@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, 1470-8728},
	url = {https://portlandpress.com/biochemj/article/478/8/1515/228429/Pyrophosphate-as-an-alternative-energy-currency-in},
	doi = {10/gj4qmj},
	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{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{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{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{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{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{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{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_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{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{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{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_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{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_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{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{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{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{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{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_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{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{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{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{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{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{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{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{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{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{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{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{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 = {10.1016/S0981-9428(02)01452-3},
	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.