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Kipkorir T, Polgar P, Barker D, D’Halluin A, Patel Z, Arnvig K. A novel regulatory interplay between atypical B12 riboswitches and uORF translation in Mycobacterium tuberculosis. Nucleic Acids Res 2024; 52:7876-7892. [PMID: 38709884 PMCID: PMC11260477 DOI: 10.1093/nar/gkae338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 04/10/2024] [Accepted: 04/17/2024] [Indexed: 05/08/2024] Open
Abstract
Vitamin B12 is an essential cofactor in all domains of life and B12-sensing riboswitches are some of the most widely distributed riboswitches. Mycobacterium tuberculosis, the causative agent of tuberculosis, harbours two B12-sensing riboswitches. One controls expression of metE, encoding a B12-independent methionine synthase, the other controls expression of ppe2 of uncertain function. Here, we analysed ligand sensing, secondary structure and gene expression control of the metE and ppe2 riboswitches. Our results provide the first evidence of B12 binding by these riboswitches and show that they exhibit different preferences for individual isoforms of B12, use distinct regulatory and structural elements and act as translational OFF switches. Based on our results, we propose that the ppe2 switch represents a new variant of Class IIb B12-sensing riboswitches. Moreover, we have identified short translated open reading frames (uORFs) upstream of metE and ppe2, which modulate the expression of their downstream genes. Translation of the metE uORF suppresses MetE expression, while translation of the ppe2 uORF is essential for PPE2 expression. Our findings reveal an unexpected regulatory interplay between B12-sensing riboswitches and the translational machinery, highlighting a new level of cis-regulatory complexity in M. tuberculosis. Attention to such mechanisms will be critical in designing next-level intervention strategies.
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Affiliation(s)
- Terry Kipkorir
- Institute for Structural and Molecular Biology, University College London, Gower Street, WC1E 6BT London, UK
| | - Peter Polgar
- Institute for Structural and Molecular Biology, University College London, Gower Street, WC1E 6BT London, UK
| | - Declan Barker
- Institute for Structural and Molecular Biology, University College London, Gower Street, WC1E 6BT London, UK
| | - Alexandre D’Halluin
- Institute for Structural and Molecular Biology, University College London, Gower Street, WC1E 6BT London, UK
| | - Zaynah Patel
- Institute for Structural and Molecular Biology, University College London, Gower Street, WC1E 6BT London, UK
| | - Kristine B Arnvig
- Institute for Structural and Molecular Biology, University College London, Gower Street, WC1E 6BT London, UK
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2
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Garg R, Manhas I, Chaturvedi D. Unveiling the orchestration: mycobacterial small RNAs as key mediators in host-pathogen interactions. Front Microbiol 2024; 15:1399280. [PMID: 38903780 PMCID: PMC11188477 DOI: 10.3389/fmicb.2024.1399280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 05/21/2024] [Indexed: 06/22/2024] Open
Abstract
Small RNA (sRNA) molecules, a class of non-coding RNAs, have emerged as pivotal players in the regulation of gene expression and cellular processes. Mycobacterium tuberculosis and other pathogenic mycobacteria produce diverse small RNA species that modulate bacterial physiology and pathogenesis. Recent advances in RNA sequencing have enabled identification of novel small RNAs and characterization of their regulatory functions. This review discusses the multifaceted roles of bacterial small RNAs, covering their biogenesis, classification, and functional diversity. Small RNAs (sRNAs) play pivotal roles in orchestrating diverse cellular processes, ranging from gene silencing to epigenetic modifications, across a broad spectrum of organisms. While traditionally associated with eukaryotic systems, recent research has unveiled their presence and significance within bacterial domains as well. Unlike their eukaryotic counterparts, which primarily function within the context of RNA interference (RNAi) pathways, bacterial sRNAs predominantly act through base-pairing interactions with target mRNAs, leading to post-transcriptional regulation. This fundamental distinction underscores the necessity of elucidating the unique roles and regulatory mechanisms of bacterial sRNAs in bacterial adaptation and survival. By doing these myriad functions, they regulate bacterial growth, metabolism, virulence, and drug resistance. In Mycobacterium tuberculosis, apart from having various roles in the bacillus itself, small RNA molecules have emerged as key regulators of gene expression and mediators of host-pathogen interactions. Understanding sRNA regulatory networks in mycobacteria can drive our understanding of significant role they play in regulating virulence and adaptation to the host environment. Detailed functional characterization of Mtb sRNAs at the host-pathogen interface is required to fully elucidate the complex sRNA-mediated gene regulatory networks deployed by Mtb, to manipulate the host. A deeper understanding of this aspect could pave the development of novel diagnostic and therapeutic strategies for tuberculosis.
