1
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Niet SVD, Green KD, Schimmel IM, Bakker JD, Lodder B, Reits EA, Garneau-Tsodikova S, van der Wel NN. Zafirlukast induces DNA condensation and has bactericidal effect on replicating Mycobacterium abscessus. Antimicrob Agents Chemother 2024:e0002924. [PMID: 38990015 DOI: 10.1128/aac.00029-24] [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: 01/05/2024] [Accepted: 06/09/2024] [Indexed: 07/12/2024] Open
Abstract
Mycobacterium abscessus infections are emerging in cystic fibrosis patients, and treatment success rate in these patients is only 33% due to extreme antibiotic resistance. Thus, new treatment options are essential. An interesting target could be Lsr2, a nucleoid-associated protein involved in mycobacterial virulence. Zafirlukast is a Food and Drug Administration (FDA)-approved drug against asthma that was shown to bind Lsr2. In this study, zafirlukast treatment is shown to reduce M. abscessus growth, with a minimal inhibitory concentration of 16 µM and a bactericidal concentration of 64 µM in replicating bacteria only. As an initial response, DNA condensation, a known stress response of mycobacteria, occurs after 1 h of treatment with zafirlukast. During continued zafirlukast treatment, the morphology of the bacteria alters and the structural integrity of the bacteria is lost. After 4 days of treatment, reduced viability is measured in different culture media, and growth of M. abscessus is reduced in a dose-dependent manner. Using transmission electron microscopy, we demonstrated that the hydrophobic multilayered cell wall and periplasm are disorganized and ribosomes are reduced in size and relocalized. In summary, our data demonstrate that zafirlukast alters the morphology of M. abscessus and is bactericidal at 64 µM. The bactericidal concentration of zafirlukast is relatively high, and it is only effective on replicating bacteria but as zafirlukast is an FDA-approved drug, and currently used as an anti-asthma treatment, it could be an interesting drug to further study in in vivo experiments to determine whether it could be used as an antibiotic for M. abscessus infections.
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Affiliation(s)
- Sanne van der Niet
- Electron Microscopy Centre Amsterdam, Amsterdam University Medical Centre, Amsterdam, the Netherlands
| | - Keith D Green
- College of Pharmacy, University of Kentucky, Lexington, Kentucky, USA
| | - Irene M Schimmel
- Electron Microscopy Centre Amsterdam, Amsterdam University Medical Centre, Amsterdam, the Netherlands
| | - Jordy de Bakker
- Electron Microscopy Centre Amsterdam, Amsterdam University Medical Centre, Amsterdam, the Netherlands
| | - Bastiaan Lodder
- Electron Microscopy Centre Amsterdam, Amsterdam University Medical Centre, Amsterdam, the Netherlands
| | - Eric A Reits
- Electron Microscopy Centre Amsterdam, Amsterdam University Medical Centre, Amsterdam, the Netherlands
| | | | - Nicole N van der Wel
- Electron Microscopy Centre Amsterdam, Amsterdam University Medical Centre, Amsterdam, the Netherlands
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2
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Santoshi M, Tare P, Nagaraja V. Nucleoid-associated proteins of mycobacteria come with a distinctive flavor. Mol Microbiol 2024. [PMID: 38922783 DOI: 10.1111/mmi.15287] [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: 02/16/2024] [Revised: 05/31/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024]
Abstract
In every bacterium, nucleoid-associated proteins (NAPs) play crucial roles in chromosome organization, replication, repair, gene expression, and other DNA transactions. Their central role in controlling the chromatin dynamics and transcription has been well-appreciated in several well-studied organisms. Here, we review the diversity, distribution, structure, and function of NAPs from the genus Mycobacterium. We highlight the progress made in our understanding of the effects of these proteins on various processes and in responding to environmental stimuli and stress of mycobacteria in their free-living as well as during distinctive intracellular lifestyles. We project them as potential drug targets and discuss future studies to bridge the information gap with NAPs from well-studied systems.
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Affiliation(s)
- Meghna Santoshi
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - Priyanka Tare
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
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3
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Ng WL, Rego EH. A nucleoid-associated protein is involved in the emergence of antibiotic resistance by promoting the frequent exchange of the replicative DNA polymerase in Mycobacterium smegmatis. mSphere 2024; 9:e0012224. [PMID: 38591887 PMCID: PMC11237743 DOI: 10.1128/msphere.00122-24] [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: 03/04/2024] [Accepted: 03/16/2024] [Indexed: 04/10/2024] Open
Abstract
Antibiotic resistance in Mycobacterium tuberculosis exclusively originates from chromosomal mutations, either during normal DNA replication or under stress, when the expression of error-prone DNA polymerases increases to repair damaged DNA. To bypass DNA lesions and catalyze error-prone DNA synthesis, translesion polymerases must be able to access the DNA, temporarily replacing the high-fidelity replicative polymerase. The mechanisms that govern polymerase exchange are not well understood, especially in mycobacteria. Here, using a suite of quantitative fluorescence imaging techniques, we discover that in Mycobacterium smegmatis, as in other bacterial species, the replicative polymerase, DnaE1, exchanges at a timescale much faster than that of DNA replication. Interestingly, this fast exchange rate depends on an actinobacteria-specific nucleoid-associated protein (NAP), Lsr2. In cells missing lsr2, DnaE1 exchanges less frequently, and the chromosome is replicated more faithfully. Additionally, in conditions that damage DNA, cells lacking lsr2 load the complex needed to bypass DNA lesions less effectively and, consistently, replicate with higher fidelity but exhibit growth defects. Together, our results show that Lsr2 promotes dynamic flexibility of the mycobacterial replisome, which is critical for robust cell growth and lesion repair in conditions that damage DNA. IMPORTANCE Unlike many other pathogens, Mycobacterium tuberculosis has limited ability for horizontal gene transfer, a major mechanism for developing antibiotic resistance. Thus, the mechanisms that facilitate chromosomal mutagenesis are of particular importance in mycobacteria. Here, we show that Lsr2, a nucleoid-associated protein, has a novel role in DNA replication and mutagenesis in the model mycobacterium Mycobacterium smegmatis. We find that Lsr2 promotes the fast exchange rate of the replicative DNA polymerase, DnaE1, at the replication fork and is important for the effective loading of the DnaE2-ImuA'-ImuB translesion complex. Without lsr2, M. smegmatis replicates its chromosome more faithfully and acquires resistance to rifampin at a lower rate, but at the cost of impaired survival to DNA damaging agents. Together, our work establishes Lsr2 as a potential factor in the emergence of mycobacterial antibiotic resistance.
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Affiliation(s)
- Wei L Ng
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
| | - E Hesper Rego
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
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4
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Gerges E, Rodríguez-Ordoñez MDP, Durand N, Herrmann JL, Crémazy F. Lsr2, a pleiotropic regulator at the core of the infectious strategy of Mycobacterium abscessus. Microbiol Spectr 2024; 12:e0352823. [PMID: 38353553 PMCID: PMC10913753 DOI: 10.1128/spectrum.03528-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 01/22/2024] [Indexed: 03/06/2024] Open
Abstract
Mycobacterium abscessus is a non-tuberculous mycobacterium, causing lung infections in cystic fibrosis patients. During pulmonary infection, M. abscessus switches from smooth (Mabs-S) to rough (Mabs-R) morphotypes, the latter being hyper-virulent. Previously, we isolated the lsr2 gene as differentially expressed during S-to-R transition. lsr2 encodes a pleiotropic transcription factor that falls under the superfamily of nucleoid-associated proteins. Here, we used two functional genomic methods, RNA-seq and chromatin immunoprecipitation-sequencing (ChIP-seq), to elucidate the molecular role of Lsr2 in the pathobiology of M. abscessus. Transcriptomic analysis shows that Lsr2 differentially regulates gene expression across both morphotypes, most of which are involved in several key cellular processes of M. abscessus, including host adaptation and antibiotic resistance. These results were confirmed through quantitative real-time PCR, as well as by minimum inhibitory concentration tests and infection tests on macrophages in the presence of antibiotics. ChIP-seq analysis revealed that Lsr2 extensively binds the M. abscessus genome at AT-rich sequences and appears to form long domains that participate in the repression of its target genes. Unexpectedly, the genomic distribution of Lsr2 revealed no distinctions between Mabs-S and Mabs-R, implying more intricate mechanisms at play for achieving target selectivity.IMPORTANCELsr2 is a crucial transcription factor and chromosome organizer involved in intracellular growth and virulence in the smooth and rough morphotypes of Mycobacterium abscessus. Using RNA-seq and chromatin immunoprecipitation-sequencing (ChIP-seq), we investigated the molecular role of Lsr2 in gene expression regulation along with its distribution on M. abscessus genome. Our study demonstrates the pleiotropic regulatory role of Lsr2, regulating the expression of many genes coordinating essential cellular and molecular processes in both morphotypes. In addition, we have elucidated the role of Lsr2 in antibiotic resistance both in vitro and in vivo, where lsr2 mutant strains display heightened sensitivity to antibiotics. Through ChIP-seq, we reported the widespread distribution of Lsr2 on M. abscessus genome, revealing a direct repressive effect due to its extensive binding on promoters or coding sequences of its targets. This study unveils the significant regulatory role of Lsr2, intricately intertwined with its function in shaping the organization of the M. abscessus genome.
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Affiliation(s)
- Elias Gerges
- Université Paris-Saclay, UVSQ, Inserm, Infection et inflammation, Montigny-Le-Bretonneux, France
| | - María del Pilar Rodríguez-Ordoñez
- Université Paris-Saclay, Université d’Evry, Laboratoire Européen de Recherche pour la Polyarthrite rhumatoïde-Genhotel, Evry, France
| | - Nicolas Durand
- Université Paris-Saclay, UVSQ, Inserm, Infection et inflammation, Montigny-Le-Bretonneux, France
| | - Jean-Louis Herrmann
- Université Paris-Saclay, UVSQ, Inserm, Infection et inflammation, Montigny-Le-Bretonneux, France
- APHP, GHU Paris-Saclay, Hôpital Raymond Poincaré, Service de Microbiologie, Garches, France
| | - Frédéric Crémazy
- Université Paris-Saclay, UVSQ, Inserm, Infection et inflammation, Montigny-Le-Bretonneux, France
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5
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Li Y, Wei Y, Guo X, Li X, Lu L, Hu L, He Z. Insertion sequence transposition activates antimycobacteriophage immunity through an lsr2-silenced lipid metabolism gene island. MLIFE 2024; 3:87-100. [PMID: 38827510 PMCID: PMC11139207 DOI: 10.1002/mlf2.12106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/16/2024] [Accepted: 01/26/2024] [Indexed: 06/04/2024]
Abstract
Insertion sequences (ISs) exist widely in bacterial genomes, but their roles in the evolution of bacterial antiphage defense remain to be clarified. Here, we report that, under the pressure of phage infection, the IS1096 transposition of Mycobacterium smegmatis into the lsr2 gene can occur at high frequencies, which endows the mutant mycobacterium with a broad-spectrum antiphage ability. Lsr2 functions as a negative regulator and directly silences expression of a gene island composed of 11 lipid metabolism-related genes. The complete or partial loss of the gene island leads to a significant decrease of bacteriophage adsorption to the mycobacterium, thus defending against phage infection. Strikingly, a phage that has evolved mutations in two tail-filament genes can re-escape from the lsr2 inactivation-triggered host defense. This study uncovered a new signaling pathway for activating antimycobacteriophage immunity by IS transposition and provided insight into the natural evolution of bacterial antiphage defense.
