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Chauvier A, Walter NG. Regulation of bacterial gene expression by non-coding RNA: It is all about time! Cell Chem Biol 2024; 31:71-85. [PMID: 38211587 DOI: 10.1016/j.chembiol.2023.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 12/05/2023] [Accepted: 12/12/2023] [Indexed: 01/13/2024]
Abstract
Commensal and pathogenic bacteria continuously evolve to survive in diverse ecological niches by efficiently coordinating gene expression levels in their ever-changing environments. Regulation through the RNA transcript itself offers a faster and more cost-effective way to adapt than protein-based mechanisms and can be leveraged for diagnostic or antimicrobial purposes. However, RNA can fold into numerous intricate, not always functional structures that both expand and obscure the plethora of roles that regulatory RNAs serve within the cell. Here, we review the current knowledge of bacterial non-coding RNAs in relation to their folding pathways and interactions. We posit that co-transcriptional folding of these transcripts ultimately dictates their downstream functions. Elucidating the spatiotemporal folding of non-coding RNAs during transcription therefore provides invaluable insights into bacterial pathogeneses and predictive disease diagnostics. Finally, we discuss the implications of co-transcriptional folding andapplications of RNAs for therapeutics and drug targets.
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Affiliation(s)
- Adrien Chauvier
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA.
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Neff SL, Hampton TH, Koeppen K, Sarkar S, Latario CJ, Ross BD, Stanton BA. Rocket-miR, a translational launchpad for miRNA-based antimicrobial drug development. mSystems 2023; 8:e0065323. [PMID: 37975659 PMCID: PMC10734502 DOI: 10.1128/msystems.00653-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/06/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Antimicrobial-resistant infections contribute to millions of deaths worldwide every year. In particular, the group of bacteria collectively known as ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter sp.) pathogens are of considerable medical concern due to their virulence and exceptional ability to develop antibiotic resistance. New kinds of antimicrobial therapies are urgently needed to treat patients for whom existing antibiotics are ineffective. The Rocket-miR application predicts targets of human miRNAs in bacterial and fungal pathogens, rapidly identifying candidate miRNA-based antimicrobials. The application's target audience are microbiologists that have the laboratory resources to test the application's predictions. The Rocket-miR application currently supports 24 recognized human pathogens that are relevant to numerous diseases including cystic fibrosis, chronic obstructive pulmonary disease (COPD), urinary tract infections, and pneumonia. Furthermore, the application code was designed to be easily extendible to other human pathogens that commonly cause hospital-acquired infections.
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Affiliation(s)
- Samuel L. Neff
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Thomas H. Hampton
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Katja Koeppen
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Sharanya Sarkar
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Casey J. Latario
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Benjamin D. Ross
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Bruce A. Stanton
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
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Shavkunov KS, Markelova NY, Glazunova OA, Kolzhetsov NP, Panyukov VV, Ozoline ON. The Fate and Functionality of Alien tRNA Fragments in Culturing Medium and Cells of Escherichia coli. Int J Mol Sci 2023; 24:12960. [PMID: 37629141 PMCID: PMC10455298 DOI: 10.3390/ijms241612960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Numerous observations have supported the idea that various types of noncoding RNAs, including tRNA fragments (tRFs), are involved in communications between the host and its microbial community. The possibility of using their signaling function has stimulated the study of secreted RNAs, potentially involved in the interspecies interaction of bacteria. This work aimed at identifying such RNAs and characterizing their maturation during transport. We applied an approach that allowed us to detect oligoribonucleotides secreted by Prevotella copri (Segatella copri) or Rhodospirillum rubrum inside Escherichia coli cells. Four tRFs imported by E. coli cells co-cultured with these bacteria were obtained via chemical synthesis, and all of them affected the growth of E. coli. Their successive modifications in the culture medium and recipient cells were studied by high-throughput cDNA sequencing. Instead of the expected accidental exonucleolysis, in the milieu, we observed nonrandom cleavage by endonucleases continued in recipient cells. We also found intramolecular rearrangements of synthetic oligonucleotides, which may be considered traces of intermediate RNA circular isomerization. Using custom software, we estimated the frequency of such events in transcriptomes and secretomes of E. coli and observed surprising reproducibility in positions of such rare events, assuming the functionality of ring isoforms or their permuted derivatives in bacteria.
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Affiliation(s)
- Konstantin S. Shavkunov
- Department of Functional Genomics of Prokaryotes, Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Natalia Yu. Markelova
- Department of Functional Genomics of Prokaryotes, Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Olga A. Glazunova
- Department of Functional Genomics of Prokaryotes, Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Nikolay P. Kolzhetsov
- Department of Functional Genomics of Prokaryotes, Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Valery V. Panyukov
- Institute of Mathematical Problems of Biology RAS—The Branch of Keldysh Institute of Applied Mathematics of the Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Olga N. Ozoline
- Department of Functional Genomics of Prokaryotes, Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, 142290 Pushchino, Russia
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The Burden of Survivors: How Can Phage Infection Impact Non-Infected Bacteria? Int J Mol Sci 2023; 24:ijms24032733. [PMID: 36769055 PMCID: PMC9917116 DOI: 10.3390/ijms24032733] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/16/2023] [Accepted: 01/26/2023] [Indexed: 02/04/2023] Open
Abstract
The contemporary understanding of complex interactions in natural microbial communities and the numerous mechanisms of bacterial communication challenge the classical concept of bacteria as unicellular organisms. Microbial populations, especially those in densely populated habitats, appear to behave cooperatively, coordinating their reactions in response to different stimuli and behaving as a quasi-tissue. The reaction of such systems to viral infection is likely to go beyond each cell or species tackling the phage attack independently. Bacteriophage infection of a fraction of the microbial community may also exert an influence on the physiological state and/or phenotypic features of those cells that have not yet had direct contact with the virus or are even intrinsically unable to become infected by the particular virus. These effects may be mediated by sensing the chemical signals released by lysing or by infected cells as well as by more indirect mechanisms.
