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Benda M, Woelfel S, Faßhauer P, Gunka K, Klumpp S, Poehlein A, Kálalová D, Šanderová H, Daniel R, Krásný L, Stülke J. Quasi-essentiality of RNase Y in Bacillus subtilis is caused by its critical role in the control of mRNA homeostasis. Nucleic Acids Res 2021; 49:7088-7102. [PMID: 34157109 PMCID: PMC8266666 DOI: 10.1093/nar/gkab528] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 05/28/2021] [Accepted: 06/08/2021] [Indexed: 01/18/2023] Open
Abstract
RNA turnover is essential in all domains of life. The endonuclease RNase Y (rny) is one of the key components involved in RNA metabolism of the model organism Bacillus subtilis. Essentiality of RNase Y has been a matter of discussion, since deletion of the rny gene is possible, but leads to severe phenotypic effects. In this work, we demonstrate that the rny mutant strain rapidly evolves suppressor mutations to at least partially alleviate these defects. All suppressor mutants had acquired a duplication of an about 60 kb long genomic region encompassing genes for all three core subunits of the RNA polymerase—α, β, β′. When the duplication of the RNA polymerase genes was prevented by relocation of the rpoA gene in the B. subtilis genome, all suppressor mutants carried distinct single point mutations in evolutionary conserved regions of genes coding either for the β or β’ subunits of the RNA polymerase that were not tolerated by wild type bacteria. In vitro transcription assays with the mutated polymerase variants showed a severe decrease in transcription efficiency. Altogether, our results suggest a tight cooperation between RNase Y and the RNA polymerase to establish an optimal RNA homeostasis in B. subtilis cells.
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Affiliation(s)
- Martin Benda
- Department of General Microbiology, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Simon Woelfel
- Department of General Microbiology, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Patrick Faßhauer
- Department of General Microbiology, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Katrin Gunka
- Department of General Microbiology, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Stefan Klumpp
- Institute for the Dynamics of Complex Systems, Georg-August-University Göttingen, Göttingen, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Debora Kálalová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Hana Šanderová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Libor Krásný
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jörg Stülke
- Department of General Microbiology, GZMB, Georg-August-University Göttingen, Göttingen, Germany
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Laalami S, Cavaiuolo M, Roque S, Chagneau C, Putzer H. Escherichia coli RNase E can efficiently replace RNase Y in Bacillus subtilis. Nucleic Acids Res 2021; 49:4643-4654. [PMID: 33788929 PMCID: PMC8096251 DOI: 10.1093/nar/gkab216] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 03/11/2021] [Accepted: 03/17/2021] [Indexed: 02/06/2023] Open
Abstract
RNase Y and RNase E are disparate endoribonucleases that govern global mRNA turnover/processing in the two evolutionary distant bacteria Bacillus subtilis and Escherichia coli, respectively. The two enzymes share a similar in vitro cleavage specificity and subcellular localization. To evaluate the potential equivalence in biological function between the two enzymes in vivo we analyzed whether and to what extent RNase E is able to replace RNase Y in B. subtilis. Full-length RNase E almost completely restores wild type growth of the rny mutant. This is matched by a surprising reversal of transcript profiles both of individual genes and on a genome-wide scale. The single most important parameter to efficient complementation is the requirement for RNase E to localize to the inner membrane while truncation of the C-terminal sequences corresponding to the degradosome scaffold has only a minor effect. We also compared the in vitro cleavage activity for the major decay initiating ribonucleases Y, E and J and show that no conclusions can be drawn with respect to their activity in vivo. Our data confirm the notion that RNase Y and RNase E have evolved through convergent evolution towards a low specificity endonuclease activity universally important in bacteria.
