Photosynthetic eukaryotes have undergone evolutionary shifts from aquatic to terrestrial habitats, accompanied by changes in genome organization and gene regulation. Yet, the evolution of transfer RNA (tRNA) gene repertoires has received limited attention despite their central role in translation. Here, we review how tRNA gene content, structure, and genomic organization diversified across photosynthetic lineages, mainly Archaeplastida, and how changes relate to evolutionary transitions. We show that tRNA gene repertoires are shaped by ecological transitions, genome architecture, and translational demands. We highlight terrestrialization as a shift in tRNA evolution, marked by loss of selenocysteine and its dedicated tRNA, and changes in intron prevalence and structure. Copy number variation correlates with codon usage and amino acid composition, and in angiosperms, nuclear tRNA genes display reinforced cis-regulatory elements consistent with increased translational demands. We show that plant tRNA genes exhibit evenly dispersed arrangements, except in some algae enriched in clustered configurations. Together, these observations support a model in which tRNA gene repertoires are drivers of genome evolution, integrating translational demand, genomic organization, and ecological adaptation across photosynthetic lineages. This review examines how tRNA gene repertoires diversified across photosynthetic lineages, highlighting how terrestrialization, genome architecture and translational demands have shaped their evolution.

In plants, polar cell growth is essential for processes such as root hair and pollen tube growth, but how it integrates with nuclear movement, cytoskeletal organization, and cell mechanics is not fully understood. We conducted high-resolution live imaging of Arabidopsis thaliana root hairs throughout their development using a microfluidic device. We identified 3 distinct stages--fast growth, slow growth, and early maturation--and quantified growth kinetics at high temporal resolution. The transition from fast to slow growth was consistent with cytoskeletal dynamics causing reduced tip growth and decreased nucleus-tip distance. Based on these observations, we developed a mathematical model linking cytoskeletal dynamics with tip growth and nuclear dynamics. Through genetic and pharmacological approaches, we were able to disrupt or trigger this transition, supporting the model and revealing the existence of essential crosstalk between actin filaments and microtubules. Additionally, vacuole dynamics, root hair diameter, and cell stiffness changed during the fast-to-slow transition, indicating a coordinated regulation of multiple subcellular systems. Together, these results connect nuclear, cytoskeletal, and mechanical dynamics during root hair development, offering an integrated view of the subcellular processes behind the control of polar cell growth in plants.

Transfer RNAs (tRNAs) are essential components of the translation machinery. Their abundance and diversity shape decoding capacity as well as the efficiency and accuracy of protein synthesis. Because tRNA abundance is encoded in the genome through tDNA copy number, chromosomal organization, and cis-regulatory sequences controlling transcription, these features are expected to influence the translational system. However, the principles governing nuclear tDNA organization remain poorly understood. Here, we analyzed nuclear tDNA repertoires across 53 photosynthetic eukaryotes spanning major Archaeplastida lineages and secondary endosymbionts, along with seven non-plant eukaryotic outgroups, using comparative genomic approaches at sequence, chromosomal, and genome-wide scales. To standardize these analyses and enable interactive exploration of tDNA organization, we developed ShinytRNA (https://nebula.ibmp.unistra.fr/shinytRNA/), a web application for genome-scale analysis of chromosomal tDNA organization. Nuclear tDNA copy numbers vary by more than two orders of magnitude across species, yet the relative representation of tRNA families corresponding to each amino acid remains strikingly conserved across lineages, revealing strong evolutionary constraints on tDNA dosage. Angiosperm tDNAs exhibit coordinated enrichment of cis-regulatory elements involved in RNA polymerase III transcription, including expanded AT-rich upstream regions, positional enrichment of CAA motifs, and extended poly(T) termination stretches. At the chromosomal scale, tDNAs are predominantly dispersed along chromosome arms, with homogeneous spacing that scales with genome size, while also showing non-random chromosomal distribution, exclusion from centromeric regions, and occasional clustering. Together, these patterns reveal conserved yet lineage-specific principles governing nuclear tDNA organization in plants and highlight how multiple genomic constraints shape the evolution of nuclear tDNA repertoires.

