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Microorganisms
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Novel Insights into the Mechanisms of Microbial Transcription and Translation
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Novel Insights into the Mechanisms of Microbial Transcription and Translation

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Molecular Microbiology and Immunology".

Deadline for manuscript submissions: closed (31 March 2023) | Viewed by 11166

Special Issue Editor

Dr. Peter Sarin

E-Mail Website
Guest Editor
RNAcious Laboratory, Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
Interests: transfer RNA; post-transcriptional nucleoside modification; translation; RNA-based translation regulation; host–pathogen interaction; viruses

Special Issue Information

Dear Colleagues,

Converting genetic code into functional proteins is dependent on the concerted action of the cell’s transcription and translation machinery. This seemingly straightforward process has become increasingly multifaceted as structural studies have revealed detailed insights into the initiation, elongation, and termination mechanism of both complexes. Advances in enabling techniques, such as next-generation sequencing, have permitted a deeper understanding of the intricate ways by which coding and non-coding RNA components and epigenetic factors modulate these processes. Furthermore, post-transcriptional RNA modifications have emerged as versatile translational regulators that dynamically respond to changes in environmental conditions. For example, transfer RNA anticodon loop modifications are critical for the efficient translation of stress-induced messenger RNA transcripts in bacteria, whereas perturbed RNA modification impairs protein homeostasis upon physiological stress in fungi. It is intriguing how the regulatory roles conferred by these seemingly simple chemical modifications are conserved across evolutionary distinct species, including bacteria, archaea, protists, and other unicellular organisms. Despite the growing appreciation for the complexity of the regulatory mechanisms that govern microbial transcription and translation, our understanding of the functional dynamics of these macromolecular machines is still in its infancy.

For this Special Issue, we invite you to send contributions on key aspects of the microbial transcription and translation machinery, with particular focus given to the regulatory functions of coding and non-coding RNAs.

Dr. Peter Sarin
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • transcription
  • RNA polymerase
  • messenger RNA
  • post-transcriptional modification
  • transfer RNA
  • non-coding RNA
  • translation
  • ribosome
  • transcriptional regulation
  • translational regulation
  • stress

Published Papers (6 papers)

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Editorial

Jump to: Research, Review, Other

3 pages, 179 KiB  
Editorial
Novel Insights into the Mechanisms of Microbial Transcription and Translation
by L. Peter Sarin
Microorganisms 2023, 11(7), 1720; https://doi.org/10.3390/microorganisms11071720 - 30 Jun 2023
Viewed by 848
Abstract
For the better part of the century, microbes have been a treasure trove for deciphering the inner workings of the cell, from early insights into DNA replication and restriction-enzyme-mediated antiviral responses, to unravelling the complexities of metabolic pathways and understanding gene expression and [...] Read more.
For the better part of the century, microbes have been a treasure trove for deciphering the inner workings of the cell, from early insights into DNA replication and restriction-enzyme-mediated antiviral responses, to unravelling the complexities of metabolic pathways and understanding gene expression and its regulatory mechanisms [...] Full article
(This article belongs to the Special Issue Novel Insights into the Mechanisms of Microbial Transcription and Translation)

