose/glucose-dependent Sus1 expression was strongly induced in transgenic Arabidopsis HXK-overexpressing (OE) plants, whereas mannose-dependent Sus1 expression markedly decreased in OE, but not in HXK-“antisense”, Arabidopsis plants. Feeding with sucrose resulted in a marked increase of glucose content in leaves, suggesting that it is glucose rather than sucrose that serves as a signal in upregulating Sus1 expression in sucrose-fed plants. The data suggest that Sus1 is regulated by a HXK-dependent pathway, with glucose and mannose effects differentially sensed/transmitted via the HXK step.},
	language = {en},
	number = {11},
	urldate = {2021-10-19},
	journal = {Plant Physiology and Biochemistry},
	author = {Ciereszko, Iwona and Kleczkowski, Leszek A.},
	month = nov,
	year = {2002},
	keywords = {Arabidopsis thaliana, Gene expression, Sucrose synthesis, Sus1, UDP-glucose synthesis},
	pages = {907--911},
}

Sucrose synthase (SuSy) is an important enzyme involved in sucrose synthesis/breakdown in all plants. Sus1, a major SuSy gene in Arabidopsis thaliana, was upregulated by sucrose, glucose and D-mannose, but not 3-O-methylglucose, when those compounds were fed to excised leaves. Mannose was more effective than glucose or sucrose in the induction of Sus1, with strong effects observed at a concentration as low as 20 mM. When fed to the excised leaves, N-acetyl-glucosamine, an inhibitor of hexokinase (HXK) enzymatic activity, decreased sucrose- and glucose-dependent, but not mannose-dependent, upregulation of Sus1. The sucrose/glucose-dependent Sus1 expression was strongly induced in transgenic Arabidopsis HXK-overexpressing (OE) plants, whereas mannose-dependent Sus1 expression markedly decreased in OE, but not in HXK-“antisense”, Arabidopsis plants. Feeding with sucrose resulted in a marked increase of glucose content in leaves, suggesting that it is glucose rather than sucrose that serves as a signal in upregulating Sus1 expression in sucrose-fed plants. The data suggest that Sus1 is regulated by a HXK-dependent pathway, with glucose and mannose effects differentially sensed/transmitted via the HXK step.

@article{johansson_molecular_2002,
	title = {Molecular cloning and characterization of a {cDNA} encoding poplar {UDP}-glucose dehydrogenase, a key gene of hemicellulose/pectin formation},
	volume = {1576},
	issn = {0167-4781},
	url = {https://www.sciencedirect.com/science/article/pii/S0167478102002920},
	doi = {10.1016/S0167-4781(02)00292-0},
	abstract = {Plant UDP-glucose dehydrogenase (UGDH) is an important enzyme in the formation of hemicellulose and pectin, the components of newly formed cell walls. A cDNA clone (Ugdh) corresponding to UGDH was isolated from a cDNA library prepared from cambial zone of poplar (Populus tremula x tremuloides). Within the 1824-nucleotide (nt)-long clone, an open reading frame encoded a protein of 481 amino acids (aa), with a calculated molecular weight of 53.1 kDa. The derived aa sequence showed 90\% and 63\% identity with UGDHs from soybean and bovine liver, respectively, and had highly conserved aa motifs believed to be of importance for nt binding and catalytic efficiency. In poplar, the Ugdh corresponds to one or two genes, as found by genomic Southern analysis. The gene was expressed predominantly in differentiating xylem and young leaves, with little expression in the phloem zone of the stem. The expression pattern matched that of UGDH protein, as found by immunoblotting. In leaves, the Ugdh expression was upregulated by a short-term feeding with sucrose, sorbitol and polyethylene glycol, and this effect was to some extent mimicked by light exposure. The data suggest that Ugdh is regulated via an osmoticum-dependent pathway, possibly related to the availability of osmotically active carbohydrate precursors to UDP-glucose, a substrate of UGDH.},
	language = {en},
	number = {1},
	urldate = {2021-10-19},
	journal = {Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression},
	author = {Johansson, Henrik and Sterky, Fredrik and Amini, Bahram and Lundeberg, Joakim and Kleczkowski, Leszek A.},
	month = jun,
	year = {2002},
	keywords = {Glucuronate, Hemicellulose, Pectin, UDP-glucose metabolism, Wood formation},
	pages = {53--58},
}

Plant UDP-glucose dehydrogenase (UGDH) is an important enzyme in the formation of hemicellulose and pectin, the components of newly formed cell walls. A cDNA clone (Ugdh) corresponding to UGDH was isolated from a cDNA library prepared from cambial zone of poplar (Populus tremula x tremuloides). Within the 1824-nucleotide (nt)-long clone, an open reading frame encoded a protein of 481 amino acids (aa), with a calculated molecular weight of 53.1 kDa. The derived aa sequence showed 90% and 63% identity with UGDHs from soybean and bovine liver, respectively, and had highly conserved aa motifs believed to be of importance for nt binding and catalytic efficiency. In poplar, the Ugdh corresponds to one or two genes, as found by genomic Southern analysis. The gene was expressed predominantly in differentiating xylem and young leaves, with little expression in the phloem zone of the stem. The expression pattern matched that of UGDH protein, as found by immunoblotting. In leaves, the Ugdh expression was upregulated by a short-term feeding with sucrose, sorbitol and polyethylene glycol, and this effect was to some extent mimicked by light exposure. The data suggest that Ugdh is regulated via an osmoticum-dependent pathway, possibly related to the availability of osmotically active carbohydrate precursors to UDP-glucose, a substrate of UGDH.