Saline and arid ecosystems are recognized as promising reservoirs of novel Actinomycetota with unique adaptations and secondary metabolic potential. In this study, a halotolerant Actinomycetota strain, designated ZS3416R2A, was isolated from saline soil in the hypersaline wetland of Lake Zima, Morocco. Phylogenetic analysis based on the 16S rRNA gene sequence showed 99.03

Members of the phylum Actinomycetota are widely distributed across diverse environments and are well known for their metabolic versatility and capacity to produce bioactive compounds. In this study, strain ZE1316R2Aᵀ was isolated from the saline water collected from Lake Zima (Morocco) and subjected to comprehensive polyphasic taxonomic characterisation. Phylogenetic analysis based on the 16 S rRNA gene placed strain ZE1316R2Aᵀ within the genus Streptomyces, showing highest sequence similarity with S. albidoflavus DSM 40,455T (99.71

Plant growth-promoting rhizobacteria (PGPR) enhance plant growth and development through diverse mechanisms, including phytohormone production, nutrient acquisition, and stress mitigation. This study describes the isolation and characterization of two bacterial strains, DT1 and S10, from the rhizospheres of Diplotaxis tenuifolia and Cynodon dactylon, respectively that exhibit multiple plant growth‑promoting traits, including phosphate and zinc solubilization, nitrogen metabolism and the production of indole acetic acid (IAA) and siderophores. Using whole genome sequencing and taxonomic analyses, these two strains were identified as Acinetobacter calcoaceticus (DT1) and Citrobacter braakii (S10). Functional genomic annotation revealed numerous genes associated with key plant growth-promoting traits, including those involved in indole-3-acetic acid (IAA) (trpABCDE, ipdC), cytokinin (miaABE), and riboflavin biosynthesis, which were further supported by targeted metabolomic analyses. In addition, genes associated with nitrogen metabolism, including nitrate/nitrite reduction (nirB, narGHI), as well as phosphate solubilization (gcd, phoARP, pstABCS, pqqEFG) were identified and supported by phenotypic assays. Interestingly, biosynthetic gene clusters for the secondary metabolites enterobactin, bacillibactin, and staphyloferrin B, known to contribute to plant growth promotion, were identified in both genomes. Both strains also harbored genes potentially involved in stress-related metabolic processes. Furthermore, non-targeted metabolomic analysis revealed that DT1 and S10 produced a range of intracellular and extracellular metabolites associated with plant growth promotion and stress resilience, including cadaverine, biotin, arginine, and GABA. Collectively, these findings position DT1 and S10 as promising bioinoculant candidates, offering an integrative genomic and metabolic foundation for their application in next-generation sustainable agricultural strategies.

Polycomb Group (PcG) proteins, including members of Polycomb Repressive Complex 1 and 2 (PRC1 and PRC2), regulate many key developmental processes through transcriptional gene repression. While the molecular mechanisms of PRC2 and its histone methyltransferase involved in depositing histone 3 lysine 27 trimethylation (H3K27me3) are well understood, the components and E3 ubiquitin ligase functions of PRC1 in plants remain largely elusive. In Arabidopsis, AtRING1 is a key PRC1 component, containing an N-terminal RING-finger domain and a C-terminal RAWUL domain. Previous studies have relied on T-DNA insertion mutants in the investigation of AtRING1 function. By editing AtRING1A using CRISPR/Cas9 technology in the atring1b-1 background, here we have generated and characterized one N-terminal stop mutant atring1ko and two C-terminal deletion mutants atring1▵C-terminal lacking the RAWUL domain. We show evidence that atring1ko represents the strongest loss-of-function mutant, exhibiting embryonic callus-like structures, demonstrating the essential role of AtRING1 in cell differentiation. Remarkably, the atring1▵C-terminal mutants exhibit mild developmental defects, suggesting that the RING domain alone retains partial function, while the RAWUL domain fine-tunes PRC1 activity. Our molecular analyses support a model in which AtRING1/PRC1-mediated H2A monoubiquitination (H2Aub1) often precedes PRC2-mediated H3K27me3 deposition at some target loci. Strikingly, the RAWUL domain is required for efficient H2Aub1 enrichment and influences H3K27me3 deposition in a locus-specific manner. Taken together, our study provides new insights into the molecular mechanism underlying PRC1 E3 ligase activity, supporting that PRC1 function facilitates PRC2 activity in epigenetic gene silencing.