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Affiliation(s)
- Rajni Garg
- Department of Human Genetics and Molecular Medicine, Amity School of Health Sciences, Amity University, Mohali, Punjab, India
| | - Ishali Manhas
- Department of Biotechnology, Amity School of Biological Sciences, Amity University, Mohali, Punjab, India
| | - Diksha Chaturvedi
- Department of Biotechnology and Medical Engineering, National Institute of Technology, Rourkela, Odisha, India
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3
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Li G, Feng Z, Song H, Wang Y, Zhu L, Li Y. Long non-coding RNA expression in PBMCs of patients with active pulmonary tuberculosis. Front Microbiol 2023; 14:1257267. [PMID: 38156018 PMCID: PMC10753990 DOI: 10.3389/fmicb.2023.1257267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 11/06/2023] [Indexed: 12/30/2023] Open
Abstract
Purpose Mycobacterium tuberculosis (Mtb) infection is the primary cause of the chronic infectious illness tuberculosis (TB). Long non-coding RNAs (lncRNAs) are functional RNA molecules that cannot be translated into proteins and play a crucial role in regulating the immune system's innate and adaptive responses. It has been demonstrated that the dysregulation of lncRNA expression is associated with various human diseases. However, the mechanism underlying the involvement of so many lncRNAs in the immune response to TB infection remains unclear. The objective of our current study was to identify a number of significantly differentially expressed lncRNAs in peripheral blood mononuclear cells (PBMCs) from TB patients and to select the most indicative lncRNAs as potential biomarkers for active pulmonary tuberculosis. Methods Microarray analysis was performed to determine the lncRNA and mRNA expression profiles in TB patients using a case-control model. The differentially expressed lncRNAs were subjected to gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis to investigate potential roles and pathways associated with the pathogenesis of TB infection, and to screen lncRNAs specifically linked to TB infection. Using real-time fluorescence quantitative PCR (QRT-PCR), specific lncRNAs were identified in TB patients and latent infections. Results Our findings revealed that various signaling pathways were differentially expressed in TB-infected individuals, suggesting a potential role for lncRNAs in the immunological responses driven by TB infection. This study provides crucial guidelines for future functional research. Upregulated lncRNAs were mainly enriched in Neutrophil extracellular trap formation and Chemokine signaling pathways, while downregulated lncRNAs were enriched in Neuroactive ligand-receptor interaction and Cushing syndrome in TB PBMCs. Furthermore, we found that lnc-XPNPEP1-5, lnc-CASKIN2-2, lnc-HSPA13-6, lnc-CLIC5-1, and LINC02502 were significantly downregulated in TB-infected patients, while LINC00528, lnc-SLC45A4-3, and LINC00926 were significantly upregulated in TB patients and latent infections. These eight lncRNAs, identified as novel biological marker candidates for diagnosing TB infection, were validated by real-time fluorescence quantitative PCR (QRT-PCR). Conclusion The abnormally expressed lncRNAs identified in this research may provide crucial information for understanding the pathophysiological characteristics of TB patients and the dysfunction of PBMCs. Our findings reveal potential targets for early TB diagnosis and therapy, as well as offer new insights into the mechanisms underlying TB infection.
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Affiliation(s)
- Guoli Li
- Department of Chronic Communicable Disease, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Zhelong Feng
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Honghuan Song
- Department of Chronic Communicable Disease, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Yajing Wang
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Limei Zhu
- Department of Chronic Communicable Disease, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Yan Li
- Integrated Service and Management Office, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
- Department of Chronic Communicable Disease, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
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4
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Pandey M, Talwar S, Pal R, Nain V, Johri S, Singhal A, Pandey AK. Transcription factor mce3R modulates antibiotics and disease persistence in Mycobacteriumtuberculosis. Res Microbiol 2023; 174:104082. [PMID: 37244349 DOI: 10.1016/j.resmic.2023.104082] [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: 02/18/2023] [Revised: 05/17/2023] [Accepted: 05/19/2023] [Indexed: 05/29/2023]
Abstract
Transcription factors (TFs) of Mycobacterium tuberculosis (Mtb), an etiological agent of tuberculosis, regulate a network of pathways that help prolong the survival of Mtb inside the host. In this study, we have characterized a transcription repressor gene (mce3R) from the TetR family, that encodes for Mce3R protein in Mtb. We demonstrated that the mce3R gene is dispensable for the growth of Mtb on cholesterol. Gene expression analysis suggests that the transcription of genes belonging to the mce3R regulon is independent of the carbon source. We found that, in comparison to the wild type, the mce3R deleted strain (Δmce3R) generated more intracellular ROS and demonstrated reduced susceptibility to oxidative stress. Total lipid analysis suggests that mce3R regulon encoded proteins modulate the biosynthesis of cell wall lipids in Mtb. Interestingly, the absence of Mce3R increased the frequency of generation of antibiotic persisters in Mtb and imparted in-vivo growth advantage phenotype in guinea pigs. In conclusion, genes belonging to the mce3R regulon modulate the frequency of generation of persisters in Mtb. Hence, targeting mce3R regulon encoded proteins could potentiate the current regimen by eliminating persisters during Mtb infection.
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Affiliation(s)
- Manitosh Pandey
- Mycobacterial Pathogenesis Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana, India; Department of Life Science, ITM University, Gwalior, Madhya Pradesh, India
| | - Sakshi Talwar
- Mycobacterial Pathogenesis Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Rahul Pal
- Mycobacterial Pathogenesis Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Vaibhav Nain
- Mycobacterial Pathogenesis Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Sonia Johri
- Department of Life Science, ITM University, Gwalior, Madhya Pradesh, India
| | - Amit Singhal
- Infectious Diseases Labs (ID Labs), Agency for Science Technology and Research (A∗STAR), Singapore 138648, Republic of Singapore; Singapore Immunology Network (SIgN), A∗STAR, Singapore 138648, Republic of Singapore
| | - Amit Kumar Pandey
- Mycobacterial Pathogenesis Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana, India.
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5
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Grigorov AS, Skvortsova YV, Bychenko OS, Aseev LV, Koledinskaya LS, Boni IV, Azhikina TL. Dynamic Transcriptional Landscape of Mycobacterium smegmatis under Cold Stress. Int J Mol Sci 2023; 24:12706. [PMID: 37628885 PMCID: PMC10454040 DOI: 10.3390/ijms241612706] [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: 07/10/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Bacterial adaptation to cold stress requires wide transcriptional reprogramming. However, the knowledge of molecular mechanisms underlying the cold stress response of mycobacteria is limited. We conducted comparative transcriptomic analysis of Mycobacterium smegmatis subjected to cold shock. The growth of M. smegmatis cultivated at 37 °C was arrested just after exposure to cold (acclimation phase) but later (by 24 h) was resumed at a much slower rate (adaptation phase). Transcriptomic analyses revealed distinct gene expression patterns corresponding to the two phases. During the acclimation phase, differential expression was observed for genes associated with cell wall remodeling, starvation response, and osmotic pressure stress, in parallel with global changes in the expression of transcription factors and the downregulation of ribosomal genes, suggesting an energy-saving strategy to support survival. At the adaptation phase, the expression profiles were recovered, indicating restoration of the processes repressed earlier. Comparison of transcriptional responses in M. smegmatis with those in other bacteria revealed unique adaptation strategies developed by mycobacteria. Our findings shed light on the molecular mechanisms underlying M. smegmatis survival under cold stress. Further research should clarify whether the discovered transcriptional mechanisms exist in other mycobacterial species, including pathogenic Mycobacterium tuberculosis, which could be important for transmission control.