@article{kleczkowski_new_2001,
	title = {A new player in the starch field},
	volume = {39},
	issn = {0981-9428},
	url = {https://www.sciencedirect.com/science/article/pii/S0981942801012943},
	doi = {10/dtg44w},
	abstract = {A possible role of a newly discovered ADP-glucose pyrophosphatase (AGPPase) is discussed in the context of starch synthesis. The enzyme hydrolyses ADP-glucose (starch precursor) and may potentially divert the flow of carbon from starch synthase, resulting in a ‘futile cycle’ when ‘coupled’ with ADP-glucose pyrophosphorylase. The activity of AGPPase is inversely related to starch yield in sink tissues, and may be prone to inhibition by Pi and certain other products of the starch pathway. The AGPPase likely belongs to a ‘nudix’ family of enzymes that in animal tissues and yeast are known to regulate levels of activated sugars. Some strategies for future research are underlined.},
	language = {en},
	number = {9},
	urldate = {2021-11-02},
	journal = {Plant Physiology and Biochemistry},
	author = {Kleczkowski, Leszek A.},
	month = sep,
	year = {2001},
	keywords = {ADP-glucose pyrophosphatase, ADP-glucose pyrophosphorylase, nudix hydrolase, starch synthase},
	pages = {759--761},
}

A possible role of a newly discovered ADP-glucose pyrophosphatase (AGPPase) is discussed in the context of starch synthesis. The enzyme hydrolyses ADP-glucose (starch precursor) and may potentially divert the flow of carbon from starch synthase, resulting in a ‘futile cycle’ when ‘coupled’ with ADP-glucose pyrophosphorylase. The activity of AGPPase is inversely related to starch yield in sink tissues, and may be prone to inhibition by Pi and certain other products of the starch pathway. The AGPPase likely belongs to a ‘nudix’ family of enzymes that in animal tissues and yeast are known to regulate levels of activated sugars. Some strategies for future research are underlined.

@article{igamberdiev_implications_2001,
	title = {Implications of adenylate kinase-governed equilibrium of adenylates on contents of free magnesium in plant cells and compartments.},
	volume = {360},
	issn = {0264-6021},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1222221/},
	abstract = {On the basis of the equilibrium of adenylate kinase (AK; EC 2.7.4.3), which interconverts MgATP and free AMP with MgADP and free ADP, an approach has been worked out to calculate concentrations of free magnesium (Mg(2+)), based on concentrations of total ATP, ADP and AMP in plant tissues and in individual subcellular compartments. Based on reported total adenylate contents, [Mg(2+)] in plant tissues and organelles varies significantly depending on light and dark regimes, plant age and developmental stage. In steady-state conditions, [Mg(2+)] in chloroplasts is similar in light and darkness (in the millimolar range), whereas in the cytosol it is very low in the light and increases to about 0.4 mM in darkness. During the dark-to-light transition (photosynthetic induction), the [Mg(2+)] in chloroplasts falls to low values (0.2 mM or less), corresponding to a delay in photosynthetic oxygen evolution. This delay is considered to result from lower activities of Mg-dependent enzymes in the Calvin cycle. In mitochondria, the changes in [Mg(2+)] are similar but smoother. On the other hand, when the transition from light to darkness is considered, an initial increase in [Mg(2+)] occurs in both chloroplasts and mitochondria, which may be of importance for the control of key regulatory enzymes (e.g. mitochondrial malic enzyme and pyruvate dehydrogenase complex) and for processes connected with light-enhanced dark respiration. A rationale is presented for a possible role of [MgATP]/[MgADP] ratio (rather than [ATP(total)]/[ADP(total)]) as an important component of metabolic cellular control. It is postulated that assays of total adenylates may provide an accurate measure of [Mg(2+)] in plant tissues/cells and subcellular compartments, given that the adenylates are equilibrated by AK.},
	number = {Pt 1},
	urldate = {2021-11-02},
	journal = {Biochemical Journal},
	author = {Igamberdiev, A U and Kleczkowski, L A},
	month = nov,
	year = {2001},
	pmid = {11696011},
	pmcid = {PMC1222221},
	pages = {225--231},
}