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Affiliation(s)
- Yakun Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and TechnologyGuangxi UniversityNanningChina
| | - Yuyun Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and TechnologyGuangxi UniversityNanningChina
| | - Xiao Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and TechnologyGuangxi UniversityNanningChina
| | - Xiaohui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and TechnologyGuangxi UniversityNanningChina
| | - Lining Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and TechnologyGuangxi UniversityNanningChina
| | - Lihua Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and TechnologyGuangxi UniversityNanningChina
| | - Zheng‐Guo He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and TechnologyGuangxi UniversityNanningChina
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6
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Gerges E, Herrmann JL, Crémazy F. [Lsr2: A Nucleoid Associated Protein (NAP) and a transcription factor in mycobacteria]. Med Sci (Paris) 2024; 40:154-160. [PMID: 38411423 DOI: 10.1051/medsci/2023218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024] Open
Abstract
Lsr2, a small protein mainly found in actinobacteria, plays a crucial role in the virulence and adaptation of mycobacteria to environmental conditions. As a member of the nucleoid-associated protein (NAPs) superfamily, Lsr2 influences DNA organization by facilitating the formation of chromosomal loops in vitro and, therefore, may be a major player in the three-dimensional folding of the genome. Additionally, Lsr2 also acts as a transcription factor, regulating the expression of numerous genes responsible for coordinating a myriad of cellular and molecular processes essential for the actinobacteria. Similar to the H-NS protein, its ortholog in enterobacteria, its role in transcriptional repression likely relies on oligomerization, rigidifying, and bridging of DNA, thereby disrupting RNA polymerase recruitment as well as the elongation of RNA transcripts.
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Affiliation(s)
- Elias Gerges
- Université Paris-Saclay, UVSQ, Inserm, Infection et inflammation, 78180 Montigny-Le-Bretonneux, France
| | - Jean-Louis Herrmann
- Université Paris-Saclay, UVSQ, Inserm, Infection et inflammation, 78180 Montigny-Le-Bretonneux, France
| | - Frédéric Crémazy
- Université Paris-Saclay, UVSQ, Inserm, Infection et inflammation, 78180 Montigny-Le-Bretonneux, France
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7
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Ling X, Liu X, Wang K, Guo M, Ou Y, Li D, Xiang Y, Zheng J, Hu L, Zhang H, Li W. Lsr2 acts as a cyclic di-GMP receptor that promotes keto-mycolic acid synthesis and biofilm formation in mycobacteria. Nat Commun 2024; 15:695. [PMID: 38267428 PMCID: PMC10808224 DOI: 10.1038/s41467-024-44774-6] [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: 05/29/2023] [Accepted: 01/03/2024] [Indexed: 01/26/2024] Open
Abstract
Cyclic di-GMP (c-di-GMP) is a second messenger that promotes biofilm formation in several bacterial species, but the mechanisms are often unclear. Here, we report that c-di-GMP promotes biofilm formation in mycobacteria in a manner dependent on the nucleoid-associated protein Lsr2. We show that c-di-GMP specifically binds to Lsr2 at a ratio of 1:1. Lsr2 upregulates the expression of HadD, a (3R)-hydroxyacyl-ACP dehydratase, thus promoting the synthesis of keto-mycolic acid and biofilm formation. Thus, Lsr2 acts as a c-di-GMP receptor that links the second messenger's function to lipid synthesis and biofilm formation in mycobacteria.
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Affiliation(s)
- Xiaocui Ling
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Xiao Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Kun Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Minhao Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Yanzhe Ou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Danting Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Yulin Xiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Jiachen Zheng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Lihua Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Hongyun Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Weihui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China.
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8
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Ng WL, Rego EH. A nucleoid-associated protein is involved in the emergence of antibiotic resistance by promoting the frequent exchange of the replicative DNA polymerase in M. smegmatis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.12.544663. [PMID: 38260554 PMCID: PMC10802252 DOI: 10.1101/2023.06.12.544663] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Antibiotic resistance in M. tuberculosis exclusively originates from chromosomal mutations, either during normal DNA replication or under stress, when the expression of error-prone DNA polymerases increases to repair damaged DNA. To bypass DNA lesions and catalyze error-prone DNA synthesis, translesion polymerases must be able to access the DNA, temporarily replacing the high-fidelity replicative polymerase. The mechanisms that govern polymerase exchange are not well understood, especially in mycobacteria. Here, using a suite of quantitative fluorescence imaging techniques, we discover that, as in other bacterial species, in M. smegmatis, the replicative polymerase, DnaE1, exchanges at a timescale much faster than that of DNA replication. Interestingly, this fast exchange rate depends on an actinobacteria-specific nucleoid-associated protein (NAP), Lsr2. In cells missing lsr2, DnaE1 exchanges less frequently, and the chromosome is replicated more faithfully. Additionally, in conditions that damage DNA, cells lacking lsr2 load the complex needed to bypass DNA lesions less effectively and, consistently, replicate with higher fidelity but exhibit growth defects. Together, our results show that Lsr2 promotes dynamic flexibility of the mycobacterial replisome, which is critical for robust cell growth and lesion repair in conditions that damage DNA.
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Affiliation(s)
- Wei L. Ng
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, 06519
| | - E. Hesper Rego
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, 06519
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9
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Barton IS, Ren Z, Cribb CB, Pitzer JE, Baglivo I, Martin DW, Wang X, Roop RM. Brucella MucR acts as an H-NS-like protein to silence virulence genes and structure the nucleoid. mBio 2023; 14:e0220123. [PMID: 37847580 PMCID: PMC10746212 DOI: 10.1128/mbio.02201-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 08/21/2023] [Indexed: 10/19/2023] Open
Abstract
IMPORTANCE Histone-like nucleoid structuring (H-NS) and H-NS-like proteins coordinate host-associated behaviors in many pathogenic bacteria, often through forming silencer/counter-silencer pairs with signal-responsive transcriptional activators to tightly control gene expression. Brucella and related bacteria do not encode H-NS or homologs of known H-NS-like proteins, and it is unclear if they have other proteins that perform analogous functions during pathogenesis. In this work, we provide compelling evidence for the role of MucR as a novel H-NS-like protein in Brucella. We show that MucR possesses many of the known functions attributed to H-NS and H-NS-like proteins, including the formation of silencer/counter-silencer pairs to control virulence gene expression and global structuring of the nucleoid. These results uncover a new role for MucR as a nucleoid structuring protein and support the importance of temporal control of gene expression in Brucella and related bacteria.
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Affiliation(s)
- Ian S. Barton
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Zhongqing Ren
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Connor B. Cribb
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Joshua E. Pitzer
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Ilaria Baglivo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Caserta, Italy
| | - Daniel W. Martin
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Xindan Wang
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - R. Martin Roop
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
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10
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Keshavam CC, Naz S, Gupta A, Sanyal P, Kochar M, Gangwal A, Sangwan N, Kumar N, Tyagi E, Goel S, Singh NK, Sowpati DT, Khare G, Ganguli M, Raze D, Locht C, Basu-Modak S, Gupta M, Nandicoori VK, Singh Y. The heparin-binding hemagglutinin protein of Mycobacterium tuberculosis is a nucleoid-associated protein. J Biol Chem 2023; 299:105364. [PMID: 37865319 PMCID: PMC10665949 DOI: 10.1016/j.jbc.2023.105364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/05/2023] [Accepted: 10/10/2023] [Indexed: 10/23/2023] Open
Abstract
Nucleoid-associated proteins (NAPs) regulate multiple cellular processes such as gene expression, virulence, and dormancy throughout bacterial species. NAPs help in the survival and adaptation of Mycobacterium tuberculosis (Mtb) within the host. Fourteen NAPs have been identified in Escherichia coli; however, only seven NAPs are documented in Mtb. Given its complex lifestyle, it is reasonable to assume that Mtb would encode for more NAPs. Using bioinformatics tools and biochemical experiments, we have identified the heparin-binding hemagglutinin (HbhA) protein of Mtb as a novel sequence-independent DNA-binding protein which has previously been characterized as an adhesion molecule required for extrapulmonary dissemination. Deleting the carboxy-terminal domain of HbhA resulted in a complete loss of its DNA-binding activity. Atomic force microscopy showed HbhA-mediated architectural modulations in the DNA, which may play a regulatory role in transcription and genome organization. Our results showed that HbhA colocalizes with the nucleoid region of Mtb. Transcriptomics analyses of a hbhA KO strain revealed that it regulates the expression of ∼36% of total and ∼29% of essential genes. Deletion of hbhA resulted in the upregulation of ∼73% of all differentially expressed genes, belonging to multiple pathways suggesting it to be a global repressor. The results show that HbhA is a nonessential NAP regulating gene expression globally and acting as a plausible transcriptional repressor.
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Affiliation(s)
| | - Saba Naz
- Department of Zoology, University of Delhi, Delhi, India; CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Aanchal Gupta
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Priyadarshini Sanyal
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India; Academy of Scientific and Innovative Research (AcSIR), CSIR- Centre for Cellular and Molecular Biology (CSIR-CCMB) Campus, Hyderabad, India
| | - Manisha Kochar
- Department of Zoology, University of Delhi, Delhi, India; CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | | | - Nitika Sangwan
- Department of Zoology, University of Delhi, Delhi, India
| | - Nishant Kumar
- Department of Zoology, University of Delhi, Delhi, India
| | - Ekta Tyagi
- Department of Zoology, University of Delhi, Delhi, India
| | - Simran Goel
- Department of Zoology, University of Delhi, Delhi, India
| | | | | | - Garima Khare
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Munia Ganguli
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Dominique Raze
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR9017 - CIIL - Centre for Infection and Immunity of Lille, Lille, France
| | - Camille Locht
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR9017 - CIIL - Centre for Infection and Immunity of Lille, Lille, France
| | | | - Meetu Gupta
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.
| | - Vinay Kumar Nandicoori
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India; Academy of Scientific and Innovative Research (AcSIR), CSIR- Centre for Cellular and Molecular Biology (CSIR-CCMB) Campus, Hyderabad, India; National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India.
| | - Yogendra Singh
- Department of Zoology, University of Delhi, Delhi, India; Delhi School of Public Health, Institution of Eminence, University of Delhi, Delhi, India.