Research

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16 pages, 1582 KiB  
Article
Bacteriophage Infection of the Marine Bacterium Shewanella glacialimarina Induces Dynamic Changes in tRNA Modifications
by Mirka Lampi, Pavlina Gregorova, M. Suleman Qasim, Niklas C. V. Ahlblad and L. Peter Sarin
Microorganisms 2023, 11(2), 355; https://doi.org/10.3390/microorganisms11020355 - 31 Jan 2023
Cited by 3 | Viewed by 1657
Abstract
Viruses are obligate intracellular parasites that, throughout evolution, have adapted numerous strategies to control the translation machinery, including the modulation of post-transcriptional modifications (PTMs) on transfer RNA (tRNA). PTMs are critical translation regulators used to further host immune responses as well as the [...] Read more.
Viruses are obligate intracellular parasites that, throughout evolution, have adapted numerous strategies to control the translation machinery, including the modulation of post-transcriptional modifications (PTMs) on transfer RNA (tRNA). PTMs are critical translation regulators used to further host immune responses as well as the expression of viral proteins. Yet, we lack critical insight into the temporal dynamics of infection-induced changes to the tRNA modification landscape (i.e., ‘modificome’). In this study, we provide the first comprehensive quantitative characterization of the tRNA modificome in the marine bacterium Shewanella glacialimarina during Shewanella phage 1/4 infection. Specifically, we show that PTMs can be grouped into distinct categories based on modification level changes at various infection stages. Furthermore, we observe a preference for the UAC codon in viral transcripts expressed at the late stage of infection, which coincides with an increase in queuosine modification. Queuosine appears exclusively on tRNAs with GUN anticodons, suggesting a correlation between phage codon usage and PTM modification. Importantly, this work provides the basis for further studies into RNA-based regulatory mechanisms employed by bacteriophages to control the prokaryotic translation machinery. Full article
(This article belongs to the Special Issue Novel Insights into the Mechanisms of Microbial Transcription and Translation)
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15 pages, 2907 KiB  
Article
The Spatial Organization of Bacterial Transcriptional Regulatory Networks
by Liu Tian, Tong Liu, Kang-Jian Hua, Xiao-Pan Hu and Bin-Guang Ma
Microorganisms 2022, 10(12), 2366; https://doi.org/10.3390/microorganisms10122366 - 30 Nov 2022
Cited by 2 | Viewed by 1218
Abstract
The transcriptional regulatory network (TRN) is the central pivot of a prokaryotic organism to receive, process and respond to internal and external environmental information. However, little is known about its spatial organization so far. In recent years, chromatin interaction data of bacteria such [...] Read more.
The transcriptional regulatory network (TRN) is the central pivot of a prokaryotic organism to receive, process and respond to internal and external environmental information. However, little is known about its spatial organization so far. In recent years, chromatin interaction data of bacteria such as Escherichia coli and Bacillus subtilis have been published, making it possible to study the spatial organization of bacterial transcriptional regulatory networks. By combining TRNs and chromatin interaction data of E. coli and B. subtilis, we explored the spatial organization characteristics of bacterial TRNs in many aspects such as regulation directions (positive and negative), central nodes (hubs, bottlenecks), hierarchical levels (top, middle, bottom) and network motifs (feed-forward loops and single input modules) of the TRNs and found that the bacterial TRNs have a variety of stable spatial organization features under different physiological conditions that may be closely related with biological functions. Our findings provided new insights into the connection between transcriptional regulation and the spatial organization of chromosome in bacteria and might serve as a factual foundation for trying spatial-distance-based gene circuit design in synthetic biology. Full article
(This article belongs to the Special Issue Novel Insights into the Mechanisms of Microbial Transcription and Translation)
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Review