Chromatin modifications are deemed to correlate with gene expression patterns, yet their direct causal effect on transcription and cell fate remains unestablished. The H3K27me3 modification, highly conserved in eukaryotes, is strongly associated with the repression of developmental genes. Here, we establish the genuine function of H3K27me3 in planta by leveraging a CRISPR-dCas9-based epigenetic editing tool to specifically remove this methylation mark at the Arabidopsis CUP SHAPED COTYLEDON 3 (CUC3) boundary gene. Targeted recruitment of the JMJ13 H3K27me3 demethylase to the CUC3 locus induces ectopic transcription and gene expression patterns, leading to altered leaf morphology and meristem integrity. Combining molecular and phenotypic analyses, we thus establish evidence directly linking H3K27me3-mediated repression to developmental outcomes. Our study highlights locus-specific epigenetic editing as a powerful approach to dissect the functional impacts of histone modifications on transcription and morphogenesis, and provides a framework for unveiling the causal role of chromatin dynamics in plant developmental plasticity.

The target of rapamycin (TOR) kinase is a critical regulator of plant growth and development, integrating environmental and internal signals to modulate cellular processes. This review explores the emerging role of TOR in chromatin regulation, focusing on its nuclear activities and interactions with chromatin remodeling factors. We highlight the mechanisms by which TOR influences chromatin structure and gene expression, including its involvement in histone modifications and DNA methylation. Additionally, we discuss the interplay between TOR signaling, the cytoskeleton, and nuclear functions, emphasizing the potential of TOR to act as a bridge between cytoskeletal dynamics and chromatin regulation. Finally, besides TOR-mediated cyto-nuclear shuttling and metabolic regulation, we address the translational control of chromatin components by TOR as additional layers impacting the chromatin landscape. We also propose future research directions to further elucidate the complex regulatory network governed by TOR in plant cells.

Nuclear dynamics refers to global/local changes in the molecular and spatial organization of genomic DNA that can occur during development or in response to environmental stress signals and eventually impact genomic functions. In plants, nuclear dynamics relies notably on the connection of the nucleus with the cytoskeleton during development. It orchestrates genomic functions in response to developmental and environmental cues. This is particularly true in the plant root system, which is constantly exposed to a wide range of internal and external stimuli. Currently, studying nuclear dynamics in a growing root is challenging due to limitations regarding real-time imaging for quantitative analyses under controlled conditions. Microfluidic systems for plant cell studies are valuable analytical tools that provide precise control of culture conditions together with live-imaging capabilities at high temporal and spatial resolutions. Herein, we describe a microfluidic platform to unravel dynamically and noninvasively nuclear organization in the seedling root system exposed to various treatments. As exemplified here, our microfluidic platform can be conveniently used for real-time microscopy imaging and quantitative analysis of fine nuclear morphological changes upon modifying cytoskeleton dynamics. Importantly, our system can be applied to a wide variety of microscopic means including high-resolution microscopy to investigate diverse subcellular compartments or nuclear domains in Arabidopsis thaliana roots.

Polar cell growth is a fundamental process across organisms, yet its coordination with nuclear movement and cytoskeleton dynamics remains underexplored. Focusing on Arabidopsis thaliana root hairs, we investigate these processes using high-resolution live imaging within microfluidics-based experiments. By incorporating data on cytoskeletal dynamics, nuclear positioning, and tip growth into a mathematical model, we analyse how their interactions shape the different growth phases that we reveal for the first time in this study. Chemical treatments and mutant analyses further support our model, revealing that timely cytoskeletal changes drive transitions between these growth phases, and correlate with shifts in nuclear movement and morphology. This regulation suggests a microtubule-actin crosstalk in the root hair subapical region. Additionally, we present novel findings on vacuole movement and cell stiffness, further refining our understanding of tip growth dynamics. Collectively, our work provides a comprehensive framework for understanding how transitions between growth phases are orchestrated in plant tip-growing cells. ### Competing Interest Statement The authors have declared no competing interest.