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11
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Born SEM, Reichlen MJ, Bartek IL, Benoit JB, Frank DN, Voskuil MI. Population heterogeneity in Mycobacterium smegmatis and Mycobacterium abscessus. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001402. [PMID: 37862100 PMCID: PMC10634367 DOI: 10.1099/mic.0.001402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 10/06/2023] [Indexed: 10/21/2023]
Abstract
Bacteria use population heterogeneity, the presence of more than one phenotypic variant in a clonal population, to endure diverse environmental challenges - a 'bet-hedging' strategy. Phenotypic variants have been described in many bacteria, but the phenomenon is not well-understood in mycobacteria, including the environmental factors that influence heterogeneity. Here, we describe three reproducible morphological variants in M. smegmatis - smooth, rough, and an intermediate morphotype that predominated under typical laboratory conditions. M. abscessus has two recognized morphotypes, smooth and rough. Interestingly, M. tuberculosis exists in only a rough form. The shift from smooth to rough in both M. smegmatis and M. abscessus was observed over time in extended static culture, however the frequency of the rough morphotype was high in pellicle preparations compared to planktonic culture, suggesting a role for an aggregated microenvironment in the shift to the rough form. Differences in growth rate, biofilm formation, cell wall composition, and drug tolerance were noted among M. smegmatis and M. abscessus variants. Deletion of the global regulator lsr2 shifted the M. smegmatis intermediate morphotype to a smooth form but did not fully phenocopy the naturally generated smooth morphotype, indicating Lsr2 is likely downstream of the initiating regulatory cascade that controls these morphotypes. Rough forms typically correlate with higher invasiveness and worse outcomes during infection and our findings indicate the shift to this rough form is promoted by aggregation. Our findings suggest that mycobacterial population heterogeneity, reflected in colony morphotypes, is a reproducible, programmed phenomenon that plays a role in adaptation to unique environments and this heterogeneity may influence infection progression and response to treatment.
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Affiliation(s)
- Sarah E. M. Born
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Matthew J. Reichlen
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Iona L. Bartek
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Jeanne B. Benoit
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Daniel N. Frank
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Martin I. Voskuil
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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12
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Nelson SJ, Williams JT, Buglino JA, Nambi S, Lojek LJ, Glickman MS, Ioerger TR, Sassetti CM. The Rip1 intramembrane protease contributes to iron and zinc homeostasis in Mycobacterium tuberculosis. mSphere 2023; 8:e0038922. [PMID: 37318217 PMCID: PMC10449499 DOI: 10.1128/msphere.00389-22] [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: 08/11/2022] [Accepted: 04/28/2023] [Indexed: 06/16/2023] Open
Abstract
Mycobacterium tuberculosis is exposed to a variety of stresses during a chronic infection, as the immune system simultaneously produces bactericidal compounds and starves the pathogen of essential nutrients. The intramembrane protease, Rip1, plays an important role in the adaptation to these stresses, at least partially by the cleavage of membrane-bound transcriptional regulators. Although Rip1 is known to be critical for surviving copper intoxication and nitric oxide exposure, these stresses do not fully account for the regulatory protein's essentiality during infection. In this work, we demonstrate that Rip1 is also necessary for growth in low-iron and low-zinc conditions, similar to those imposed by the immune system. Using a newly generated library of sigma factor mutants, we show that the known regulatory target of Rip1, SigL, shares this defect. Transcriptional profiling under iron-limiting conditions supported the coordinated activity of Rip1 and SigL and demonstrated that the loss of these proteins produces an exaggerated iron starvation response. These observations demonstrate that Rip1 coordinates several aspects of metal homeostasis and suggest that a Rip1- and SigL-dependent pathway is necessary to thrive in the iron-deficient environments encountered during infection. IMPORTANCE Metal homeostasis represents a critical point of interaction between the mammalian immune system and potential pathogens. While the host attempts to intoxicate microbes with high concentrations of copper or starve the invader of iron and zinc, successful pathogens have acquired mechanisms to overcome these defenses. Our work identifies a regulatory pathway consisting of the Rip1 intramembrane protease and the sigma factor, SigL, that is essential for the important human pathogen, Mycobacterium tuberculosis, to grow in low-iron or low-zinc conditions such as those encountered during infection. In conjunction with Rip1's known role in resisting copper toxicity, our work implicates this protein as a critical integration point that coordinates the multiple metal homeostatic systems required for this pathogen to survive in host tissue.
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Affiliation(s)
- Samantha J. Nelson
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - John T. Williams
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - John A. Buglino
- Immunology Program, Sloan Kettering Institute, New York City, New York, USA
| | - Subhalaxmi Nambi
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Lisa J. Lojek
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | | | - Thomas R. Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, Texas, USA
| | - Christopher M. Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
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13
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Rashid FZM, Dame RT. Three-dimensional chromosome re-modelling: The integral mechanism of transcription regulation in bacteria. Mol Microbiol 2023; 120:60-70. [PMID: 37433047 DOI: 10.1111/mmi.15062] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 07/13/2023]
Abstract
Nucleoid-associated proteins (NAPs) are architectural proteins of the bacterial chromosome and transcription factors that dynamically organise the chromosome and regulate gene expression in response to physicochemical environmental signals. While the architectural and regulatory functions of NAPs have been verified independently, the coupling between these functions in vivo has not been conclusively proven. Here we describe a model NAP - histone-like nucleoid structuring protein (H-NS) - as a coupled sensor-effector that directly regulates gene expression by chromatin re-modelling in response to physicochemical environmental signals. We outline how H-NS-binding partners and post-translational modifications modulate the role of H-NS as a transcription factor by influencing its DNA structuring properties. We consolidate our ideas in models of how H-NS may regulate the expression of the proVWX and hlyCABD operons by chromatin re-modelling. The interplay between chromosome structure and gene expression may be a common - but, at present, under-appreciated - concept of transcription regulation in bacteria.
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Affiliation(s)
- Fatema-Zahra M Rashid
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands
| | - Remus T Dame
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands
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14
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Dulberger CL, Guerrero-Bustamante CA, Owen SV, Wilson S, Wuo MG, Garlena RA, Serpa LA, Russell DA, Zhu J, Braunecker BJ, Squyres GR, Baym M, Kiessling LL, Garner EC, Rubin EJ, Hatfull GF. Mycobacterial nucleoid-associated protein Lsr2 is required for productive mycobacteriophage infection. Nat Microbiol 2023; 8:695-710. [PMID: 36823286 PMCID: PMC10066036 DOI: 10.1038/s41564-023-01333-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/23/2023] [Indexed: 02/25/2023]
Abstract
Mycobacteriophages are a diverse group of viruses infecting Mycobacterium with substantial therapeutic potential. However, as this potential becomes realized, the molecular details of phage infection and mechanisms of resistance remain ill-defined. Here we use live-cell fluorescence microscopy to visualize the spatiotemporal dynamics of mycobacteriophage infection in single cells and populations, showing that infection is dependent on the host nucleoid-associated Lsr2 protein. Mycobacteriophages preferentially adsorb at Mycobacterium smegmatis sites of new cell wall synthesis and following DNA injection, Lsr2 reorganizes away from host replication foci to establish zones of phage DNA replication (ZOPR). Cells lacking Lsr2 proceed through to cell lysis when infected but fail to generate consecutive phage bursts that trigger epidemic spread of phage particles to neighbouring cells. Many mycobacteriophages code for their own Lsr2-related proteins, and although their roles are unknown, they do not rescue the loss of host Lsr2.
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Affiliation(s)
- Charles L Dulberger
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | | | - Siân V Owen
- Department of Biomedical Informatics and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Sean Wilson
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Michael G Wuo
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rebecca A Garlena
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lexi A Serpa
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel A Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Junhao Zhu
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Ben J Braunecker
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Georgia R Squyres
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Michael Baym
- Department of Biomedical Informatics and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Laura L Kiessling
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ethan C Garner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Eric J Rubin
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
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15
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Erkelens AM, Qin L, van Erp B, Miguel-Arribas A, Abia D, Keek HGJ, Markus D, Cajili MKM, Schwab S, Meijer WJJ, Dame R. The B. subtilis Rok protein is an atypical H-NS-like protein irresponsive to physico-chemical cues. Nucleic Acids Res 2022; 50:12166-12185. [PMID: 36408910 PMCID: PMC9757077 DOI: 10.1093/nar/gkac1064] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 10/20/2022] [Accepted: 10/26/2022] [Indexed: 11/22/2022] Open
Abstract
Nucleoid-associated proteins (NAPs) play a central role in chromosome organization and environment-responsive transcription regulation. The Bacillus subtilis-encoded NAP Rok binds preferentially AT-rich regions of the genome, which often contain genes of foreign origin that are silenced by Rok binding. Additionally, Rok plays a role in chromosome architecture by binding in genomic clusters and promoting chromosomal loop formation. Based on this, Rok was proposed to be a functional homolog of E. coli H-NS. However, it is largely unclear how Rok binds DNA, how it represses transcription and whether Rok mediates environment-responsive gene regulation. Here, we investigated Rok's DNA binding properties and the effects of physico-chemical conditions thereon. We demonstrate that Rok is a DNA bridging protein similar to prototypical H-NS-like proteins. However, unlike these proteins, the DNA bridging ability of Rok is not affected by changes in physico-chemical conditions. The DNA binding properties of the Rok interaction partner sRok are affected by salt concentration. This suggests that in a minority of Bacillus strains Rok activity can be modulated by sRok, and thus respond indirectly to environmental stimuli. Despite several functional similarities, the absence of a direct response to physico-chemical changes establishes Rok as disparate member of the H-NS family.
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Affiliation(s)
| | | | - Bert van Erp
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands,Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands,Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands
| | - Andrés Miguel-Arribas
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - David Abia
- Bioinformatics Facility, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
| | - Helena G J Keek
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands
| | - Dorijn Markus
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands
| | - Marc K M Cajili
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands,Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands,Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands
| | - Samuel Schwab
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands,Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands,Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands
| | - Wilfried J J Meijer
- Correspondence may also be addressed to Wilfried J.J. Meijer. Tel: +34 91 196 4539;
| | - Remus T Dame
- To whom correspondence should be addressed. Tel: +31 71 527 5605;
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16
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Boopathi S, Ramasamy S, Haridevamuthu B, Murugan R, Veerabadhran M, Jia AQ, Arockiaraj J. Intercellular communication and social behaviors in mycobacteria. Front Microbiol 2022; 13:943278. [PMID: 36177463 PMCID: PMC9514802 DOI: 10.3389/fmicb.2022.943278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Cell-to-cell communication is a fundamental process of bacteria to exert communal behaviors. Sputum samples of patients with cystic fibrosis have often been observed with extensive mycobacterial genetic diversity. The emergence of heterogenic mycobacterial populations is observed due to subtle changes in their morphology, gene expression level, and distributive conjugal transfer (DCT). Since each subgroup of mycobacteria has different hetero-resistance, they are refractory against several antibiotics. Such genetically diverse mycobacteria have to communicate with each other to subvert the host immune system. However, it is still a mystery how such heterogeneous strains exhibit synchronous behaviors for the production of quorum sensing (QS) traits, such as biofilms, siderophores, and virulence proteins. Mycobacteria are characterized by division of labor, where distinct sub-clonal populations contribute to the production of QS traits while exchanging complimentary products at the community level. Thus, active mycobacterial cells ensure the persistence of other heterogenic clonal populations through cooperative behaviors. Additionally, mycobacteria are likely to establish communication with neighboring cells in a contact-independent manner through QS signals. Hence, this review is intended to discuss our current knowledge of mycobacterial communication. Understanding mycobacterial communication could provide a promising opportunity to develop drugs to target key pathways of mycobacteria.