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Affiliation(s)
- Artem S. Grigorov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | | | | | | | | | | | - Tatyana L. Azhikina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
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6
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Martini BA, Grigorov AS, Skvortsova YV, Bychenko OS, Salina EG, Azhikina TL. Small RNA MTS1338 Configures a Stress Resistance Signature in Mycobacterium tuberculosis. Int J Mol Sci 2023; 24:ijms24097928. [PMID: 37175635 PMCID: PMC10178195 DOI: 10.3390/ijms24097928] [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: 04/02/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
In the course of evolution, Mycobacterium tuberculosis (Mtb), the etiological agent of tuberculosis, has developed sophisticated strategies to evade host immune response, including the synthesis of small non-coding RNAs (sRNAs), which regulate post-transcriptional pathways involved in the stress adaptation of mycobacteria. sRNA MTS1338 is upregulated in Mtb during its infection of cultured macrophages and in the model of chronic tuberculosis, suggesting involvement in host-pathogen interactions. Here, we analyzed the role of MTS1338 in the Mtb response to macrophage-like stresses in vitro. The Mtb strain overexpressing MTS1338 demonstrated enhanced survival ability under low pH, nitrosative, and oxidative stress conditions simulating the antimicrobial environment inside macrophages. Transcriptomic analysis revealed that in MTS1338-overexpressing Mtb, the stress factors led to the activation of a number of transcriptional regulators, toxin-antitoxin modules, and stress chaperones, about half of which coincided with the genes induced in Mtb phagocytosed by macrophages. We determined the MTS1338 "core regulon", consisting of 11 genes that were activated in all conditions under MTS1338 overexpression. Our findings indicate that MTS1338 is a stress-induced sRNA that promotes Mtb survival in macrophages by triggering adaptive transcriptional mechanisms in response to host antimicrobial defense reactions.
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Affiliation(s)
- Billy A Martini
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Artem S Grigorov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Yulia V Skvortsova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Oksana S Bychenko
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Elena G Salina
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Tatyana L Azhikina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
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7
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D’Halluin A, Polgar P, Kipkorir T, Patel Z, Cortes T, Arnvig KB. Premature termination of transcription is shaped by Rho and translated uORFS in Mycobacterium tuberculosis. iScience 2023; 26:106465. [PMID: 37096044 PMCID: PMC10122055 DOI: 10.1016/j.isci.2023.106465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 01/29/2023] [Accepted: 03/17/2023] [Indexed: 04/05/2023] Open
Abstract
Little is known about the decisions behind transcription elongation versus termination in the human pathogen Mycobacterium tuberculosis (M.TB). By applying Term-seq to M.TB we found that the majority of transcription termination is premature and associated with translated regions, i.e., within previously annotated or newly identified open reading frames. Computational predictions and Term-seq analysis, upon depletion of termination factor Rho, suggests that Rho-dependent transcription termination dominates all transcription termination sites (TTS), including those associated with regulatory 5' leaders. Moreover, our results suggest that tightly coupled translation, in the form of overlapping stop and start codons, may suppress Rho-dependent termination. This study provides detailed insights into novel M.TB cis-regulatory elements, where Rho-dependent, conditional termination of transcription and translational coupling together play major roles in gene expression control. Our findings contribute to a deeper understanding of the fundamental regulatory mechanisms that enable M.TB adaptation to the host environment offering novel potential points of intervention.
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Affiliation(s)
- Alexandre D’Halluin
- Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Peter Polgar
- Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Terry Kipkorir
- Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Zaynah Patel
- Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Teresa Cortes
- Instituto de Biomedicina de Valencia, CSIC, Valencia 46010, Spain
| | - Kristine B. Arnvig
- Structural and Molecular Biology, University College London, London WC1E 6BT, UK
- Corresponding author
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8
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Stiens J, Tan YY, Joyce R, Arnvig KB, Kendall SL, Nobeli I. Using a whole genome co-expression network to inform the functional characterisation of predicted genomic elements from Mycobacterium tuberculosis transcriptomic data. Mol Microbiol 2023; 119:381-400. [PMID: 36924313 DOI: 10.1111/mmi.15055] [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: 11/18/2022] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023]
Abstract
A whole genome co-expression network was created using Mycobacterium tuberculosis transcriptomic data from publicly available RNA-sequencing experiments covering a wide variety of experimental conditions. The network includes expressed regions with no formal annotation, including putative short RNAs and untranslated regions of expressed transcripts, along with the protein-coding genes. These unannotated expressed transcripts were among the best-connected members of the module sub-networks, making up more than half of the 'hub' elements in modules that include protein-coding genes known to be part of regulatory systems involved in stress response and host adaptation. This data set provides a valuable resource for investigating the role of non-coding RNA, and conserved hypothetical proteins, in transcriptomic remodelling. Based on their connections to genes with known functional groupings and correlations with replicated host conditions, predicted expressed transcripts can be screened as suitable candidates for further experimental validation.