On the basis of the equilibrium of adenylate kinase (AK; EC 2.7.4.3), which interconverts MgATP and free AMP with MgADP and free ADP, an approach has been worked out to calculate concentrations of free magnesium (Mg(2+)), based on concentrations of total ATP, ADP and AMP in plant tissues and in individual subcellular compartments. Based on reported total adenylate contents, [Mg(2+)] in plant tissues and organelles varies significantly depending on light and dark regimes, plant age and developmental stage. In steady-state conditions, [Mg(2+)] in chloroplasts is similar in light and darkness (in the millimolar range), whereas in the cytosol it is very low in the light and increases to about 0.4 mM in darkness. During the dark-to-light transition (photosynthetic induction), the [Mg(2+)] in chloroplasts falls to low values (0.2 mM or less), corresponding to a delay in photosynthetic oxygen evolution. This delay is considered to result from lower activities of Mg-dependent enzymes in the Calvin cycle. In mitochondria, the changes in [Mg(2+)] are similar but smoother. On the other hand, when the transition from light to darkness is considered, an initial increase in [Mg(2+)] occurs in both chloroplasts and mitochondria, which may be of importance for the control of key regulatory enzymes (e.g. mitochondrial malic enzyme and pyruvate dehydrogenase complex) and for processes connected with light-enhanced dark respiration. A rationale is presented for a possible role of [MgATP]/[MgADP] ratio (rather than [ATP(total)]/[ADP(total)]) as an important component of metabolic cellular control. It is postulated that assays of total adenylates may provide an accurate measure of [Mg(2+)] in plant tissues/cells and subcellular compartments, given that the adenylates are equilibrated by AK.

@article{ciereszko_phosphate_2001,
	title = {Phosphate status affects the gene expression, protein content and enzymatic activity of {UDP}-glucose pyrophosphorylase in wild-type and pho mutants of {Arabidopsis}},
	volume = {212},
	issn = {1432-2048},
	url = {https://doi.org/10.1007/s004250000424},
	doi = {10/ct6jfd},
	abstract = {The effects of inorganic phosphate (Pi) deficiency on the expression of the UDP-glucose pyrophosphorylase (UGPase) gene (Ugp), involved in sucrose synthesis/metabolism, and on carbohydrate status were investigated in different tissues of Arabidopsis thaliana (L.) Heynh. For leaves, a decrease in internal Pi status caused by growth of plants on a medium lacking Pi (−P conditions) led to an increase in the overall content of glucose and starch, but had little effect on sucrose content. The Pi deficiency also led to an increased carbohydrate content in stems/flowers, but not in roots. The expression of Ugp was upregulated in both leaves and roots, but not in stems/flowers. The effects of Pi status on Ugp expression were confirmed using leaves of both pho1-2 and pho2-1 mutants of Arabidopsis (Pi-deficient and Pi-accumulating, respectively) and by feeding the leaves with d-mannose, which acts as a sink for Pi. The Pi-status-dependent changes in Ugp expression followed the same patterns as those of ApS, a gene encoding the small subunit of ADP-glucose pyrophosphorylase, a key enzyme of starch synthesis. The changes in Ugp mRNA levels, depending on internal Pi status, were generally correlated with changes in UGPase protein content and enzymatic activity. This was demonstrated both for wild-type plants grown under Pi-deficiency and for Pi mutants. The data suggest that, under Pi-deficiency, UGPase represents a transcriptionally regulated step in sucrose synthesis/metabolism, involved in homeostatic mechanisms readjusting the nutritional status of a plant under Pi-stress conditions.},
	language = {en},
	number = {4},
	urldate = {2021-11-02},
	journal = {Planta},
	author = {Ciereszko, Iwona and Johansson, Henrik and Hurry, Vaughan and Kleczkowski, Leszek A.},
	month = mar,
	year = {2001},
	pages = {598--605},
}

The effects of inorganic phosphate (Pi) deficiency on the expression of the UDP-glucose pyrophosphorylase (UGPase) gene (Ugp), involved in sucrose synthesis/metabolism, and on carbohydrate status were investigated in different tissues of Arabidopsis thaliana (L.) Heynh. For leaves, a decrease in internal Pi status caused by growth of plants on a medium lacking Pi (−P conditions) led to an increase in the overall content of glucose and starch, but had little effect on sucrose content. The Pi deficiency also led to an increased carbohydrate content in stems/flowers, but not in roots. The expression of Ugp was upregulated in both leaves and roots, but not in stems/flowers. The effects of Pi status on Ugp expression were confirmed using leaves of both pho1-2 and pho2-1 mutants of Arabidopsis (Pi-deficient and Pi-accumulating, respectively) and by feeding the leaves with d-mannose, which acts as a sink for Pi. The Pi-status-dependent changes in Ugp expression followed the same patterns as those of ApS, a gene encoding the small subunit of ADP-glucose pyrophosphorylase, a key enzyme of starch synthesis. The changes in Ugp mRNA levels, depending on internal Pi status, were generally correlated with changes in UGPase protein content and enzymatic activity. This was demonstrated both for wild-type plants grown under Pi-deficiency and for Pi mutants. The data suggest that, under Pi-deficiency, UGPase represents a transcriptionally regulated step in sucrose synthesis/metabolism, involved in homeostatic mechanisms readjusting the nutritional status of a plant under Pi-stress conditions.

