@article{diamanti_comparative_2022,
	title = {Comparative structural analysis provides new insights into the function of {R2}-like ligand-binding oxidase},
	volume = {596},
	copyright = {© 2022 The Authors. FEBS Letters published by John Wiley \& Sons Ltd on behalf of Federation of European Biochemical Societies},
	issn = {1873-3468},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/1873-3468.14319},
	doi = {10.1002/1873-3468.14319},
	abstract = {R2-like ligand-binding oxidase (R2lox) is a ferritin-like protein that harbours a heterodinuclear manganese–iron active site. Although R2lox function is yet to be established, the enzyme binds a fatty acid ligand coordinating the metal centre and catalyses the formation of a tyrosine–valine ether cross-link in the protein scaffold upon O2 activation. Here, we characterized the ligands copurified with R2lox by mass spectrometry-based metabolomics. Moreover, we present the crystal structures of two new homologs of R2lox, from Saccharopolyspora erythraea and Sulfolobus acidocaldarius, at 1.38 Å and 2.26 Å resolution, respectively, providing the highest resolution structure for R2lox, as well as new insights into putative mechanisms regulating the function of the enzyme.},
	language = {en},
	number = {12},
	urldate = {2022-06-30},
	journal = {FEBS Letters},
	author = {Diamanti, Riccardo and Srinivas, Vivek and Johansson, Annika I. and Nordström, Anders and Griese, Julia J. and Lebrette, Hugo and Högbom, Martin},
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/1873-3468.14319},
	keywords = {R2-like ligand-binding oxidase, R2lox, aldehyde deformylating oxygenase, ferritin-like protein, hydroxy fatty acids, long-chain fatty acids},
	pages = {1600--1610},
}

R2-like ligand-binding oxidase (R2lox) is a ferritin-like protein that harbours a heterodinuclear manganese–iron active site. Although R2lox function is yet to be established, the enzyme binds a fatty acid ligand coordinating the metal centre and catalyses the formation of a tyrosine–valine ether cross-link in the protein scaffold upon O2 activation. Here, we characterized the ligands copurified with R2lox by mass spectrometry-based metabolomics. Moreover, we present the crystal structures of two new homologs of R2lox, from Saccharopolyspora erythraea and Sulfolobus acidocaldarius, at 1.38 Å and 2.26 Å resolution, respectively, providing the highest resolution structure for R2lox, as well as new insights into putative mechanisms regulating the function of the enzyme.

@article{ranjan_molecular_2022,
	title = {Molecular basis of differential adventitious rooting competence in poplar genotypes},
	volume = {73},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/erac126},
	doi = {10.1093/jxb/erac126},
	abstract = {Recalcitrant adventitious root (AR) development is a major hurdle in propagating commercially important woody plants. Although significant progress has been made to identify genes involved in subsequent steps of AR development, the molecular basis of differences in apparent recalcitrance to form AR between easy-to-root and difficult-to-root genotypes remains unknown. To address this, we generated cambium tissue-specific transcriptomic data from stem cuttings of hybrid aspen, T89 (difficult-to-root) and hybrid poplar OP42 (easy-to-root), and used transgenic approaches to verify the role of several transcription factors in the control of adventitious rooting. Increased peroxidase activity was positively correlated with better rooting. We found differentially expressed genes encoding reactive oxygen species scavenging proteins to be enriched in OP42 compared with T89. A greater number of differentially expressed transcription factors in cambium cells of OP42 compared with T89 was revealed by a more intense transcriptional reprograming in the former. PtMYC2, a potential negative regulator, was less expressed in OP42 compared with T89. Using transgenic approaches, we demonstrated that PttARF17.1 and PttMYC2.1 negatively regulate adventitious rooting. Our results provide insights into the molecular basis of genotypic differences in AR and implicate differential expression of the master regulator MYC2 as a critical player in this process.},
	number = {12},
	urldate = {2022-06-30},
	journal = {Journal of Experimental Botany},
	author = {Ranjan, Alok and Perrone, Irene and Alallaq, Sanaria and Singh, Rajesh and Rigal, Adeline and Brunoni, Federica and Chitarra, Walter and Guinet, Frederic and Kohler, Annegret and Martin, Francis and Street, Nathaniel R and Bhalerao, Rishikesh and Legué, Valérie and Bellini, Catherine},
	month = jun,
	year = {2022},
	pages = {4046--4064},
}

