The Plant Journal最新文献

Seed germination is crucial for agricultural reproduction. A deep understanding of this process can secure healthy growth at the early phases of plant development and therefore yield. Recent research indicates that germination is a complex process involving translational regulation. A large group of seed-stored mRNAs together with newly synthesized transcripts are regulated by post-transcriptional mechanisms and selectively translated at different stages to support the germination process. To investigate the mechanism of translational control, we performed ribosome profiling on mRNAs of distinct physiological stages during Arabidopsis thaliana seed germination. The presence of ribosome association on mRNAs with three-nucleotide periodicity indicates their capacity for translation. Dry seeds, in which translation is on hold, are characterized by a unique ribosome association landscape with a higher ribosome association at the 5′ and 3′ UTR, compared with physiological stages that show active translation. Start codon-specific stalling of ribosomes in dry seeds is associated with an adenine-enriched sequence motif. Throughout germination, codons encoding glycine, aspartate, tyrosine, and proline are the most frequent ribosome pausing sites. Moreover, the non-coding ribosome-associated RNAs that we identified are indeed translated, as was revealed by investigating total seed proteome data. Seed-specific upstream open reading frames (uORFs) have been identified that may play a role in translational regulation of early seed germination. Altogether, we present a first ribosome profiling analysis across seed germination that illuminates various regulatory mechanisms that potentially contribute to the seed's survival strategy.

Protein synthesis is an essential process for all living organisms and is tightly regulated to ensure the proper production of proteins needed for growth, development, and stress responses. As sessile organisms, plants have evolved distinct mechanisms to regulate translation, allowing them to adapt to their environment. In this review, we highlight the general translation process, discuss the translational machinery in plants, and examine cis-regulatory elements that influence translation. Additionally, we explore recent studies on how plants regulate translation in response to environmental and developmental cues.

Physcomitrium patens is a bryophyte model system particularly valuable for evolutionary developmental and comparative genomics studies. Sexual reproduction in bryophytes offers unique insights into the evolution of land plant reproduction. Unlike seed plants, bryophytes have a dominant gametophyte phase and provide significant advantages for studying sexual reproduction, such as the possibility to maintain embryo-lethal mutants through vegetative propagation or the presence of motile male gametes. More than 25 years after the first publications of transcriptomic data for P. patens, expression data of most developmental stages of P. patens as well as its responses to various biotic and abiotic perturbations have been represented by microarrays or RNA-seq datasets. To facilitate the use of such data, we introduce the MAdLandExpression atlas as a successor of PEATmoss (Physcomitrium Expression Atlas Tool), integrating its 109 P. patens expression experiments and expanding it with 20 recently published RNA-seq samples of sexual reproduction stages, thus completing the coverage of the P. patens life cycle. The MAdLandExpression atlas also introduces new features for data visualization and analysis, such as the comparison of samples from multiple datasets and gene set normalization. Using this tool, the sexual reproduction dataset was analyzed, identifying genes potentially important for egg and sperm cell development, and confirming the behavior of known key genes in sexual development observed in previous studies.

Plants actively monitor the state of their cell walls and adapt their structure and composition as needed. THESEUS1 (THE1), a receptor kinase from the Catharanthus roseus RECEPTOR-LIKE KINASE 1-LIKE (CrRLK1L) family, was the first receptor kinase described to be involved in this maintenance of cell wall integrity in Arabidopsis thaliana. It contributes to the regulation of cell wall stiffness, participates in lateral root development, and modulates production of the stress hormones abscisic acid and jasmonic acid. Besides, it is required for responses to cellulose biosynthesis inhibition, such as growth inhibition and ectopic lignification. The THE1 ligand, RAPID ALKALINIZATION FACTOR 34, and one intracellular interaction partner, GUANINE EXCHANGE FACTOR 4, have been identified. However, relatively little is known about other interaction partners and mechanisms by which THE1 influences downstream responses. Given that FERONIA, a related member of the CrRLK1L family, has dozens of interaction partners, it is likely that there is a wealth of interactors waiting to be described for THE1. Here, we shed light on the evolutionary origin of THE1 and describe the many open questions surrounding THE1-dependent signaling processes. We expect that many of these questions will be answered in the coming years and that these answers will provide more insight into the molecular mechanism of cell wall integrity maintenance mediated by THE1.

Microalgae modulate lipid metabolism in response to nutrient stress, offering a promising avenue for sustainable biofuel production. However, a mechanistic understanding of the transcriptional programs driving triacylglycerol (TAG) accumulation remains limited, particularly in non-model species. Here, we employ a systems-level approach to dissect the regulatory basis of TAG biosynthesis in two Chlorella sorokiniana strains exhibiting contrasting lipid accumulation phenotypes under nitrogen (N) and phosphorus (P) deprivation. Through physiological, metabolic, and transcriptomic analyses, we confirmed C. sorokiniana DOE1412 (CsDOE1412) as a high TAG-accumulator and C. sorokiniana UTEX1228 (Cs1228) as a low TAG-accumulator, providing a comparative framework for inferring transcriptional regulatory networks (TRNs). Both stressors induced rapid TAG accumulation within 6 h, with CsDOE1412 reaching 40% TAG content by 48 h under N conditions. While N deprivation primarily promoted TAG accumulation, P starvation favored diacylglyceryl trimethylhomoserine biosynthesis, reaching up to 21 and 30% of the lipid composition in Cs1228 and CsDOE1412, respectively. TRNs analysis revealed a distinct regulatory logic between strains: CsDOE1412 exhibited a stress-specific, narrowly focused transcriptional response, with five transcription factors (TFs) identified as leading regulators based on centrality measures, whereas Cs1228 mounted a broader, overlapping response, with 30 key TFs across conditions. A detailed analysis of the inferred TRNs identified 15 and 14 candidate TFs in CsDOE1412 and Cs1228, respectively, with predicted interactions involving key steps in carbon metabolism and lipid biosynthesis, suggesting their involvement in metabolic rewiring during nutrient stress. Among them, we found two CH3-type ortholog pairs, Cs1228_21g10473/CsDOE1412_2079g07848 and Cs1228_02g00899/CsDOE1412_2296g01133, showing upregulation in TAG-accumulating conditions; and one AP2-type ortholog pair, Cs1228_04g03113/CsDOE1412_2160g02163, with contrasting transcription profiles, pointing to transcriptional regulatory pathways with shared and unique regulators between strains. These findings expand the repertoire of regulatory components associated with algal lipid metabolism and highlight C. sorokiniana as a robust model for elucidating complex transcriptional responses to environmental cues. Furthermore, this study provides candidate TFs for engineering enhanced lipid productivity in microalgae.