@article{ciereszko_sucrose_2001,
	title = {Sucrose and light regulation of a cold-inducible {UDP}-glucose pyrophosphorylase gene via a hexokinase-independent and abscisic acid-insensitive pathway in {Arabidopsis}.},
	volume = {354},
	issn = {0264-6021},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1221629/},
	abstract = {UDP-glucose pyrophosphorylase (UGPase) is a key enzyme producing UDP-glucose, which is involved in an array of metabolic pathways concerned with, among other functions, the synthesis of sucrose and cellulose. An Arabidopsis thaliana UGPase-encoding gene, Ugp, was profoundly up-regulated by feeding sucrose to the excised leaves and by an exposure of plants to low temperature (5 degrees C). The UGPase activity and its protein content also increased under conditions of sucrose feeding and exposure to cold. The sucrose effect on Ugp was apparently specific and was mimicked by exposure of dark-adapted leaves to light. Drought and O2 deficiency had some down-regulating effects on expression of Ugp. The sugar-signalling pathway for Ugp regulation was independent of hexokinase, as was found by using transgenic plants with increased and decreased expression of the corresponding gene. Subjecting mutants deficient in abscisic acid (ABA) to cold stress conditions had no effect on Ugp expression profiles. Okadaic acid was a powerful inhibitor of Ugp expression, whereas it up-regulated the gene encoding sucrose synthase (Sus1), indicating distinct transduction pathways in transmitting the sugar signal for the two genes in A. thaliana. We suggest that Ugp gene expression is mediated via a hexokinase-independent and ABA-insensitive pathway that involves an okadaic acid-responsive protein phosphatase. The data point towards Ugp as a possible regulatory entity that is closely involved in the homoeostatic readjustment of plant responses to environmental signals.},
	number = {Pt 1},
	urldate = {2021-11-02},
	journal = {Biochemical Journal},
	author = {Ciereszko, I and Johansson, H and Kleczkowski, L A},
	month = feb,
	year = {2001},
	pmid = {11171080},
	pmcid = {PMC1221629},
	pages = {67--72},
}

UDP-glucose pyrophosphorylase (UGPase) is a key enzyme producing UDP-glucose, which is involved in an array of metabolic pathways concerned with, among other functions, the synthesis of sucrose and cellulose. An Arabidopsis thaliana UGPase-encoding gene, Ugp, was profoundly up-regulated by feeding sucrose to the excised leaves and by an exposure of plants to low temperature (5 degrees C). The UGPase activity and its protein content also increased under conditions of sucrose feeding and exposure to cold. The sucrose effect on Ugp was apparently specific and was mimicked by exposure of dark-adapted leaves to light. Drought and O2 deficiency had some down-regulating effects on expression of Ugp. The sugar-signalling pathway for Ugp regulation was independent of hexokinase, as was found by using transgenic plants with increased and decreased expression of the corresponding gene. Subjecting mutants deficient in abscisic acid (ABA) to cold stress conditions had no effect on Ugp expression profiles. Okadaic acid was a powerful inhibitor of Ugp expression, whereas it up-regulated the gene encoding sucrose synthase (Sus1), indicating distinct transduction pathways in transmitting the sugar signal for the two genes in A. thaliana. We suggest that Ugp gene expression is mediated via a hexokinase-independent and ABA-insensitive pathway that involves an okadaic acid-responsive protein phosphatase. The data point towards Ugp as a possible regulatory entity that is closely involved in the homoeostatic readjustment of plant responses to environmental signals.