Recalcitrant adventitious root (AR) development is a major hurdle in propagating commercially important woody plants. Although significant progress has been made to identify genes involved in subsequent steps of AR development, the molecular basis of differences in apparent recalcitrance to form AR between easy-to-root and difficult-to-root genotypes remains unknown. To address this, we generated cambium tissue-specific transcriptomic data from stem cuttings of hybrid aspen, T89 (difficult-to-root) and hybrid poplar OP42 (easy-to-root), and used transgenic approaches to verify the role of several transcription factors in the control of adventitious rooting. Increased peroxidase activity was positively correlated with better rooting. We found differentially expressed genes encoding reactive oxygen species scavenging proteins to be enriched in OP42 compared with T89. A greater number of differentially expressed transcription factors in cambium cells of OP42 compared with T89 was revealed by a more intense transcriptional reprograming in the former. PtMYC2, a potential negative regulator, was less expressed in OP42 compared with T89. Using transgenic approaches, we demonstrated that PttARF17.1 and PttMYC2.1 negatively regulate adventitious rooting. Our results provide insights into the molecular basis of genotypic differences in AR and implicate differential expression of the master regulator MYC2 as a critical player in this process.

@article{fataftah_nitrate_2022,
	title = {Nitrate fertilization may delay autumn leaf senescence, while amino acid treatments do not},
	volume = {174},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.13690},
	doi = {10.1111/ppl.13690},
	abstract = {Fertilization with nitrogen (N)-rich compounds leads to increased growth but may compromise phenology and winter survival of trees in boreal regions. During autumn, N is remobilized from senescing leaves and stored in other parts of the tree to be used in the next growing season. However, the mechanism behind the N fertilization effect on winter survival is not well understood, and it is unclear how N levels or forms modulate autumn senescence. We performed fertilization experiments and showed that treating Populus saplings with inorganic nitrogen resulted in a delay in senescence. In addition, by using precise delivery of solutes into the xylem stream of Populus trees in their natural environment, we found that delay of autumn senescence was dependent on the form of N administered: inorganic N (NO3−) delayed senescence, but amino acids (Arg, Glu, Gln, and Leu) did not. Metabolite profiling of leaves showed that the levels of tricarboxylic acids, arginine catabolites (ammonium, ornithine), glycine, glycine-serine ratio and overall carbon-to-nitrogen (C/N) ratio were affected differently by the way of applying NO3− and Arg treatments. In addition, the onset of senescence did not coincide with soluble sugar accumulation in control trees or in any of the treatments. We propose that different regulation of C and N status through direct molecular signaling of NO3− and/or different allocation of N between tree parts depending on N forms could account for the contrasting effects of NO3− and tested here amino acids (Arg, Glu, Gln, and Leu) on autumn senescence.},
	language = {en},
	number = {3},
	urldate = {2022-06-30},
	journal = {Physiologia Plantarum},
	author = {Fataftah, Nazeer and Edlund, Erik and Lihavainen, Jenna and Bag, Pushan and Björkén, Lars and Näsholm, Torgny and Jansson, Stefan},
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.13690},
	pages = {e13690},
}

