1
|
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.
Collapse
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
| |
Collapse
|
2
|
Bar-Oz M, Martini MC, Alonso MN, Meir M, Lore NI, Miotto P, Riva C, Angala SK, Xiao J, Masiello CS, Misiakou MA, Sun H, Moy JK, Jackson M, Johansen HK, Cirillo DM, Shell SS, Barkan D. The small non-coding RNA B11 regulates multiple facets of Mycobacterium abscessus virulence. PLoS Pathog 2023; 19:e1011575. [PMID: 37603560 PMCID: PMC10470900 DOI: 10.1371/journal.ppat.1011575] [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: 01/11/2023] [Revised: 08/31/2023] [Accepted: 07/24/2023] [Indexed: 08/23/2023] Open
Abstract
Mycobacterium abscessus causes severe disease in patients with cystic fibrosis. Little is known in M. abscessus about the roles of small regulatory RNAs (sRNA) in gene regulation. We show that the sRNA B11 controls gene expression and virulence-associated phenotypes in this pathogen. B11 deletion from the smooth strain ATCC_19977 produced a rough strain, increased pro-inflammatory signaling and virulence in multiple infection models, and increased resistance to antibiotics. Examination of clinical isolate cohorts identified isolates with B11 mutations or reduced expression. We used RNAseq and proteomics to investigate the effects of B11 on gene expression and test the impact of mutations found in clinical isolates. Over 200 genes were differentially expressed in the deletion mutant. Strains with the clinical B11 mutations showed expression trends similar to the deletion mutant, suggesting partial loss of function. Among genes upregulated in the B11 mutant, there was a strong enrichment for genes with B11-complementary sequences in their predicted ribosome binding sites (RBS), consistent with B11 functioning as a negative regulator that represses translation via base-pairing to RBSs. Comparing the proteomes similarly revealed that upregulated proteins were strongly enriched for B11-complementary sequences. Intriguingly, genes upregulated in the absence of B11 included components of the ESX-4 secretion system, critical for M. abscessus virulence. Many of these genes had B11-complementary sequences at their RBSs, which we show is sufficient to mediate repression by B11 through direct binding. Altogether, our data show that B11 acts as a direct negative regulator and mediates (likely indirect) positive regulation with pleiotropic effects on gene expression and clinically important phenotypes in M. abscessus. The presence of hypomorphic B11 mutations in clinical strains is consistent with the idea that lower B11 activity may be advantageous for M. abscessus in some clinical contexts. This is the first report on an sRNA role in M. abscessus.
Collapse
Affiliation(s)
- Michal Bar-Oz
- Koret School of Veterinary Medicine, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Maria Carla Martini
- Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | - Maria Natalia Alonso
- Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | | | | | - Paolo Miotto
- IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Camilla Riva
- IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Shiva K Angala
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Junpei Xiao
- Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | - Catherine S Masiello
- Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | - Maria-Anna Misiakou
- Center for Genomic Medicine, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
| | - Huaming Sun
- Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | - Justin K Moy
- Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | | | | | - Scarlet S Shell
- Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | - Daniel Barkan
- Koret School of Veterinary Medicine, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Ostrik AA, Grigorov AS, Bocharova IV, Kaprelyants AS, Azhikina TL, Salina EG. Small RNAs Mcr11 and DrrS of Mycobacterium tuberculosis as Possible Regulators of Glycerol Metabolism. APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s0003683822040135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
6
|
Khabibullina NF, Kutuzova DM, Burmistrova IA, Lyadova IV. The Biological and Clinical Aspects of a Latent Tuberculosis Infection. Trop Med Infect Dis 2022; 7:tropicalmed7030048. [PMID: 35324595 PMCID: PMC8955876 DOI: 10.3390/tropicalmed7030048] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/04/2022] [Accepted: 03/04/2022] [Indexed: 01/22/2023] Open
Abstract
Tuberculosis (TB), caused by bacilli from the Mycobacterium tuberculosis complex, remains a serious global public health problem, representing one of the main causes of death from infectious diseases. About one quarter of the world’s population is infected with Mtb and has a latent TB infection (LTBI). According to the World Health Organization (WHO), an LTBI is characterized by a lasting immune response to Mtb antigens without any TB symptoms. Current LTBI diagnoses and treatments are based on this simplified definition, although an LTBI involves a broad range of conditions, including when Mtb remains in the body in a persistent form and the immune response cannot be detected. The study of LTBIs has progressed in recent years; however, many biological and medical aspects of an LTBI are still under discussion. This review focuses on an LTBI as a broad spectrum of states, both of the human body, and of Mtb cells. The problems of phenotypic insusceptibility, diagnoses, chemoprophylaxis, and the necessity of treatment are discussed. We emphasize the complexity of an LTBI diagnosis and its treatment due to its ambiguous nature. We consider alternative ways of differentiating an LTBI from active TB, as well as predicting TB reactivation based on using mycobacterial “latency antigens” for interferon gamma release assay (IGRA) tests and the transcriptomic analysis of human blood cells.
