Biology subjects

Rojas-Murcia, N.

Publications and source records attributed to Rojas-Murcia, N..

4 recordsLinked to original sources

bioRxiv2024

Time and temperature-resolved transcriptomic analysis of Arabidopsis splicing-related mutants

Temperature plays a crucial role in plant growth and development, influencing numerous physiological processes throughout the plant life cycle. Ambient temperature fluctuations can significantly affect transcriptomic adjustments, which are essential for plants to adapt to ever-changing environmental conditions. Despite the known impacts of extreme temperatures on plant physiology, there remains a knowledge gap regarding the specific effects of moderate changes in ambient temperatures on transcriptomic responses. This study employs strand-specific mRNA sequencing (RNA-seq) to assess how different splicing-related mutants respond to varying ambient temperatures, providing a valuable resource to the research community. Analysis of our time-resolved temperature-regulated alternative RNA splicing data reveals that common and exclusive use of the splicing machinery plays pivotal roles in thermoresponsive growth. Furthermore, our analyses demonstrate that moderate temperature changes are translated into widespread transcriptomic responses, including adjustments of the circadian clock and significant splicing changes in light and temperature genes. These results highlight the importance of these particular signaling pathways in adapting to new temperature regimes and suggest future experiments to study the role of alternative RNA splicing in temperature adaptation. Taken together, our results provide insights regarding the role of RNA splicing in plant responses to ambient temperature changes, highlighting the biological relevance of transcriptomic adjustments in enhancing plant resilience and adaptation to climate variability. SIGNIFICANCE STATEMENT- This is the first comprehensive study on how mutants involved in multiple steps of the splicing process modulate splicing activity in response to low and high ambient temperature changes. - We assessed early and acclimated transcriptomic responses and created a valuable resource to investigate the biological outputs.

plant biology↗

bioRxiv2024

The Arabidopsis thaliana core splicing factor PORCUPINE/SmE1 requires intron-mediated expression

Plants are prone to genome duplications and tend to preserve multiple gene copies. This is also the case for the genes encoding the Sm proteins of Arabidopsis thaliana (L). The Sm proteins are best known for their roles in RNA processing such as pre-mRNA splicing and nonsense-mediated mRNA decay. In this study, we have taken a closer look at the phylogeny and differential regulation of the SmE-coding genes found in A. thaliana, PCP/SmE1, best known for its cold-sensitive phenotype, and its paralog, PCPL/SmE2. The phylogeny of the PCP homologs in the green lineage shows that SmE duplications happened multiple times independently in different plant clades and that the duplication that gave rise to PCP and PCPL occurred only in the Brassicaceae family. Our analysis revealed that A. thaliana PCP and PCPL proteins, which only differ in two amino acids, exhibit a very high level of functional conservation and are able to perform the same function in the cell. However, our results indicate that PCP is the prevailing copy of the two SmE genes in A. thaliana as it is more highly expressed and that the main difference between PCP and PCPL resides in their transcriptional regulation, which is strongly linked to intronic sequences.

plant biology↗

bioRxiv2023

Temperature-dependent regulation of Arabidopsis thaliana growth and development by LSM7

Temperature affects plant growth by modulating the expression of genes and subsequent processing of RNAs that govern essential physiological processes. Here, we show that Arabidopsis thaliana Sm-like7 (LSM7), a core component of the splicing and decapping machinery, is indispensable for embryogenesis and development. Hypomorphic lsm7-2 mutants display severe developmental defects that are exacerbated by high temperatures. Transcriptome analysis verified LSM7s extensive role in gene regulation. In particular, we found that the key regulator of thermomorphogenesis, PHYTOCHROME INTERACTING FACTOR 4 (PIF4), and auxin-related genes, including SMALL AUXIN UP-REGULATED (SAUR) genes, are misregulated in lsm7-2. Auxin metabolic profiling confirmed that auxin homeostasis was disturbed in lsm7-2. Importantly, overexpression of the auxin-responsive SAUR19 gene partially restored thermomorphogenesis defects in lsm7-2 under high ambient temperature. Taken together, our research provides mechanistic insights into the interplay between RNA processing, hormone homeostasis, and the response to temperature regulation in plants and elucidates LSM7s essential function in plant temperature acclimation and resilience. Significance StatementGiven their sessile nature, plants cannot escape adverse environmental conditions such as cold or heat. Instead, they continuously adjust their gene expression and RNA processing to regulate growth and physiology in response to their surroundings. In this study, we investigated the role of the core RNA processing factor LSM7 in temperature acclimation in Arabidopsis thaliana. We found that LSM7 knockdown mutants were impaired in thermomorphogenesis and, as a result, were hypersensitive to elevated temperatures. At the molecular level, we demonstrated that this temperature sensitivity was caused by the misregulation of key regulators of thermomorphogenesis, including PIF4, auxin homeostasis and signaling, and SAUR genes. Our findings provide valuable insights into the role of RNA processing in plant temperature acclimation.

plant biology↗

bioRxiv2020

High-order mutants reveal an essential requirement for peroxidases but not laccases in Casparian strip lignification

The invention of lignin has been at the heart of plants capacity to colonize land, allowing them to grow tall, transport water within their bodies and protect themselves against various stresses. Consequently, this polyphenolic polymer, that impregnates the cellulosic plant cell walls, now represents the second most abundant polymer on Earth, after cellulose itself. Yet, despite its great physiological, ecological and economical importance, our knowledge of lignin biosynthesis in vivo, especially the crucial last steps of polymerization within the cell wall, remains vague. Specifically, the respective roles and importance of the two main polymerizing enzymes classes, laccases and peroxidases have remained obscure. One reason for this lies in the very high numbers of laccases and peroxidases encoded by 17 and 73 homologous genes, respectively, in the Arabidopsis genome. Here, we have focused on a specific lignin structure, the ring-like Casparian strips (CS) within the endodermis of Arabidopsis roots. By reducing the number of possible candidate genes using cellular resolution expression and localization data and by boosting the levels of mutants that can be stacked using CRISPR/Cas9, we were able to knock-out more than half of all laccases in the Arabidopsis genome in a nonuple mutant - abolishing the vast majority of laccases with detectable endodermal-expression. Yet, we were unable to detect even slight defects in CS formation. By contrast, we were able to induce a complete absence of CS formation in a quintuple peroxidase mutant. Our findings are in stark contrast to the strong requirement of xylem vessels for laccase action and indicate that lignin in different cell types can be polymerized in very distinct ways. We speculate that cells lignify differently depending on whether they deposit lignin in a localized or ubiquitous fashion, whether they stay alive during and after lignification as well as the composition of the cell wall.

plant biology↗