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1. m ⁶ A modification plays an integral role in mRNA stability and translation during pattern-triggered immunity

   https://doi.org/10.1073/pnas.2411100121  

   Chen, Tianyuan; Greene, George H; Motley, Jonathan; Mwimba, Musoki; Luo, Guan-Zheng; Xu, Guoyong; Karapetyan, Sargis; Xiang, Yezi; Liu, Chang; He, Chuan; et al (August 2024, Proceedings of the National Academy of Sciences)

   Plants employ distinct mechanisms to respond to environmental changes. Modification of mRNA byN⁶-methyladenosine (m⁶A), known to affect the fate of mRNA, may be one such mechanism to reprogram mRNA processing and translatability upon stress. However, it is difficult to distinguish a direct role from a pleiotropic effect for this modification due to its prevalence in RNA. Through characterization of the transient knockdown-mutants of m⁶A writer components and mutants of specific m⁶A readers, we demonstrate the essential role that m⁶A plays in basal resistance and pattern-triggered immunity (PTI). A global m⁶A profiling of mock and PTI-inducedArabidopsisplants as well as formaldehyde fixation and cross-linking immunoprecipitation-sequencing of the m⁶A reader, EVOLUTIONARILY CONSERVED C-TERMINAL REGION2 (ECT2) showed that while dynamic changes in m⁶A modification and binding by ECT2 were detected upon PTI induction, most of the m⁶A sites and their association with ECT2 remained static. Interestingly, RNA degradation assay identified a dual role of m⁶A in stabilizing the overall transcriptome while facilitating rapid turnover of immune-induced mRNAs during PTI. Moreover, polysome profiling showed that m⁶A enhances immune-associated translation by binding to the ECT2/3/4 readers. We propose that m⁶A plays a positive role in plant immunity by destabilizing defense mRNAs while enhancing their translation efficiency to create a transient surge in the production of defense proteins. 

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2. RNA N6-Methyladenosine Affects Copper-Induced Oxidative Stress Response in Arabidopsis thaliana

   https://doi.org/10.3390/ncrna10010008  

   Sharma, Bishwas; Govindan, Ganesan; Li, Yongfang; Sunkar, Ramanjulu; Gregory, Brian D (February 2024, Non-Coding RNA)

   Recently, post-transcriptional regulation of mRNA mediated by N6-methyladenosine (m6A) has been found to have profound effects on transcriptome regulation during plant responses to various abiotic stresses. However, whether this RNA modification can affect an oxidative stress response in plants has not been studied. To assess the role of m6A modifications during copper-induced oxidative stress responses, m6A-IP-seq was performed in Arabidopsis seedlings exposed to high levels of copper sulfate. This analysis revealed large-scale shifts in this modification on the transcripts most relevant for oxidative stress. This altered epitranscriptomic mark is known to influence transcript abundance and translation; therefore we scrutinized these possibilities. We found an increased abundance of copper-enriched m6A-containing transcripts. Similarly, we also found increased ribosome occupancy of copper-enriched m6A-containing transcripts, specifically those encoding proteins involved with stress responses relevant to oxidative stressors. Furthermore, the significance of the m6A epitranscriptome on plant oxidative stress tolerance was uncovered by assessing germination and seedling development of the mta (N6-methyladenosine RNA methyltransferase A mutant complemented with ABI3:MTA) mutant exposed to high copper treatment. These analyses suggested hypersensitivity of the mta mutant compared to the wild-type plants in response to copper-induced oxidative stress. Overall, our findings suggest an important role for m6A in the oxidative stress response of Arabidopsis. 

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3. The vacuolar Ca ²⁺ transporter CATION EXCHANGER 2 regulates cytosolic calcium homeostasis, hypoxic signaling, and response to flooding in Arabidopsis thaliana

   https://doi.org/10.1111/nph.19274  

   Bakshi, Arkadipta; Choi, Won‐Gyu; Kim, Su‐Hwa; Gilroy, Simon (September 2023, New Phytologist)

   Summary Flooding represents a major threat to global agricultural productivity and food security, but plants are capable of deploying a suite of adaptive responses that can lead to short‐ or longer‐term survival to this stress. One cellular pathway thought to help coordinate these responses is via flooding‐triggered Ca²⁺signaling.We have mined publicly available transcriptomic data from Arabidopsis subjected to flooding or low oxygen stress to identify rapidly upregulated, Ca²⁺‐related transcripts. We then focused on transporters likely to modulate Ca²⁺signals. Candidates emerging from this analysis includedAUTOINHIBITED Ca²⁺ATPASE 1andCATION EXCHANGER 2. We therefore assayed mutants in these genes for flooding sensitivity at levels from growth to patterns of gene expression and the kinetics of flooding‐related Ca²⁺changes.Knockout mutants inCAX2especially showed enhanced survival to soil waterlogging coupled with suppressed induction of many marker genes for hypoxic response and constitutive activation of others.CAX2mutants also generated larger and more sustained Ca²⁺signals in response to both flooding and hypoxic challenges.CAX2 is a Ca²⁺transporter located on the tonoplast, and so these results are consistent with an important role for vacuolar Ca²⁺transport in the signaling systems that trigger flooding response. 