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Affiliation(s)
- Seenivasan Boopathi
- Key Laboratory of Tropical Biological Resources of Ministry Education, School of Pharmaceutical Sciences, Hainan University, Haikou, China
- Department of Biotechnology, College of Science and Humanities, SRM Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Subbiah Ramasamy
- Department of Biochemistry, Cardiac Metabolic Disease Laboratory, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - B. Haridevamuthu
- Department of Biotechnology, College of Science and Humanities, SRM Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Raghul Murugan
- Department of Biotechnology, College of Science and Humanities, SRM Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Maruthanayagam Veerabadhran
- Biofouling and Biofilm Processes Section, Water and Steam Chemistry Division, Bhabha Atomic Research Centre Facilities, Kalpakkam, Tamil Nadu, India
| | - Ai-Qun Jia
- Key Laboratory of Tropical Biological Resources of Ministry Education, School of Pharmaceutical Sciences, Hainan University, Haikou, China
- *Correspondence: Ai-Qun Jia
| | - Jesu Arockiaraj
- Department of Biotechnology, College of Science and Humanities, SRM Institute of Science and Technology, Chennai, Tamil Nadu, India
- Jesu Arockiaraj ;
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17
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Kapoor I, Shaw A, Naha A, Emam EAF, Varshney U. Role of the nucleotide excision repair pathway proteins (UvrB and UvrD2) in recycling UdgB, a base excision repair enzyme in Mycobacterium smegmatis. DNA Repair (Amst) 2022; 113:103316. [PMID: 35306347 DOI: 10.1016/j.dnarep.2022.103316] [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: 10/19/2021] [Revised: 01/30/2022] [Accepted: 03/02/2022] [Indexed: 11/24/2022]
Abstract
Cross-talks between DNA repair pathways are emerging as a crucial strategy in the maintenance of the genomic integrity. A double-stranded (ds) DNA specific DNA glycosylase, UdgB is known to excise uracil, hypoxanthine and ethenocytosine. We earlier showed that Mycobacterium smegmatis (Msm) UdgB stays back on the AP-sites it generates in the DNA upon excision of the damaged bases. Here, we show that in an Msm strain deleted for a nucleotide excision repair (NER) protein, UvrB (uvrB-), UdgB expression is toxic, and its deletion from the genome (udgB-) rescues the strain from the genotoxic stress. However, UdgB bound AP-site is not a direct substrate for NER in vitro. We show that UvrD2 and UvrB, known helicases with single-stranded (ss) DNA translocase activity, facilitate recycling of UdgB from AP-DNA. Our studies reveal that the helicases play an important role in exposing the AP-sites in DNA and make them available for further repair.
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Affiliation(s)
- Indu Kapoor
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Abhirup Shaw
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Arindam Naha
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Elhassan Ali Fathi Emam
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India.
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18
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Mycobacterium tuberculosis Transcription Factor EmbR Regulates the Expression of Key Virulence Factors That Aid in Ex Vivo and In Vivo Survival. mBio 2022; 13:e0383621. [PMID: 35471080 PMCID: PMC9239209 DOI: 10.1128/mbio.03836-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium tuberculosis encodes ~200 transcription factors that modulate gene expression under different microenvironments in the host. Even though high-throughput chromatin immunoprecipitation sequencing and transcriptome sequencing (RNA-seq) studies have identified the regulatory network for ~80% of transcription factors, many transcription factors remain uncharacterized. EmbR is one such transcription factor whose in vivo regulon and biological function are yet to be elucidated. Previous in vitro studies suggested that phosphorylation of EmbR by PknH upregulates the embCAB operon. Using a gene replacement mutant of embR, we investigated its role in modulating cellular morphology, antibiotic resistance, and survival in the host. Contrary to the prevailing hypothesis, under normal growth conditions, EmbR is neither phosphorylated nor impacted by ethambutol resistance through the regulation of the embCAB operon. The embR deletion mutant displayed attenuated M. tuberculosis survival in vivo. RNA-seq analysis suggested that EmbR regulates operons involved in the secretion pathway, lipid metabolism, virulence, and hypoxia, including well-known hypoxia-inducible genes devS and hspX. Lipidome analysis revealed that EmbR modulates levels of all lysophospholipids, several phospholipids, and M. tuberculosis-specific lipids, which is more pronounced under hypoxic conditions. We found that the EmbR mutant is hypersusceptible to hypoxic stress, and RNA sequencing performed under hypoxic conditions indicated that EmbR majorly regulates genes involved in response to acidic pH, hypoxia, and fatty acid metabolism. We observed condition-specific phosphorylation of EmbR, which contributes to EmbR-mediated transcription of several essential genes, ensuring enhanced survival. Collectively, the study establishes EmbR as a key modulator of hypoxic response that facilitates mycobacterial survival in the host.
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19
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Lata S, Mahatha AC, Mal S, Gupta UD, Kundu M, Basu J. Unravelling novel roles of the Mycobacterium tuberculosis transcription factor Rv0081 in regulation of the nucleoid-associated proteins Lsr2 and EspR, cholesterol utilization and subversion of lysosomal trafficking in macrophages. Mol Microbiol 2022; 117:1104-1120. [PMID: 35304930 DOI: 10.1111/mmi.14895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 11/30/2022]
Abstract
The transcriptional network of Mycobacterium tuberculosis is designed to enable the organism to withstand host-associated stresses and to exploit the host milieu for its own survival and multiplication. Rv0081 (MT0088) is a transcriptional regulator whose interplay with other gene regulatory proteins and role in enabling M. tuberculosis to thrive within its host is incompletely understood. M. tuberculosis utilizes cholesterol within the granuloma. We show that deletion of Rv0081 compromises the ability of M. tuberculosis to utilize cholesterol as sole carbon source, to subvert lysosomal trafficking, and to form granulomas in vitro. Rv0081 downregulates expression of the nucleoid associated repressor Lsr2, leading to increased expression of the cholesterol catabolism-linked gene kshA and genes of the cholesterol importing operon, accounting for the requirement of Rv0081 in cholesterol utilization. Further, Rv0081 activates EspR which is required for secretion of ESX-1 substrates, which in turn are involved in subversion of lysosomal traffickingof M. tuberculosisand granuloma expansion. These results provide new insight into the role of Rv0081 under conditions which resemble the environment encountered by M. tuberculosis within its host. Rv0081 emergesas a central regulator of genes linked to various pathways which are crucial for the survival of the bacterium in vivo.
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Affiliation(s)
- Suruchi Lata
- Department of Chemistry, Bose Institute, 93/1 Acharya Prafulla Chandra Road, Kolkata, 700009, India
| | - Amar Chandra Mahatha
- Department of Chemistry, Bose Institute, 93/1 Acharya Prafulla Chandra Road, Kolkata, 700009, India
| | - Soumya Mal
- Department of Chemistry, Bose Institute, 93/1 Acharya Prafulla Chandra Road, Kolkata, 700009, India
| | - Umesh D Gupta
- National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra 282004, India
| | - Manikuntala Kundu
- Department of Chemistry, Bose Institute, 93/1 Acharya Prafulla Chandra Road, Kolkata, 700009, India
| | - Joyoti Basu
- Department of Chemistry, Bose Institute, 93/1 Acharya Prafulla Chandra Road, Kolkata, 700009, India
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20
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Li Q, Peng Z, Fu X, Wang H, Zhao Z, Pang Y, Chen L. Rv3737 is required for Mycobacterium tuberculosis growth in vitro and in vivo and correlates with bacterial load and disease severity in human tuberculosis. BMC Infect Dis 2022; 22:256. [PMID: 35287590 PMCID: PMC8919692 DOI: 10.1186/s12879-021-06967-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 12/07/2021] [Indexed: 11/13/2022] Open
Abstract
Background Rv3737 is the sole homologue of multifunctional transporter ThrE in Mycobacterium tuberculosis (Mtb). In this study, we aimed to investigate whether this transporter participates in vitro and in vivo survival of Mtb. Methods To characterize the role of Rv3737, we constructed and characterized a Mtb H37RvΔRv3737. This strain was evaluated for altered growth rate and macrophage survival using a cell model of infection. In addition, the comparative analysis was conducted to determine the association between Rv3737 mRNA expression and disease severity in active pulmonary TB patients. Results The H37RvΔRv3737 strain exhibited significantly slow growth rate compared to H37Rv-WT strain in standard culture medium. Additionally, the survival rate of H37Rv-WT strain in macrophages was 2 folds higher than that of H37RvΔRv3737 at 72 h. A significantly higher level of TNF-α and IL-6 mRNA expression was observed in macrophages infected with H37RvΔRv3737 as compared to H37Rv-WT. Of note, Rv3737 expression was significantly increased in clinical Mtb isolates than H37Rv-WT. The relative expression level of Rv3737 was positively correlated with lung cavity number of TB patients. Similarly, the higher Rv3737 mRNA level resulted in lower C(t) value by Xpert MTB/RIF assay, demonstrating that a positive correlation between Rv3737 expression and bacterial load in TB patients. Conclusions Our data takes the lead in demonstrate that the threonine transporter Rv3737 is required for in vitro growth and survival of bacteria inside macrophages. In addition, the expression level of Rv3737 may be associated with bacterial load and disease severity in pulmonary tuberculosis patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-06967-y.
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Affiliation(s)
- Qing Li
- Tuberculosis Division of Respiratory and Critical Care Medicine, Affiliated Hospital of Zunyi Medical University, No. 149, Dalian Road, Huichuan District, Zunyi City, 563000, Guizhou Province, China.,Department of Bacteriology and Immunology, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Area 2, Yard 9, Beiguan Street, Yongzhun Town, Tongzhou District, Beijing, 101100, China
| | - Zhangli Peng
- Tuberculosis Division of Respiratory and Critical Care Medicine, Affiliated Hospital of Zunyi Medical University, No. 149, Dalian Road, Huichuan District, Zunyi City, 563000, Guizhou Province, China
| | - Xuefeng Fu
- Tuberculosis Division of Respiratory and Critical Care Medicine, Affiliated Hospital of Zunyi Medical University, No. 149, Dalian Road, Huichuan District, Zunyi City, 563000, Guizhou Province, China
| | - Hong Wang
- Tuberculosis Division of Respiratory and Critical Care Medicine, Affiliated Hospital of Zunyi Medical University, No. 149, Dalian Road, Huichuan District, Zunyi City, 563000, Guizhou Province, China
| | - Zhaoliang Zhao
- Tuberculosis Division of Respiratory and Critical Care Medicine, Affiliated Hospital of Zunyi Medical University, No. 149, Dalian Road, Huichuan District, Zunyi City, 563000, Guizhou Province, China
| | - Yu Pang
- Department of Bacteriology and Immunology, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Area 2, Yard 9, Beiguan Street, Yongzhun Town, Tongzhou District, Beijing, 101100, China.
| | - Ling Chen
- Tuberculosis Division of Respiratory and Critical Care Medicine, Affiliated Hospital of Zunyi Medical University, No. 149, Dalian Road, Huichuan District, Zunyi City, 563000, Guizhou Province, China.