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Affiliation(s)
- Jennifer Stiens
- Institute of Structural and Molecular Biology, Biological Sciences, Birkbeck, University of London, London, UK
| | - Yen Yi Tan
- Institute of Structural and Molecular Biology, Biological Sciences, Birkbeck, University of London, London, UK
| | - Rosanna Joyce
- Institute of Structural and Molecular Biology, Biological Sciences, Birkbeck, University of London, London, UK
| | - Kristine B Arnvig
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
| | - Sharon L Kendall
- Royal Veterinary College, Centre for Emerging, Endemic and Exotic Diseases, Pathobiology and Population Sciences, Hatfield, UK
| | - Irene Nobeli
- Institute of Structural and Molecular Biology, Biological Sciences, Birkbeck, University of London, London, UK
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9
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Miotto P, Sorrentino R, De Giorgi S, Provvedi R, Cirillo DM, Manganelli R. Transcriptional regulation and drug resistance in Mycobacterium tuberculosis. Front Cell Infect Microbiol 2022; 12:990312. [PMID: 36118045 PMCID: PMC9480834 DOI: 10.3389/fcimb.2022.990312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
Bacterial drug resistance is one of the major challenges to present and future human health, as the continuous selection of multidrug resistant bacteria poses at serious risk the possibility to treat infectious diseases in the near future. One of the infection at higher risk to become incurable is tuberculosis, due to the few drugs available in the market against Mycobacterium tuberculosis. Drug resistance in this species is usually due to point mutations in the drug target or in proteins required to activate prodrugs. However, another interesting and underexplored aspect of bacterial physiology with important impact on drug susceptibility is represented by the changes in transcriptional regulation following drug exposure. The main regulators involved in this phenomenon in M. tuberculosis are the sigma factors, and regulators belonging to the WhiB, GntR, XRE, Mar and TetR families. Better understanding the impact of these regulators in survival to drug treatment might contribute to identify new drug targets and/or to design new strategies of intervention.
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Affiliation(s)
- Paolo Miotto
- Emerging Bacterial Pathogens Unit, Div. of Immunology, Transplantation and Infectious Diseases IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Rita Sorrentino
- Emerging Bacterial Pathogens Unit, Div. of Immunology, Transplantation and Infectious Diseases IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Stefano De Giorgi
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | | | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Div. of Immunology, Transplantation and Infectious Diseases IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Riccardo Manganelli
- Department of Molecular Medicine, University of Padova, Padova, Italy
- *Correspondence: Riccardo Manganelli,
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10
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Dawson CC, Cummings JE, Starkey JM, Slayden RA. Discovery of a novel type IIb RelBE toxin-antitoxin system in Mycobacterium tuberculosis defined by co-regulation with an antisense RNA. Mol Microbiol 2022; 117:1419-1433. [PMID: 35526138 PMCID: PMC9325379 DOI: 10.1111/mmi.14917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 04/30/2022] [Accepted: 05/05/2022] [Indexed: 11/29/2022]
Abstract
Toxin‐antitoxin loci regulate adaptive responses to stresses associated with the host environment and drug exposure. Phylogenomic studies have shown that Mycobacterium tuberculosis encodes a naturally expanded type II toxin‐antitoxin system, including ParDE/RelBE superfamily members. Type II toxins are presumably regulated exclusively through protein–protein interactions with type II antitoxins. However, experimental observations in M. tuberculosis indicated that additional control mechanisms regulate RelBE2 type II loci under host‐associated stress conditions. Herein, we describe for the first time a novel antisense RNA, termed asRelE2, that co‐regulates RelE2 production via targeted processing by the Mtb RNase III, Rnc. We find that convergent expression of this coding‐antisense hybrid TA locus, relBE2‐asrelE2, is controlled in a cAMP‐dependent manner by the essential cAMP receptor protein transcription factor, Crp, in response to the host‐associated stresses of low pH and nutrient limitation. Ex vivo survival studies with relE2 and asrelE2 knockout strains showed that RelE2 contributes to Mtb survival in activated macrophages and low pH to nutrient limitation. To our knowledge, this is the first report of a novel tripartite type IIb TA loci and antisense post‐transcriptional regulation of a type II TA loci.
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Affiliation(s)
- Clinton C Dawson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins.,Endolytix Technology, Inc. Beverly, 01915
| | - Jason E Cummings
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins
| | - Julie M Starkey
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins
| | - Richard A Slayden
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins
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11
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Stiens J, Arnvig KB, Kendall SL, Nobeli I. Challenges in defining the functional, non-coding, expressed genome of members of the Mycobacterium tuberculosis complex. Mol Microbiol 2021; 117:20-31. [PMID: 34894010 DOI: 10.1111/mmi.14862] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 12/14/2022]
Abstract
A definitive transcriptome atlas for the non-coding expressed elements of the members of the Mycobacterium tuberculosis complex (MTBC) does not exist. Incomplete lists of non-coding transcripts can be obtained for some of the reference genomes (e.g., M. tuberculosis H37Rv) but to what extent these transcripts have homologues in closely related species or even strains is not clear. This has implications for the analysis of transcriptomic data; non-coding parts of the transcriptome are often ignored in the absence of formal, reliable annotation. Here, we review the state of our knowledge of non-coding RNAs in pathogenic mycobacteria, emphasizing the disparities in the information included in commonly used databases. We then proceed to review ways of combining computational solutions for predicting the non-coding transcriptome with experiments that can help refine and confirm these predictions.
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Affiliation(s)
- Jennifer Stiens
- Institute of Structural and Molecular Biology, Biological Sciences, Birkbeck, University of London, London, UK
| | - Kristine B Arnvig
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
| | - Sharon L Kendall
- Centre for Emerging, Endemic and Exotic Diseases, Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, UK
| | - Irene Nobeli
- Institute of Structural and Molecular Biology, Biological Sciences, Birkbeck, University of London, London, UK
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12
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Singh S, Nirban R, Dutta T. MTS1338 in Mycobacterium tuberculosis promotes detoxification of reactive oxygen species under oxidative stress. Tuberculosis (Edinb) 2021; 131:102142. [PMID: 34773773 DOI: 10.1016/j.tube.2021.102142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 09/22/2021] [Accepted: 10/31/2021] [Indexed: 11/29/2022]
Abstract
Diverse mechanisms exist in Mycobacterium tuberculosis for adaptation to stresses leading to its persistence in the hostile environment of macrophages. Small RNA (sRNA)-mediated regulatory mechanisms have been scarcely explored in M. tuberculosis. MTS1338, a sRNA present only in pathogenic mycobacteria, was discovered to be highly abundant during infection and significantly contributes to host-pathogen interaction. A variety of stresses have been implicated for its accumulation. Herein, we showed that MTS1338 is an oxidative stress induced sRNA, which promotes the detoxification of reactive oxygen species (ROS) under oxidative stress. Current study identified a new role of MTS1338 in M. tuberculosis under oxidative stress.
