@article{grenzi_long-distance_2023,
	title = {Long-distance turgor pressure changes induce local activation of plant glutamate receptor-like channels},
	issn = {0960-9822},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982223000763},
	doi = {10.1016/j.cub.2023.01.042},
	abstract = {In Arabidopsis thaliana, local wounding and herbivore feeding provoke leaf-to-leaf propagating Ca2+ waves that are dependent on the activity of members of the glutamate receptor-like channels (GLRs). In systemic tissues, GLRs are needed to sustain the synthesis of jasmonic acid (JA) with the subsequent activation of JA-dependent signaling response required for the plant acclimation to the perceived stress. Even though the role of GLRs is well established, the mechanism through which they are activated remains unclear. Here, we report that in vivo, the amino-acid-dependent activation of the AtGLR3.3 channel and systemic responses require a functional ligand-binding domain. By combining imaging and genetics, we show that leaf mechanical injury, such as wounds and burns, as well as hypo-osmotic stress in root cells, induces the systemic apoplastic increase of L-glutamate (L-Glu), which is largely independent of AtGLR3.3 that is instead required for systemic cytosolic Ca2+ elevation. Moreover, by using a bioelectronic approach, we show that the local release of minute concentrations of L-Glu in the leaf lamina fails to induce any long-distance Ca2+ waves.},
	language = {en},
	urldate = {2023-03-23},
	journal = {Current Biology},
	author = {Grenzi, Matteo and Buratti, Stefano and Parmagnani, Ambra Selene and Abdel Aziz, Ilaria and Bernacka-Wojcik, Iwona and Resentini, Francesca and Šimura, Jan and Doccula, Fabrizio Gandolfo and Alfieri, Andrea and Luoni, Laura and Ljung, Karin and Bonza, Maria Cristina and Stavrinidou, Eleni and Costa, Alex},
	month = feb,
	year = {2023},
	keywords = {glutamate receptor-like channels, implantable bioelectronic device, ligand-binding domain, long-distance Ca signaling},
}

In Arabidopsis thaliana, local wounding and herbivore feeding provoke leaf-to-leaf propagating Ca2+ waves that are dependent on the activity of members of the glutamate receptor-like channels (GLRs). In systemic tissues, GLRs are needed to sustain the synthesis of jasmonic acid (JA) with the subsequent activation of JA-dependent signaling response required for the plant acclimation to the perceived stress. Even though the role of GLRs is well established, the mechanism through which they are activated remains unclear. Here, we report that in vivo, the amino-acid-dependent activation of the AtGLR3.3 channel and systemic responses require a functional ligand-binding domain. By combining imaging and genetics, we show that leaf mechanical injury, such as wounds and burns, as well as hypo-osmotic stress in root cells, induces the systemic apoplastic increase of L-glutamate (L-Glu), which is largely independent of AtGLR3.3 that is instead required for systemic cytosolic Ca2+ elevation. Moreover, by using a bioelectronic approach, we show that the local release of minute concentrations of L-Glu in the leaf lamina fails to induce any long-distance Ca2+ waves.

@article{bernacka-wojcik_flexible_2023,
	title = {Flexible {Organic} {Electronic} {Ion} {Pump} for {Flow}-{Free} {Phytohormone} {Delivery} into {Vasculature} of {Intact} {Plants}},
	volume = {n/a},
	issn = {2198-3844},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/advs.202206409},
	doi = {10.1002/advs.202206409},
	abstract = {Plant vasculature transports molecules that play a crucial role in plant signaling including systemic responses and acclimation to diverse environmental conditions. Targeted controlled delivery of molecules to the vascular tissue can be a biomimetic way to induce long distance responses, providing a new tool for the fundamental studies and engineering of stress-tolerant plants. Here, a flexible organic electronic ion pump, an electrophoretic delivery device, for controlled delivery of phytohormones directly in plant vascular tissue is developed. The c-OEIP is based on polyimide-coated glass capillaries that significantly enhance the mechanical robustness of these microscale devices while being minimally disruptive for the plant. The polyelectrolyte channel is based on low-cost and commercially available precursors that can be photocured with blue light, establishing much cheaper and safer system than the state-of-the-art. To trigger OEIP-induced plant response, the phytohormone abscisic acid (ABA) in the petiole of intact Arabidopsis plants is delivered. ABA is one of the main phytohormones involved in plant stress responses and induces stomata closure under drought conditions to reduce water loss and prevent wilting. The OEIP-mediated ABA delivery triggered fast and long-lasting stomata closure far away from the delivery point demonstrating systemic vascular transport of the delivered ABA, verified delivering deuterium-labeled ABA.},
	language = {en},
	number = {n/a},
	urldate = {2023-03-21},
	journal = {Advanced Science},
	author = {Bernacka-Wojcik, Iwona and Talide, Loïc and Abdel Aziz, Ilaria and Simura, Jan and Oikonomou, Vasileios K. and Rossi, Stefano and Mohammadi, Mohsen and Dar, Abdul Manan and Seitanidou, Maria and Berggren, Magnus and Simon, Daniel T. and Tybrandt, Klas and Jonsson, Magnus P. and Ljung, Karin and Niittylä, Totte and Stavrinidou, Eleni},
	month = mar,
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/advs.202206409},
	keywords = {bioelectronic devices, drug delivery, photo-crosslinking, plants vasculature, polyelectrolytes},
	pages = {2206409},
}

Plant vasculature transports molecules that play a crucial role in plant signaling including systemic responses and acclimation to diverse environmental conditions. Targeted controlled delivery of molecules to the vascular tissue can be a biomimetic way to induce long distance responses, providing a new tool for the fundamental studies and engineering of stress-tolerant plants. Here, a flexible organic electronic ion pump, an electrophoretic delivery device, for controlled delivery of phytohormones directly in plant vascular tissue is developed. The c-OEIP is based on polyimide-coated glass capillaries that significantly enhance the mechanical robustness of these microscale devices while being minimally disruptive for the plant. The polyelectrolyte channel is based on low-cost and commercially available precursors that can be photocured with blue light, establishing much cheaper and safer system than the state-of-the-art. To trigger OEIP-induced plant response, the phytohormone abscisic acid (ABA) in the petiole of intact Arabidopsis plants is delivered. ABA is one of the main phytohormones involved in plant stress responses and induces stomata closure under drought conditions to reduce water loss and prevent wilting. The OEIP-mediated ABA delivery triggered fast and long-lasting stomata closure far away from the delivery point demonstrating systemic vascular transport of the delivered ABA, verified delivering deuterium-labeled ABA.

@article{routier_chitosan-modified_2023,
	title = {Chitosan-{Modified} {Polyethyleneimine} {Nanoparticles} for {Enhancing} the {Carboxylation} {Reaction} and {Plants}’ {CO2} {Uptake}},
	volume = {17},
	issn = {1936-0851},
	url = {https://doi.org/10.1021/acsnano.2c09255},
	doi = {10.1021/acsnano.2c09255},
	abstract = {Increasing plants’ photosynthetic efficiency is a major challenge that must be addressed in order to cover the food demands of the growing population in the changing climate. Photosynthesis is greatly limited at the initial carboxylation reaction, where CO2 is converted to the organic acid 3-PGA, catalyzed by the RuBisCO enzyme. RuBisCO has poor affinity for CO2, but also the CO2 concentration at the RuBisCO site is limited by the diffusion of atmospheric CO2 through the various leaf compartments to the reaction site. Beyond genetic engineering, nanotechnology can offer a materials-based approach for enhancing photosynthesis, and yet, it has mostly been explored for the light-dependent reactions. In this work, we developed polyethyleneimine-based nanoparticles for enhancing the carboxylation reaction. We demonstrate that the nanoparticles can capture CO2 in the form of bicarbonate and increase the CO2 that reacts with the RuBisCO enzyme, enhancing the 3-PGA production in in vitro assays by 20\%. The nanoparticles can be introduced to the plant via leaf infiltration and, because of the functionalization with chitosan oligomers, they do not induce any toxic effect to the plant. In the leaves, the nanoparticles localize in the apoplastic space but also spontaneously reach the chloroplasts where photosynthetic activity takes place. Their CO2 loading-dependent fluorescence verifies that, in vivo, they maintain their ability to capture CO2 and can be therefore reloaded with atmospheric CO2 while in planta. Our results contribute to the development of a nanomaterials-based CO2-concentrating mechanism in plants that can potentially increase photosynthetic efficiency and overall plants’ CO2 storage.},
	number = {4},
	urldate = {2023-03-10},
	journal = {ACS Nano},
	author = {Routier, Cyril and Vallan, Lorenzo and Daguerre, Yohann and Juvany, Marta and Istif, Emin and Mantione, Daniele and Brochon, Cyril and Hadziioannou, Georges and Strand, Åsa and Näsholm, Torgny and Cloutet, Eric and Pavlopoulou, Eleni and Stavrinidou, Eleni},
	month = feb,
	year = {2023},
	note = {Publisher: American Chemical Society},
	pages = {3430--3441},
}