Plants constantly face adverse environmental conditions, including temperature drops that can severely impair growth and productivity. To cope with such stresses, they have evolved complex mechanisms of transcriptional reprogramming. While various cold-responsive pathways have been described, the contribution of chromatin-level regulation, and in particular histone modifications, remains largely obscure. Here, we identify the histone methyltransferase SET DOMAIN GROUP 26 (SDG26) as a positive regulator of cold stress responses in Arabidopsis thaliana . We show that SDG26 is transcriptionally induced and post-transcriptionally stabilized by cold, and that its loss of function leads to increased freezing tolerance but reduced drought tolerance. At the molecular level, SDG26 promotes expression of cold-responsive genes, including members of the CBF-COR regulon, through direct binding and histone H3 lysine 36 trimethylation (H3K36me3) at their chromatin. Concomitantly, SDG26 modulates abscisic acid (ABA) biosynthesis, catabolism, and transport, thereby promoting ABA accumulation, stomatal closure, and drought tolerance. Collectively, our results reveal that SDG26 integrates ABA-dependent and ABA-independent pathways to fine-tune Arabidopsis responses to abiotic stresses. We further establish SDG26 as a chromatin modifier contributing to stress-responsive H3K36me3 enrichment at specific loci. Together, our work identifies SDG26 as a chromatin-based hub balancing cold acclimation with water conservation, thereby enhancing plant resilience. ### Competing Interest Statement The authors have declared no competing interest.

The target of rapamycin (TOR)-Polycomb repressive complex 2 (PRC2) pathway is a crucial link that translates environmental and developmental cues into chromatin, thus reprogramming transcription. While the PRC2 methyltransferase Curly leaf (CLF) is known to be specifically involved, the underlying mechanism remains unclear. This study sheds light on how TOR fine-tunes CLF protein levels by promoting translation re-initiation mediated by eIF3h. We found that the second upstream open reading frame (uORF) located in the 5' leader region of the CLF transcript significantly represses its translation (by 50%). Plants lacking this uORF leader displayed reduced sensitivity to TOR inhibition and impaired induction of stress-responsive genes. Interestingly, this uORF sequence exhibits partial conservation across diverse plant species, suggesting a potential role in adaptation to various environmental conditions. Our findings reveal a dynamic mechanism within the TOR-PRC2 pathway, highlighting its responsiveness to environmental stimuli. ### Competing Interest Statement The authors have declared no competing interest.

In eukaryotes, accurate chromosome segregation during cell division relies on the centromeric histone H3 variant, CENH3. Our previous work identified KINETOCHORE NULL2 (alpha KNL2) as a plant CENH3 assembly factor, which contains a centromere-targeting motif, CENPC-k, analogous to the CENPC motif found in CENP-C. We also demonstrated that alpha KNL2 can bind DNA in vitro in a sequence-independent manner, without the involvement of its CENPC-k motif. In this study, we show that the CENPC-k and CENPC motifs alone are insufficient for centromere targeting in Nicotiana benthamiana and Arabidopsis thaliana. In silico analysis identified adjacent DNA-binding regions near the CENPC-k and CENPC motifs, suggesting their role in centromeric DNA interaction. We further demonstrated that protein fragments containing these motifs effectively target centromeres. Deletion of these DNA-binding domains reduced the centromeric localization of alpha KNL2-C, while fusing CENPC-k to the non-specific DNA-binding domain of histone-like nucleoid structuring protein from Escherichia coli successfully targeted it to centromeres. Our findings suggest that the centromeric targeting of alpha KNL2 and CENP-C proteins relies on the CENPC-k/CENPC motifs, and that their sequence-independent DNA-binding activity enhances their centromere anchoring. These insights into the mechanisms of alpha KNL2 and CENP-C targeting may facilitate the engineering of kinetochore structures by directing chromatin-modifying proteins to centromeres.

Chromatin modifications are deemed to associate with gene expression patterns, yet their causal function on transcription and cell fate remains unestablished. Here, we demonstrate the direct impact of an epigenome editing tool designed to remove a key chromatin modification at a precise locus in living plants, with outcomes from the molecular to the developmental scale.The manipulated mark, H3K27me3, deposited at Lysine 27 of Histone 3 by the methyltransferase Polycomb PRC2 complex, is associated with the repression of developmental genes. As a new approach to investigate this histone mark genuine function, we used a dCas9-derived tool to bring a specific demethylase function at the CUP SHAPED COTYLEDON 3 ( CUC3) organ frontier gene, aiming to remove the trimethyl mark at H3K27. We show that the removal of H3K27me3 at the locus causally induces activation of CUC3 expression within its regular territory, as well as ectopically. Our precise perturbation strategy reveals that alterations in a chromatin mark lead to changes in transcription and developmental gene expression patterning, with sharp consequences on plant morphogenesis and growth.Our work thus constitutes a proof of concept for the effective use of epigenome editing tools in unveiling the causal role of mark dynamics, supported by both molecular and developmental evidences.### Competing Interest StatementThe authors have declared no competing interest.