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Affiliation(s)
- Saumya Singh
- RNA Biology Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Reena Nirban
- RNA Biology Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India; School of Interdisciplinary Research, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Tanmay Dutta
- RNA Biology Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India; School of Interdisciplinary Research, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
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13
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Grigorov A, Bychenko O, Salina EG, Skvortsova Y, Mazurova A, Skvortsov T, Kaprelyants A, Azhikina T. Small RNA F6 Provides Mycobacterium smegmatis Entry into Dormancy. Int J Mol Sci 2021; 22:11536. [PMID: 34768965 PMCID: PMC8583896 DOI: 10.3390/ijms222111536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 11/16/2022] Open
Abstract
Regulatory small non-coding RNAs play a significant role in bacterial adaptation to changing environmental conditions. Various stresses such as hypoxia and nutrient starvation cause a reduction in the metabolic activity of Mycobacterium smegmatis, leading to entry into dormancy. We investigated the functional role of F6, a small RNA of M. smegmatis, and constructed an F6 deletion strain of M. smegmatis. Using the RNA-seq approach, we demonstrated that gene expression changes that accompany F6 deletion contributed to bacterial resistance against oxidative stress. We also found that F6 directly interacted with 5'-UTR of MSMEG_4640 mRNA encoding RpfE2, a resuscitation-promoting factor, which led to the downregulation of RpfE2 expression. The F6 deletion strain was characterized by the reduced ability to enter into dormancy (non-culturability) in the potassium deficiency model compared to the wild-type strain, indicating that F6 significantly contributes to bacterial adaptation to non-optimal growth conditions.
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Affiliation(s)
- Artem Grigorov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (A.G.); (O.B.); (Y.S.); (A.M.)
| | - Oksana Bychenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (A.G.); (O.B.); (Y.S.); (A.M.)
| | - Elena G. Salina
- Research Center of Biotechnology, Bach Institute of Biochemistry, 119071 Moscow, Russia; (E.G.S.); (A.K.)
| | - Yulia Skvortsova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (A.G.); (O.B.); (Y.S.); (A.M.)
| | - Arina Mazurova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (A.G.); (O.B.); (Y.S.); (A.M.)
| | - Timofey Skvortsov
- School of Pharmacy, Queen’s University Belfast, Belfast BT9 7BL, UK;
| | - Arseny Kaprelyants
- Research Center of Biotechnology, Bach Institute of Biochemistry, 119071 Moscow, Russia; (E.G.S.); (A.K.)
| | - Tatyana Azhikina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (A.G.); (O.B.); (Y.S.); (A.M.)
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14
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Bahoua B, Sevdalis SE, Soto AM. Effect of Sequence on the Interactions of Divalent Cations with M-Box Riboswitches from Mycobacterium tuberculosis and Bacillus subtilis. Biochemistry 2021; 60:2781-2794. [PMID: 34472844 DOI: 10.1021/acs.biochem.1c00371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
RNA is highly negatively charged and often acquires complex structures that require the presence of divalent cations. Subtle changes in conformation resulting from changes in sequence can affect the way ions associate with RNA. Riboswitches are RNA molecules that are involved in the control of gene expression in bacteria and are excellent systems for testing the effects of sequence variations on the conformation of RNA because they contain a highly conserved binding pocket but present sequence variability among different organisms. In this work, we have compared the aptamer domain of a proposed M-box riboswitch from Mycobacterium tuberculosis with the aptamer domain of a validated M-box riboswitch from Bacillus subtilis. We have in vitro transcribed and purified wild-type (WT) M-box riboswitches from M. tuberculosis and B. subtilis as well as a variety of mutated aptamers in which regions from one riboswitch have been replaced with regions from the other riboswitch. We have used ultraviolet unfolding experiments and circular dichroism to characterize the interactions of WT and related M-box riboswitches with divalent cations. Our results show that M-box from M. tuberculosis associates with Mg2+ and Sr2+ in a similar fashion while M-box from B. subtilis discriminates between these two ions and appears to associate better with Mg2+. Our overall results show that M-box from M. tuberculosis interacts differently with cations than M-box from B. subtilis and suggest conformational differences between these two riboswitches.
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15
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Ostrik AA, Azhikina TL, Salina EG. Small Noncoding RNAs and Their Role in the Pathogenesis of Mycobacterium tuberculosis Infection. BIOCHEMISTRY (MOSCOW) 2021; 86:S109-S119. [PMID: 33827403 PMCID: PMC7905965 DOI: 10.1134/s000629792114008x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Mycobacterium tuberculosis possesses a significant arsenal of strategies to combat immune defense of the host organism. Small noncoding RNAs, which constitute the largest group of regulatory RNAs, play an important role in the host–pathogen interactions and represent one of the levels of the regulation of interactions of microbial cells with their environment. The regulatory role of small RNAs in pathogenic bacteria is essential when rapid adaptation to the changing environmental conditions with further synchronization of metabolic reactions are required to ensure microbial survival and infection progression. During the past few years, eight small RNAs from M. tuberculosis have been functionally characterized, and targets for four of them have been identified. Small RNAs from M. tuberculosis and other pathogenic microorganisms were found to be one of the most important functional factors in the adaptive response to changing environmental conditions.
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Affiliation(s)
- Albina A Ostrik
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 119071, Russia
| | - Tatyana L Azhikina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Elena G Salina
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 119071, Russia.