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21
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Ferrell KC, Johansen MD, Triccas JA, Counoupas C. Virulence Mechanisms of Mycobacterium abscessus: Current Knowledge and Implications for Vaccine Design. Front Microbiol 2022; 13:842017. [PMID: 35308378 PMCID: PMC8928063 DOI: 10.3389/fmicb.2022.842017] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 02/08/2022] [Indexed: 12/22/2022] Open
Abstract
Mycobacterium abscessus is a member of the non-tuberculous mycobacteria (NTM) group, responsible for chronic infections in individuals with cystic fibrosis (CF) or those otherwise immunocompromised. While viewed traditionally as an opportunistic pathogen, increasing research into M. abscessus in recent years has highlighted its continued evolution into a true pathogen. This is demonstrated through an extensive collection of virulence factors (VFs) possessed by this organism which facilitate survival within the host, particularly in the harsh environment of the CF lung. These include VFs resembling those of other Mycobacteria, and non-mycobacterial VFs, both of which make a notable contribution in shaping M. abscessus interaction with the host. Mycobacterium abscessus continued acquisition of VFs is cause for concern and highlights the need for novel vaccination strategies to combat this pathogen. An effective M. abscessus vaccine must be suitably designed for target populations (i.e., individuals with CF) and incorporate current knowledge on immune correlates of protection against M. abscessus infection. Vaccination strategies must also build upon lessons learned from ongoing efforts to develop novel vaccines for other pathogens, particularly Mycobacterium tuberculosis (M. tb); decades of research into M. tb has provided insight into unconventional and innovative vaccine approaches that may be applied to M. abscessus. Continued research into M. abscessus pathogenesis will be critical for the future development of safe and effective vaccines and therapeutics to reduce global incidence of this emerging pathogen.
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Affiliation(s)
- Kia C. Ferrell
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia
- Tuberculosis Research Program, Centenary Institute, Sydney, NSW, Australia
- *Correspondence: Kia C. Ferrell,
| | - Matt D. Johansen
- Centre for Inflammation, Centenary Institute, University of Technology, Sydney, NSW, Australia
- Faculty of Science, School of Life Sciences, University of Technology, Sydney, NSW, Australia
| | - James A. Triccas
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia
- Sydney Institute for Infectious Diseases and the Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia
| | - Claudio Counoupas
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia
- Tuberculosis Research Program, Centenary Institute, Sydney, NSW, Australia
- Sydney Institute for Infectious Diseases and the Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia
- Claudio Counoupas,
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22
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Balasubramanian D, López-Pérez M, Grant TA, Ogbunugafor CB, Almagro-Moreno S. Molecular mechanisms and drivers of pathogen emergence. Trends Microbiol 2022; 30:898-911. [DOI: 10.1016/j.tim.2022.02.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 02/05/2022] [Accepted: 02/10/2022] [Indexed: 12/21/2022]
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23
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Peterson EJR, Abidi AA, Arrieta-Ortiz ML, Aguilar B, Yurkovich JT, Kaur A, Pan M, Srinivas V, Shmulevich I, Baliga NS. Intricate Genetic Programs Controlling Dormancy in Mycobacterium tuberculosis. Cell Rep 2021; 31:107577. [PMID: 32348771 PMCID: PMC7605849 DOI: 10.1016/j.celrep.2020.107577] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 12/18/2019] [Accepted: 04/06/2020] [Indexed: 11/24/2022] Open
Abstract
Mycobacterium tuberculosis (MTB) displays the remarkable ability to transition in and out of dormancy, a hallmark of the pathogen’s capacity to evade the immune system and exploit susceptible individuals. Uncovering the gene regulatory programs that underlie the phenotypic shifts in MTB during disease latency and reactivation has posed a challenge. We develop an experimental system to precisely control dissolved oxygen levels in MTB cultures in order to capture the transcriptional events that unfold as MTB transitions into and out of hypoxia-induced dormancy. Using a comprehensive genome-wide transcription factor binding map and insights from network topology analysis, we identify regulatory circuits that deterministically drive sequential transitions across six transcriptionally and functionally distinct states encompassing more than three-fifths of the MTB genome. The architecture of the genetic programs explains the transcriptional dynamics underlying synchronous entry of cells into a dormant state that is primed to infect the host upon encountering favorable conditions. Mycobacterium tuberculosis (MTB) persists within the host by counteracting disparate stressors including hypoxia. Peterson et al. report a transcriptional program that coordinates sequential state transitions to drive MTB in and out of hypoxia-induced dormancy. Among varied properties, this program encodes advanced preparedness to infect the host in favorable conditions.
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Affiliation(s)
| | - Abrar A Abidi
- Institute for Systems Biology, Seattle, WA 98109, USA
| | | | - Boris Aguilar
- Institute for Systems Biology, Seattle, WA 98109, USA
| | | | - Amardeep Kaur
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Min Pan
- Institute for Systems Biology, Seattle, WA 98109, USA
| | | | | | - Nitin S Baliga
- Institute for Systems Biology, Seattle, WA 98109, USA; Molecular and Cellular Biology Program, Departments of Microbiology and Biology, University of Washington, Seattle, WA; Lawrence Berkeley National Laboratories, Berkeley, CA.
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24
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Lsr2 and Its Novel Paralogue Mediate the Adjustment of Mycobacterium smegmatis to Unfavorable Environmental Conditions. mSphere 2021; 6:6/3/e00290-21. [PMID: 33980681 PMCID: PMC8125055 DOI: 10.1128/msphere.00290-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Nucleoid-associated proteins (NAPs) are the most abundant proteins involved in bacterial chromosome organization and global transcription regulation. The mycobacterial NAP family includes many diverse proteins; some are unique to actinobacteria, and many are crucial for survival under stress (e.g., HupB and Lsr2) and/or optimal growth conditions (e.g., mycobacterial integration host factor [mIHF]). Lsr2 is a nucleoid-associated protein (NAP) that has been found strictly in actinobacteria, including mycobacteria. It is a functional homolog of histone-like nucleoid-structuring protein (H-NS); it acts as a DNA-bridging protein that plays a role in chromosomal organization and transcriptional regulation. To date, the studies on Lsr2 have focused mainly on Mycobacterium tuberculosis. In this study, we analyze the role of Lsr2 as a transcription factor in Mycobacterium smegmatis, a saprophytic bacterium whose natural habitat (soil and water) substantially differs from those of the obligatory mycobacterial pathogens. Our chromatin immunoprecipitation-sequencing (ChIP-seq) data revealed that Lsr2 binds preferentially to AT-rich regions of the M. smegmatis chromosome. We found that Lsr2 acts mainly as a repressor, controlling gene expression either directly by binding promoter regions or indirectly through DNA loop formation and DNA coating. One of the Lsr2-repressed genes encodes polyketide synthase (MSMEG_4727), which is involved in the synthesis of lipooligosaccharides (LOSs). An M. smegmatis strain deprived of Lsr2 produces more LOSs, which is mirrored by changes in the smoothness of cells and their susceptibilities to antibiotics. Unlike M. tuberculosis, M. smegmatis additionally encodes a paralogue of Lsr2, MSMEG_1060, which is a novel member of the mycobacterial NAP family. The Lsr2 and MSMEG_1060 proteins exhibit different DNA binding specificities and chromosomal localizations. Our results suggest that these proteins help M. smegmatis cells cope with stress conditions, including hypoxia and exposure to antibiotics. Thus, the present work provides novel insight into the role of Lsr2 paralogues in the ability of a saprophytic mycobacterial species to adjust to environmental changes. IMPORTANCE Nucleoid-associated proteins (NAPs) are the most abundant proteins involved in bacterial chromosome organization and global transcription regulation. The mycobacterial NAP family includes many diverse proteins; some are unique to actinobacteria, and many are crucial for survival under stress (e.g., HupB and Lsr2) and/or optimal growth conditions (e.g., mycobacterial integration host factor [mIHF]). Here, we present a comprehensive study concerning two functional homologues of mycobacterial H-NS: Lsr2 and its paralogue from M. smegmatis, MSMEG_1060. We found that Lsr2 plays a role in transcriptional regulation, mainly by repressing gene expression via DNA loop formation and/or DNA-coating mechanisms. Intriguingly, the number of Lsr2-mediated genes was found to increase under hypoxia. Compared to Lsr2, MSMEG_1060 exhibits a different DNA binding specificity and chromosomal localization. Since tuberculosis remains a serious worldwide health problem, studies on stress response-mediating agents, such as Lsr2, may contribute to the development of novel antituberculosis drugs.
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25
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Abo-Zed A, Yassin M, Phan T. Tuberculosis of the rare azygos lobe of the right lung. Respir Med Case Rep 2021; 33:101424. [PMID: 34401270 PMCID: PMC8348907 DOI: 10.1016/j.rmcr.2021.101424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 04/09/2021] [Accepted: 05/07/2021] [Indexed: 11/23/2022] Open
Abstract
Mycobacterium tuberculosis is the etiological agent of tuberculosis in humans. Tuberculosis is not only a highly contagious infectious disease, but also one of the top causes of death globally, especially in developing countries. Tuberculosis generally affects the lungs, and tuberculosis of the azygos lobe of the lung is extremely rare. This case report presents such a unique finding. Mycobacterium tuberculosis causes tuberculosis in humans. Tuberculosis is a highly contagious infectious disease. Tuberculosis of the rare azygos lobe of the right lung is reported.
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Affiliation(s)
- Abdelrhman Abo-Zed
- Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Mohamed Yassin
- Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Tung Phan
- Division of Clinical Microbiology, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA, USA
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26
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Niño-Padilla EI, Velazquez C, Garibay-Escobar A. Mycobacterial biofilms as players in human infections: a review. BIOFOULING 2021; 37:410-432. [PMID: 34024206 DOI: 10.1080/08927014.2021.1925886] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 04/18/2021] [Accepted: 04/28/2021] [Indexed: 06/12/2023]
Abstract
The role of biofilms in pathogenicity and treatment strategies is often neglected in mycobacterial infections. In recent years, the emergence of nontuberculous mycobacterial infections has necessitated the development of novel prophylactic strategies and elucidation of the mechanisms underlying the establishment of chronic infections. More importantly, the question arises whether members of the Mycobacterium tuberculosis complex can form biofilms and contribute to latent tuberculosis and drug resistance because of the long-lasting and recalcitrant nature of its infections. This review discusses some of the molecular mechanisms by which biofilms could play a role in infection or pathological events in humans.