@article{igamberdiev_capacity_2000,
	title = {Capacity for {NADPH}/{NADP} turnover in the cytosol of barley seed endosperm: {The} role of {NADPH}-dependent hydroxypyruvate reductase},
	volume = {38},
	issn = {0981-9428},
	shorttitle = {Capacity for {NADPH}/{NADP} turnover in the cytosol of barley seed endosperm},
	url = {https://www.sciencedirect.com/science/article/pii/S0981942800011876},
	doi = {10/dps4mx},
	abstract = {Barley (Hordeum vulgare L.) endosperm from developing seeds was found to contain relatively high activities of cytosolic NAD(P)H-dependent hydroxypyruvate reductase (HPR-2) and isocitrate dehydrogenase (ICDH). In contrast, activities of peroxisomal NADH-dependent hydroxypyruvate reductase (HPR-1) and glycolate oxidase as well as cytosolic NAD(P)H-dependent glyoxylate reductase were very low or absent in the endosperm both during maturation and seed germination, indicating the lack of a complete glycolate cycle in this tissue. In addition, activities of cytosolic glucose-6-phosphate dehydrogenase and glyceraldehyde-3-phosphate dehydrogenase were low or absent in the endosperm. The endosperm HPR-2 exhibited similar properties to those of an earlier described HPR-2 from green leaves, e.g. activities with both hydroxypyruvate and glyoxylate, utilization of both NADPH and NADH as cofactors, and a strong uncompetitive inhibition by oxalate (Ki in the order of micromolar). In etiolated leaves, both HPR-1 and HPR-2 were present with the same activity as in green leaves, indicating that the lack of HPR-1 in the endosperm is not a general feature of non-photosynthetic tissues. We conclude that the endosperm has considerable capacity for cytosolic NADP/NADPH cycling via HPR-2 and ICDH, the former being possibly involved in the utilization of a serine-derived carbon.},
	language = {en},
	number = {10},
	urldate = {2021-11-08},
	journal = {Plant Physiology and Biochemistry},
	author = {Igamberdiev, Abir U. and Kleczkowski, Leszek A.},
	month = oct,
	year = {2000},
	keywords = {cytosol, glyoxylate, hydroxypyruvate reductase, seed germination, starch synthesis, sucrose synthesis},
	pages = {747--753},
}

Barley (Hordeum vulgare L.) endosperm from developing seeds was found to contain relatively high activities of cytosolic NAD(P)H-dependent hydroxypyruvate reductase (HPR-2) and isocitrate dehydrogenase (ICDH). In contrast, activities of peroxisomal NADH-dependent hydroxypyruvate reductase (HPR-1) and glycolate oxidase as well as cytosolic NAD(P)H-dependent glyoxylate reductase were very low or absent in the endosperm both during maturation and seed germination, indicating the lack of a complete glycolate cycle in this tissue. In addition, activities of cytosolic glucose-6-phosphate dehydrogenase and glyceraldehyde-3-phosphate dehydrogenase were low or absent in the endosperm. The endosperm HPR-2 exhibited similar properties to those of an earlier described HPR-2 from green leaves, e.g. activities with both hydroxypyruvate and glyoxylate, utilization of both NADPH and NADH as cofactors, and a strong uncompetitive inhibition by oxalate (Ki in the order of micromolar). In etiolated leaves, both HPR-1 and HPR-2 were present with the same activity as in green leaves, indicating that the lack of HPR-1 in the endosperm is not a general feature of non-photosynthetic tissues. We conclude that the endosperm has considerable capacity for cytosolic NADP/NADPH cycling via HPR-2 and ICDH, the former being possibly involved in the utilization of a serine-derived carbon.

@article{kleczkowski_is_2000,
	title = {Is leaf {ADP}-glucose pyrophosphorylase an allosteric enzyme?},
	volume = {1476},
	issn = {0167-4838},
	url = {https://www.sciencedirect.com/science/article/pii/S0167483899002290},
	doi = {10.1016/S0167-4838(99)00229-0},
	abstract = {Barley leaf ADP-glucose pyrophosphorylase (AGPase), a key enzyme of starch synthesis in the chloroplast stroma, was analysed, in both directions of the reaction, with respect to details of its regulation by 3-phosphoglycerate (PGA) and inorganic phosphate (Pi) which serve as activator and inhibitor, respectively. AGPase was found to catalyse a close-to-equilibrium reaction, with the Keq value of approximately 0.5, i.e. slightly favouring the pyrophosphorolytic direction. When the enzyme was analysed by substrate kinetics, PGA acted either as a linear (hyperbolic response) ‘non-competitive’ activator (forward reaction) or a linear near-‘competitive’ activator (reverse reaction). When the activation and inhibition patterns with PGA and Pi, respectively, were studied in detail by Dixon plots, the response curves to effectors also followed hyperbolic kinetics, with the experimentally determined Ka and Ki values on the order of micromolar. The results suggest that the regulation of AGPase proceeds via a non-cooperative mechanism, where neither of the effectors, when considered separately, induces any allosteric response. The evidence, discussed in terms of an overall kinetic mechanism/regulation of leaf AGPase, prompts caution in classifying the protein as an ‘allosteric enzyme’.},
	language = {en},
	number = {1},
	urldate = {2021-11-08},
	journal = {Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology},
	author = {Kleczkowski, Leszek A},
	month = jan,
	year = {2000},
	keywords = {Allosteric regulation, Cooperative kinetics, Starch synthesis},
	pages = {103--108},
}