Fertilization with nitrogen (N)-rich compounds leads to increased growth but may compromise phenology and winter survival of trees in boreal regions. During autumn, N is remobilized from senescing leaves and stored in other parts of the tree to be used in the next growing season. However, the mechanism behind the N fertilization effect on winter survival is not well understood, and it is unclear how N levels or forms modulate autumn senescence. We performed fertilization experiments and showed that treating Populus saplings with inorganic nitrogen resulted in a delay in senescence. In addition, by using precise delivery of solutes into the xylem stream of Populus trees in their natural environment, we found that delay of autumn senescence was dependent on the form of N administered: inorganic N (NO3−) delayed senescence, but amino acids (Arg, Glu, Gln, and Leu) did not. Metabolite profiling of leaves showed that the levels of tricarboxylic acids, arginine catabolites (ammonium, ornithine), glycine, glycine-serine ratio and overall carbon-to-nitrogen (C/N) ratio were affected differently by the way of applying NO3− and Arg treatments. In addition, the onset of senescence did not coincide with soluble sugar accumulation in control trees or in any of the treatments. We propose that different regulation of C and N status through direct molecular signaling of NO3− and/or different allocation of N between tree parts depending on N forms could account for the contrasting effects of NO3− and tested here amino acids (Arg, Glu, Gln, and Leu) on autumn senescence.

@article{arshad_kaleidoscope_2022,
	title = {A kaleidoscope of photosynthetic antenna proteins and their emerging roles},
	volume = {189},
	issn = {1532-2548},
	doi = {10.1093/plphys/kiac175},
	abstract = {Photosynthetic light-harvesting antennae are pigment-binding proteins that perform one of the most fundamental tasks on Earth, capturing light and transferring energy that enables life in our biosphere. Adaptation to different light environments led to the evolution of an astonishing diversity of light-harvesting systems. At the same time, several strategies have been developed to optimize the light energy input into photosynthetic membranes in response to fluctuating conditions. The basic feature of these prompt responses is the dynamic nature of antenna complexes, whose function readily adapts to the light available. High-resolution microscopy and spectroscopic studies on membrane dynamics demonstrate the crosstalk between antennae and other thylakoid membrane components. With the increased understanding of light-harvesting mechanisms and their regulation, efforts are focusing on the development of sustainable processes for effective conversion of sunlight into functional bio-products. The major challenge in this approach lies in the application of fundamental discoveries in light-harvesting systems for the improvement of plant or algal photosynthesis. Here, we underline some of the latest fundamental discoveries on the molecular mechanisms and regulation of light harvesting that can potentially be exploited for the optimization of photosynthesis.},
	language = {eng},
	number = {3},
	journal = {Plant Physiology},
	author = {Arshad, Rameez and Saccon, Francesco and Bag, Pushan and Biswas, Avratanu and Calvaruso, Claudio and Bhatti, Ahmad Farhan and Grebe, Steffen and Mascoli, Vincenzo and Mahbub, Moontaha and Muzzopappa, Fernando and Polyzois, Alexandros and Schiphorst, Christo and Sorrentino, Mirella and Streckaité, Simona and van Amerongen, Herbert and Aro, Eva-Mari and Bassi, Roberto and Boekema, Egbert J. and Croce, Roberta and Dekker, Jan and van Grondelle, Rienk and Jansson, Stefan and Kirilovsky, Diana and Kouřil, Roman and Michel, Sylvie and Mullineaux, Conrad W. and Panzarová, Klára and Robert, Bruno and Ruban, Alexander V. and van Stokkum, Ivo and Wientjes, Emilie and Büchel, Claudia},
	month = jun,
	year = {2022},
	pmid = {35512089},
	keywords = {Adaptation, Physiological, Light-Harvesting Protein Complexes, Photosynthesis, Plants, Thylakoids},
	pages = {1204--1219},
}

Photosynthetic light-harvesting antennae are pigment-binding proteins that perform one of the most fundamental tasks on Earth, capturing light and transferring energy that enables life in our biosphere. Adaptation to different light environments led to the evolution of an astonishing diversity of light-harvesting systems. At the same time, several strategies have been developed to optimize the light energy input into photosynthetic membranes in response to fluctuating conditions. The basic feature of these prompt responses is the dynamic nature of antenna complexes, whose function readily adapts to the light available. High-resolution microscopy and spectroscopic studies on membrane dynamics demonstrate the crosstalk between antennae and other thylakoid membrane components. With the increased understanding of light-harvesting mechanisms and their regulation, efforts are focusing on the development of sustainable processes for effective conversion of sunlight into functional bio-products. The major challenge in this approach lies in the application of fundamental discoveries in light-harvesting systems for the improvement of plant or algal photosynthesis. Here, we underline some of the latest fundamental discoveries on the molecular mechanisms and regulation of light harvesting that can potentially be exploited for the optimization of photosynthesis.