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Affiliation(s)
| | - Carlos Velazquez
- Departamento de Ciencias Químico Biológicas, Universidad de Sonora, Hermosillo, Sonora, México
| | - Adriana Garibay-Escobar
- Departamento de Ciencias Químico Biológicas, Universidad de Sonora, Hermosillo, Sonora, México
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27
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Szafran MJ, Jakimowicz D, Elliot MA. Compaction and control-the role of chromosome-organizing proteins in Streptomyces. FEMS Microbiol Rev 2021; 44:725-739. [PMID: 32658291 DOI: 10.1093/femsre/fuaa028] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 07/09/2020] [Indexed: 12/17/2022] Open
Abstract
Chromosomes are dynamic entities, whose organization and structure depend on the concerted activity of DNA-binding proteins and DNA-processing enzymes. In bacteria, chromosome replication, segregation, compaction and transcription are all occurring simultaneously, and to ensure that these processes are appropriately coordinated, all bacteria employ a mix of well-conserved and species-specific proteins. Unusually, Streptomyces bacteria have large, linear chromosomes and life cycle stages that include multigenomic filamentous hyphae and unigenomic spores. Moreover, their prolific secondary metabolism yields a wealth of bioactive natural products. These different life cycle stages are associated with profound changes in nucleoid structure and chromosome compaction, and require distinct repertoires of architectural-and regulatory-proteins. To date, chromosome organization is best understood during Streptomyces sporulation, when chromosome segregation and condensation are most evident, and these processes are coordinated with synchronous rounds of cell division. Advances are, however, now being made in understanding how chromosome organization is achieved in multigenomic hyphal compartments, in defining the functional and regulatory interplay between different architectural elements, and in appreciating the transcriptional control exerted by these 'structural' proteins.
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Affiliation(s)
- Marcin J Szafran
- Laboratory of Molecular Microbiology, Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland
| | - Dagmara Jakimowicz
- Laboratory of Molecular Microbiology, Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland
| | - Marie A Elliot
- Department of Biology, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, L8S 4K1, Canada
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28
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Swain SS, Sharma D, Hussain T, Pati S. Molecular mechanisms of underlying genetic factors and associated mutations for drug resistance in Mycobacterium tuberculosis. Emerg Microbes Infect 2021; 9:1651-1663. [PMID: 32573374 PMCID: PMC7473167 DOI: 10.1080/22221751.2020.1785334] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nowadays, drug-resistant tuberculosis (DR-TB) and co-infected tuberculosis (CI-TB) strains are the leading cause for the enhancement of long-term morbidity and unpredicted mortality rates from this ghoulish acid fast-bacterium infection, globally. Unfortunately, the lack of/ample lethargic towards the development of compelling anti-TB regimens with a large-scale prevalence rate is a great challenge towards control of the pandemic situation. Indeed, the recent improvement in genomic studies for early diagnosis and understanding the mechanisms of drug resistance, as well as the identification of newer drug targets is quite remarkable and promising. Mainly, identification of such genetic factors, chromosomal mutations and associated pathways gives new ray of hope in current anti-TB drug discovery. This focused review provides molecular insights into the updated drug resistance mechanisms with encoded bacilli genetic factors as a novel target and potential source of development with screened-out newer anti-TB agents towards the control of MDR-TB soon.
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Affiliation(s)
- Shasank S Swain
- Division of Microbiology and NCDs, ICMR-Regional Medical Research Centre, Bhubaneswar, India
| | - Divakar Sharma
- CRF, Mass Spectrometry Laboratory, Kusuma School of Biological Sciences (KSBS), Indian Institute of Technology-Delhi (IIT-D), Delhi, India
| | - Tahziba Hussain
- Division of Microbiology and NCDs, ICMR-Regional Medical Research Centre, Bhubaneswar, India
| | - Sanghamitra Pati
- Division of Public Health and Research, ICMR-Regional Medical Research Centre, Bhubaneswar, India
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29
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Lsr2, a nucleoid-associated protein influencing mycobacterial cell cycle. Sci Rep 2021; 11:2910. [PMID: 33536448 PMCID: PMC7858621 DOI: 10.1038/s41598-021-82295-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 01/04/2021] [Indexed: 01/30/2023] Open
Abstract
Nucleoid-associated proteins (NAPs) are responsible for maintaining highly organized and yet dynamic chromosome structure in bacteria. The genus Mycobacterium possesses a unique set of NAPs, including Lsr2, which is a DNA-bridging protein. Importantly, Lsr2 is essential for the M. tuberculosis during infection exhibiting pleiotropic activities including regulation of gene expression (mainly as a repressor). Here, we report that deletion of lsr2 gene profoundly impacts the cell morphology of M. smegmatis, which is a model organism for studying the cell biology of M. tuberculosis and other mycobacterial pathogens. Cells lacking Lsr2 are shorter, wider, and more rigid than the wild-type cells. Using time-lapse fluorescent microscopy, we showed that fluorescently tagged Lsr2 forms large and dynamic nucleoprotein complexes, and that the N-terminal oligomerization domain of Lsr2 is indispensable for the formation of nucleoprotein complexes in vivo. Moreover, lsr2 deletion exerts a significant effect on the replication time and replisome dynamics. Thus, we propose that the Lsr2 nucleoprotein complexes may contribute to maintaining the proper organization of the newly synthesized DNA and therefore influencing mycobacterial cell cycle.
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30
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Young AT, Carette X, Helmel M, Steen H, Husson RN, Quackenbush J, Platig J. Multi-omic regulatory networks capture downstream effects of kinase inhibition in Mycobacterium tuberculosis. NPJ Syst Biol Appl 2021; 7:8. [PMID: 33514755 PMCID: PMC7846781 DOI: 10.1038/s41540-020-00164-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 12/07/2020] [Indexed: 11/30/2022] Open
Abstract
The ability of Mycobacterium tuberculosis (Mtb) to adapt to diverse stresses in its host environment is crucial for pathogenesis. Two essential Mtb serine/threonine protein kinases, PknA and PknB, regulate cell growth in response to environmental stimuli, but little is known about their downstream effects. By combining RNA-Seq data, following treatment with either an inhibitor of both PknA and PknB or an inactive control, with publicly available ChIP-Seq and protein–protein interaction data for transcription factors, we show that the Mtb transcription factor (TF) regulatory network propagates the effects of kinase inhibition and leads to widespread changes in regulatory programs involved in cell wall integrity, stress response, and energy production, among others. We also observe that changes in TF regulatory activity correlate with kinase-specific phosphorylation of those TFs. In addition to characterizing the downstream regulatory effects of PknA/PknB inhibition, this demonstrates the need for regulatory network approaches that can incorporate signal-driven transcription factor modifications.
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Affiliation(s)
- Albert T Young
- School of Medicine, University of California, San Francisco, USA
| | - Xavier Carette
- Division of Infectious Diseases, Boston Children's Hospital, Boston, USA.,Harvard Medical School, Boston, USA
| | - Michaela Helmel
- Harvard Medical School, Boston, USA.,Department of Pathology, Boston Children's Hospital, Boston, USA
| | - Hanno Steen
- Division of Infectious Diseases, Boston Children's Hospital, Boston, USA.,Harvard Medical School, Boston, USA.,Department of Pathology, Boston Children's Hospital, Boston, USA
| | - Robert N Husson
- Division of Infectious Diseases, Boston Children's Hospital, Boston, USA.,Harvard Medical School, Boston, USA
| | - John Quackenbush
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, USA.,Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, USA
| | - John Platig
- Harvard Medical School, Boston, USA. .,Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, USA.
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31
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Hołówka J, Zakrzewska-Czerwińska J. Nucleoid Associated Proteins: The Small Organizers That Help to Cope With Stress. Front Microbiol 2020; 11:590. [PMID: 32373086 PMCID: PMC7177045 DOI: 10.3389/fmicb.2020.00590] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 03/18/2020] [Indexed: 12/11/2022] Open
Abstract
The bacterial chromosome must be efficiently compacted to fit inside the small and crowded cell while remaining accessible for the protein complexes involved in replication, transcription, and DNA repair. The dynamic organization of the nucleoid is a consequence of both intracellular factors (i.e., simultaneously occurring cell processes) and extracellular factors (e.g., environmental conditions, stress agents). Recent studies have revealed that the bacterial chromosome undergoes profound topological changes under stress. Among the many DNA-binding proteins that shape the bacterial chromosome structure in response to various signals, NAPs (nucleoid associated proteins) are the most abundant. These small, basic proteins bind DNA with low specificity and can influence chromosome organization under changing environmental conditions (i.e., by coating the chromosome in response to stress) or regulate the transcription of specific genes (e.g., those involved in virulence).
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Affiliation(s)
- Joanna Hołówka
- Department of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
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32
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Kriel NL, Heunis T, Sampson SL, Gey van Pittius NC, Williams MJ, Warren RM. Identifying nucleic acid-associated proteins in Mycobacterium smegmatis by mass spectrometry-based proteomics. BMC Mol Cell Biol 2020; 21:19. [PMID: 32293251 PMCID: PMC7092591 DOI: 10.1186/s12860-020-00261-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 03/09/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Transcriptional responses required to maintain cellular homeostasis or to adapt to environmental stress, is in part mediated by several nucleic-acid associated proteins. In this study, we sought to establish an affinity purification-mass spectrometry (AP-MS) approach that would enable the collective identification of nucleic acid-associated proteins in mycobacteria. We hypothesized that targeting the RNA polymerase complex through affinity purification would allow for the identification of RNA- and DNA-associated proteins that not only maintain the bacterial chromosome but also enable transcription and translation. RESULTS AP-MS analysis of the RNA polymerase β-subunit cross-linked to nucleic acids identified 275 putative nucleic acid-associated proteins in the model organism Mycobacterium smegmatis under standard culturing conditions. The AP-MS approach successfully identified proteins that are known to make up the RNA polymerase complex, as well as several other known RNA polymerase complex-associated proteins such as a DNA polymerase, sigma factors, transcriptional regulators, and helicases. Gene ontology enrichment analysis of the identified proteins revealed that this approach selected for proteins with GO terms associated with nucleic acids and cellular metabolism. Importantly, we identified several proteins of unknown function not previously known to be associated with nucleic acids. Validation of several candidate nucleic acid-associated proteins demonstrated for the first time DNA association of ectopically expressed MSMEG_1060, MSMEG_2695 and MSMEG_4306 through affinity purification. CONCLUSIONS Effective identification of nucleic acid-associated proteins, which make up the RNA polymerase complex as well as other DNA- and RNA-associated proteins, was facilitated by affinity purification of the RNA polymerase β-subunit in M. smegmatis. The successful identification of several transcriptional regulators suggest that our approach could be sensitive enough to investigate the nucleic acid-associated proteins that maintain cellular functions and mediate transcriptional and translational change in response to environmental stress.
