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1. 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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2. Regulatory links between the circadian clock and stress-induced biomolecular condensates

   https://doi.org/10.1038/s44323-025-00036-2  

   Brown, Gabriela; Nagel, Dawn H (December 2025, npj Biological Timing and Sleep)

   The circadian clock is a conserved timekeeping mechanism that is essential for integrating different environmental cues such as light and temperature to coordinate biological processes with the time of day. While much is known about transcriptional regulation by the clock, the role of post-transcriptional regulation, particularly through sequestration into biomolecular condensate such as stress granules, remains less understood. Stress granules are dynamic RNA-protein assemblies that play a critical role in the cellular response to stress by sequestering mRNAs to regulate translation during stressful conditions. In animals and fungi, the circadian clock regulates stress granule formation and mRNA translation by controlling key factors such as eIF2α, which orchestrates the rhythmic sequestration and translation of specific mRNAs. In plants, it has been shown that some transcripts, despite coming from arrhythmic expression, are rhythmically translated. In addition, some clock-controlled genes (CCGs) are induced in response to heat stress only at the transcriptional level and not at the translational level. Together this highlights a layer of clock regulation beyond transcription. This review discusses the intersection between the circadian clock and heat stress-related biomolecular condensates across eukaryotes, with a particular focus on plants. We discuss how the clock may regulate stress granule dynamics and preferential translation of mRNAs at specific times of the day or during stress responses, thereby enhancing cellular function and energy efficiency. By integrating evidence from animals, fungi, and plants, we highlight emerging questions regarding the role of biomolecular condensates as post-transcriptional mechanisms in controlling circadian rhythms and stress tolerance in plants. 

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3. PELOTA and HBS1 suppress co‐translational messenger RNA decay in Arabidopsis

   https://doi.org/10.1002/pld3.553  

   Guo, Rong; Gregory, Brian D. (December 2023, Plant Direct)

   Abstract Various messenger RNA (mRNA) decay mechanisms play major roles in controlling mRNA quality and quantity in eukaryotic organisms under different conditions. While it is known that the recently discovered co‐translational mRNA decay (CTRD), the mechanism that allows mRNAs to be degraded while still being actively translated, is prevalent in yeast, humans, and various angiosperms, the regulation of this decay mechanism is less well studied. Moreover, it is still unclear whether this decay mechanism plays any role in the regulation of specific physiological processes in eukaryotes. Here, by re‐analyzing the publicly available polysome profiling or ribosome footprinting and degradome sequencing datasets, we discovered that highly translated mRNAs tend to have lower co‐translational decay levels. Based on this finding, we then identified Pelota and Hbs1, the translation‐related ribosome rescue factors, as suppressors of co‐translational mRNA decay in Arabidopsis. Furthermore, we found that Pelota and Hbs1 null mutants have lower germination rates compared to the wild‐type plants, implying that proper regulation of co‐translational mRNA decay is essential for normal developmental processes. In total, our study provides further insights into the regulation of CTRD in Arabidopsis and demonstrates that this decay mechanism does play important roles in Arabidopsis physiological processes. 

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4. What, where, and how: Regulation of translation and the translational landscape in plants

   https://doi.org/10.1093/plcell/koad197  

   Wu, Hsin-Yen Larry; Jen, Joey; Hsu, Polly Yingshan (July 2023, The Plant Cell)

   Abstract Translation is a crucial step in gene expression and plays a vital role in regulating various aspects of plant development and environmental responses. It is a dynamic and complex program that involves interactions between mRNAs, tRNAs, and the ribosome machinery, through both cis- and trans-regulation, while integrating internal and external signals. Translational control can act in a global (transcriptome-wide) or mRNA-specific manner. Recent advances in genome-wide techniques, particularly ribosome profiling and proteomics, have led to numerous exciting discoveries in both global and mRNA-specific translation. In this review, we aim to provide a ‘primer’ that introduces readers to this fascinating yet complex cellular process and provide a big picture of how essential components connect within the network. We begin with an overview of mRNA translation, followed by a discussion of the experimental approaches and recent findings in the field, focusing on unannotated translation events and translational control through cis-regulatory elements on mRNAs and trans-acting factors, as well as signaling networks through three conserved translational regulators TOR, SnRK1, and GCN2. Finally, we briefly touch on the spatial regulation of mRNAs in translational control. Here, we focus on cytosolic mRNAs, and translation in organelles and viruses is not covered in this review. 

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5. CRISPR-Cas tools for simultaneous transcription & translation control in bacteria

   https://doi.org/10.1093/nar/gkae275  

   Cardiff, Ryan A_L; Faulkner, Ian D.; Beall, Juliana G.; Carothers, James_M; Zalatan, Jesse G. (April 2024, Nucleic Acids Research)

   Abstract Robust control over gene translation at arbitrary mRNA targets is an outstanding challenge in microbial synthetic biology. The development of tools that can regulate translation will greatly expand our ability to precisely control genes across the genome. In Escherichia coli, most genes are contained in multi-gene operons, which are subject to polar effects where targeting one gene for repression leads to silencing of other genes in the same operon. These effects pose a challenge for independently regulating individual genes in multi-gene operons. Here, we use CRISPR-dCas13 to address this challenge. We find dCas13-mediated repression exhibits up to 6-fold lower polar effects compared to dCas9. We then show that we can selectively activate single genes in a synthetic multi-gene operon by coupling dCas9 transcriptional activation of an operon with dCas13 translational repression of individual genes within the operon. We also show that dCas13 and dCas9 can be multiplexed for improved biosynthesis of a medically-relevant human milk oligosaccharide. Taken together, our findings suggest that combining transcriptional and translational control can access effects that are difficult to achieve with either mode independently. These combined tools for gene regulation will expand our abilities to precisely engineer bacteria for biotechnology and perform systematic genetic screens. 

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