Biology subjects

Pedmale, U. V.

Publications and source records attributed to Pedmale, U. V..

8 recordsLinked to original sources

bioRxiv2024

The microRNA156/SPL9 module mediates auxin response to facilitate apical hook maintenance in Arabidopsis

Auxin coordinates cell growth by promoting or inhibiting cell expansion during etiolated seedling development, but whether and how microRNA modules participate in this process remains unclear. Here, we show the miRNA156/SQUAMOSA PROMOTER-BINDING-PROTEIN-LIKE9 (miR156/SPL9) module is critical for skotomorphogenesis. Perturbation of the miR156/SPL9 module affected skotomorphogenesis, as the loss of miR156 function or SPL9 de-repression led to shorter hypocotyl, higher hook angle, and delayed hook opening. Opposing phenotypes were observed in dark-grown spl9 and miR156-overexpressing seedlings. Importantly, loss of miR156-dependent SPL9 regulation triggered apical hook formation even under reduced levels of endogenous auxin. miR156-targeted SPL9 arrested cell expansion by repressing small auxin-up RNA19 (SAUR19) gene in a FRUITFULL (FUL)-dependent and independent manner. The conserved miR156/SPL9/15 module also affects skotomorphogenesis in tomato, impacting its successful soil emergence. Our findings unravel how the miR156/SPL9 module plays a pivotal role in the auxin network coordinating apical hook development to enable appropriate seedling emergence.

plant biology↗

bioRxiv2024

Reticulate leaf venation in Pilea peperomioides is a Voronoi diagram

Reticulate leaf venation, characterized by the presence of loops, is a distinguishing feature of many flowering plants. However, our understanding of both the geometry and the morphogenesis of reticulate vein patterns is far from complete. We show that in the Chinese money plant (Pilea peperomioides), major veins form an approximate Voronoi diagram surrounding secretory pores known as hydathodes. We also propose a mechanistic model based on polar transport of the plant hormone auxin to produce Voronoi patterns. In contrast with classical models where veins directly connect auxin sources to sinks, our model generates veins that bisect the space between adjacent auxin sources, collectively forming loops. The paradigm change offered by this model may open the door to study reticulate vein formation in other species.

plant biology↗

bioRxiv2023

Light and temperature regulate m6A-RNA modification to regulate growth in plants

N6-methyladenosine is a highly dynamic, abundant mRNA modification which is an excellent potential mechanism for fine tuning gene expression. Plants adapt to their surrounding light and temperature environment using complex gene regulatory networks. The role of m6A in controlling gene expression in response to variable environmental conditions has so far been unexplored. Here, we map the transcriptome-wide m6A landscape under various light and temperature environments. Identified m6A-modifications show a highly specific spatial distribution along transcripts with enrichment occurring in 5UTR regions and around transcriptional end sites. We show that the position of m6A modifications on transcripts might influence cellular transcript localization and the presence of m6A-modifications is associated with alternative polyadenylation, a process which results in multiple RNA isoforms with varying 3UTR lengths. RNA with m6A-modifications exhibit a higher preference for shorter 3UTRs. These shorter 3UTR regions might directly influence transcript abundance and localization by including or excluding cis-regulatory elements. We propose that environmental stimuli might change the m6A landscape of plants as one possible way of fine tuning gene regulation through alternative polyadenylation and transcript localization.

plant biology↗

bioRxiv2023

Cryptochromes and UBP12/13 deubiquitinases antagonistically regulate DNA damage response in Arabidopsis

Cryptochromes (CRYs) are evolutionarily conserved blue-light receptors that evolved from bacterial photolyases that repair damaged DNA. Today, CRYs have lost their ability to repair damaged DNA; however, prior reports suggest that human CRYs can respond to DNA damage. Currently, the role of CRYs in the DNA damage response (DDR) is lacking, especially in plants. Therefore, we evaluated the role of plant CRYs in DDR along with UBP12/13 deubiquitinases, which interact with and regulate the CRY2 protein. We found that cry1cry2 was hypersensitive, while ubp12ubp13 was hyposensitive to UVC-induced DNA damage. Elevated UV-induced cyclobutane pyrimidine dimers (CPDs) and the lack of DNA repair protein RAD51 accumulation in cry1cry2 plants indicate that CRYs are required for DNA repair. On the contrary, CPD levels diminished and RAD51 protein levels elevated in plants lacking UBP12 and UBP13, indicating their role in DDR repression. Temporal transcriptomic analysis revealed that DDR-induced transcriptional responses were subdued in cry1cry2, but elevated in ubp12ubp13 compared to WT. Through transcriptional modeling of the timecourse transcriptome, we found that genes quickly induced by UVC (15 min) are targets of CAMTA 1-3 transcription factors, which we found are required for DDR. This transcriptional regulation seems, however, diminished in the cry1cry2 mutant, indicating that CAMTAs are required for CRY2-mediated DDR. Furthermore, we observed enhanced CRY2-UBP13 interaction and formation of CRY2 nuclear speckles under UVC, suggesting that UVC activates CRY2 similarly to blue light. Together, our data reveal the temporal dynamics of the transcriptional events underlying UVC-induced genotoxicity and expand our knowledge of the role of CRY and UBP12/13 in DDR.