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4. Glucosinolates can act as signals to modulate intercellular trafficking via plasmodesmata

   https://doi.org/10.1111/nph.70032  

   Fernandez, Jessica C; Azim, Mohammad F; Adams, Nicole; Strong, Morgan; Piya, Sarbottam; Xu, Min; Brunkard, Jacob O; Hewezi, Tarek; Sams, Carl E; Burch‐Smith, Tessa M (May 2025, New Phytologist)

   Summary Plasmodesmata (PD) allow direct communication across the cellulosic plant cell wall, facilitating the intercellular movement of metabolites and signaling molecules within the symplast. InArabidopsis thalianaembryos with reduced levels of the chloroplast RNA helicase ISE2, intercellular trafficking and the number of branched PD were increased. We therefore investigated the relationship between alteredISE2expression and intercellular trafficking.Gene expression analyses in Arabidopsis tissues whereISE2expression was increased or decreased identified genes associated with the metabolism of glucosinolates (GLSs) as highly affected.Concomitant with changes in the expression of GLS‐related genes, plants with abnormalISE2expression contained altered GLS metabolic profiles compared with wild‐type (WT) counterparts. Indeed, changes in the expression of GLS‐associated genes led to altered intercellular trafficking in Arabidopsis leaves. Exogenous application of GLSs but not their breakdown products also resulted in altered intercellular trafficking.These changes in trafficking may be mediated by callose levels at PD as exogenous GLS treatment was sufficient to modulate plasmodesmal callose in WT plants. Furthermore, auxin metabolism was perturbed in plants with increased indole‐type GLS levels. These findings suggest that GLSs, which are themselves transported between cells via PD, can act on PD to regulate plasmodesmal trafficking capacity. 

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5. The Impact of Leadered and Leaderless Gene Structures on Translation Efficiency, Transcript Stability, and Predicted Transcription Rates in Mycobacterium smegmatis

   https://doi.org/10.1128/JB.00746-19  

   Nguyen, Tien G.; Vargas-Blanco, Diego A.; Roberts, Louis A.; Shell, Scarlet S. (April 2020, Journal of Bacteriology)

   Henkin, Tina M. (Ed.)

   ABSTRACT Regulation of gene expression is critical for Mycobacterium tuberculosis to tolerate stressors encountered during infection and for nonpathogenic mycobacteria such as Mycobacterium smegmatis to survive environmental stressors. Unlike better-studied models, mycobacteria express ∼14% of their genes as leaderless transcripts. However, the impacts of leaderless transcript structures on mRNA half-life and translation efficiency in mycobacteria have not been directly tested. For leadered transcripts, the contributions of 5′ untranslated regions (UTRs) to mRNA half-life and translation efficiency are similarly unknown. In M. tuberculosis and M. smegmatis , the essential sigma factor, SigA, is encoded by a transcript with a relatively short half-life. We hypothesized that the long 5′ UTR of sigA causes this instability. To test this, we constructed fluorescence reporters and measured protein abundance, mRNA abundance, and mRNA half-life and calculated relative transcript production rates. The sigA 5′ UTR conferred an increased transcript production rate, shorter mRNA half-life, and decreased apparent translation rate compared to a synthetic 5′ UTR commonly used in mycobacterial expression plasmids. Leaderless transcripts appeared to be translated with similar efficiency as those with the sigA 5′ UTR but had lower predicted transcript production rates. A global comparison of M. tuberculosis mRNA and protein abundances failed to reveal systematic differences in protein/mRNA ratios for leadered and leaderless transcripts, suggesting that variability in translation efficiency is largely driven by factors other than leader status. Our data are also discussed in light of an alternative model that leads to different conclusions and suggests leaderless transcripts may indeed be translated less efficiently. IMPORTANCE Tuberculosis, caused by Mycobacterium tuberculosis , is a major public health problem killing 1.5 million people globally each year. During infection, M. tuberculosis must alter its gene expression patterns to adapt to the stress conditions it encounters. Understanding how M. tuberculosis regulates gene expression may provide clues for ways to interfere with the bacterium’s survival. Gene expression encompasses transcription, mRNA degradation, and translation. Here, we used Mycobacterium smegmatis as a model organism to study how 5′ untranslated regions affect these three facets of gene expression in multiple ways. We furthermore provide insight into the expression of leaderless mRNAs, which lack 5′ untranslated regions and are unusually prevalent in mycobacteria. 

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