Barley leaf ADP-glucose pyrophosphorylase (AGPase), a key enzyme of starch synthesis in the chloroplast stroma, was analysed, in both directions of the reaction, with respect to details of its regulation by 3-phosphoglycerate (PGA) and inorganic phosphate (Pi) which serve as activator and inhibitor, respectively. AGPase was found to catalyse a close-to-equilibrium reaction, with the Keq value of approximately 0.5, i.e. slightly favouring the pyrophosphorolytic direction. When the enzyme was analysed by substrate kinetics, PGA acted either as a linear (hyperbolic response) ‘non-competitive’ activator (forward reaction) or a linear near-‘competitive’ activator (reverse reaction). When the activation and inhibition patterns with PGA and Pi, respectively, were studied in detail by Dixon plots, the response curves to effectors also followed hyperbolic kinetics, with the experimentally determined Ka and Ki values on the order of micromolar. The results suggest that the regulation of AGPase proceeds via a non-cooperative mechanism, where neither of the effectors, when considered separately, induces any allosteric response. The evidence, discussed in terms of an overall kinetic mechanism/regulation of leaf AGPase, prompts caution in classifying the protein as an ‘allosteric enzyme’.

@article{t_nucleotide_2000,
	title = {Nucleotide sequence of the {ADP}-glucose pyrophosphorylase promoter of barley ({Hordeum} vulgare {L}.), a gene involved in endosperm starch formation.},
	volume = {122},
	journal = {Plant physiology},
	author = {T, Thorbjørnsen and P, Villand and VE, Ramstad and Kleczkowski, Leszek and O-A, Olsen and HG, Opsahl-Ferstad},
	month = jan,
	year = {2000},
	keywords = {⛔ No DOI found},
	pages = {1457 (Plant Gene Register)},
}

@article{siedlecka_relationship_1999,
	title = {A {Relationship} between {Carbonic} {Anhydrase} and {Rubisco} in {Response} to {Moderate} {Cadmium} {Stress} during {Light} {Activation} of {Photosynthesis}},
	volume = {54},
	issn = {1865-7125},
	url = {https://www.degruyter.com/document/doi/10.1515/znc-1999-9-1023/html},
	doi = {10.1515/znc-1999-9-1023},
	abstract = {In our previous research, we showed that low Cd concentration increases the effectiveness of the processes leading to activation of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). This stimulation was dependent on carbonic anhydrase (CA) activity and resulted in protecting Rubisco activity against Cd toxicity. The aim of the present paper was to test whether this mechanism has any influence on light activation of photosynthesis during the first 2 h of illumination. Both the “activation mechanism” of plant response to Cd-stress conditions and its full efficiency at low Cd concentration were confirmed. The CA-dependent light activation of Rubisco at low Cd level was correlated with accelerated attaining of the maximum Rubisco activity by these plants. The amount of Rubisco was also Cd- and timedependent and varied from continuous accumulation in control plants till reaching the maximum level within 30 minutes for the high Cd concentration. An increase in CA activity that was found to be parallel to the decrease of the amount of CA suggested activation of the enzyme by low Cd concentration},
	language = {en},
	number = {9-10},
	urldate = {2021-11-08},
	journal = {Zeitschrift für Naturforschung C},
	author = {Siedlecka, Anna and Gardeström, Per and Samuelsson, Göran and Kleczkowski, Leszek A. and Krupa, Zbigniew},
	month = oct,
	year = {1999},
	note = {Publisher: De Gruyter},
	pages = {759--763},
}

In our previous research, we showed that low Cd concentration increases the effectiveness of the processes leading to activation of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). This stimulation was dependent on carbonic anhydrase (CA) activity and resulted in protecting Rubisco activity against Cd toxicity. The aim of the present paper was to test whether this mechanism has any influence on light activation of photosynthesis during the first 2 h of illumination. Both the “activation mechanism” of plant response to Cd-stress conditions and its full efficiency at low Cd concentration were confirmed. The CA-dependent light activation of Rubisco at low Cd level was correlated with accelerated attaining of the maximum Rubisco activity by these plants. The amount of Rubisco was also Cd- and timedependent and varied from continuous accumulation in control plants till reaching the maximum level within 30 minutes for the high Cd concentration. An increase in CA activity that was found to be parallel to the decrease of the amount of CA suggested activation of the enzyme by low Cd concentration

@article{kleczkowski_phosphoglycerate_1999,
	title = {A phosphoglycerate to inorganic phosphate ratio is the major factor in controlling starch levels in chloroplasts via {ADP}-glucose pyrophosphorylase regulation},
	volume = {448},
	copyright = {FEBS Letters 448 (1999) 1873-3468 © 2015 Federation of European Biochemical Societies},
	issn = {1873-3468},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1016/S0014-5793%2899%2900346-4},
	doi = {10/cvszx8},
	abstract = {Purified barley leaf ADP-glucose pyrophosphorylase, a key enzyme of the starch synthesis in the chloroplast stroma, was analysed with respect to its possible regulation by factors defining the metabolic/effector status of the chloroplast during light and dark conditions. The enzyme required 3-phosphoglyceric acid for the maximal activity and was inhibited by inorganic phosphate. The optimal pH for the enzyme was at circa 7.0, regardless of the presence or absence of 3-phosphoglyceric acid, whereas the maximal activation by 3-phosphoglyceric acid was observed at pH 8.5 and higher. Changes in the concentration of Mg2+ and dithiothreitol had little or no effect on the enzymatic activity of AGPase. It has been directly demonstrated for the first time that a 3-phosphoglyceric acid/inorganic phosphate ratio, a crucial regulatory parameter, could be directly related to a defined activation state of the enzyme, allowing the prediction of a relative AGPase activity under given conditions. The predicted changes in the enzyme activity were directly correlated with earlier reported responses of starch levels to the 3-phosphoglyceric acid/inorganic phosphate ratio in chloroplasts. Consequences of this for the starch biosynthesis are discussed.},
	language = {en},
	number = {1},
	urldate = {2021-11-08},
	journal = {FEBS Letters},
	author = {Kleczkowski, Leszek A},
	year = {1999},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1016/S0014-5793\%2899\%2900346-4},
	keywords = {Allosteric effector, Light regulation, Photosynthesis, Starch synthesis},
	pages = {153--156},
}