Increasing plants’ photosynthetic efficiency is a major challenge that must be addressed in order to cover the food demands of the growing population in the changing climate. Photosynthesis is greatly limited at the initial carboxylation reaction, where CO2 is converted to the organic acid 3-PGA, catalyzed by the RuBisCO enzyme. RuBisCO has poor affinity for CO2, but also the CO2 concentration at the RuBisCO site is limited by the diffusion of atmospheric CO2 through the various leaf compartments to the reaction site. Beyond genetic engineering, nanotechnology can offer a materials-based approach for enhancing photosynthesis, and yet, it has mostly been explored for the light-dependent reactions. In this work, we developed polyethyleneimine-based nanoparticles for enhancing the carboxylation reaction. We demonstrate that the nanoparticles can capture CO2 in the form of bicarbonate and increase the CO2 that reacts with the RuBisCO enzyme, enhancing the 3-PGA production in in vitro assays by 20%. The nanoparticles can be introduced to the plant via leaf infiltration and, because of the functionalization with chitosan oligomers, they do not induce any toxic effect to the plant. In the leaves, the nanoparticles localize in the apoplastic space but also spontaneously reach the chloroplasts where photosynthetic activity takes place. Their CO2 loading-dependent fluorescence verifies that, in vivo, they maintain their ability to capture CO2 and can be therefore reloaded with atmospheric CO2 while in planta. Our results contribute to the development of a nanomaterials-based CO2-concentrating mechanism in plants that can potentially increase photosynthetic efficiency and overall plants’ CO2 storage.

@article{pateras_short_2023,
	title = {Short term starvation potentiates the efficacy of chemotherapy in triple negative breast cancer via metabolic reprogramming},
	volume = {21},
	issn = {1479-5876},
	url = {https://doi.org/10.1186/s12967-023-03935-9},
	doi = {10.1186/s12967-023-03935-9},
	abstract = {Chemotherapy (CT) is central to the treatment of triple negative breast cancer (TNBC), but drug toxicity and resistance place strong restrictions on treatment regimes. Fasting sensitizes cancer cells to a range of chemotherapeutic agents and also ameliorates CT-associated adverse effects. However, the molecular mechanism(s) by which fasting, or short-term starvation (STS), improves the efficacy of CT is poorly characterized.},
	number = {1},
	urldate = {2023-03-10},
	journal = {Journal of Translational Medicine},
	author = {Pateras, Ioannis S. and Williams, Chloe and Gianniou, Despoina D. and Margetis, Aggelos T. and Avgeris, Margaritis and Rousakis, Pantelis and Legaki, Aigli-Ioanna and Mirtschink, Peter and Zhang, Wei and Panoutsopoulou, Konstantina and Delis, Anastasios D. and Pagakis, Stamatis N. and Tang, Wei and Ambs, Stefan and Warpman Berglund, Ulrika and Helleday, Thomas and Varvarigou, Anastasia and Chatzigeorgiou, Antonios and Nordström, Anders and Tsitsilonis, Ourania E. and Trougakos, Ioannis P. and Gilthorpe, Jonathan D. and Frisan, Teresa},
	month = mar,
	year = {2023},
	keywords = {Breast cancer, Caloric restriction, Fasting, Metabolic reprogramming, Mitochondria, Oncological treatment, Oxidative stress, Reactive oxygen species, Starvation, Triple negative breast cancer},
	pages = {169},
}

Chemotherapy (CT) is central to the treatment of triple negative breast cancer (TNBC), but drug toxicity and resistance place strong restrictions on treatment regimes. Fasting sensitizes cancer cells to a range of chemotherapeutic agents and also ameliorates CT-associated adverse effects. However, the molecular mechanism(s) by which fasting, or short-term starvation (STS), improves the efficacy of CT is poorly characterized.

@article{hallberg-sramek_combining_2023,
	title = {Combining scientific and local knowledge improves evaluating future scenarios of forest ecosystem services},
	volume = {60},
	issn = {2212-0416},
	url = {https://www.sciencedirect.com/science/article/pii/S2212041623000049},
	doi = {10.1016/j.ecoser.2023.101512},
	abstract = {Forest scenario analysis can help tackle sustainability issues by generating insight into the potential long-term effects of present-day management. In northern Sweden, forests provide important benefits including climate change mitigation, biodiversity conservation, reindeer husbandry, local livelihoods, and recreation. Informed by local stakeholders’ views on how forests can be enabled to deliver these benefits, we created four forest management scenarios: the close-to-nature scenario (CTN) which emphasises biodiversity conservation, the classic management scenario (CLA) optimising the forests’ net present value, the intensified scenario (INT) maximising harvested wood from the forest, and the combined scenario (COM) applying a combination of measures from the CTN and INT. The scenarios were applied to the local forest landscape and modelled over a 100-year simulation period, and the results of the modelling were then evaluated by a diverse group of stakeholders. For most ecosystem services, there was a time lag of 10–50 years before noticeable effects and differences between the scenarios became evident, highlighting the need to consider both the short- and long-term effects of forest management. Evaluation by the stakeholders put the modelled results into a local context. They raised considerations relating to wildlife and hunting, climate change risks, social acceptability, and conflict, highlighting the value of evaluating the scenarios qualitatively as well as quantitatively. Overall, stakeholders thought that the CTN and CLA scenarios promoted more ecosystem services and posed fewer climate risks, while also creating less conflict among stakeholders. Our results emphasise the value of combining scientific and local knowledge when developing and evaluating future forest scenarios.},
	language = {en},
	urldate = {2023-03-10},
	journal = {Ecosystem Services},
	author = {Hallberg-Sramek, Isabella and Nordström, Eva-Maria and Priebe, Janina and Reimerson, Elsa and Mårald, Erland and Nordin, Annika},
	month = apr,
	year = {2023},
	keywords = {Forest management, Indigenous and local knowledge, Inter- and transdisciplinary research, Knowledge co-production, Scenario modelling, Stakeholder participation},
	pages = {101512},
}

Forest scenario analysis can help tackle sustainability issues by generating insight into the potential long-term effects of present-day management. In northern Sweden, forests provide important benefits including climate change mitigation, biodiversity conservation, reindeer husbandry, local livelihoods, and recreation. Informed by local stakeholders’ views on how forests can be enabled to deliver these benefits, we created four forest management scenarios: the close-to-nature scenario (CTN) which emphasises biodiversity conservation, the classic management scenario (CLA) optimising the forests’ net present value, the intensified scenario (INT) maximising harvested wood from the forest, and the combined scenario (COM) applying a combination of measures from the CTN and INT. The scenarios were applied to the local forest landscape and modelled over a 100-year simulation period, and the results of the modelling were then evaluated by a diverse group of stakeholders. For most ecosystem services, there was a time lag of 10–50 years before noticeable effects and differences between the scenarios became evident, highlighting the need to consider both the short- and long-term effects of forest management. Evaluation by the stakeholders put the modelled results into a local context. They raised considerations relating to wildlife and hunting, climate change risks, social acceptability, and conflict, highlighting the value of evaluating the scenarios qualitatively as well as quantitatively. Overall, stakeholders thought that the CTN and CLA scenarios promoted more ecosystem services and posed fewer climate risks, while also creating less conflict among stakeholders. Our results emphasise the value of combining scientific and local knowledge when developing and evaluating future forest scenarios.

@article{derba-maceluch_xylan_2023,
	title = {Xylan glucuronic acid side chains fix suberin-like aliphatic compounds to wood cell walls},
	volume = {238},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.18712},
	doi = {10.1111/nph.18712},
	abstract = {Wood is the most important repository of assimilated carbon in the biosphere, in the form of large polymers (cellulose, hemicelluloses including glucuronoxylan, and lignin) that interactively form a composite, together with soluble extractives including phenolic and aliphatic compounds. Molecular interactions among these compounds are not fully understood. We have targeted the expression of a fungal α-glucuronidase to the wood cell wall of aspen (Populus tremula L. × tremuloides Michx.) and Arabidopsis (Arabidopsis thaliana (L.) Heynh), to decrease contents of the 4-O-methyl glucuronopyranose acid (mGlcA) substituent of xylan, to elucidate mGlcA's functions. The enzyme affected the content of aliphatic insoluble cell wall components having composition similar to suberin, which required mGlcA for binding to cell walls. Such suberin-like compounds have been previously identified in decayed wood, but here, we show their presence in healthy wood of both hardwood and softwood species. By contrast, γ-ester bonds between mGlcA and lignin were insensitive to cell wall-localized α-glucuronidase, supporting the intracellular formation of these bonds. These findings challenge the current view of the wood cell wall composition and reveal a novel function of mGlcA substituent of xylan in fastening of suberin-like compounds to cell wall. They also suggest an intracellular initiation of lignin–carbohydrate complex assembly.},
	language = {en},
	number = {1},
	urldate = {2023-03-10},
	journal = {New Phytologist},
	author = {Derba-Maceluch, Marta and Mitra, Madhusree and Hedenström, Mattias and Liu, Xiaokun and Gandla, Madhavi L. and Barbut, Félix R. and Abreu, Ilka N. and Donev, Evgeniy N. and Urbancsok, János and Moritz, Thomas and Jönsson, Leif J. and Tsang, Adrian and Powlowski, Justin and Master, Emma R. and Mellerowicz, Ewa J.},
	month = jan,
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.18712},
	keywords = {Populus, lignin-carbohydrate complexes (LCCs), lignin–carbohydrate complexes, saccharification, suberin, wood cell wall, xylan},
	pages = {297--312},
}

