@article{le_bail_essential_2025,
	title = {Essential developmental processes in {Physcomitrium} patens require distinct levels of total activity provided by functionally redundant {PpROP} {GTPases}},
	volume = {248},
	copyright = {© 2025 The Author(s). New Phytologist © 2025 New Phytologist Foundation.},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.70603},
	doi = {10.1111/nph.70603},
	abstract = {RHO (RAS homologous) GTPases regulate important cellular and developmental processes in most eukaryotes. Plant-specific ROP (RHO of plants) GTPase families expanded and functionally diversified during the evolution of vascular plants, but contain few members in nonvascular extant relatives of early land plants. Here, a systematic investigation of essential PpROP functions in the development of the nonvascular moss Physcomitrium patens is presented. This investigation was based on: knocking out individually or all possible combinations of each of the four PpROP genes, which encode nearly identical proteins; complementing knockout lines with wild-type (WT) or mutated PpROPs, or with heterologous homologs; and inducing PpROP overexpression. PpROPs were found to have previously unknown functions in cell proliferation, caulonema differentiation, and gametophore formation. PpROP functions were observed to display variable dependence on guanosine diphosphate (GDP)/guanosine triphosphate (GTP) cycling and to rely on distinct downstream signaling. Different cellular and developmental processes were determined to require distinct levels of total PpROP activity, rather than individual PpROPs. These observations provide important insights into PpROP functions and signaling in P. patens, enhancing our understanding of the evolution of the regulation of developmental processes by ROP/RHO GTPases. The evolutionary origin of the remarkable functional integration and sequence conservation within the PpROP family is discussed.},
	language = {en},
	number = {6},
	urldate = {2025-11-21},
	journal = {New Phytologist},
	author = {Le Bail, Aude and Kost, Benedikt and Nüssel, Janina and Lolis, Tamara Isabeau and Koch, David and Voll, Hildegard and Schulmeister, Sylwia and Kaier, Alexander and Ljung, Karin and Ntefidou, Maria},
	year = {2025},
	note = {\_eprint: https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.70603},
	keywords = {GTP/GDP cycling, Physcomitrium patens, RHO/ROP GTPases, apical initial cells, caulonema differentiation, gametophore development, plant evolution, polarity},
	pages = {2865--2890},
}

RHO (RAS homologous) GTPases regulate important cellular and developmental processes in most eukaryotes. Plant-specific ROP (RHO of plants) GTPase families expanded and functionally diversified during the evolution of vascular plants, but contain few members in nonvascular extant relatives of early land plants. Here, a systematic investigation of essential PpROP functions in the development of the nonvascular moss Physcomitrium patens is presented. This investigation was based on: knocking out individually or all possible combinations of each of the four PpROP genes, which encode nearly identical proteins; complementing knockout lines with wild-type (WT) or mutated PpROPs, or with heterologous homologs; and inducing PpROP overexpression. PpROPs were found to have previously unknown functions in cell proliferation, caulonema differentiation, and gametophore formation. PpROP functions were observed to display variable dependence on guanosine diphosphate (GDP)/guanosine triphosphate (GTP) cycling and to rely on distinct downstream signaling. Different cellular and developmental processes were determined to require distinct levels of total PpROP activity, rather than individual PpROPs. These observations provide important insights into PpROP functions and signaling in P. patens, enhancing our understanding of the evolution of the regulation of developmental processes by ROP/RHO GTPases. The evolutionary origin of the remarkable functional integration and sequence conservation within the PpROP family is discussed.

@article{ye_cambium_2025,
	title = {Cambium {LBDs} promote radial growth by regulating {PLL}-mediated pectin metabolism},
	copyright = {2025 The Author(s)},
	issn = {2055-0278},
	url = {https://www.nature.com/articles/s41477-025-02151-1},
	doi = {10.1038/s41477-025-02151-1},
	abstract = {Plant growth originates from the interlinked action of cell division and cell growth. During radial growth of secondary tissues, bifacial cambial stem cells grow and divide to produce xylem and phloem precursors, which subsequently undergo expansion characteristic of their respective differentiation processes. In Arabidopsis roots, cytokinins and four downstream LATERAL ORGAN BOUNDARIES DOMAIN (LBD) transcription factors are key players in promoting radial growth, though the underlying mechanisms remain unknown. Here our results indicate that these LBD genes primarily regulate cell growth rather than proliferation. Through a large-scale CRISPR–Cas9-aided reverse genetic screen, we identified a set of PECTATE LYASE-LIKE (PLL) genes that function downstream of cytokinin and the LBDs in the regulation of radial growth. We show that at least one of these PLLs, PLL18, possesses pectate lyase activity. In accordance with this activity, PLLs and LBDs promote radial growth by modifying the pectin composition and mechanical properties of the primary cell wall. Our findings thus connect the central role of cytokinins in radial growth with cell wall remodelling and pave a way for further research on hormone-mediated plant growth regulation and cell wall metabolism.},
	language = {en},
	urldate = {2025-11-21},
	journal = {Nature Plants},
	author = {Ye, Lingling and Wang, Xin and Valle-Delgado, Juan José and Vainonen, Julia P. and Wopereis, Isaac and Kesari, Kavindra Kumar and Takahashi, Junko and Sierla, Maija and Mähönen, Ari Pekka},
	month = nov,
	year = {2025},
	note = {Publisher: Nature Publishing Group},
	keywords = {Cell wall, Cytokinin, Plant morphogenesis, Transgenic plants},
	pages = {1--16},
}