Collapse
|
7
|
Alvarez-Eraso KLF, Muñoz-Martínez LM, Alzate JF, Barrera LF, Baena A. Modulatory Impact of the sRNA Mcr11 in Two Clinical Isolates of Mycobacterium tuberculosis. Curr Microbiol 2022; 79:39. [PMID: 34982251 DOI: 10.1007/s00284-021-02733-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 11/30/2021] [Indexed: 11/26/2022]
Abstract
Mycobacterium tuberculosis (Mtb) is a successful pathogen causing tuberculosis (TB) disease in humans. It has been shown, that some circulating strains of Mtb in TB endemic populations, are more virulent and more transmissible than others, which may be related to their evolved adaptations to modulate the host immune responses. Underlying these adaptations to the stressful conditions, different genetic regulatory networks involved sRNAs that are mostly unknown for Mtb. We have previously shown that Mcr11 is one of the main sRNAs that determine transcriptomic differences among the Colombian clinical isolates UT127 and UT205 compared to the laboratory strain H37Rv. We found that the knock-down of mcr11 using CRISPRi has a major impact on phenotypic traits, especially in the clinical isolate UT205. Through the analysis of RNA-seq during the knock-down of mcr11 in UT205, we found a downregulation of genes mainly involved in lipid synthesis, lipid metabolism, ribosomal proteins, transport systems, respiratory and energy systems, membrane and cell wall components, intermediary metabolism, lipoproteins and virulence genes. One of the most interesting genes showing transcriptomic changes is OprA (encoded by the gene rv0516c), which has been involved in the K+ regulation. Overall, our data may suggest that one of the prominent roles of the sRNA Mcr11 is to regulate genes that control Mtb growth and osmoregulation.
Collapse
Affiliation(s)
| | | | - Juan F Alzate
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Carrera 53 No. 61-30, Medellín, Colombia
- Centro Nacional de Secuenciación Genómica-CNSG, Medellín, Colombia
- Sede de Investigación Universitaria-SIU, Medellín, Colombia
| | - Luis F Barrera
- Grupo de Inmunología Celular e Inmunogenética (GICIG), Medellín, Colombia
- Sede de Investigación Universitaria-SIU, Medellín, Colombia
- Instituto de Investigaciones Médicas, Universidad de Antioquia, Medellín, Colombia
| | - Andres Baena
- Grupo de Inmunología Celular e Inmunogenética (GICIG), Medellín, Colombia.
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Carrera 53 No. 61-30, Medellín, Colombia.
- Sede de Investigación Universitaria-SIU, Medellín, Colombia.
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Small RNAs Asserting Big Roles in Mycobacteria. Noncoding RNA 2021; 7:ncrna7040069. [PMID: 34842799 PMCID: PMC8628891 DOI: 10.3390/ncrna7040069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/20/2021] [Accepted: 10/26/2021] [Indexed: 02/07/2023] Open
Abstract
Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (Mtb), with 10.4 million new cases per year reported in the human population. Recent studies on the Mtb transcriptome have revealed the abundance of noncoding RNAs expressed at various phases of mycobacteria growth, in culture, in infected mammalian cells, and in patients. Among these noncoding RNAs are both small RNAs (sRNAs) between 50 and 350 nts in length and smaller RNAs (sncRNA) < 50 nts. In this review, we provide an up-to-date synopsis of the identification, designation, and function of these Mtb-encoded sRNAs and sncRNAs. The methodological advances including RNA sequencing strategies, small RNA antagonists, and locked nucleic acid sequence-specific RNA probes advancing the studies on these small RNA are described. Initial insights into the regulation of the small RNA expression and putative processing enzymes required for their synthesis and function are discussed. There are many open questions remaining about the biological and pathogenic roles of these small non-coding RNAs, and potential research directions needed to define the role of these mycobacterial noncoding RNAs are summarized.
Collapse
|
10
|
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.
Collapse
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.
| |
Collapse
|
11
|
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.