Purified barley leaf ADP-glucose pyrophosphorylase, a key enzyme of the starch synthesis in the chloroplast stroma, was analysed with respect to its possible regulation by factors defining the metabolic/effector status of the chloroplast during light and dark conditions. The enzyme required 3-phosphoglyceric acid for the maximal activity and was inhibited by inorganic phosphate. The optimal pH for the enzyme was at circa 7.0, regardless of the presence or absence of 3-phosphoglyceric acid, whereas the maximal activation by 3-phosphoglyceric acid was observed at pH 8.5 and higher. Changes in the concentration of Mg2+ and dithiothreitol had little or no effect on the enzymatic activity of AGPase. It has been directly demonstrated for the first time that a 3-phosphoglyceric acid/inorganic phosphate ratio, a crucial regulatory parameter, could be directly related to a defined activation state of the enzyme, allowing the prediction of a relative AGPase activity under given conditions. The predicted changes in the enzyme activity were directly correlated with earlier reported responses of starch levels to the 3-phosphoglyceric acid/inorganic phosphate ratio in chloroplasts. Consequences of this for the starch biosynthesis are discussed.

@article{krupa_cadmium-affected_1999,
	title = {Cadmium-affected level of inorganic phosphate in rye leaves influences {Rubisco} subunits},
	volume = {21},
	issn = {1861-1664},
	url = {https://doi.org/10.1007/s11738-999-0040-x},
	doi = {10.1007/s11738-999-0040-x},
	abstract = {Heavy metals, like Cd, decrease intracellular levels of essential mineral nutrient elements. Here we show the effects of the interaction between Cd and inorganic phosphate and its effects on some aspects of the photosynthetic competence of first rye leaves. The decrease in the level of small and large Rubisco subunits in the leaves of Cd-treated seedlings is discussed both in terms of the recovering effect of an additional Pi supply to the leaves, as well as of direct and indirect mechanisms of Cd-toxicity towards photosynthesis.},
	language = {en},
	number = {3},
	urldate = {2021-11-08},
	journal = {Acta Physiologiae Plantarum},
	author = {Krupa, Zbigniew and Siedlecka, Anna and Kleczkowski, Leszek A.},
	month = sep,
	year = {1999},
	pages = {257--261},
}

Heavy metals, like Cd, decrease intracellular levels of essential mineral nutrient elements. Here we show the effects of the interaction between Cd and inorganic phosphate and its effects on some aspects of the photosynthetic competence of first rye leaves. The decrease in the level of small and large Rubisco subunits in the leaves of Cd-treated seedlings is discussed both in terms of the recovering effect of an additional Pi supply to the leaves, as well as of direct and indirect mechanisms of Cd-toxicity towards photosynthesis.

@article{f_cloning_1999,
	title = {Cloning of a {cDNA} encoding soluble inorganic pyrophosphatase from cambium of poplar ({Populus} tremula x tremuloides).},
	volume = {120},
	journal = {Plant physiology},
	author = {F, Sterky and Lundeberg, Joakim and Kleczkowski, Leszek},
	month = jan,
	year = {1999},
	keywords = {⛔ No DOI found},
	pages = {934 (Plant Gene Register)},
}