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16
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Small Noncoding RNAs MTS0997 and MTS1338 Affect the Adaptation and Virulence of Mycobacterium tuberculosis. MICROBIOLOGY RESEARCH 2021. [DOI: 10.3390/microbiolres12010014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Tuberculosis (TB) is currently the leading cause of death among bacterial infectious diseases. The spectrum of disease manifestations depends on both host immune responses and the ability of Mycobacterium tuberculosis to resist it. Small non-coding RNAs are known to regulate gene expression; however, their functional role in the relationship of M. tuberculosis with the host is poorly understood. Here, we investigated the effect of small non-coding sRNAs MTS1338 and MTS0997 on M. tuberculosis properties by creating knockout strains. We also assessed the effect of small non-coding RNAs on the survival of wild type and mutant mycobacteria in primary cultures of human alveolar macrophages and the virulence of these strains in a mouse infection model. Wild-type and mutants survived differentially in human alveolar macrophages. Infection of I/St mice with KO M. tuberculosis H37RV strains provided beneficial effects onto major TB phenotypes. We observed attenuated tuberculosis-specific inflammatory responses, including reduced cellular infiltration and decreased granuloma formation in the lungs. Infections caused by KO strains were characterized by significantly lower inflammation of mouse lung tissue and increased survival time of infected animals. Thus, the deletion of MTS0997 and MTS1338 lead to a significant decrease in the virulence of M. tuberculosis.
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17
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Kolbe K, Bell AC, Prosser GA, Assmann M, Yang HJ, Forbes HE, Gallucci S, Mayer-Barber KD, Boshoff HI, Barry Iii CE. Development and Optimization of Chromosomally-Integrated Fluorescent Mycobacterium tuberculosis Reporter Constructs. Front Microbiol 2020; 11:591866. [PMID: 33362741 PMCID: PMC7755994 DOI: 10.3389/fmicb.2020.591866] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 11/13/2020] [Indexed: 11/25/2022] Open
Abstract
Mycobacterium tuberculosis resides in the lungs in various lesion types with unique microenvironmental conditions. This diversity is in line with heterogeneous disease progression and divergent drug efficiency. Fluorescent reporter strains can be used to decipher the micromilieu and to guide future treatment regimens. Current reporters using replicating plasmids, however, are not suitable for long-term mouse infections or studies in non-human primates. Using a combination of recombinant DNA and protein optimization techniques, we have developed reporter strains based on integrative plasmids, which exhibit stimulus-response characteristics and fluorescence intensities comparable to those based on replicating plasmids. We successfully applied the concepts by constructing a multi-color reporter strain able to detect simultaneous changes in environmental pH, Mg2+ concentrations, and protein expression levels.
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Affiliation(s)
- Katharina Kolbe
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Alice C Bell
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Gareth A Prosser
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States.,Drug Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee, United Kingdom
| | - Maike Assmann
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Hee-Jeong Yang
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - He Eun Forbes
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Sophia Gallucci
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Katrin D Mayer-Barber
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Helena I Boshoff
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Clifton E Barry Iii
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
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18
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Mejía-Almonte C, Busby SJW, Wade JT, van Helden J, Arkin AP, Stormo GD, Eilbeck K, Palsson BO, Galagan JE, Collado-Vides J. Redefining fundamental concepts of transcription initiation in bacteria. Nat Rev Genet 2020; 21:699-714. [PMID: 32665585 PMCID: PMC7990032 DOI: 10.1038/s41576-020-0254-8] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2020] [Indexed: 12/15/2022]
Abstract
Despite enormous progress in understanding the fundamentals of bacterial gene regulation, our knowledge remains limited when compared with the number of bacterial genomes and regulatory systems to be discovered. Derived from a small number of initial studies, classic definitions for concepts of gene regulation have evolved as the number of characterized promoters has increased. Together with discoveries made using new technologies, this knowledge has led to revised generalizations and principles. In this Expert Recommendation, we suggest precise, updated definitions that support a logical, consistent conceptual framework of bacterial gene regulation, focusing on transcription initiation. The resulting concepts can be formalized by ontologies for computational modelling, laying the foundation for improved bioinformatics tools, knowledge-based resources and scientific communication. Thus, this work will help researchers construct better predictive models, with different formalisms, that will be useful in engineering, synthetic biology, microbiology and genetics.
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Affiliation(s)
- Citlalli Mejía-Almonte
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Morelos, Cuernavaca, México
| | | | - Joseph T Wade
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Jacques van Helden
- Aix-Marseille University, INSERM UMR S 1090, Theory and Approaches of Genome Complexity (TAGC), Marseille, France
- CNRS, Institut Français de Bioinformatique, IFB-core, UMS 3601, Evry, France
| | - Adam P Arkin
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Gary D Stormo
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Karen Eilbeck
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - James E Galagan
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Julio Collado-Vides
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Morelos, Cuernavaca, México.
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.
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19
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Bancroft PJ, Turapov O, Jagatia H, Arnvig KB, Mukamolova GV, Green J. Coupling of Peptidoglycan Synthesis to Central Metabolism in Mycobacteria: Post-transcriptional Control of CwlM by Aconitase. Cell Rep 2020; 32:108209. [PMID: 32997986 PMCID: PMC7527780 DOI: 10.1016/j.celrep.2020.108209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 06/18/2020] [Accepted: 09/09/2020] [Indexed: 10/25/2022] Open
Abstract
Mycobacterium tuberculosis causes human tuberculosis, and a better understanding of its biology is required to identify vulnerabilities that might be exploited in developing new therapeutics. The iron-sulfur cluster of the essential M. tuberculosis central metabolic enzyme, aconitase (AcnA), disassembles when exposed to oxidative/nitrosative stress or iron chelators. The catalytically inactive apo-AcnA interacts with a sequence resembling an iron-responsive element (IRE) located within the transcript of another essential protein, CwlM, a regulator of peptidoglycan synthesis. A Mycobacterium smegmatis cwlM conditional mutant complemented with M. tuberculosis cwlM with a disrupted IRE is unable to recover from combinations of oxidative, nitrosative, and iron starvation stresses. An equivalent M. tuberculosis cwlM conditional mutant complemented with the cwlM gene lacking a functional IRE exhibits a growth defect in THP-1 macrophages. It appears that AcnA acts to couple peptidoglycan synthesis and central metabolism, and disruption of this coupling potentially leaves mycobacteria vulnerable to attack by macrophages.