Wood is the most important repository of assimilated carbon in the biosphere, in the form of large polymers (cellulose, hemicelluloses including glucuronoxylan, and lignin) that interactively form a composite, together with soluble extractives including phenolic and aliphatic compounds. Molecular interactions among these compounds are not fully understood. We have targeted the expression of a fungal α-glucuronidase to the wood cell wall of aspen (Populus tremula L. × tremuloides Michx.) and Arabidopsis (Arabidopsis thaliana (L.) Heynh), to decrease contents of the 4-O-methyl glucuronopyranose acid (mGlcA) substituent of xylan, to elucidate mGlcA's functions. The enzyme affected the content of aliphatic insoluble cell wall components having composition similar to suberin, which required mGlcA for binding to cell walls. Such suberin-like compounds have been previously identified in decayed wood, but here, we show their presence in healthy wood of both hardwood and softwood species. By contrast, γ-ester bonds between mGlcA and lignin were insensitive to cell wall-localized α-glucuronidase, supporting the intracellular formation of these bonds. These findings challenge the current view of the wood cell wall composition and reveal a novel function of mGlcA substituent of xylan in fastening of suberin-like compounds to cell wall. They also suggest an intracellular initiation of lignin–carbohydrate complex assembly.

@article{chowdhury_fluorogenic_2023,
	title = {Fluorogenic properties of 4-dimethylaminocinnamaldehyde ({DMACA}) enable high resolution imaging of cell-wall-bound proanthocyanidins in plant root tissues},
	volume = {13},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2022.1060804},
	doi = {10.3389/fpls.2022.1060804},
	abstract = {Proanthocyanidins (PAs) are polymeric phenolic compounds found in plants and used in many industrial applications. Despite strong evidence of herbivore and pathogen resistance-related properties of PAs, their in planta function is not fully understood. Determining the location and dynamics of PAs in plant tissues and cellular compartments is crucial to understand their mode of action. Such an approach requires microscopic localization with fluorescent dyes that specifically bind to PAs. Such dyes have hitherto been lacking. Here, we show that 4-dimethylaminocinnamaldehyde (DMACA) can be used as a PA-specific fluorescent dye that allows localization of PAs at high resolution in cell walls and inside cells using confocal microscopy, revealing features of previously unreported wall-bound PAs. We demonstrate several novel usages of DMACA as a fluorophore by taking advantage of its double staining compatibility with other fluorescent dyes. We illustrate the use of the dye alone and its co-localization with cell wall polymers in different Populus root tissues. The easy-to-use fluorescent staining method, together with its high photostability and compatibility with other fluorogenic dyes, makes DMACA a valuable tool for uncovering the biological function of PAs at a cellular level in plant tissues. DMACA can also be used in other plant tissues than roots, however care needs to be taken when tissues contain compounds that autofluoresce in the red spectral region which can be confounded with the PA-specific DMACA signal.},
	urldate = {2023-02-10},
	journal = {Frontiers in Plant Science},
	author = {Chowdhury, Jamil and Ferdous, Jannatul and Lihavainen, Jenna and Albrectsen, Benedicte Riber and Lundberg-Felten, Judith},
	month = feb,
	year = {2023},
	keywords = {⛔ No DOI found},
}

Proanthocyanidins (PAs) are polymeric phenolic compounds found in plants and used in many industrial applications. Despite strong evidence of herbivore and pathogen resistance-related properties of PAs, their in planta function is not fully understood. Determining the location and dynamics of PAs in plant tissues and cellular compartments is crucial to understand their mode of action. Such an approach requires microscopic localization with fluorescent dyes that specifically bind to PAs. Such dyes have hitherto been lacking. Here, we show that 4-dimethylaminocinnamaldehyde (DMACA) can be used as a PA-specific fluorescent dye that allows localization of PAs at high resolution in cell walls and inside cells using confocal microscopy, revealing features of previously unreported wall-bound PAs. We demonstrate several novel usages of DMACA as a fluorophore by taking advantage of its double staining compatibility with other fluorescent dyes. We illustrate the use of the dye alone and its co-localization with cell wall polymers in different Populus root tissues. The easy-to-use fluorescent staining method, together with its high photostability and compatibility with other fluorogenic dyes, makes DMACA a valuable tool for uncovering the biological function of PAs at a cellular level in plant tissues. DMACA can also be used in other plant tissues than roots, however care needs to be taken when tissues contain compounds that autofluoresce in the red spectral region which can be confounded with the PA-specific DMACA signal.

@article{siddique_molecular_2023,
	title = {Molecular studies of rust on {European} aspen suggest an autochthonous relationship shaped by genotype},
	volume = {14},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2023.1111001},
	doi = {10.3389/fpls.2023.1111001},
	abstract = {Forests are at increasing risk from pathogen outbreak. Climate change for example enhance the risk of local disease outbreaks, and naturalization of exotic pathogens may follow human activities, warranting robust pest surveillance routines to support forest management. Melampsora pinitorqua (pine twisting rust) is of concern in Swedish forestry, and here we evaluate the use of visible rust scores (VRS) on its obligate summer host, European aspen (Populus tremula) as a tool for quantification of the pathogen. With use of species-specific primers, we could detect the native rust, but we failed to detect two exotic rusts (M. medusae and M. larici-populina). We found that aspen genotype determined the presence of fungal genetic markers (amplifying the ITS2 region of the fungal rDNA sequence) as well as DNA sequences specific to M. pinitorqua. We correlated VRS with the amount of fungal DNA in the same leaf, and we related the findings to aspen genotype-specific parameters such as the ability to synthesize and store leaf condensed tannins (CT).  At the genotype level both positive and negative relationships were observed between CTs, fungal markers, and rust infestations. However, at the population level, foliar CT concentrations correlated negatively with general fungal- and rust-specific marker abundances.  Our results, therefore, do not support the use of VRS to assess Melampsora infestation in Aspen. They do, however, suggest that the relationship between European aspen and rust infestation may be characterized as autochthonous in northern Sweden.},
	urldate = {2023-02-24},
	journal = {Frontiers in Plant Science},
	author = {Siddique, Abu Bakar and Menke, Laura and Dinedurga, Melis and Albrectsen, Benedicte Riber},
	month = feb,
	year = {2023},
}

Forests are at increasing risk from pathogen outbreak. Climate change for example enhance the risk of local disease outbreaks, and naturalization of exotic pathogens may follow human activities, warranting robust pest surveillance routines to support forest management. Melampsora pinitorqua (pine twisting rust) is of concern in Swedish forestry, and here we evaluate the use of visible rust scores (VRS) on its obligate summer host, European aspen (Populus tremula) as a tool for quantification of the pathogen. With use of species-specific primers, we could detect the native rust, but we failed to detect two exotic rusts (M. medusae and M. larici-populina). We found that aspen genotype determined the presence of fungal genetic markers (amplifying the ITS2 region of the fungal rDNA sequence) as well as DNA sequences specific to M. pinitorqua. We correlated VRS with the amount of fungal DNA in the same leaf, and we related the findings to aspen genotype-specific parameters such as the ability to synthesize and store leaf condensed tannins (CT). At the genotype level both positive and negative relationships were observed between CTs, fungal markers, and rust infestations. However, at the population level, foliar CT concentrations correlated negatively with general fungal- and rust-specific marker abundances. Our results, therefore, do not support the use of VRS to assess Melampsora infestation in Aspen. They do, however, suggest that the relationship between European aspen and rust infestation may be characterized as autochthonous in northern Sweden.