Plant growth originates from the interlinked action of cell division and cell growth. During radial growth of secondary tissues, bifacial cambial stem cells grow and divide to produce xylem and phloem precursors, which subsequently undergo expansion characteristic of their respective differentiation processes. In Arabidopsis roots, cytokinins and four downstream LATERAL ORGAN BOUNDARIES DOMAIN (LBD) transcription factors are key players in promoting radial growth, though the underlying mechanisms remain unknown. Here our results indicate that these LBD genes primarily regulate cell growth rather than proliferation. Through a large-scale CRISPR–Cas9-aided reverse genetic screen, we identified a set of PECTATE LYASE-LIKE (PLL) genes that function downstream of cytokinin and the LBDs in the regulation of radial growth. We show that at least one of these PLLs, PLL18, possesses pectate lyase activity. In accordance with this activity, PLLs and LBDs promote radial growth by modifying the pectin composition and mechanical properties of the primary cell wall. Our findings thus connect the central role of cytokinins in radial growth with cell wall remodelling and pave a way for further research on hormone-mediated plant growth regulation and cell wall metabolism.

@incollection{shankar_microproteins_2026,
	address = {New York, NY},
	title = {Microproteins: {Uncovering} {Hidden} {Layers} of the {Proteome}},
	isbn = {978-1-07-165013-4},
	shorttitle = {Microproteins},
	url = {https://doi.org/10.1007/978-1-0716-5013-4_1},
	abstract = {Once dismissed as nonfunctional transcriptional noise, small open reading frames (sORFs) and their encoded microproteins have rapidly emerged as key players in diverse biological processes. Ranging from just a few to about 150 amino acids in length, microproteins are now recognized for their ability to modulate cellular functions, often acting as dominant-negative regulators, scaffolds, or signaling intermediates. Initially overlooked due to technical and conceptual limitations, they are increasingly being detected thanks to advances in high-resolution proteomics, ribosome profiling, and integrative bioinformatics. In this chapter, we provide a concise overview of the discovery, origins, functions, and biological significance of microproteins. We also introduce the structure of this methods book, which captures the latest experimental and computational tools used to identify, characterize, and functionally dissect microproteins across a wide range of organisms and research disciplines. This emerging field exemplifies the power of cross-disciplinary collaboration, and we hope this volume will support and inspire further research in this exciting and rapidly expanding area.},
	language = {en},
	urldate = {2025-11-21},
	booktitle = {Microproteins: {Methods} and {Protocols}},
	publisher = {Springer US},
	author = {Shankar, Naveen and Wenkel, Stephan},
	editor = {Wenkel, Stephan},
	year = {2026},
	doi = {10.1007/978-1-0716-5013-4_1},
	keywords = {Evolution, Microproteins, Protein structure, lncRNAs, sORFs},
	pages = {3--18},
}

Once dismissed as nonfunctional transcriptional noise, small open reading frames (sORFs) and their encoded microproteins have rapidly emerged as key players in diverse biological processes. Ranging from just a few to about 150 amino acids in length, microproteins are now recognized for their ability to modulate cellular functions, often acting as dominant-negative regulators, scaffolds, or signaling intermediates. Initially overlooked due to technical and conceptual limitations, they are increasingly being detected thanks to advances in high-resolution proteomics, ribosome profiling, and integrative bioinformatics. In this chapter, we provide a concise overview of the discovery, origins, functions, and biological significance of microproteins. We also introduce the structure of this methods book, which captures the latest experimental and computational tools used to identify, characterize, and functionally dissect microproteins across a wide range of organisms and research disciplines. This emerging field exemplifies the power of cross-disciplinary collaboration, and we hope this volume will support and inspire further research in this exciting and rapidly expanding area.

@article{skalicky_illuminating_2025,
	title = {Illuminating the {Subcellular} {Maze}: {Fluorescence}-{Activated} {Organelle} {Sorting} in {Plant} {Sciences}},
	issn = {0022-0957},
	shorttitle = {Illuminating the {Subcellular} {Maze}},
	url = {https://doi.org/10.1093/jxb/eraf490},
	doi = {10.1093/jxb/eraf490},
	abstract = {The isolation of organelles is critical for gaining a deeper understanding of their functions in intracellular processes, not only at the cellular but also at the multicellular, organ and organism levels. Isolating them into pure fractions allows for the reduction of sample complexity, thereby ensuring high quality downstream analysis, such as in protein localization studies. Since the mid-20th century, new methods of subcellular fractionation have constantly emerged. Conventional fractionation approaches based on (ultra)centrifugation typically focus on isolating only one type of organelle. Moreover, their resolving power may be inadequate for improving the limit of detection of downstream applications. Fluorescence activated-organelle sorting (FAOS) is a versatile and advanced technique that is gaining popularity due to its high efficiency. This efficiency refers to the ability to monitor organelle isolation live and to sort multiple organelle populations simultaneously from a single sample. This review offers an overview of the usage of FAOS and highlights its promising prospects within the realm of plant sciences. FAOS shows great potential for applications in both the functional and structural analysis of plant organelles while serving as a valuable isolation tool for downstream applications, including ‘omics’ studies.},
	urldate = {2025-11-21},
	journal = {Journal of Experimental Botany},
	author = {Skalický, Vladimír and Antoniadi, Ioanna and Ljung, Karin and Novák, Ondřej},
	month = nov,
	year = {2025},
	pages = {eraf490},
}