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Affiliation(s)
- Nastassja L Kriel
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 19063, Tygerberg, Cape Town, 7505, South Africa.
| | - Tiaan Heunis
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 19063, Tygerberg, Cape Town, 7505, South Africa
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Samantha L Sampson
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 19063, Tygerberg, Cape Town, 7505, South Africa
| | - Nico C Gey van Pittius
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 19063, Tygerberg, Cape Town, 7505, South Africa
| | - Monique J Williams
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 19063, Tygerberg, Cape Town, 7505, South Africa
- Present address: Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Robin M Warren
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 19063, Tygerberg, Cape Town, 7505, South Africa
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Hade MD, Sethi D, Datta H, Singh S, Thakur N, Chhaya A, Dikshit KL. Truncated Hemoglobin O Carries an Autokinase Activity and Facilitates Adaptation of Mycobacterium tuberculosis Under Hypoxia. Antioxid Redox Signal 2020; 32:351-362. [PMID: 31218881 DOI: 10.1089/ars.2018.7708] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aims: Although the human pathogen, Mycobacterium tuberculosis (Mtb), is strictly aerobic and requires efficient supply of oxygen, it can survive long stretches of severe hypoxia. The mechanism responsible for this metabolic flexibility is unknown. We have investigated a novel mechanism by which hemoglobin O (HbO), operates and supports its host under oxygen stress. Results: We discovered that the HbO exists in a phospho-bound state in Mtb and remains associated with the cell membrane under hypoxia. Deoxy-HbO carries an autokinase activity that disrupts its dimeric assembly into monomer and facilitates its association with the cell membrane, supporting survival and adaptation of Mtb under low oxygen conditions. Consistent with these observations, deletion of the glbO gene in Mycobacterium bovis bacillus Calmette-Guerin, which is identical to the glbO gene of Mtb, attenuated its survival under hypoxia and complementation of the glbO gene of Mtb rescued this inhibition, but phosphorylation-deficient mutant did not. These results demonstrated that autokinase activity of the HbO modulates its physiological function and plays a vital role in supporting the survival of its host under hypoxia. Innovation and Conclusion: Our study demonstrates that the redox-dependent autokinase activity regulates oligomeric state and membrane association of HbO that generates a reservoir of oxygen in the proximity of respiratory membranes to sustain viability of Mtb under hypoxia. These results thus provide a novel insight into the physiological function of the HbO and demonstrate its pivotal role in supporting the survival and adaptation of Mtb under hypoxia.
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Affiliation(s)
| | - Deepti Sethi
- CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Himani Datta
- CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Sandeep Singh
- CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Naveen Thakur
- CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Ajay Chhaya
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Kanak L Dikshit
- CSIR-Institute of Microbial Technology, Chandigarh, India.,Department of Biotechnology, Panjab University, Chandigarh, India
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Horizontally Acquired Homologs of Xenogeneic Silencers: Modulators of Gene Expression Encoded by Plasmids, Phages and Genomic Islands. Genes (Basel) 2020; 11:genes11020142. [PMID: 32013150 PMCID: PMC7074111 DOI: 10.3390/genes11020142] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 01/19/2020] [Accepted: 01/20/2020] [Indexed: 02/08/2023] Open
Abstract
Acquisition of mobile elements by horizontal gene transfer can play a major role in bacterial adaptation and genome evolution by providing traits that contribute to bacterial fitness. However, gaining foreign DNA can also impose significant fitness costs to the host bacteria and can even produce detrimental effects. The efficiency of horizontal acquisition of DNA is thought to be improved by the activity of xenogeneic silencers. These molecules are a functionally related group of proteins that possess affinity for the acquired DNA. Binding of xenogeneic silencers suppresses the otherwise uncontrolled expression of genes from the newly acquired nucleic acid, facilitating their integration to the bacterial regulatory networks. Even when the genes encoding for xenogeneic silencers are part of the core genome, homologs encoded by horizontally acquired elements have also been identified and studied. In this article, we discuss the current knowledge about horizontally acquired xenogeneic silencer homologs, focusing on those encoded by genomic islands, highlighting their distribution and the major traits that allow these proteins to become part of the host regulatory networks.
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35
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Alqaseer K, Turapov O, Barthe P, Jagatia H, De Visch A, Roumestand C, Wegrzyn M, Bartek IL, Voskuil MI, O'Hare HM, Ajuh P, Bottrill AR, Witney AA, Cohen-Gonsaud M, Waddell SJ, Mukamolova GV. Protein kinase B controls Mycobacterium tuberculosis growth via phosphorylation of the transcriptional regulator Lsr2 at threonine 112. Mol Microbiol 2019; 112:1847-1862. [PMID: 31562654 PMCID: PMC6906086 DOI: 10.1111/mmi.14398] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2019] [Indexed: 01/23/2023]
Abstract
Mycobacterium tuberculosis (Mtb) is able to persist in the body through months of multi‐drug therapy. Mycobacteria possess a wide range of regulatory proteins, including the protein kinase B (PknB) which controls peptidoglycan biosynthesis during growth. Here, we observed that depletion of PknB resulted in specific transcriptional changes that are likely caused by reduced phosphorylation of the H‐NS‐like regulator Lsr2 at threonine 112. The activity of PknB towards this phosphosite was confirmed with purified proteins, and this site was required for adaptation of Mtb to hypoxic conditions, and growth on solid media. Like H‐NS, Lsr2 binds DNA in sequence‐dependent and non‐specific modes. PknB phosphorylation of Lsr2 reduced DNA binding, measured by fluorescence anisotropy and electrophoretic mobility shift assays, and our NMR structure of phosphomimetic T112D Lsr2 suggests that this may be due to increased dynamics of the DNA‐binding domain. Conversely, the phosphoablative T112A Lsr2 had increased binding to certain DNA sites in ChIP‐sequencing, and Mtb containing this variant showed transcriptional changes that correspond with the change in DNA binding. In summary, PknB controls Mtb growth and adaptations to the changing host environment by phosphorylating the global transcriptional regulator Lsr2.
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Affiliation(s)
- Kawther Alqaseer
- Leicester Tuberculosis Research Group, Department of Respiratory Sciences, University of Leicester, Leicester, LE2 9HN, UK.,Department of Basic Science, Faculty of Nursing, University of Kufa, Najaf Governorate, P.O. Box 21, Kufa, Najaf, Iraq
| | - Obolbek Turapov
- Leicester Tuberculosis Research Group, Department of Respiratory Sciences, University of Leicester, Leicester, LE2 9HN, UK
| | - Philippe Barthe
- Centre de Biochimie Structurale, CNRS, INSERM, University of Montpellier, 34090, Montpellier, France
| | - Heena Jagatia
- Wellcome Trust Brighton and Sussex Centre for Global Health Research, Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PX, UK
| | - Angélique De Visch
- Centre de Biochimie Structurale, CNRS, INSERM, University of Montpellier, 34090, Montpellier, France
| | - Christian Roumestand
- Centre de Biochimie Structurale, CNRS, INSERM, University of Montpellier, 34090, Montpellier, France
| | - Malgorzata Wegrzyn
- Core Biotechnology Services, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Iona L Bartek
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Martin I Voskuil
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Helen M O'Hare
- Leicester Tuberculosis Research Group, Department of Respiratory Sciences, University of Leicester, Leicester, LE2 9HN, UK.,LISCB, Department of Molecular and Cell Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Paul Ajuh
- Gemini Biosciences Ltd, Liverpool Science Park, Liverpool, L7 8TX, UK
| | - Andrew R Bottrill
- Protein Nucleic Acid Laboratory, University of Leicester, Leicester, LE1 7RH, UK
| | - Adam A Witney
- Institute for Infection and Immunity, St George's University of London, London, SW17 0RE, UK
| | - Martin Cohen-Gonsaud
- Centre de Biochimie Structurale, CNRS, INSERM, University of Montpellier, 34090, Montpellier, France
| | - Simon J Waddell
- Wellcome Trust Brighton and Sussex Centre for Global Health Research, Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PX, UK
| | - Galina V Mukamolova
- Leicester Tuberculosis Research Group, Department of Respiratory Sciences, University of Leicester, Leicester, LE2 9HN, UK
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Gordhan BG, Peters J, Kana BD. Application of model systems to study adaptive responses of Mycobacterium tuberculosis during infection and disease. ADVANCES IN APPLIED MICROBIOLOGY 2019; 108:115-161. [PMID: 31495404 DOI: 10.1016/bs.aambs.2019.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Tuberculosis (TB) claims more human lives than any other infectious organism. The lethal synergy between TB-HIV infection and the rapid emergence of drug resistant strains has created a global public health threat that requires urgent attention. Mycobacterium tuberculosis, the causative agent of TB is an exquisitely well-adapted human pathogen, displaying the ability to promptly remodel metabolism when encountering stressful environments during pathogenesis. A careful study of the mechanisms that enable this adaptation will enhance the understanding of key aspects related to the microbiology of TB disease. However, these efforts require microbiological model systems that mimic host conditions in the laboratory. Herein, we describe several in vitro model systems that generate non-replicating and differentially culturable mycobacteria. The changes that occur in the metabolism of M. tuberculosis in some of these models and how these relate to those reported for human TB disease are discussed. We describe mechanisms that tubercle bacteria use to resuscitate from these non-replicating conditions, together with phenotypic heterogeneity in terms of culturabiliy of M. tuberculosis in sputum. Transcriptional changes in M. tuberculosis that allow for adaptation of the organism to the lung environment are also summarized. Finally, given the emerging importance of the microbiome in various infectious diseases, we provide a description of how the lung and gut microbiome affect susceptibility to TB infection and response to treatment. Consideration of these collective aspects will enhance the understanding of basic metabolism, physiology, drug tolerance and persistence in M. tuberculosis to enable development of new therapeutic interventions.
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Affiliation(s)
- Bhavna Gowan Gordhan
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Julian Peters
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Bavesh Davandra Kana
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa.
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Le Moigne V, Bernut A, Cortès M, Viljoen A, Dupont C, Pawlik A, Gaillard JL, Misguich F, Crémazy F, Kremer L, Herrmann JL. Lsr2 Is an Important Determinant of Intracellular Growth and Virulence in Mycobacterium abscessus. Front Microbiol 2019; 10:905. [PMID: 31114557 PMCID: PMC6503116 DOI: 10.3389/fmicb.2019.00905] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 04/09/2019] [Indexed: 12/30/2022] Open
Abstract
Mycobacterium abscessus, a pathogen responsible for severe lung infections in cystic fibrosis patients, exhibits either smooth (S) or rough (R) morphotypes. The S-to-R transition correlates with inhibition of the synthesis and/or transport of glycopeptidolipids (GPLs) and is associated with an increase of pathogenicity in animal and human hosts. Lsr2 is a small nucleoid-associated protein highly conserved in mycobacteria, including M. abscessus, and is a functional homolog of the heat-stable nucleoid-structuring protein (H-NS). It is essential in Mycobacterium tuberculosis but not in the non-pathogenic model organism Mycobacterium smegmatis. It acts as a master transcriptional regulator of multiple genes involved in virulence and immunogenicity through binding to AT-rich genomic regions. Previous transcriptomic studies, confirmed here by quantitative PCR, showed increased expression of lsr2 (MAB_0545) in R morphotypes when compared to their S counterparts, suggesting a possible role of this protein in the virulence of the R form. This was addressed by generating lsr2 knock-out mutants in both S (Δlsr2-S) and R (Δlsr2-R) variants, demonstrating that this gene is dispensable for M. abscessus growth. We show that the wild-type S variant, Δlsr2-S and Δlsr2-R strains were more sensitive to H2O2 as compared to the wild-type R variant of M. abscessus. Importantly, virulence of the Lsr2 mutants was considerably diminished in cellular models (macrophage and amoeba) as well as in infected animals (mouse and zebrafish). Collectively, these results emphasize the importance of Lsr2 in M. abscessus virulence.