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Affiliation(s)
- Peter J Bancroft
- Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Obolbek Turapov
- Leicester Tuberculosis Research Group, Department of Respiratory Sciences, University of Leicester, Maurice Shock Medical Sciences Building, University Road, Leicester, LE1 9HN, UK
| | - Heena Jagatia
- Leicester Tuberculosis Research Group, Department of Respiratory Sciences, University of Leicester, Maurice Shock Medical Sciences Building, University Road, Leicester, LE1 9HN, UK
| | - Kristine B Arnvig
- Institute for Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Galina V Mukamolova
- Leicester Tuberculosis Research Group, Department of Respiratory Sciences, University of Leicester, Maurice Shock Medical Sciences Building, University Road, Leicester, LE1 9HN, UK.
| | - Jeffrey Green
- Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK.
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20
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Zebrafish Embryo Model for Assessment of Drug Efficacy on Mycobacterial Persisters. Antimicrob Agents Chemother 2020; 64:AAC.00801-20. [PMID: 32778551 DOI: 10.1128/aac.00801-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/03/2020] [Indexed: 01/21/2023] Open
Abstract
Tuberculosis continues to kill millions of people each year. The main difficulty in eradication of the disease is the prolonged duration of treatment, which takes at least 6 months. Persister cells have long been associated with failed treatment and disease relapse because of their phenotypical, though transient, tolerance to drugs. By targeting these persisters, the duration of treatment could be shortened, leading to improved tuberculosis treatment and a reduction in transmission. The unique in vivo environment drives the generation of persisters; however, appropriate in vivo mycobacterial persister models enabling optimized drug screening are lacking. To set up a persister infection model that is suitable for this, we infected zebrafish embryos with in vitro-starved Mycobacterium marinum In vitro starvation resulted in a persister-like phenotype with the accumulation of stored neutral lipids and concomitant increased tolerance to ethambutol. However, these starved wild-type M. marinum organisms rapidly lost their persister phenotype in vivo To prolong the persister phenotype in vivo, we subsequently generated and analyzed mutants lacking functional resuscitation-promoting factors (Rpfs). Interestingly, the ΔrpfAB mutant, lacking two Rpfs, established an infection in vivo, whereas a nutrient-starved ΔrpfAB mutant did maintain its persister phenotype in vivo This mutant was, after nutrient starvation, also tolerant to ethambutol treatment in vivo, as would be expected for persisters. We propose that this zebrafish embryo model with ΔrpfAB mutant bacteria is a valuable addition for drug screening purposes and specifically screens to target mycobacterial persisters.
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21
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Bossi L, Figueroa-Bossi N, Bouloc P, Boudvillain M. Regulatory interplay between small RNAs and transcription termination factor Rho. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194546. [PMID: 32217107 DOI: 10.1016/j.bbagrm.2020.194546] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 02/12/2020] [Accepted: 03/20/2020] [Indexed: 12/14/2022]
Abstract
The largest and best studied group of regulatory small RNAs (sRNAs) in bacteria act by modulating translation or turnover of messenger RNAs (mRNAs) through base-pairing interactions that typically take place near the 5' end of the mRNA. This allows the sRNA to bind the complementary target sequence while the remainder of the mRNA is still being made, creating conditions whereby the action of the sRNA can extend to transcriptional steps, most notably transcription termination. Increasing evidence corroborates the existence of a functional interplay between sRNAs and termination factor Rho. Two general mechanisms have emerged. One mechanism operates in translated regions subjected to sRNA repression. By inhibiting ribosome binding co-transcriptionally, the sRNA uncouples translation from transcription, allowing Rho to bind the nascent RNA and promote termination. In the second mechanism, which functions in 5' untranslated regions, the sRNA antagonizes termination directly by interfering with Rho binding to the RNA or the subsequent translocation along the RNA. Here, we review the above literature in the context of other mechanisms that underlie the participation of Rho-dependent transcription termination in gene regulation. This article is part of a Special Issue entitled: RNA and gene control in bacteria edited by Dr. M. Guillier and F. Repoila.
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Affiliation(s)
- Lionello Bossi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Nara Figueroa-Bossi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Philippe Bouloc
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Marc Boudvillain
- Centre de Biophysique Moléculaire, CNRS UPR4301, rue Charles Sadron, 45071 Orléans cedex 2, France
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22
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Salina EG, Grigorov A, Skvortsova Y, Majorov K, Bychenko O, Ostrik A, Logunova N, Ignatov D, Kaprelyants A, Apt A, Azhikina T. MTS1338, A Small Mycobacterium tuberculosis RNA, Regulates Transcriptional Shifts Consistent With Bacterial Adaptation for Entering Into Dormancy and Survival Within Host Macrophages. Front Cell Infect Microbiol 2019; 9:405. [PMID: 31850238 PMCID: PMC6901956 DOI: 10.3389/fcimb.2019.00405] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 11/12/2019] [Indexed: 11/13/2022] Open
Abstract
Small non-coding RNAs play a significant role in bacterial adaptation to changing environmental conditions. We investigated the dynamics of expression of MTS1338, a small non-coding RNA of Mycobacterium tuberculosis, in the mouse model in vivo, regulation of its expression in the infected macrophages, and the consequences of its overexpression in bacterial cultures. Here we demonstrate that MTS1338 significantly contributes to host-pathogen interactions. Activation of the host immune system triggered NO-inducible up-regulation of MTS1338 in macrophage-engulfed mycobacteria. Constitutive overexpression of MTS1338 in cultured mycobacteria improved their survival in vitro under low pH conditions. MTS1338 up-regulation launched a spectrum of shifts in the transcriptome profile similar to those reported for M. tuberculosis adaptation to hostile intra-macrophage environment. Using the RNA-seq approach, we demonstrate that gene expression changes accompanying MTS1338 overexpression indicate reduction in translational activity and bacterial growth. These changes indicate mycobacteria entering the dormant state. Taken together, our results suggest a direct involvement of this sRNA in the interplay between mycobacteria and the host immune system during infectious process.