@article{ntefidou_physcomitrium_2023,
	title = {Physcomitrium patens {PpRIC}, an ancestral {CRIB}-domain {ROP} effector, inhibits auxin-induced differentiation of apical initial cells},
	volume = {42},
	issn = {2211-1247},
	url = {https://www.cell.com/cell-reports/abstract/S2211-1247(23)00141-9},
	doi = {10.1016/j.celrep.2023.112130},
	abstract = {RHO guanosine triphosphatases are important eukaryotic regulators of cell differentiation and behavior. Plant ROP (RHO of plant) family members activate specific, incompletely characterized downstream signaling. The structurally simple land plant Physcomitrium patens is missing homologs of key animal and flowering plant RHO effectors but contains a single CRIB (CDC42/RAC interactive binding)-domain-containing RIC (ROP-interacting CRIB-containing) protein (PpRIC). Protonemal P. patens filaments elongate based on regular division and PpROP-dependent tip growth of apical initial cells, which upon stimulation by the hormone auxin differentiate caulonemal characteristics. PpRIC interacts with active PpROP1, co-localizes with this protein at the plasma membrane at the tip of apical initial cells, and accumulates in the nucleus. Remarkably, PpRIC is not required for tip growth but is targeted to the nucleus to block caulonema differentiation downstream of auxin-controlled gene expression. These observations establish functions of PpRIC in mediating crosstalk between ROP and auxin signaling, which contributes to the maintenance of apical initial cell identity.},
	language = {English},
	number = {2},
	urldate = {2023-02-23},
	journal = {Cell Reports},
	author = {Ntefidou, Maria and Eklund, D. Magnus and Bail, Aude Le and Schulmeister, Sylwia and Scherbel, Franziska and Brandl, Lisa and Dörfler, Wolfgang and Eichstädt, Chantal and Bannmüller, Anna and Ljung, Karin and Kost, Benedikt},
	month = feb,
	year = {2023},
	pmid = {36790931},
	note = {Publisher: Elsevier},
	keywords = {CP: Developmental biology, CP: Plants, CRIB domain, Physcomitrium patens, RHO/ROP GTPases, RHO/ROP effectors, auxin, cell differentiation, initial cells, land plant evolution, nuclear targeting, tip growth},
}

RHO guanosine triphosphatases are important eukaryotic regulators of cell differentiation and behavior. Plant ROP (RHO of plant) family members activate specific, incompletely characterized downstream signaling. The structurally simple land plant Physcomitrium patens is missing homologs of key animal and flowering plant RHO effectors but contains a single CRIB (CDC42/RAC interactive binding)-domain-containing RIC (ROP-interacting CRIB-containing) protein (PpRIC). Protonemal P. patens filaments elongate based on regular division and PpROP-dependent tip growth of apical initial cells, which upon stimulation by the hormone auxin differentiate caulonemal characteristics. PpRIC interacts with active PpROP1, co-localizes with this protein at the plasma membrane at the tip of apical initial cells, and accumulates in the nucleus. Remarkably, PpRIC is not required for tip growth but is targeted to the nucleus to block caulonema differentiation downstream of auxin-controlled gene expression. These observations establish functions of PpRIC in mediating crosstalk between ROP and auxin signaling, which contributes to the maintenance of apical initial cell identity.

@article{le_provost_oak_2023,
	title = {Oak stands along an elevation gradient have different molecular strategies for regulating bud phenology},
	volume = {23},
	issn = {1471-2229},
	url = {https://doi.org/10.1186/s12870-023-04069-2},
	doi = {10.1186/s12870-023-04069-2},
	abstract = {Global warming raises serious concerns about the persistence of species and populations locally adapted to their environment, simply because of the shift it produces in their adaptive landscape. For instance, the phenological cycle of tree species may be strongly affected by higher winter temperatures and late frost in spring. Given the variety of ecosystem services they provide, the question of forest tree adaptation has received increasing attention in the scientific community and catalyzed research efforts in ecology, evolutionary biology and functional genomics to study their adaptive capacity to respond to such perturbations.},
	number = {1},
	urldate = {2023-03-03},
	journal = {BMC Plant Biology},
	author = {Le Provost, Gregoire and Lalanne, Céline and Lesur, Isabelle and Louvet, Jean-Marc and Delzon, Sylvain and Kremer, Antoine and Labadie, Karine and Aury, Jean-Marc and Da Silva, Corinne and Moritz, Thomas and Plomion, Christophe},
	month = feb,
	year = {2023},
	keywords = {Bud phenology, Elevation cline, Gene expression, Hormone quantification, Response to temperature, Sessile oak},
	pages = {108},
}

Global warming raises serious concerns about the persistence of species and populations locally adapted to their environment, simply because of the shift it produces in their adaptive landscape. For instance, the phenological cycle of tree species may be strongly affected by higher winter temperatures and late frost in spring. Given the variety of ecosystem services they provide, the question of forest tree adaptation has received increasing attention in the scientific community and catalyzed research efforts in ecology, evolutionary biology and functional genomics to study their adaptive capacity to respond to such perturbations.

@article{nie_gapless_2023,
	title = {Gapless genome assembly of azalea and multi-omics investigation into divergence between two species with distinct flower color},
	volume = {10},
	issn = {2052-7276},
	url = {https://doi.org/10.1093/hr/uhac241},
	doi = {10.1093/hr/uhac241},
	abstract = {The genus Rhododendron (Ericaceae), with more than 1000 species highly diverse in flower color, is providing distinct ornamental values and a model system for flower color studies. Here, we investigated the divergence between two parental species with different flower color widely used for azalea breeding. Gapless genome assembly was generated for the yellow-flowered azalea, Rhododendron molle. Comparative genomics found recent proliferation of  long terminal repeat retrotransposons (LTR-RTs), especially Gypsy, has resulted in a 125 Mb (19\%) genome size increase in species-specific regions, and a significant amount of dispersed gene duplicates (13 402) and pseudogenes (17 437). Metabolomic assessment revealed that yellow flower coloration is attributed to the dynamic changes of carotenoids/flavonols biosynthesis and chlorophyll degradation. Time-ordered gene co-expression networks (TO-GCNs) and the comparison confirmed the metabolome and uncovered the specific gene regulatory changes underpinning the distinct flower pigmentation. B3 and ERF TFs were found dominating the gene regulation of carotenoids/flavonols characterized pigmentation in R. molle, while WRKY, ERF, WD40, C2H2, and NAC TFs collectively regulated the anthocyanins characterized pigmentation in the red-flowered R simsii. This study employed a multi-omics strategy in disentangling the complex divergence between two important azaleas and provided references for further functional genetics and molecular breeding.},
	number = {1},
	urldate = {2023-03-03},
	journal = {Horticulture Research},
	author = {Nie, Shuai and Zhao, Shi-Wei and Shi, Tian-Le and Zhao, Wei and Zhang, Ren-Gang and Tian, Xue-Chan and Guo, Jing-Fang and Yan, Xue-Mei and Bao, Yu-Tao and Li, Zhi-Chao and Kong, Lei and Ma, Hai-Yao and Chen, Zhao-Yang and Liu, Hui and El-Kassaby, Yousry A and Porth, Ilga and Yang, Fu-Sheng and Mao, Jian-Feng},
	month = jan,
	year = {2023},
	pages = {uhac241},
}

The genus Rhododendron (Ericaceae), with more than 1000 species highly diverse in flower color, is providing distinct ornamental values and a model system for flower color studies. Here, we investigated the divergence between two parental species with different flower color widely used for azalea breeding. Gapless genome assembly was generated for the yellow-flowered azalea, Rhododendron molle. Comparative genomics found recent proliferation of long terminal repeat retrotransposons (LTR-RTs), especially Gypsy, has resulted in a 125 Mb (19%) genome size increase in species-specific regions, and a significant amount of dispersed gene duplicates (13 402) and pseudogenes (17 437). Metabolomic assessment revealed that yellow flower coloration is attributed to the dynamic changes of carotenoids/flavonols biosynthesis and chlorophyll degradation. Time-ordered gene co-expression networks (TO-GCNs) and the comparison confirmed the metabolome and uncovered the specific gene regulatory changes underpinning the distinct flower pigmentation. B3 and ERF TFs were found dominating the gene regulation of carotenoids/flavonols characterized pigmentation in R. molle, while WRKY, ERF, WD40, C2H2, and NAC TFs collectively regulated the anthocyanins characterized pigmentation in the red-flowered R simsii. This study employed a multi-omics strategy in disentangling the complex divergence between two important azaleas and provided references for further functional genetics and molecular breeding.