plant biology↗

bioRxiv2022

Systematic histone H4 replacement in Arabidopsis thaliana reveals a role for H4R17 in regulating flowering time

Despite the broad array of roles for epigenetic mechanisms on regulating diverse processes in eukaryotes, no experimental system for the direct assessment of histone function is currently available in plants. In this work, we present the development of a genetic strategy in Arabidopsis thaliana in which modified H4 transgenes can completely replace the expression of endogenous histone H4. Using this strategy, we established a collection of plants expressing different H4 point mutants targeting residues that may be post-translationally modified in vivo. To demonstrate the utility of this new H4 mutant collection, we screened it to uncover substitutions in H4 that alter flowering time. We identified different mutations in the tail (H4R17A) and the globular domain (H4R36A, H4R39K, H4R39A, and H4K44A) of H4 that strongly accelerate the floral transition. Furthermore, we found a conserved regulatory relationship between H4R17 and the ISWI chromatin remodeling complex in plants. Similar to other biological systems, H4R17 regulates nucleosome spacing via ISWI. Overall, this work provides a large set of H4 mutants to the plant epigenetics community that can be used to systematically assess histone H4 function in A. thaliana and a roadmap to replicate this strategy for studying other histone proteins in plants.

plant biology↗

bioRxiv2021

Shade-induced WRKY transcription factors restrict root growth during the shade avoidance response

Shade-intolerant plants rapidly elongate their stems, branches, and leaf stalks to compete with their neighboring vegetation to maximize sunlight capture for photosynthesis. This rapid growth adaptation, known as the shade avoidance response (SAR), comes at a cost; reduced biomass, crop yield, and root growth. Significant progress has been made on the mechanistic understanding of hypocotyl elongation during SAR; however, the molecular account of how root growth is repressed is not well understood. Here, we explore the mechanisms by which low red:far-red induced SAR restrict the primary and lateral root (LR) growth. By analyzing whole-genome transcriptome, we identified a core set of shade-induced genes in the roots of Arabidopsis and tomato seedlings grown in the shade. Abiotic and biotic stressors also induce many of these shade-induced genes and are predominantly regulated by the WRKY transcription factors. Correspondingly, a majority of the WRKYs were also among the shade-induced genes. Functional analysis using transgenics of these shade-induced WRKYs revealed their role is essentially to restrict primary root and LR growth in the shade, and captivatingly, they did not affect hypocotyl elongation. Similarly, we also show that ethylene hormone signaling is necessary to limit root growth in the shade. Our study proposes that during SAR, shade-induced WRKY26, 45, and 75, and ethylene reprogram gene expression in the root to restrict its growth and development. The reduced growth of root organs helps the plant divert its critical resources to the elongating organs in the shoot to ensure competitiveness under limiting photosynthetic radiation. One sentence summaryShade represses root growth by inducing WRKY transcription factors.

plant biology↗

bioRxiv2021

UBP12 and UBP13 deubiquitinases destabilize the CRY2 blue-light receptor to regulate growth

All organisms undergo growth, which is precisely controlled by exogenous and endogenous signals. Unchecked growth often leads to neoplasia and other developmental defects, severely affecting an organisms fitness. Light is a vital exogenous signal sensed by cryptochrome (CRY) blue light receptors to modulate growth and the circadian clock in plants and animals. Yet, how CRYs interpret light quantity to regulate growth in plants remains poorly understood. We show that UBP12 and UBP13 deubiquitinases physically interact with CRY2 in light. UBP12/13 negatively regulated CRY2 protein levels by promoting its ubiquitination and turnover to fine-tune growth. Unexpectedly, the destabilization of CRY2 by UBP12/13 is contrary to the general view that deubiquitinases stabilize proteins by preventing their degradation. Growth and development were explicitly affected in blue light when UBP12/13 was disrupted or overexpressed, indicating their role alongside CRY2. UBP12/13 also interacted and stabilized COP1, which is partially required for the turnover of CRY2. Despite decades of studies on deubiquitinases, the knowledge on how they are regulated is limited. Our study offers an insight into how exogenous signals and their receptors regulate deubiquitinase activity by protein-protein interaction. Altogether, our results provide a new module of cryptochromes and deubiquitinases in sensing and interpreting light cues to control growth at the most appropriate time.

plant biology↗

bioRxiv2020

Rapid expression of COVID-19 proteins by transient expression in tobacco.

In 2020 we suffered from a major global pandemic caused by the SARS-CoV-2 coronavirus. Efforts to contain the virus include the development of rapid tests and vaccines, which require a ready supply of viral proteins. Here we report the production of two SARS-CoV-2 proteins by transient transformation of tobacco, leading to high expression within three days, and subsequent purification of the intact proteins. Such efforts may help to develop testing resources to alleviate the major impacts of this global pandemic.

plant biology↗