The isolation of organelles is critical for gaining a deeper understanding of their functions in intracellular processes, not only at the cellular but also at the multicellular, organ and organism levels. Isolating them into pure fractions allows for the reduction of sample complexity, thereby ensuring high quality downstream analysis, such as in protein localization studies. Since the mid-20th century, new methods of subcellular fractionation have constantly emerged. Conventional fractionation approaches based on (ultra)centrifugation typically focus on isolating only one type of organelle. Moreover, their resolving power may be inadequate for improving the limit of detection of downstream applications. Fluorescence activated-organelle sorting (FAOS) is a versatile and advanced technique that is gaining popularity due to its high efficiency. This efficiency refers to the ability to monitor organelle isolation live and to sort multiple organelle populations simultaneously from a single sample. This review offers an overview of the usage of FAOS and highlights its promising prospects within the realm of plant sciences. FAOS shows great potential for applications in both the functional and structural analysis of plant organelles while serving as a valuable isolation tool for downstream applications, including ‘omics’ studies.

@article{renzi_creatine_2025,
	title = {Creatine kinase {B} regulates glycolysis and \textit{de novo} lipogenesis pathways to control lipid accumulation during adipogenesis},
	volume = {44},
	issn = {2211-1247},
	url = {https://www.sciencedirect.com/science/article/pii/S2211124725012604},
	doi = {10.1016/j.celrep.2025.116489},
	abstract = {White adipocyte differentiation or adipogenesis requires coordination of metabolic sensing and transcriptional modifications to orchestrate lipid storage. Creatine and its kinases are implicated in adipose energy buffering, but the roles of cytosolic (CKB) and mitochondrial (CKMT2) creatine kinases in adipogenesis are unclear. We find that both CKB and CKMT2 are progressively upregulated during differentiation. Functional studies show that CKB restrains de novo lipogenesis (DNL) by limiting activation of carbohydrate-responsive element-binding protein (ChREBP), a key regulator of lipogenic genes. Mechanistically, CKB interacts with AKT and regulates its activation in response to insulin. Loss of CKB causes persistent AKT-mTORC1 signaling, increases glycolytic flux, and enhances ChREBP activation, thereby promoting glucose-derived lipid synthesis. Thus, CKB acts as a metabolic rheostat linking creatine-kinase activity to insulin signaling and nutrient-responsive transcription. We propose a CKB-AKT-ChREBP regulatory axis that contributes to metabolic remodeling and lipid homeostasis during adipocyte differentiation.},
	number = {11},
	urldate = {2025-11-14},
	journal = {Cell Reports},
	author = {Renzi, Gianluca and Higos, Romane and Vlassakev, Ivan and Bello, Abdoul Akim and Omar-Hmeadi, Muhmmad and Hansen, Mattias and Merabtene, Fatiha and Rouault, Christine and Hodek, Ondrej and Massier, Lucas and Antonny, Bruno and Marcelin, Geneviève and Rahbani, Janane F. and Lecoutre, Simon and Maqdasy, Salwan},
	month = nov,
	year = {2025},
	keywords = {AKT-mTORC, CKB, ChREBP, adipogenesis, creatine kinase, lipogenesis, white adipocyte},
	pages = {116489},
}

White adipocyte differentiation or adipogenesis requires coordination of metabolic sensing and transcriptional modifications to orchestrate lipid storage. Creatine and its kinases are implicated in adipose energy buffering, but the roles of cytosolic (CKB) and mitochondrial (CKMT2) creatine kinases in adipogenesis are unclear. We find that both CKB and CKMT2 are progressively upregulated during differentiation. Functional studies show that CKB restrains de novo lipogenesis (DNL) by limiting activation of carbohydrate-responsive element-binding protein (ChREBP), a key regulator of lipogenic genes. Mechanistically, CKB interacts with AKT and regulates its activation in response to insulin. Loss of CKB causes persistent AKT-mTORC1 signaling, increases glycolytic flux, and enhances ChREBP activation, thereby promoting glucose-derived lipid synthesis. Thus, CKB acts as a metabolic rheostat linking creatine-kinase activity to insulin signaling and nutrient-responsive transcription. We propose a CKB-AKT-ChREBP regulatory axis that contributes to metabolic remodeling and lipid homeostasis during adipocyte differentiation.