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12 pages, 2295 KiB  
Review
How to Shut Down Transcription in Archaea during Virus Infection
by Simona Pilotto and Finn Werner
Microorganisms 2022, 10(9), 1824; https://doi.org/10.3390/microorganisms10091824 - 13 Sep 2022
Cited by 2 | Viewed by 1453
Abstract
Multisubunit RNA polymerases (RNAPs) carry out transcription in all domains of life; during virus infection, RNAPs are targeted by transcription factors encoded by either the cell or the virus, resulting in the global repression of transcription with distinct outcomes for different host–virus combinations. [...] Read more.
Multisubunit RNA polymerases (RNAPs) carry out transcription in all domains of life; during virus infection, RNAPs are targeted by transcription factors encoded by either the cell or the virus, resulting in the global repression of transcription with distinct outcomes for different host–virus combinations. These repressors serve as versatile molecular probes to study RNAP mechanisms, as well as aid the exploration of druggable sites for the development of new antibiotics. Here, we review the mechanisms and structural basis of RNAP inhibition by the viral repressor RIP and the crenarchaeal negative regulator TFS4, which follow distinct strategies. RIP operates by occluding the DNA-binding channel and mimicking the initiation factor TFB/TFIIB. RIP binds tightly to the clamp and locks it into one fixed position, thereby preventing conformational oscillations that are critical for RNAP function as it progresses through the transcription cycle. TFS4 engages with RNAP in a similar manner to transcript cleavage factors such as TFS/TFIIS through the NTP-entry channel; TFS4 interferes with the trigger loop and bridge helix within the active site by occlusion and allosteric mechanisms, respectively. The conformational changes in RNAP described above are universally conserved and are also seen in inactive dimers of eukaryotic RNAPI and several inhibited RNAP complexes of both bacterial and eukaryotic RNA polymerases, including inactive states that precede transcription termination. A comparison of target sites and inhibitory mechanisms reveals that proteinaceous repressors and RNAP-specific antibiotics use surprisingly common ways to inhibit RNAP function. Full article
(This article belongs to the Special Issue Novel Insights into the Mechanisms of Microbial Transcription and Translation)
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10 pages, 1293 KiB  
Review
Regulation of Leaderless mRNA Translation in Bacteria
by Lorenzo Eugenio Leiva and Assaf Katz
Microorganisms 2022, 10(4), 723; https://doi.org/10.3390/microorganisms10040723 - 28 Mar 2022
Cited by 12 | Viewed by 4124
Abstract
In bacteria, the translation of genetic information can begin through at least three different mechanisms: canonical or Shine-Dalgarno-led initiation, readthrough or 70S scanning initiation, or leaderless initiation. Here, we discuss the main features and regulation of the last, which is characterized mainly by [...] Read more.
In bacteria, the translation of genetic information can begin through at least three different mechanisms: canonical or Shine-Dalgarno-led initiation, readthrough or 70S scanning initiation, or leaderless initiation. Here, we discuss the main features and regulation of the last, which is characterized mainly by the ability of 70S ribosomal particles to bind to AUG located at or near the 5′ end of mRNAs to initiate translation. These leaderless mRNAs (lmRNAs) are rare in enterobacteria, such as Escherichia coli, but are common in other bacteria, such as Mycobacterium tuberculosis and Deinococcus deserti, where they may represent more than 20% and even up to 60% of the genes. Given that lmRNAs are devoid of a 5′ untranslated region and the Shine-Dalgarno sequence located within it, the mechanism of translation regulation must depend on molecular strategies that are different from what has been observed in the Shine-Dalgarno-led translation. Diverse regulatory mechanisms have been proposed, including the processing of ribosomal RNA and changes in the abundance of translation factors, but all of them produce global changes in the initiation of lmRNA translation. Thus, further research will be required to understand how the initiation of the translation of particular lmRNA genes is regulated. Full article
(This article belongs to the Special Issue Novel Insights into the Mechanisms of Microbial Transcription and Translation)
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Other

7 pages, 661 KiB  
Perspective
Learning from the Invaders: What Viruses Teach Us about RNA-Based Regulation in Microbes
by L. Peter Sarin
Microorganisms 2022, 10(11), 2106; https://doi.org/10.3390/microorganisms10112106 - 25 Oct 2022
Cited by 2 | Viewed by 1253
Abstract
Viruses feature an evolutionary shaped minimal genome that is obligately dependent on the cellular transcription and translation machinery for propagation. To suppress host cell immune responses and ensure efficient replication, viruses employ numerous tactics to favor viral gene expression and protein synthesis. This [...] Read more.
Viruses feature an evolutionary shaped minimal genome that is obligately dependent on the cellular transcription and translation machinery for propagation. To suppress host cell immune responses and ensure efficient replication, viruses employ numerous tactics to favor viral gene expression and protein synthesis. This necessitates a carefully balanced network of virus- and host-encoded components, of which the RNA-based regulatory mechanisms have emerged as particularly interesting albeit insufficiently studied, especially in unicellular organisms such as archaea, bacteria, and yeasts. Here, recent advances that further our understanding of RNA-based translation regulation, mainly through post-transcriptional chemical modification of ribonucleosides, codon usage, and (virus-encoded) transfer RNAs, will be discussed in the context of viral infection. Full article
(This article belongs to the Special Issue Novel Insights into the Mechanisms of Microbial Transcription and Translation)
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