@article{boussardon_tissue-specific_2023,
	title = {Tissue-{Specific} {Isolation} of {Tagged} {Arabidopsis} {Plastids}},
	volume = {3},
	issn = {2691-1299},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/cpz1.673},
	doi = {10.1002/cpz1.673},
	abstract = {Plastids are found in all plant cell types. However, most extraction methods to study these organelles are performed at the organ level (e.g., leaf, root, fruit) and do not allow for tissue-specific resolution, which hinders our understanding of their physiology. Therefore, IPTACT (Isolation of Plastids TAgged in specific Cell Types) was developed to isolate plastids in a tissue-specific manner in Arabidopsis thaliana (Arabidopsis). Plastids are biotinylated using one-shot transgenic lines, and tissue specificity is achieved with a suitable promoter as long as such a promoter exists. Cell-specific biotinylated plastids are then isolated with 2.8-µm streptavidin beads. Plastids extracted by IPTACT are suitable for RNA or protein isolation and subsequent tissue-specific OMICs analyses. This method provides the user with a powerful tool to investigate plastidial functions at cell-type resolution. Furthermore, it can easily be combined with studies using diverse genetic backgrounds and/or different developmental or stress conditions. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Promoter cloning and plant selection Basic Protocol 2: Isolation of biotinylated plastids Basic Protocol 3: Quality control of isolated plastids},
	language = {en},
	number = {2},
	urldate = {2023-02-22},
	journal = {Current Protocols},
	author = {Boussardon, Clément and Keech, Olivier},
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/cpz1.673},
	keywords = {Arabidopsis, biotin-streptavidin interaction, editable Golden Gate plasmids, plastids, tissue-specific isolation},
	pages = {e673},
}

Plastids are found in all plant cell types. However, most extraction methods to study these organelles are performed at the organ level (e.g., leaf, root, fruit) and do not allow for tissue-specific resolution, which hinders our understanding of their physiology. Therefore, IPTACT (Isolation of Plastids TAgged in specific Cell Types) was developed to isolate plastids in a tissue-specific manner in Arabidopsis thaliana (Arabidopsis). Plastids are biotinylated using one-shot transgenic lines, and tissue specificity is achieved with a suitable promoter as long as such a promoter exists. Cell-specific biotinylated plastids are then isolated with 2.8-µm streptavidin beads. Plastids extracted by IPTACT are suitable for RNA or protein isolation and subsequent tissue-specific OMICs analyses. This method provides the user with a powerful tool to investigate plastidial functions at cell-type resolution. Furthermore, it can easily be combined with studies using diverse genetic backgrounds and/or different developmental or stress conditions. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Promoter cloning and plant selection Basic Protocol 2: Isolation of biotinylated plastids Basic Protocol 3: Quality control of isolated plastids

@article{donev_field_2023,
	title = ,
	issn = {1467-7652},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pbi.14012},
	doi = {10.1111/pbi.14012},
	abstract = {Trees constitute promising renewable feedstocks for biorefinery using biochemical conversion, but their recalcitrance restricts their attractiveness for the industry. To obtain trees with reduced recalcitrance, large-scale genetic engineering experiments were performed in hybrid aspen blindly targeting genes expressed during wood formation and 32 lines representing seven constructs were selected for characterization in the field. Here we report phenotypes of five-year old trees considering 49 traits related to growth and wood properties. The best performing construct considering growth and glucose yield in saccharification with acid pretreatment had suppressed expression of the gene encoding an uncharacterized 2-oxoglutarate-dependent dioxygenase (2OGD). It showed minor changes in wood chemistry but increased nanoporosity and glucose conversion. Suppressed levels of SUCROSE SYNTHASE, (SuSy), CINNAMATE 4-HYDROXYLASE (C4H), and increased levels of GTPase activating protein for ADP-ribosylation factor ZAC led to significant growth reductions and anatomical abnormalities. However, C4H and SuSy constructs greatly improved glucose yields in saccharification without and with pretreatment, respectively. Traits associated with high glucose yields were different for saccharification with and without pretreatment. While carbohydrates, phenolics and tension wood contents positively impacted the yields without pretreatment and growth, lignin content and S/G ratio were negative factors, the yields with pretreatment positively correlated with S lignin, and negatively with carbohydrate contents. The genotypes with high glucose yields had increased nanoporosity and mGlcA/Xyl ratio, and some had shorter polymers extractable with subcritical water compared to wild-type. The pilot-scale industrial-like pretreatment of best performing 2OGD construct confirmed its superior sugar yields, supporting our strategy.},
	language = {en},
	urldate = {2023-01-26},
	journal = {Plant Biotechnology Journal},
	author = {Donev, Evgeniy N. and Derba-Maceluch, Marta and Yassin, Zakiya and Gandla, Madhavi Latha and Sivan, Pramod and Heinonen, Saara E. and Kumar, Vikash and Scheepers, Gerhard and Vilaplana, Francisco and Johansson, Ulf and Hertzberg, Magnus and Sundberg, Björn and Winestrand, Sandra and Hörnberg, Andreas and Alriksson, Björn and Jönsson, Leif J. and Mellerowicz, Ewa J.},
	month = jan,
	year = {2023},
	keywords = {BET analysis, Populus, SilviScan, enzymatic saccharification, field trial, secondary cell wall, subcritical water extraction, transgenic trees, wood quality},
}

Trees constitute promising renewable feedstocks for biorefinery using biochemical conversion, but their recalcitrance restricts their attractiveness for the industry. To obtain trees with reduced recalcitrance, large-scale genetic engineering experiments were performed in hybrid aspen blindly targeting genes expressed during wood formation and 32 lines representing seven constructs were selected for characterization in the field. Here we report phenotypes of five-year old trees considering 49 traits related to growth and wood properties. The best performing construct considering growth and glucose yield in saccharification with acid pretreatment had suppressed expression of the gene encoding an uncharacterized 2-oxoglutarate-dependent dioxygenase (2OGD). It showed minor changes in wood chemistry but increased nanoporosity and glucose conversion. Suppressed levels of SUCROSE SYNTHASE, (SuSy), CINNAMATE 4-HYDROXYLASE (C4H), and increased levels of GTPase activating protein for ADP-ribosylation factor ZAC led to significant growth reductions and anatomical abnormalities. However, C4H and SuSy constructs greatly improved glucose yields in saccharification without and with pretreatment, respectively. Traits associated with high glucose yields were different for saccharification with and without pretreatment. While carbohydrates, phenolics and tension wood contents positively impacted the yields without pretreatment and growth, lignin content and S/G ratio were negative factors, the yields with pretreatment positively correlated with S lignin, and negatively with carbohydrate contents. The genotypes with high glucose yields had increased nanoporosity and mGlcA/Xyl ratio, and some had shorter polymers extractable with subcritical water compared to wild-type. The pilot-scale industrial-like pretreatment of best performing 2OGD construct confirmed its superior sugar yields, supporting our strategy.

@article{jonsson_multiple_2023,
	title = {Multiple mechanisms behind plant bending},
	volume = {9},
	copyright = {2022 Springer Nature Limited},
	issn = {2055-0278},
	url = {https://www.nature.com/articles/s41477-022-01310-y},
	doi = {10.1038/s41477-022-01310-y},
	abstract = {To survive, plants constantly adapt their body shape to their environment. This often involves remarkably rapid bending of their organs such as stems, leaves and roots. Since plant cells are enclosed by stiff cell walls, they use various strategies for bending their organs, which differ from bending mechanisms of soft animal tissues and involve larger physical forces. Here we attempt to summarize and link different viewpoints on bending mechanisms: genes and signalling, mathematical modelling and biomechanics. We argue that quantifying cell growth and physical forces could open a new level in our understanding of bending and resolve some of its paradoxes.},
	language = {en},
	number = {1},
	urldate = {2023-02-03},
	journal = {Nature Plants},
	author = {Jonsson, Kristoffer and Ma, Yuan and Routier-Kierzkowska, Anne-Lise and Bhalerao, Rishikesh P.},
	month = jan,
	year = {2023},
	keywords = {Plant morphogenesis, Tropism},
	pages = {13--21},
}

To survive, plants constantly adapt their body shape to their environment. This often involves remarkably rapid bending of their organs such as stems, leaves and roots. Since plant cells are enclosed by stiff cell walls, they use various strategies for bending their organs, which differ from bending mechanisms of soft animal tissues and involve larger physical forces. Here we attempt to summarize and link different viewpoints on bending mechanisms: genes and signalling, mathematical modelling and biomechanics. We argue that quantifying cell growth and physical forces could open a new level in our understanding of bending and resolve some of its paradoxes.