@article{luo_expression_1999,
	title = {Expression of barley {ADP}-glucose pyrophosphorylase in {Escherichia} coli: processing and regulatory considerations},
	volume = {50},
	issn = {0031-9422},
	shorttitle = {Expression of barley {ADP}-glucose pyrophosphorylase in {Escherichia} coli},
	url = {https://www.sciencedirect.com/science/article/pii/S0031942298004725},
	doi = {10/dck4r3},
	abstract = {Full length cDNAs for barley ADP-glucose pyrophosphorylase (AGPase) coding for the large subunits of the endosperm and leaf homologues of the enzyme (AGPase-S1 and -S2, respectively) and for the small subunit protein from endosperm (AGPase-B1), have been expressed in Escherichia coli. The cDNAs for AGPase-S1 and -S2 required different induction conditions for their maximal expression and they encoded immunologically distinct proteins. The AGPase-S1 that was produced by E. coli had the same Mr (58 kDa) as the corresponding protein in barley crude endosperm extracts, whereas the bacteria-produced AGPase-S2 (55 kDa) was larger than its counterpart from barley leaf preparations (53 kDa). An enzymatically active AGPase expressed in E. coli from a double construct containing cDNAs for AGPase-S1 and -B1 subunits was insensitive to the activation by 3-phosphoglycerate and to inhibition by inorganic phosphate, similarly to the enzyme in barley endosperm. Neither AGPase-S1 nor -B1 were active when expressed alone in the bacteria. The data are discussed with respect to possible mechanisms of intracellular targeting of immature AGPase-S proteins in barley tissues and regarding previous data on effector regulation of the barley enzyme.},
	language = {en},
	number = {2},
	urldate = {2021-11-08},
	journal = {Phytochemistry},
	author = {Luo, Cheng and Kleczkowski, Leszek A},
	month = jan,
	year = {1999},
	keywords = {Barley, Heterologous expression, Starch synthesis, Transit peptide},
	pages = {209--214},
}

Full length cDNAs for barley ADP-glucose pyrophosphorylase (AGPase) coding for the large subunits of the endosperm and leaf homologues of the enzyme (AGPase-S1 and -S2, respectively) and for the small subunit protein from endosperm (AGPase-B1), have been expressed in Escherichia coli. The cDNAs for AGPase-S1 and -S2 required different induction conditions for their maximal expression and they encoded immunologically distinct proteins. The AGPase-S1 that was produced by E. coli had the same Mr (58 kDa) as the corresponding protein in barley crude endosperm extracts, whereas the bacteria-produced AGPase-S2 (55 kDa) was larger than its counterpart from barley leaf preparations (53 kDa). An enzymatically active AGPase expressed in E. coli from a double construct containing cDNAs for AGPase-S1 and -B1 subunits was insensitive to the activation by 3-phosphoglycerate and to inhibition by inorganic phosphate, similarly to the enzyme in barley endosperm. Neither AGPase-S1 nor -B1 were active when expressed alone in the bacteria. The data are discussed with respect to possible mechanisms of intracellular targeting of immature AGPase-S proteins in barley tissues and regarding previous data on effector regulation of the barley enzyme.

@article{igamberdiev_origins_1999,
	title = {Origins and metabolism of formate in higher plants},
	volume = {37},
	issn = {0981-9428},
	url = {https://www.sciencedirect.com/science/article/pii/S0981942800801023},
	doi = {10/fqdmdx},
	abstract = {Formate, a simple one-carbon compound, is readily metabolized in plant tissues. In greening potato tubers, similar to some procaryotes, formate is directly synthesized via a ferredoxin-dependent fixation of CO2, serving as the main precursor for carbon skeletons in biosynthetic pathways. In other plant species and tissues, formate appears as a side-product of photorespiration and of fermentation pathways, but possibly also as a product of direct CO2 reduction in chloroplasts. Formate metabolism is closely related to serine synthesis and to all subsequent reactions originating from serine. Formate may have a role in biosynthesis of numerous compounds, in energetic metabolism and in signal transduction pathways related to stress response. This review summarizes the current state of formate research, physiological/biochemical and molecular aspects.},
	language = {en},
	number = {7},
	urldate = {2021-11-08},
	journal = {Plant Physiology and Biochemistry},
	author = {Igamberdiev, Abir U. and Bykova, Natalia V. and Kleczkowski, Leszek A.},
	month = jul,
	year = {1999},
	keywords = {C1-Metabolism, formate, glyoxylate, photorespiration, photosynthesis, tetrahydrofolates},
	pages = {503--513},
}

Formate, a simple one-carbon compound, is readily metabolized in plant tissues. In greening potato tubers, similar to some procaryotes, formate is directly synthesized via a ferredoxin-dependent fixation of CO2, serving as the main precursor for carbon skeletons in biosynthetic pathways. In other plant species and tissues, formate appears as a side-product of photorespiration and of fermentation pathways, but possibly also as a product of direct CO2 reduction in chloroplasts. Formate metabolism is closely related to serine synthesis and to all subsequent reactions originating from serine. Formate may have a role in biosynthesis of numerous compounds, in energetic metabolism and in signal transduction pathways related to stress response. This review summarizes the current state of formate research, physiological/biochemical and molecular aspects.

@article{h_arabidopsis_1999,
	title = {The {Arabidopsis} thaliana {ADP} glucose pyrophosphorylase large subunit gene, adg2},
	volume = {119},
	journal = {Plant physiology},
	author = {H, Ito and L.N, Sokolov and Kleczkowski, Leszek and Okita, Tom},
	month = jan,
	year = {1999},
	pages = {1567 (Plant Gene Register)},
}