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Affiliation(s)
- Soumaya Laalami
- CNRS, UMR8261, Institut de Biologie Physico-Chimique, Université de Paris, 75005 Paris, France
| | - Marina Cavaiuolo
- CNRS, UMR8261, Institut de Biologie Physico-Chimique, Université de Paris, 75005 Paris, France
| | - Sylvain Roque
- CNRS, UMR8261, Institut de Biologie Physico-Chimique, Université de Paris, 75005 Paris, France
| | - Carine Chagneau
- CNRS, UMR8261, Institut de Biologie Physico-Chimique, Université de Paris, 75005 Paris, France
| | - Harald Putzer
- CNRS, UMR8261, Institut de Biologie Physico-Chimique, Université de Paris, 75005 Paris, France
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Lei L, Yang Y, Yang Y, Wu S, Ma X, Mao M, Hu T. Mechanisms by Which Small RNAs Affect Bacterial Activity. J Dent Res 2019; 98:1315-1323. [PMID: 31547763 DOI: 10.1177/0022034519876898] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The oral cavity contains a distinct habitat that supports diverse bacterial flora. Recent observations have provided additional evidence that sRNAs are key regulators of bacterial physiology and pathogenesis. These sRNAs have been divided into 5 functional groups: cis-encoded RNAs, trans-encoded RNAs, RNA regulators of protein activity, bacterial CRISPR (clustered regularly interspaced short palindromic repeat) RNAs, and a novel category of miRNA-size small RNAs (msRNAs). In this review, we discuss a critical group of key commensal and opportunistic oral pathogens. In general, supragingival bacterial sRNAs function synergistically to fine-tune the regulation of cellular processes and stress responses in adaptation to environmental changes. Particularly in the cariogenic bacteria Streptococcus mutans, both the antisense vicR RNA and msRNA1657 can impede the metabolism of bacterial exopolysaccharides, prevent biofilm formation, and suppress its cariogenicity. In Enterococcus faecalis, selected sRNAs control the expression of proteins involved in diverse cellular processes and stress responses. In subgingival plaques, sRNAs from periodontal pathogens can function as novel bacterial signaling molecules that mediate bacterial-human interactions in periodontal homeostasis. In Porphyromonas gingivalis, the expression profiles of putative sRNA101 and sRNA42 were found to respond to hemin availability after hemin starvation. Regarding Aggregatibacter actinomycetemcomitans (previously Actinobacillus actinomycetemcomitans), a major periodontal pathogen associated with aggressive periodontitis, the predicted sRNAs interact with several virulence genes, including those encoding leukotoxin and cytolethal distending toxin. Furthermore, in clinical isolates, these associated RNAs could be explored not only as potential biomarkers for oral disease monitoring but also as alternative types of regulators for drug design. Thus, this emerging subspecialty of bacterial regulatory RNAs could reshape our understanding of bacterial gene regulation from their key roles of endogenous regulatory RNAs to their activities in pathologic processes.
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Affiliation(s)
- L Lei
- State Key Laboratory of Oral Diseases, Department of Preventive Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Y Yang
- State Key Laboratory of Oral Diseases, Department of Preventive Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, China.,State Key Laboratory of Powder Metallurgy, Central South University, Changsha, China
| | - Y Yang
- State Key Laboratory of Oral Diseases, Department of Preventive Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - S Wu
- West China Hospital, Sichuan University, Chengdu, China
| | - X Ma
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - M Mao
- State Key Laboratory of Oral Diseases, Department of Preventive Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, China.,Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - T Hu
- State Key Laboratory of Oral Diseases, Department of Preventive Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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Pasinetti GM, Singh R, Westfall S, Herman F, Faith J, Ho L. The Role of the Gut Microbiota in the Metabolism of Polyphenols as Characterized by Gnotobiotic Mice. J Alzheimers Dis 2018; 63:409-421. [PMID: 29660942 PMCID: PMC6021178 DOI: 10.3233/jad-171151] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A growing body of experimental data suggests that microbes in the gut influence behavior and can alter brain physiology and neurochemistry. Although promising, researchers are only starting to understand the potential of the gut microbiota for use in neurological disease. Recent evidence demonstrated that gastrointestinal activities are linked to mood disorders such as anxiety, depression, and most recently, cognitive functions in age-related neurodegenerative disorders. Studies from our group and others are uncovering new evidence suggesting that the gut microbiota plays a crucial role in the metabolism and bioavailability of certain dietary compounds and synthetic drugs. Based on this evidence, this review article will discuss the implications of the gut microbiota in mechanisms of bioavailability and biotransformation with an emphasis on dietary polyphenol compounds. This will be followed by a survey of ongoing innovative research identifying the ability of individual gut bacteria to enhance the bioavailability of gut-derived, brain-penetrating, bioactive polyphenol metabolites that ultimately influence mechanisms associated with the promotion of resilience against psychological and cognitive impairment in response to stress. Lastly, current research initiatives aimed at promoting the generation of brain bioactive polyphenol metabolites by specialized gut microbes will be discussed, specifically the use of gnotobiotic mice to develop bioengineered second generation probiotics. We propose that leveraging the gut microbial ecosystem to generate brain targeted bioactive metabolites from dietary polyphenols can attenuate lifestyle risk factors and promote resilience against age-related cognitive decline.
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Affiliation(s)
- Giulio Maria Pasinetti
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Geriatric Research, Education and Clinical Center, James J. Peters Veterans Affairs Medical Center, Bronx, NY, USA
| | - Risham Singh
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Susan Westfall
- Department of Biomedical Engineering, McGill University, Montreal, QC, Canada
| | - Francis Herman
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeremiah Faith
- Department of Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lap Ho
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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