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Affiliation(s)
- Elena G. Salina
- Laboratory of Biochemistry of Stresses in Microorganisms, Bach Institute of Biochemistry, Research Center of Biotechnology, Moscow, Russia
| | - Artem Grigorov
- Laboratory of Regulatory Transcriptomics, Department of Genomics and Postgenomic Technologies, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Yulia Skvortsova
- Laboratory of Regulatory Transcriptomics, Department of Genomics and Postgenomic Technologies, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Konstantin Majorov
- Laboratory for Immunogenetics, Department of Immunology, Central Institute for Tuberculosis, Moscow, Russia
| | - Oksana Bychenko
- Laboratory of Regulatory Transcriptomics, Department of Genomics and Postgenomic Technologies, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Albina Ostrik
- Laboratory of Biochemistry of Stresses in Microorganisms, Bach Institute of Biochemistry, Research Center of Biotechnology, Moscow, Russia
| | - Nadezhda Logunova
- Laboratory for Immunogenetics, Department of Immunology, Central Institute for Tuberculosis, Moscow, Russia
| | - Dmitriy Ignatov
- Laboratory of Regulatory Transcriptomics, Department of Genomics and Postgenomic Technologies, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Arseny Kaprelyants
- Laboratory of Biochemistry of Stresses in Microorganisms, Bach Institute of Biochemistry, Research Center of Biotechnology, Moscow, Russia
| | - Alexander Apt
- Laboratory for Immunogenetics, Department of Immunology, Central Institute for Tuberculosis, Moscow, Russia
| | - Tatyana Azhikina
- Laboratory of Regulatory Transcriptomics, Department of Genomics and Postgenomic Technologies, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
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23
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Taneja S, Dutta T. On a stake-out: Mycobacterial small RNA identification and regulation. Noncoding RNA Res 2019; 4:86-95. [PMID: 32083232 PMCID: PMC7017587 DOI: 10.1016/j.ncrna.2019.05.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 04/30/2019] [Accepted: 05/12/2019] [Indexed: 12/23/2022] Open
Abstract
Persistence of mycobacteria in the hostile environment of human macrophage is pivotal for its successful pathogenesis. Rapid adaptation to diverse stresses is the key aspect for their survival in the host cells. A range of heterogeneous mechanisms operate in bacteria to retaliate stress conditions. Small RNAs (sRNA) have been implicated in many of those mechanisms in either a single or multiple regulatory networks to post-transcriptionally modulate bacterial gene expression. Although small RNA profiling in mycobacteria by advanced technologies like deep sequencing, tilling microarray etc. have identified hundreds of sRNA, however, a handful of those small RNAs have been unearthed with precise regulatory mechanism. Extensive investigations on sRNA-mediated gene regulations in eubacteria like Escherichia coli revealed the existence of a plethora of distinctive sRNA mechanisms e.g. base pairing, protein sequestration, RNA decoy etc. Increasing studies on mycobacterial sRNA also discovered several eccentric mechanisms where sRNAs act at the posttranscriptional stage to either activate or repress target gene expression that lead to promote mycobacterial survival in stresses. Several intrinsic features like high GC content, absence of any homologue of abundant RNA chaperones, Hfq and ProQ, isolate sRNA mechanisms of mycobacteria from that of other bacteria. An insightful approach has been taken in this review to describe sRNA identification and its regulations in mycobacterial species especially in Mycobacterium tuberculosis.
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Key Words
- Anti-antisense
- Antisense
- Base pairing
- CDS, coding sequence
- Gene regulation by sRNA
- IGR, intergenic region
- ORF, open reading frame
- RBS, Ribosome binding site
- RNAP, RNA polymerase
- SD, Shine Dalgarno sequence
- Small RNAs
- TF, transcription factor
- TIR, translation initiation region
- UTR, untranslated region
- nt, nucleotide
- sRNA, small RNA
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Affiliation(s)
| | - Tanmay Dutta
- RNA Biology Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
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24
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Arnvig KB. Riboswitches: choosing the best platform. Biochem Soc Trans 2019; 47:1091-1099. [PMID: 31249101 PMCID: PMC7615714 DOI: 10.1042/bst20180507] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 05/10/2019] [Accepted: 05/28/2019] [Indexed: 03/07/2024]
Abstract
Riboswitch discovery and characterisation have come a long way since the term was first coined almost two decades ago. Riboswitches themselves are likely derived from ancient ligand-binding transcripts, which have evolved into sophisticated genetic control elements that are widespread in prokaryotes. Riboswitches are associated with a multitude of cellular processes including biosynthetic pathways, transport mechanisms and stress responses leading to an ever-increasing appreciation for an in-depth understanding of their triggers and functions in order to address physiological and regulatory questions. The majority of riboswitches exert their control via transcriptional or translational expression platforms depending on their genetic context. It remains, however, to be determined precisely why one platform is favoured over another. Is this a question of the layout of the gene expression machinery, ligand availability, the degree of control required, serendipity or various combinations of these? With this review, rather than providing answers, I am hoping to plant a seed for further scientific discussions about this puzzle.
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Affiliation(s)
- Kristine B Arnvig
- Institute for Structural and Molecular Biology, University College London, London WC1E 6BT, U.K.
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25
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Kathleen M, Patrick B. Editorial: Introduction to thematic issue 'Molecular Effectors of Tuberculosis Pathogenesis'. Pathog Dis 2018; 76:5307233. [PMID: 30726953 DOI: 10.1093/femspd/fty077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- McDonough Kathleen
- Wadsworth Center, NYS Department of Health; and Department of Biomedical Sciences, University at Albany, SUNY, USA
| | - Brennan Patrick
- Department of Microbiology, Immunology and Pathology, Colorado State University, USA
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