Collapse
|
12
|
Coskun FS, Srivastava S, Raj P, Dozmorov I, Belkaya S, Mehra S, Golden NA, Bucsan AN, Chapagain ML, Wakeland EK, Kaushal D, Gumbo T, van Oers NSC. sncRNA-1 Is a Small Noncoding RNA Produced by Mycobacterium tuberculosis in Infected Cells That Positively Regulates Genes Coupled to Oleic Acid Biosynthesis. Front Microbiol 2020; 11:1631. [PMID: 32849337 PMCID: PMC7399025 DOI: 10.3389/fmicb.2020.01631] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/23/2020] [Indexed: 12/21/2022] Open
Abstract
Nearly one third of the world’s population is infected with Mycobacterium tuberculosis (Mtb). While much work has focused on the role of different Mtb encoded proteins in pathogenesis, recent studies have revealed that Mtb also transcribes many noncoding RNAs whose functions remain poorly characterized. We performed RNA sequencing and identified a subset of Mtb H37Rv-encoded small RNAs (<30 nts in length) that were produced in infected macrophages. Designated as smaller noncoding RNAs (sncRNAs), three of these predominated the read counts. Each of the three, sncRNA-1, sncRNA-6, and sncRNA-8 had surrounding sequences with predicted stable secondary RNA stem loops. Site-directed mutagenesis of the precursor sequences suggest the existence of a hairpin loop dependent RNA processing mechanism. A functional assessment of sncRNA-1 suggested that it positively regulated two mycobacterial transcripts involved in oleic acid biosynthesis. Complementary loss- and gain- of-function approaches revealed that sncRNA-1 positively supports Mtb growth and survival in nutrient-depleted cultures as well as in infected macrophages. Overall, the findings reveal that Mtb produces sncRNAs in infected cells, with sncRNA-1 modulating mycobacterial gene expression including genes coupled to oleic acid biogenesis.
Collapse
Affiliation(s)
- Fatma S Coskun
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Shashikant Srivastava
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, TX, United States
| | - Prithvi Raj
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Igor Dozmorov
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Serkan Belkaya
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Smriti Mehra
- Tulane National Primate Research Center, School of Medicine, Tulane University, Covington, LA, United States
| | - Nadia A Golden
- Tulane National Primate Research Center, School of Medicine, Tulane University, Covington, LA, United States
| | - Allison N Bucsan
- Tulane National Primate Research Center, School of Medicine, Tulane University, Covington, LA, United States
| | - Moti L Chapagain
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, TX, United States
| | - Edward K Wakeland
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Deepak Kaushal
- Tulane National Primate Research Center, School of Medicine, Tulane University, Covington, LA, United States.,Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Tawanda Gumbo
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, TX, United States
| | - Nicolai S C van Oers
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States.,Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, United States.,Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, United States
| |
Collapse
|
13
|
Girardin RC, McDonough KA. Small RNA Mcr11 requires the transcription factor AbmR for stable expression and regulates genes involved in the central metabolism of Mycobacterium tuberculosis. Mol Microbiol 2020; 113:504-520. [PMID: 31782837 PMCID: PMC7064933 DOI: 10.1111/mmi.14436] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 11/25/2019] [Accepted: 11/26/2019] [Indexed: 12/31/2022]
Abstract
Mycobacterium tuberculosis (Mtb), the etiologic agent of tuberculosis, must adapt to host-associated environments during infection by modulating gene expression. Small regulatory RNAs (sRNAs) are key regulators of bacterial gene expression, but their roles in Mtb are not well understood. Here, we address the expression and function of the Mtb sRNA Mcr11, which is associated with slow bacterial growth and chronic infections in mice. We found that stable expression of Mcr11 requires multiple factors specific to TB-complex bacteria, including the AbmR transcription factor. Bioinformatic analyses used to predict regulatory targets of Mcr11 identified 7-11 nucleotide regions with potential for direct base-pairing with Mcr11 immediately upstream of Rv3282, fadA3, and lipB. mcr11-dependent regulation of these genes was demonstrated using qRT-PCR and found to be responsive to the presence of fatty acids. Mutation of the putative Mcr11 base-pairing site upstream of lipB in a promoter reporter strain resulted in significant de-repression of lipB expression, similar to that observed in mcr11-deleted Mtb. These studies establish Mcr11's roles in regulating growth and central metabolism in Mtb. Our finding that multiple TB-complex-specific factors are required for production of stable Mcr11 also emphasizes the need to better understand mechanisms of sRNA expression and stability in TB.
Collapse
Affiliation(s)
- Roxie C. Girardin
- Department of Biomedical SciencesSchool of Public HealthUniversity at AlbanyAlbanyNY
| | - Kathleen A. McDonough
- Department of Biomedical SciencesSchool of Public HealthUniversity at AlbanyAlbanyNY
- Wadsworth Center, New York State Department of HealthAlbanyNY
| |
Collapse
|