@article{igamberdiev_toward_2023,
	title = {Toward understanding the emergence of life: {A} dual function of the system of nucleotides in the metabolically closed autopoietic organization},
	volume = {224},
	issn = {0303-2647},
	shorttitle = {Toward understanding the emergence of life},
	url = {https://www.sciencedirect.com/science/article/pii/S0303264723000126},
	doi = {10.1016/j.biosystems.2023.104837},
	abstract = {General structure of metabolism includes the reproduction of catalysts that govern metabolism. In this structure, the system becomes autopoietic in the sense of Maturana and Varela, and it is closed to efficient causation as defined by Robert Rosen. The autopoietic maintenance and operation of the catalysts takes place via the set of free nucleotides while the synthesis of catalysts occurs via the information encoded by the set of nucleotides arranged in polymers of RNA and DNA. Both energy charge and genetic information use the components of the same pool of nucleoside triphosphates, which is equilibrated by thermodynamic buffering enzymes such as nucleoside diphosphate kinase and adenylate kinase. This occurs in a way that the system becomes internally stable and metabolically closed, which initially could be realized at the level of ribozymes catalyzing basic metabolic reactions as well as own reproduction. The function of ATP, GTP, UTP, and CTP is dual, as these species participate both in the general metabolism as free nucleotides and in the transfer of genetic information via covalent polymerization to nucleic acids. The changes in their pools directly impact both bioenergetic pathways and nucleic acid turnover. Here we outline the concept of metabolic closure of biosystems grounded in the dual function of nucleotide coenzymes that serve both as energetic and informational molecules and through this duality generate the autopoietic performance and the ability for codepoietic evolutionary transformations of living systems starting from the emergence of prebiotic systems.},
	language = {en},
	urldate = {2023-01-20},
	journal = {Biosystems},
	author = {Igamberdiev, Abir U. and Kleczkowski, Leszek A.},
	month = feb,
	year = {2023},
	keywords = {Autopoiesis, Codepoiesis, Coenzyme, Metabolic closure, Nucleoside triphosphates, Ribozymes, Thermodynamic buffering},
	pages = {104837},
}

General structure of metabolism includes the reproduction of catalysts that govern metabolism. In this structure, the system becomes autopoietic in the sense of Maturana and Varela, and it is closed to efficient causation as defined by Robert Rosen. The autopoietic maintenance and operation of the catalysts takes place via the set of free nucleotides while the synthesis of catalysts occurs via the information encoded by the set of nucleotides arranged in polymers of RNA and DNA. Both energy charge and genetic information use the components of the same pool of nucleoside triphosphates, which is equilibrated by thermodynamic buffering enzymes such as nucleoside diphosphate kinase and adenylate kinase. This occurs in a way that the system becomes internally stable and metabolically closed, which initially could be realized at the level of ribozymes catalyzing basic metabolic reactions as well as own reproduction. The function of ATP, GTP, UTP, and CTP is dual, as these species participate both in the general metabolism as free nucleotides and in the transfer of genetic information via covalent polymerization to nucleic acids. The changes in their pools directly impact both bioenergetic pathways and nucleic acid turnover. Here we outline the concept of metabolic closure of biosystems grounded in the dual function of nucleotide coenzymes that serve both as energetic and informational molecules and through this duality generate the autopoietic performance and the ability for codepoietic evolutionary transformations of living systems starting from the emergence of prebiotic systems.

@article{kidwai_species-specific_2023,
	title = {Species-specific transcriptional reprogramming during adventitious root initiation},
	volume = {28},
	issn = {1360-1385},
	url = {https://www.sciencedirect.com/science/article/pii/S1360138522003028},
	doi = {10.1016/j.tplants.2022.11.003},
	abstract = {Adventitious roots or shoot-borne roots transdifferentiate from cells close to vascular tissues after cell reprogramming, which is associated with increased transcriptional activity. Recently, Garg et al. provided a genome-wide landscape of transcriptional signatures during the early stages of adventitious root initiation in rice and showed that conserved transcription factors acquire species-specific function.},
	language = {en},
	number = {2},
	urldate = {2023-01-26},
	journal = {Trends in Plant Science},
	author = {Kidwai, Maria and Mishra, Priyanka and Bellini, Catherine},
	month = feb,
	year = {2023},
	keywords = {adventitious root, dicotyledons, epigenetic regulation, monocotyledons, transcription factors},
	pages = {128--130},
}

Adventitious roots or shoot-borne roots transdifferentiate from cells close to vascular tissues after cell reprogramming, which is associated with increased transcriptional activity. Recently, Garg et al. provided a genome-wide landscape of transcriptional signatures during the early stages of adventitious root initiation in rice and showed that conserved transcription factors acquire species-specific function.

@article{rohricht_mitochondrial_2023,
	title = {Mitochondrial ferredoxin-like is essential for forming complex {I}-containing supercomplexes in {Arabidopsis}},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiad040},
	doi = {10.1093/plphys/kiad040},
	abstract = {In eukaryotes, mitochondrial ATP is mainly produced by the oxidative phosphorylation (OXPHOS) system, which is composed of five multiprotein complexes (complexes I to V). Analyses of the OXPHOS system by native gel electrophoresis have revealed an organization of OXPHOS complexes into supercomplexes, but their roles and assembly pathways remain unclear. In this study, we characterized an atypical mitochondrial ferredoxin (mitochondrial ferredoxin-like, mFDX-like). This protein was previously found to be part of the bridge domain linking the matrix and membrane arms of the complex I. Phylogenetic analysis suggested that the Arabidopsis (Arabidopsis thaliana) mFDX-like evolved from classical mitochondrial ferredoxin but lost one of the cysteines required for the coordination of the iron-sulfur (Fe-S) cluster, supposedly essential for the electron transfer function of ferredoxins. Accordingly, our biochemical study showed that AtmFDX-like does not bind an Fe-S cluster and is therefore unlikely to be involved in electron transfer reactions. To study the function of mFDX-like, we created deletion lines in Arabidopsis using a CRISPR/Cas9-based strategy. These lines did not show any abnormal phenotype under standard growth conditions. However, the characterization of the OXPHOS system demonstrated that mFDX-like is important for the assembly of complex I and essential for the formation of complex I-containing supercomplexes. We propose that mFDX-like and the bridge domain are required for the correct conformation of the membrane arm of complex I that is essential for the association of complex I with complex III to form supercomplexes.},
	urldate = {2023-01-26},
	journal = {Plant Physiology},
	author = {Röhricht, Helene and Przybyla-Toscano, Jonathan and Forner, Joachim and Boussardon, Clément and Keech, Olivier and Rouhier, Nicolas and Meyer, Etienne H},
	month = jan,
	year = {2023},
	pages = {kiad040},
}

In eukaryotes, mitochondrial ATP is mainly produced by the oxidative phosphorylation (OXPHOS) system, which is composed of five multiprotein complexes (complexes I to V). Analyses of the OXPHOS system by native gel electrophoresis have revealed an organization of OXPHOS complexes into supercomplexes, but their roles and assembly pathways remain unclear. In this study, we characterized an atypical mitochondrial ferredoxin (mitochondrial ferredoxin-like, mFDX-like). This protein was previously found to be part of the bridge domain linking the matrix and membrane arms of the complex I. Phylogenetic analysis suggested that the Arabidopsis (Arabidopsis thaliana) mFDX-like evolved from classical mitochondrial ferredoxin but lost one of the cysteines required for the coordination of the iron-sulfur (Fe-S) cluster, supposedly essential for the electron transfer function of ferredoxins. Accordingly, our biochemical study showed that AtmFDX-like does not bind an Fe-S cluster and is therefore unlikely to be involved in electron transfer reactions. To study the function of mFDX-like, we created deletion lines in Arabidopsis using a CRISPR/Cas9-based strategy. These lines did not show any abnormal phenotype under standard growth conditions. However, the characterization of the OXPHOS system demonstrated that mFDX-like is important for the assembly of complex I and essential for the formation of complex I-containing supercomplexes. We propose that mFDX-like and the bridge domain are required for the correct conformation of the membrane arm of complex I that is essential for the association of complex I with complex III to form supercomplexes.

@article{chandra_transformer-based_2023,
	title = {Transformer-based deep learning for predicting protein properties in the life sciences},
	volume = {12},
	issn = {2050-084X},
	url = {https://doi.org/10.7554/eLife.82819},
	doi = {10.7554/eLife.82819},
	abstract = {Recent developments in deep learning, coupled with an increasing number of sequenced proteins, have led to a breakthrough in life science applications, in particular in protein property prediction. There is hope that deep learning can close the gap between the number of sequenced proteins and proteins with known properties based on lab experiments. Language models from the field of natural language processing have gained popularity for protein property predictions and have led to a new computational revolution in biology, where old prediction results are being improved regularly. Such models can learn useful multipurpose representations of proteins from large open repositories of protein sequences and can be used, for instance, to predict protein properties. The field of natural language processing is growing quickly because of developments in a class of models based on a particular model—the Transformer model. We review recent developments and the use of large-scale Transformer models in applications for predicting protein characteristics and how such models can be used to predict, for example, post-translational modifications. We review shortcomings of other deep learning models and explain how the Transformer models have quickly proven to be a very promising way to unravel information hidden in the sequences of amino acids.},
	urldate = {2023-01-20},
	journal = {eLife},
	author = {Chandra, Abel and Tünnermann, Laura and Löfstedt, Tommy and Gratz, Regina},
	editor = {Dötsch, Volker},
	month = jan,
	year = {2023},
	keywords = {deep learning, life sciences, machine learning, protein property prediction, transformers},
	pages = {e82819},
}

Recent developments in deep learning, coupled with an increasing number of sequenced proteins, have led to a breakthrough in life science applications, in particular in protein property prediction. There is hope that deep learning can close the gap between the number of sequenced proteins and proteins with known properties based on lab experiments. Language models from the field of natural language processing have gained popularity for protein property predictions and have led to a new computational revolution in biology, where old prediction results are being improved regularly. Such models can learn useful multipurpose representations of proteins from large open repositories of protein sequences and can be used, for instance, to predict protein properties. The field of natural language processing is growing quickly because of developments in a class of models based on a particular model—the Transformer model. We review recent developments and the use of large-scale Transformer models in applications for predicting protein characteristics and how such models can be used to predict, for example, post-translational modifications. We review shortcomings of other deep learning models and explain how the Transformer models have quickly proven to be a very promising way to unravel information hidden in the sequences of amino acids.