In eukaryotic organisms, proper chromosome segregation during cell division depends on the centromeric histone H3 (CENH3) variant. Our previous studies identified a plant CENH3 assembly factor, Kinetochore Null2 (αKNL2), that possesses a centromere-targeting motif, CENPC-k, similar to the CENPC motif in CENP-C. Additionally, we have demonstrated that αKNL2 can bind DNA in vitro, independent of its CENPC-k motif. Thus, the mechanism underlying the binding of αKNL2 to centromeric DNA remains elusive.Our study shows that the CENPC-k and CENPC motifs alone are not sufficient to target the centromere in N. benthamiana and A. thaliana . In-silico analysis revealed flanking DNA-binding regions near the CENPC-k and CENPC motifs, suggesting their importance in interacting with centromeric DNA. Fusion of protein fragments containing these motifs to EYFP facilitated targeting to the centromere. Deletion of DNA-binding domains reduced the centromeric localization of αKNL2-C, whereas fusion of CENPC-k to the H-NS protein from E. coli targeted it to centromeres.We conclude that targeting of αKNL2 and CENP-C proteins to centromeres is dependent on the CENPC-k/CENPC motifs, and their sequence-independent DNA-binding promotes anchoring at the centromere. Understanding the targeting mechanisms of KNL2 and CENP-C may help to engineer kinetochore structure by targeting chromatin modifying proteins to centromeres.### Competing Interest StatementThe authors have declared no competing interest.

How to get a metre of DNA into a tiny space while preserving its functional characteristics? This question seems easy to pose, but the answer is far from being trivial. Facing this riddle, salvation came from technical improvements in microscopy and in situ hybridisation techniques applied to cytogenetics. Here, we would like to look into the past at one of these pure cytogenetics articles that makes a breakthrough in addressing this question in plant science. Our choice fell on the work published two decades ago by Fransz et al. (2002). Besides the elegant manner in which DNA probes were organised to bring into light the out-looping arrangement of interphase chromosomes in Arabidopsis thaliana nuclei, this article perfectly illustrates that painting is not reserved to the fine art. As for whether emotional expression prioritised by artists can sometimes hide behind scientific empirical evidence, there is only a small step to make to the general case.

Chromatin is a dynamic platform within which gene expression is controlled by epigenetic modifications, notably targeting amino acid residues of histone H3. Among them is lysine 27 of H3 (H3K27), the trimethylation of which by the Polycomb Repressive Complex 2 (PRC2) is instrumental in regulating spatiotemporal patterns of key developmental genes. H3K27 is also subjected to acetylation and is found at sites of active transcription. Most information on the function of histone residues and their associated modifications in plants was obtained from studies of loss-of-function mutants for the complexes that modify them. To decrypt the genuine function of H3K27, we expressed a non-modifiable variant of H3 at residue K27 (H3.3K27A ) in Arabidopsis, and developed a multi-scale approach combining in-depth phenotypical and cytological analyses, with transcriptomics and metabolomics. We uncovered that the H3.3K27A variant causes severe developmental defects, part of them are reminiscent of PRC2 mutants, part of them are new. They include early flowering, increased callus formation and short stems with thicker xylem cell layer. This latest phenotype correlates with mis-regulation of phenylpropanoid biosynthesis. Overall, our results reveal novel roles of H3K27 in plant cell fates and metabolic pathways, and highlight an epigenetic control point for elongation and lignin composition of the stem.

The nucleus is a central organelle of eukaryotic cells undergoing dynamic structural changes during cellular fundamental processes such as proliferation and differentiation. These changes rely on the integration of developmental and stress signals at the nuclear envelope (NE), orchestrating responses at the nucleo-cytoplasmic interface for efficient genomic functions such as DNA transcription, replication and repair. While in animals, correlation has already been established between NE dynamics and chromatin remodeling using last-generation tools and cutting-edge technologies, this topic is just emerging in plants, especially in response to mechanical cues. This review summarizes recent data obtained in this field with more emphasis on the mechanical stress response. It also highlights similarities/differences between animal and plant cells at multiples scales, from the structural organization of the nucleo-cytoplasmic continuum to the functional impacts of NE dynamics.