@article{blasko_carbon_2022,
	title = {The carbon sequestration response of aboveground biomass and soils to nutrient enrichment in boreal forests depends on baseline site productivity},
	volume = {838},
	issn = {0048-9697},
	url = {https://www.sciencedirect.com/science/article/pii/S0048969722034246},
	doi = {10.1016/j.scitotenv.2022.156327},
	abstract = {Nutrient enrichment can alleviate productivity limitations and thus substantially increase carbon (C) uptake in northern coniferous forests. Yet, factors controlling stand-to-stand variation of forest ecosystem responses to nutrient enrichment remain unclear. We used five long-term (13 years) nutrient-enrichment experiments across Sweden, where nitrogen (N), phosphorus, and potassium were applied annually to young Norway spruce forests that varied in their baseline ecosystem properties. We measured tree biomass and soil C and N stocks, litterfall C inputs, soil CO2 efflux, and shifts in composition and biomass of soil microbial communities to understand the links between above and belowground responses to nutrient enrichment. We found that the strongest responses in tree biomass occurred when baseline site productivity was lowest. High increases in tree biomass C stocks were generally balanced by weaker responses in organic soil C stocks. The average ecosystem C–N response rate was 35 kg C kg−1 N added, with a nearly five-fold greater response rate in tree biomass than in soil. The positive nutrient enrichment effects on ecosystem C sinks were driven by a 95\% increase in tree biomass C stocks, 150\% increase in litter production, 67\% increase in organic layer C stocks, and a 46\% reduction in soil CO2 efflux accompanied by compositional changes in soil microbial communities. Our results show that ecosystem C uptake in spruce forests in northern Europe can be substantially enhanced by nutrient enrichment; however, the strength of the responses and whether the enhancement occurs mainly in tree biomass or soils are dependent on baseline forest productivity.},
	language = {en},
	urldate = {2022-06-30},
	journal = {Science of The Total Environment},
	author = {Blaško, Róbert and Forsmark, Benjamin and Gundale, Michael J. and Lim, Hyungwoo and Lundmark, Tomas and Nordin, Annika},
	month = sep,
	year = {2022},
	keywords = {Ecosystem carbon stocks, Litterfall, Soil carbon, Soil microbial community, Soil nitrogen, Soil respiration},
	pages = {156327},
}

Nutrient enrichment can alleviate productivity limitations and thus substantially increase carbon (C) uptake in northern coniferous forests. Yet, factors controlling stand-to-stand variation of forest ecosystem responses to nutrient enrichment remain unclear. We used five long-term (13 years) nutrient-enrichment experiments across Sweden, where nitrogen (N), phosphorus, and potassium were applied annually to young Norway spruce forests that varied in their baseline ecosystem properties. We measured tree biomass and soil C and N stocks, litterfall C inputs, soil CO2 efflux, and shifts in composition and biomass of soil microbial communities to understand the links between above and belowground responses to nutrient enrichment. We found that the strongest responses in tree biomass occurred when baseline site productivity was lowest. High increases in tree biomass C stocks were generally balanced by weaker responses in organic soil C stocks. The average ecosystem C–N response rate was 35 kg C kg−1 N added, with a nearly five-fold greater response rate in tree biomass than in soil. The positive nutrient enrichment effects on ecosystem C sinks were driven by a 95% increase in tree biomass C stocks, 150% increase in litter production, 67% increase in organic layer C stocks, and a 46% reduction in soil CO2 efflux accompanied by compositional changes in soil microbial communities. Our results show that ecosystem C uptake in spruce forests in northern Europe can be substantially enhanced by nutrient enrichment; however, the strength of the responses and whether the enhancement occurs mainly in tree biomass or soils are dependent on baseline forest productivity.