@article{tiret_divergent_2023,
	title = {Divergent selection predating the {Last} {Glacial} {Maximum} mainly acted on macro-phenotypes in {Norway} spruce},
	volume = {16},
	issn = {1752-4571},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/eva.13519},
	doi = {10.1111/eva.13519},
	abstract = {The current distribution and population structure of many species were, to a large extent, shaped by cycles of isolation in glacial refugia and subsequent population expansions. Isolation in and postglacial expansion through heterogeneous environments led to either neutral or adaptive divergence. Norway spruce is no exception, and its current distribution is the consequence of a constant interplay between evolutionary and demographic processes. We investigated population differentiation and adaptation of Norway spruce for juvenile growth, diameter of the stem, wood density, and tracheid traits at breast height. Data from 4461 phenotyped and genotyped Norway spruce from 396 half-sib families in two progeny tests were used to test for divergent selection in the framework of QST vs. FST. We show that the macroscopic resultant trait (stem diameter), unlike its microscopic components (tracheid dimensions) and juvenile growth, was under divergent selection that predated the Last Glacial Maximum. Altogether, the current variation in these phenotypic traits in Norway spruce is better explained by local adaptation to ancestral environments than to current ones, where populations were partly preadapted, mainly through growth-related traits.},
	language = {en},
	number = {1},
	urldate = {2023-01-20},
	journal = {Evolutionary Applications},
	author = {Tiret, Mathieu and Olsson, Lars and Grahn, Thomas and Karlsson, Bo and Milesi, Pascal and Lascoux, Martin and Lundqvist, Sven-Olof and García-Gil, Maria Rosario},
	year = {2023},
	keywords = {Norway spruce, QST vs. FST, population structure, wood quality},
	pages = {163--172},
}

The current distribution and population structure of many species were, to a large extent, shaped by cycles of isolation in glacial refugia and subsequent population expansions. Isolation in and postglacial expansion through heterogeneous environments led to either neutral or adaptive divergence. Norway spruce is no exception, and its current distribution is the consequence of a constant interplay between evolutionary and demographic processes. We investigated population differentiation and adaptation of Norway spruce for juvenile growth, diameter of the stem, wood density, and tracheid traits at breast height. Data from 4461 phenotyped and genotyped Norway spruce from 396 half-sib families in two progeny tests were used to test for divergent selection in the framework of QST vs. FST. We show that the macroscopic resultant trait (stem diameter), unlike its microscopic components (tracheid dimensions) and juvenile growth, was under divergent selection that predated the Last Glacial Maximum. Altogether, the current variation in these phenotypic traits in Norway spruce is better explained by local adaptation to ancestral environments than to current ones, where populations were partly preadapted, mainly through growth-related traits.

@article{zacharaki_non-coding_2023,
	title = {The non-coding {RNA} {SVALKA} locus produces a cis- natural antisense transcript that negatively regulates the expression of {CBF1} and biomass production at normal temperatures},
	issn = {2590-3462},
	url = {https://www.sciencedirect.com/science/article/pii/S2590346223000494},
	doi = {10.1016/j.xplc.2023.100551},
	abstract = {Non-coding transcription is present in all eukaryotic genomes, but we lack fundamental knowledge about its importance for an organism’s ability to develop properly. In plants, emerging evidence highlights the essential biological role of non-coding transcription in regulating coding transcription. However, the molecular insights into the regulation are largely unknown. Here, we show that a long isoform of the long non-coding RNA, SVALKA-L (SVK-L), forms a natural antisense transcript to the host gene CBF1 and negatively regulates CBF1 mRNA levels at normal temperatures in the model plant Arabidopsis thaliana. Furthermore, we show detailed evidence for the specific mode of action for SVK-L. This pathway includes the formation of double stranded RNA that is recognized by the DICER proteins and subsequent down-regulation of CBF1 mRNA levels. Thus, the CBF1-SVK regulatory circuit is not only important for the previously known role in cold temperature acclimation but also for biomass production at normal temperatures. Our study characterizes a developmental role of SVK-L and offers mechanistic insight into how biologically important overlapping natural antisense transcripts can act on and fine-tune the steady state levels of their host gene’s mRNA.},
	language = {en},
	urldate = {2023-01-24},
	journal = {Plant Communications},
	author = {Zacharaki, Vasiliki and Meena, Shiv Kumar and Kindgren, Peter},
	month = jan,
	year = {2023},
	keywords = {cis- natural antisense transcript, non-coding transcription},
	pages = {100551},
}

Non-coding transcription is present in all eukaryotic genomes, but we lack fundamental knowledge about its importance for an organism’s ability to develop properly. In plants, emerging evidence highlights the essential biological role of non-coding transcription in regulating coding transcription. However, the molecular insights into the regulation are largely unknown. Here, we show that a long isoform of the long non-coding RNA, SVALKA-L (SVK-L), forms a natural antisense transcript to the host gene CBF1 and negatively regulates CBF1 mRNA levels at normal temperatures in the model plant Arabidopsis thaliana. Furthermore, we show detailed evidence for the specific mode of action for SVK-L. This pathway includes the formation of double stranded RNA that is recognized by the DICER proteins and subsequent down-regulation of CBF1 mRNA levels. Thus, the CBF1-SVK regulatory circuit is not only important for the previously known role in cold temperature acclimation but also for biomass production at normal temperatures. Our study characterizes a developmental role of SVK-L and offers mechanistic insight into how biologically important overlapping natural antisense transcripts can act on and fine-tune the steady state levels of their host gene’s mRNA.

@article{liu_plant_2023,
	title = {The plant trans-{Golgi} network component {ECHIDNA} regulates defense, cell death, and endoplasmic reticulum stress},
	volume = {191},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiac400},
	doi = {10.1093/plphys/kiac400},
	abstract = {The trans-Golgi network (TGN) acts as a central platform for sorting and secreting various cargoes to the cell surface, thus being essential for the full execution of plant immunity. However, the fine-tuned regulation of TGN components in plant defense and stress response has been not fully elucidated. Our study revealed that despite largely compromising penetration resistance, the loss-of-function mutation of the TGN component protein ECHIDNA (ECH) induced enhanced postinvasion resistance to powdery mildew in Arabidopsis thaliana. Genetic and transcriptome analyses and hormone profiling demonstrated that ECH loss resulted in salicylic acid (SA) hyperaccumulation via the ISOCHORISMATE SYNTHASE 1 biosynthesis pathway, thereby constitutively activating SA-dependent innate immunity that was largely responsible for the enhanced postinvasion resistance. Furthermore, the ech mutant displayed accelerated SA-independent spontaneous cell death and constitutive POWDERY MILDEW RESISTANCE 4-mediated callose depositions. In addition, ECH loss led to a chronically prolonged endoplasmic reticulum stress in the ech mutant. These results provide insights into understanding the role of TGN components in the regulation of plant immunity and stress responses.},
	number = {1},
	urldate = {2023-01-09},
	journal = {Plant Physiology},
	author = {Liu, Lijiang and Qin, Li and Safdar, Luqman Bin and Zhao, Chuanji and Cheng, Xiaohui and Xie, Meili and Zhang, Yi and Gao, Feng and Bai, Zetao and Huang, Junyan and Bhalerao, Rishikesh P and Liu, Shengyi and Wei, Yangdou},
	month = jan,
	year = {2023},
	pages = {558--574},
}

The trans-Golgi network (TGN) acts as a central platform for sorting and secreting various cargoes to the cell surface, thus being essential for the full execution of plant immunity. However, the fine-tuned regulation of TGN components in plant defense and stress response has been not fully elucidated. Our study revealed that despite largely compromising penetration resistance, the loss-of-function mutation of the TGN component protein ECHIDNA (ECH) induced enhanced postinvasion resistance to powdery mildew in Arabidopsis thaliana. Genetic and transcriptome analyses and hormone profiling demonstrated that ECH loss resulted in salicylic acid (SA) hyperaccumulation via the ISOCHORISMATE SYNTHASE 1 biosynthesis pathway, thereby constitutively activating SA-dependent innate immunity that was largely responsible for the enhanced postinvasion resistance. Furthermore, the ech mutant displayed accelerated SA-independent spontaneous cell death and constitutive POWDERY MILDEW RESISTANCE 4-mediated callose depositions. In addition, ECH loss led to a chronically prolonged endoplasmic reticulum stress in the ech mutant. These results provide insights into understanding the role of TGN components in the regulation of plant immunity and stress responses.