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Tutukina MN, Dakhnovets AI, Kaznadzey AD, Gelfand MS, Ozoline ON. Sense and antisense RNA products of the uxuR gene can affect motility and chemotaxis acting independent of the UxuR protein. Front Mol Biosci 2023; 10:1121376. [PMID: 36936992 PMCID: PMC10016265 DOI: 10.3389/fmolb.2023.1121376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 02/06/2023] [Indexed: 02/19/2023] Open
Abstract
Small non-coding and antisense RNAs are widespread in all kingdoms of life, however, the diversity of their functions in bacteria is largely unknown. Here, we study RNAs synthesised from divergent promoters located in the 3'-end of the uxuR gene, encoding transcription factor regulating hexuronate metabolism in Escherichia coli. These overlapping promoters were predicted in silico with rather high scores, effectively bound RNA polymerase in vitro and in vivo and were capable of initiating transcription in sense and antisense directions. The genome-wide correlation between in silico promoter scores and RNA polymerase binding in vitro and in vivo was higher for promoters located on the antisense strands of the genes, however, sense promoters within the uxuR gene were more active. Both regulatory RNAs synthesised from the divergent promoters inhibited expression of genes associated with the E. coli motility and chemotaxis independent of a carbon source on which bacteria had been grown. Direct effects of these RNAs were confirmed for the fliA gene encoding σ28 subunit of RNA polymerase. In addition to intracellular sRNAs, promoters located within the uxuR gene could initiate synthesis of transcripts found in the fraction of RNAs secreted in the extracellular medium. Their profile was also carbon-independent suggesting that intragenic uxuR transcripts have a specific regulatory role not directly related to the function of the protein in which gene they are encoded.
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Affiliation(s)
- Maria N. Tutukina
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
- Lab of Functional Genomics and Cellular Stress, Institute of Cell Biophysics RAS, FRC PRCBR, Pushchino, Russia
- RTC “Bioinformatics”, A. A. Kharkevich Institute for Information Transmission Problems RAS, Moscow, Russia
- *Correspondence: Maria N. Tutukina, , Olga N. Ozoline,
| | - Artemiy I. Dakhnovets
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Biotechnology, M. V. Lomonosov Moscow State University, Moscow, Russia
| | - Anna D. Kaznadzey
- RTC “Bioinformatics”, A. A. Kharkevich Institute for Information Transmission Problems RAS, Moscow, Russia
| | - Mikhail S. Gelfand
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
- RTC “Bioinformatics”, A. A. Kharkevich Institute for Information Transmission Problems RAS, Moscow, Russia
| | - Olga N. Ozoline
- Lab of Functional Genomics and Cellular Stress, Institute of Cell Biophysics RAS, FRC PRCBR, Pushchino, Russia
- *Correspondence: Maria N. Tutukina, , Olga N. Ozoline,
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Sarshar M, Scribano D, Palamara AT, Ambrosi C, Masotti A. The Acinetobacter baumannii model can explain the role of small non-coding RNAs as potential mediators of host-pathogen interactions. Front Mol Biosci 2022; 9:1088783. [PMID: 36619166 PMCID: PMC9810633 DOI: 10.3389/fmolb.2022.1088783] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
Bacterial small RNAs (sRNAs) research has accelerated over the past decade, boosted by advances in RNA-seq technologies and methodologies for capturing both protein-RNA and RNA-RNA interactions. The emerging picture is that these regulatory sRNAs play important roles in controlling complex physiological processes and are required to survive the antimicrobial challenge. In recent years, the RNA content of OMVs/EVs has also gained increasing attention, particularly in the context of infection. Secreted RNAs from several bacterial pathogens have been characterized but the exact mechanisms promoting pathogenicity remain elusive. In this review, we briefly discuss how secreted sRNAs interact with targets in infected cells, thus representing a novel perspective of host cell manipulation during bacterial infection. During the last decade, Acinetobacter baumannii became clinically relevant emerging pathogens responsible for nosocomial and community-acquired infections. Therefore, we also summarize recent findings of regulation by sRNAs in A. baumannii and discuss how this emerging bacterium utilizes many of these sRNAs to adapt to its niche and become successful human pathogen.
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Affiliation(s)
- Meysam Sarshar
- Research Laboratories, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy,*Correspondence: Meysam Sarshar, ; Andrea Masotti,
| | - Daniela Scribano
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Anna Teresa Palamara
- Laboratory Affiliated to Institute Pasteur Italia-Cenci Bolognetti Foundation, Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy,Department of Infectious Diseases, National Institute of Health, Rome, Italy
| | - Cecilia Ambrosi
- Department of Human Sciences and Promotion of the Quality of Life, San Raffaele Roma Open University, Rome, Italy,IRCCS San Raffaele Roma, Rome, Italy
| | - Andrea Masotti
- Research Laboratories, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy,*Correspondence: Meysam Sarshar, ; Andrea Masotti,
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