@article{walker_cytokinin_2023,
	title = {Cytokinin signaling regulates two-stage inflorescence arrest in {Arabidopsis}},
	volume = {191},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiac514},
	doi = {10.1093/plphys/kiac514},
	abstract = {To maximize reproductive success, flowering plants must correctly time entry and exit from the reproductive phase. While much is known about mechanisms that regulate initiation of flowering, end-of-flowering remains largely uncharacterized. End-of-flowering in Arabidopsis (Arabidopsis thaliana) consists of quasi-synchronous arrest of inflorescences, but it is unclear how arrest is correctly timed with respect to environmental stimuli and reproductive success. Here, we showed that Arabidopsis inflorescence arrest is a complex developmental phenomenon, which includes the arrest of the inflorescence meristem (IM), coupled with a separable “floral arrest” of all unopened floral primordia; these events occur well before visible inflorescence arrest. We showed that global inflorescence removal delays both IM and floral arrest, but that local fruit removal only delays floral arrest, emphasizing their separability. We tested whether cytokinin regulates inflorescence arrest, and found that cytokinin signaling dynamics mirror IM activity, while cytokinin treatment can delay both IM and floral arrest. We further showed that gain-of-function cytokinin receptor mutants can delay IM and floral arrest; conversely, loss-of-function mutants prevented the extension of flowering in response to inflorescence removal. Collectively, our data suggest that the dilution of cytokinin among an increasing number of sink organs leads to end-of-flowering in Arabidopsis by triggering IM and floral arrest.},
	number = {1},
	urldate = {2023-01-09},
	journal = {Plant Physiology},
	author = {Walker, Catriona H and Ware, Alexander and Šimura, Jan and Ljung, Karin and Wilson, Zoe and Bennett, Tom},
	month = jan,
	year = {2023},
	pages = {479--495},
}

To maximize reproductive success, flowering plants must correctly time entry and exit from the reproductive phase. While much is known about mechanisms that regulate initiation of flowering, end-of-flowering remains largely uncharacterized. End-of-flowering in Arabidopsis (Arabidopsis thaliana) consists of quasi-synchronous arrest of inflorescences, but it is unclear how arrest is correctly timed with respect to environmental stimuli and reproductive success. Here, we showed that Arabidopsis inflorescence arrest is a complex developmental phenomenon, which includes the arrest of the inflorescence meristem (IM), coupled with a separable “floral arrest” of all unopened floral primordia; these events occur well before visible inflorescence arrest. We showed that global inflorescence removal delays both IM and floral arrest, but that local fruit removal only delays floral arrest, emphasizing their separability. We tested whether cytokinin regulates inflorescence arrest, and found that cytokinin signaling dynamics mirror IM activity, while cytokinin treatment can delay both IM and floral arrest. We further showed that gain-of-function cytokinin receptor mutants can delay IM and floral arrest; conversely, loss-of-function mutants prevented the extension of flowering in response to inflorescence removal. Collectively, our data suggest that the dilution of cytokinin among an increasing number of sink organs leads to end-of-flowering in Arabidopsis by triggering IM and floral arrest.

@article{kleczkowski_magnesium_2023,
	title = {Magnesium and cell energetics: {At} the junction of metabolism of adenylate and non-adenylate nucleotides},
	volume = {280},
	issn = {0176-1617},
	shorttitle = {Magnesium and cell energetics},
	url = {https://www.sciencedirect.com/science/article/pii/S0176161722002875},
	doi = {10.1016/j.jplph.2022.153901},
	abstract = {Free magnesium (Mg2+) represents a powerful signal arising from interconversions of adenylates (ATP, ADP and AMP). This is a consequence of the involvement of adenylate kinase (AK) which equilibrates adenylates and uses defined species of Mg-complexed and Mg-free adenylates in both directions of its reaction. However, cells contain also other reversible Mg2+-dependent enzymes that equilibrate non-adenylate nucleotides (uridylates, cytidylates and guanylates), i.e. nucleoside monophosphate kinases (NMPKs) and nucleoside diphosphate kinase (NDPK). Here, we propose that AK activity is tightly coupled to activities of NMPK and NDPK, linking adenylate equilibrium to equilibria of other nucleotides, and with [Mg2+] controlling the ratios of Mg-chelated and Mg-free nucleotides. This coupling establishes main hubs for adenylate-driven equilibration of non-adenylate nucleotides, with [Mg2+] acting as signal arising from all nucleotides rather than adenylates only. Further consequences involve an overall adenylate control of UTP-, GTP- and CTP-dependent pathways and the availability of substrates for RNA and DNA synthesis.},
	language = {en},
	urldate = {2022-12-30},
	journal = {Journal of Plant Physiology},
	author = {Kleczkowski, Leszek A. and Igamberdiev, Abir U.},
	month = jan,
	year = {2023},
	keywords = {Adenylate kinase, Guanylate kinase, Magnesium signaling, Nucleoside diphosphate kinase, Nucleoside monophosphate kinase, Uridylate-cytidylate kinase},
	pages = {153901},
}

Free magnesium (Mg2+) represents a powerful signal arising from interconversions of adenylates (ATP, ADP and AMP). This is a consequence of the involvement of adenylate kinase (AK) which equilibrates adenylates and uses defined species of Mg-complexed and Mg-free adenylates in both directions of its reaction. However, cells contain also other reversible Mg2+-dependent enzymes that equilibrate non-adenylate nucleotides (uridylates, cytidylates and guanylates), i.e. nucleoside monophosphate kinases (NMPKs) and nucleoside diphosphate kinase (NDPK). Here, we propose that AK activity is tightly coupled to activities of NMPK and NDPK, linking adenylate equilibrium to equilibria of other nucleotides, and with [Mg2+] controlling the ratios of Mg-chelated and Mg-free nucleotides. This coupling establishes main hubs for adenylate-driven equilibration of non-adenylate nucleotides, with [Mg2+] acting as signal arising from all nucleotides rather than adenylates only. Further consequences involve an overall adenylate control of UTP-, GTP- and CTP-dependent pathways and the availability of substrates for RNA and DNA synthesis.

@article{lecoy_analysis_2023,
	title = {Analysis of the {ASR} and {LP3} homologous gene families reveal positive selection acting on {LP3}-3 gene},
	volume = {850},
	issn = {0378-1119},
	url = {https://www.sciencedirect.com/science/article/pii/S0378111922007557},
	doi = {10.1016/j.gene.2022.146935},
	abstract = {Drought has long been established as a major environmental stress for plants which have in turn developed several coping strategies, ranging from physiological to molecular mechanisms. LP3 that was first discovered in loblolly pine (Pinus taeda L.) is a homolog of the Abscisic Acid, Stress and Ripening (ASR) gene belonging to the ABA/WDS gene family that was first detected in tomato. LP3 has been shown to be present in four different paralogs in loblolly pine called LP3-0, LP3-1, LP3-2 and LP3-3. LP3 in loblolly pine has not been as extensively studied as the ASR in tomato. Similar to ASR, the different LP3 paralogs have been shown to be upregulated in response to water deficit stress and to act as transcription factors for genes likely involved in hexose transport. In the current study, we have investigated the evolutionary history of LP3 gene family, with the aim of relating it to that of ASR from a phylogenetic perspective and comparing the differences in selective pressure and codon usage. Phylogenetic trees revealed that LP3 is less divergent across species than ASR even when the trees were solely based on the different sub-sections of the gene. Phylogenetic, GC content, codon usage and selective pressure analyses suggest that LP3-3 is undergoing positive selection.},
	language = {en},
	urldate = {2022-10-06},
	journal = {Gene},
	author = {Lecoy, Jonathan and Ranade, Sonali Sachin and García-Gil, María Rosario},
	month = jan,
	year = {2023},
	keywords = {ABA/WDS, Codon usage, Drought resistance, GC-content, Selective pressure},
	pages = {146935},
}

Drought has long been established as a major environmental stress for plants which have in turn developed several coping strategies, ranging from physiological to molecular mechanisms. LP3 that was first discovered in loblolly pine (Pinus taeda L.) is a homolog of the Abscisic Acid, Stress and Ripening (ASR) gene belonging to the ABA/WDS gene family that was first detected in tomato. LP3 has been shown to be present in four different paralogs in loblolly pine called LP3-0, LP3-1, LP3-2 and LP3-3. LP3 in loblolly pine has not been as extensively studied as the ASR in tomato. Similar to ASR, the different LP3 paralogs have been shown to be upregulated in response to water deficit stress and to act as transcription factors for genes likely involved in hexose transport. In the current study, we have investigated the evolutionary history of LP3 gene family, with the aim of relating it to that of ASR from a phylogenetic perspective and comparing the differences in selective pressure and codon usage. Phylogenetic trees revealed that LP3 is less divergent across species than ASR even when the trees were solely based on the different sub-sections of the gene. Phylogenetic, GC content, codon usage and selective pressure analyses suggest that LP3-3 is undergoing positive selection.