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Affiliation(s)
| | - Audrey Bernut
- UMR 9004, Centre National de la Recherche Scientifique, Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, Montpellier, France
| | | | - Albertus Viljoen
- UMR 9004, Centre National de la Recherche Scientifique, Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, Montpellier, France
| | - Christian Dupont
- UMR 9004, Centre National de la Recherche Scientifique, Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, Montpellier, France
| | - Alexandre Pawlik
- Unité de Pathogénomique Mycobactérienne, Institut Pasteur, Paris, France
| | - Jean-Louis Gaillard
- 2I, UVSQ, INSERM, Université Paris-Saclay, Versailles, France.,APHP, GHU PIFO, Hôpital Raymond-Poincaré - Hôpital Ambroise-Paré, Boulogne-Billancourt, France
| | | | | | - Laurent Kremer
- UMR 9004, Centre National de la Recherche Scientifique, Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, Montpellier, France.,INSERM, Institut de Recherche en Infectiologie de Montpellier, Montpellier, France
| | - Jean-Louis Herrmann
- 2I, UVSQ, INSERM, Université Paris-Saclay, Versailles, France.,APHP, GHU PIFO, Hôpital Raymond-Poincaré - Hôpital Ambroise-Paré, Boulogne-Billancourt, France
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38
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NapA (Rv0430), a Novel Nucleoid-Associated Protein that Regulates a Virulence Operon in Mycobacterium tuberculosis in a Supercoiling-Dependent Manner. J Mol Biol 2019; 431:1576-1591. [DOI: 10.1016/j.jmb.2019.02.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 02/23/2019] [Accepted: 02/25/2019] [Indexed: 12/17/2022]
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Datta C, Jha RK, Ahmed W, Ganguly S, Ghosh S, Nagaraja V. Physical and functional interaction between nucleoid-associated proteins HU and Lsr2 of Mycobacterium tuberculosis: altered DNA binding and gene regulation. Mol Microbiol 2019; 111:981-994. [PMID: 30633392 DOI: 10.1111/mmi.14202] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/06/2019] [Indexed: 12/15/2022]
Abstract
Nucleoid-associated proteins (NAPs) in bacteria contribute to key activities such as DNA compaction, chromosome organization and regulation of gene expression. HU and Lsr2 are two principal NAPs in Mycobacterium tuberculosis (Mtb). HU is essential for Mtb survival and is one of the most abundant NAPs. It differs from other eubacterial HU proteins in having a long, flexible lysine- and arginine-rich carboxy-terminal domain. Lsr2 of Mtb is the functional analogue of the bacterial NAP commonly called H-NS. Lsr2 binds to and regulates expression of A/T-rich portions of the otherwise G/C-rich mycobacterial chromosome. Here, we demonstrate that HU and Lsr2 interact to form a complex. The interaction occurs primarily through the flexible carboxy-terminal domain of HU and the acidic amino-terminal domain of Lsr2. The resulting complex, upon binding to DNA, forms thick nucleoprotein rods, in contrast to the DNA bridging seen with Lsr2 and the DNA compaction seen with HU. Furthermore, transcription assays indicate that the HU-Lsr2 complex is a regulator of gene expression. This physical and functional interaction between two NAPs, which has not been reported previously, is likely to be important for DNA organization and gene expression in Mtb and perhaps other bacterial species.
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Affiliation(s)
- Chandreyee Datta
- Department of Microbiology and Cell Biology, Indian Institute of Science, C.V. Raman Avenue, Bangalore, 560012, India
| | - Rajiv Kumar Jha
- Department of Microbiology and Cell Biology, Indian Institute of Science, C.V. Raman Avenue, Bangalore, 560012, India
| | - Wareed Ahmed
- Department of Microbiology and Cell Biology, Indian Institute of Science, C.V. Raman Avenue, Bangalore, 560012, India
| | - Sohini Ganguly
- Department of Microbiology and Cell Biology, Indian Institute of Science, C.V. Raman Avenue, Bangalore, 560012, India
| | - Soumitra Ghosh
- Department of Microbiology and Cell Biology, Indian Institute of Science, C.V. Raman Avenue, Bangalore, 560012, India
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, C.V. Raman Avenue, Bangalore, 560012, India.,Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, 560064, India
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40
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Shur KV, Bekker OB, Zaichikova MV, Maslov DA, Akimova NI, Zakharevich NV, Chekalina MS, Danilenko VN. Genetic Aspects of Drug Resistance and Virulence in Mycobacterium tuberculosis. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418120141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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41
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Li W, Deng W, Xie J. Expression and regulatory networks of Mycobacterium tuberculosis PE/PPE family antigens. J Cell Physiol 2018; 234:7742-7751. [PMID: 30478834 DOI: 10.1002/jcp.27608] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 09/21/2018] [Indexed: 01/06/2023]
Abstract
PE/PPE family antigens are distributed mainly in pathogenic mycobacteria and serve as potential antituberculosis (TB) vaccine components. Some PE/PPE family antigens can regulate the host innate immune response, interfere with macrophage activation and phagolysosome fusion, and serve as major sources of antigenic variation. PE/PPE antigens have been associated with mycobacteria pathogenesis; pe/ppe genes are mainly found in pathogenic mycobacteria and are differentially expressed between Mtb and Mycobacterium bovis. PE/PPE proteins were essential for the growth of Mtb, and PE/PPE proteins were differentially expressed under a variety of conditions. Multiple mycobacterial-virulence-related transcription factors, sigma factors, the global transcriptional regulation factor Lsr2, MprAB, and PhoPR two-component regulatory systems, and cyclic adenine monophosphate-dependent regulators, regulate the expression of PE/PPE family antigens. Multiple-scale integrative analysis revealed the expression and regulatory networks of PE/PPE family antigens underlying the virulence and pathogenesis of Mtb, providing important clues for the discovery of new anti-TB measures.
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Affiliation(s)
- Wu Li
- Key Laboratory of Regional Characteristic Agricultural Resources, College of Life Sciences, Neijiang Normal University, Neijiang, China
| | - Wanyan Deng
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing, China
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42
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PPE11 of Mycobacterium tuberculosis can alter host inflammatory response and trigger cell death. Microb Pathog 2018; 126:45-55. [PMID: 30366125 DOI: 10.1016/j.micpath.2018.10.031] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 08/09/2018] [Accepted: 10/22/2018] [Indexed: 01/23/2023]
Abstract
Tuberculosis (TB), which is caused by Mycobacterium tuberculosis (Mtb), remains a serious global health problem. The PE/PPE family, featuring unique sequences, structures and expression in Mtb, is reported to interfere with the macrophage response to the pathogen and facilitate its infection. PPE11 (Rv0453) existed in pathogenic mycobacteria and was persistently expressed in the infected guinea pig lungs. However, the role it played in the pathogenesis remains unclear. Here, to investigate the interaction and potential mechanism of PPE11 between pathogens and hosts, we heterologously expressed PPE11 in non-pathogenic, rapidly growing Mycobacterium smegmatis strains. We found that the overexpression of the cell wall-associated protein, PPE11, can improve the viability of bacteria in the presence of lysozyme, hydrogen peroxide and acid stress. Expression of PPE11 enhanced the early survival of M. smegmatis in macrophages and sustained a higher bacterial load in mouse tissues that showed exacerbated organ pathology. Macrophages infected with recombinant M. smegmatis produced significantly greater amounts of interleukin (IL)-1β, IL-6, tumour necrosis factor (TNF)-α and an early decrease in IL-10 along with higher levels of host cell death. Similar cytokines changes were observed in the sera of infected mice. Accordingly, PPE11 protein causes histopathological changes by disrupting the dynamic balance of the inflammatory factors and promoting host-cell death, indicating a potential role in the virulence of Mtb.
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43
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Turapov O, Forti F, Kadhim B, Ghisotti D, Sassine J, Straatman-Iwanowska A, Bottrill AR, Moynihan PJ, Wallis R, Barthe P, Cohen-Gonsaud M, Ajuh P, Vollmer W, Mukamolova GV. Two Faces of CwlM, an Essential PknB Substrate, in Mycobacterium tuberculosis. Cell Rep 2018; 25:57-67.e5. [PMID: 30282038 PMCID: PMC6180346 DOI: 10.1016/j.celrep.2018.09.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 06/11/2018] [Accepted: 08/31/2018] [Indexed: 11/26/2022] Open
Abstract
Tuberculosis claims >1 million lives annually, and its causative agent Mycobacterium tuberculosis is a highly successful pathogen. Protein kinase B (PknB) is reported to be critical for mycobacterial growth. Here, we demonstrate that PknB-depleted M. tuberculosis can replicate normally and can synthesize peptidoglycan in an osmoprotective medium. Comparative phosphoproteomics of PknB-producing and PknB-depleted mycobacteria identify CwlM, an essential regulator of peptidoglycan synthesis, as a major PknB substrate. Our complementation studies of a cwlM mutant of M. tuberculosis support CwlM phosphorylation as a likely molecular basis for PknB being essential for mycobacterial growth. We demonstrate that growing mycobacteria produce two forms of CwlM: a non-phosphorylated membrane-associated form and a PknB-phosphorylated cytoplasmic form. Furthermore, we show that the partner proteins for the phosphorylated and non-phosphorylated forms of CwlM are FhaA, a fork head-associated domain protein, and MurJ, a proposed lipid II flippase, respectively. From our results, we propose a model in which CwlM potentially regulates both the biosynthesis of peptidoglycan precursors and their transport across the cytoplasmic membrane.
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Affiliation(s)
- Obolbek Turapov
- Leicester Tuberculosis Research Group, Department of Infection, Immunity and Inflammation, University of Leicester, Leicester LE1 9HN, UK
| | - Francesca Forti
- Department of Biosciences, University of Milan, Milan 20133, Italy
| | - Baleegh Kadhim
- Leicester Tuberculosis Research Group, Department of Infection, Immunity and Inflammation, University of Leicester, Leicester LE1 9HN, UK; Biology Department, College of Science, University of Al-Qadisiyah, Al-Diwaniyah 58002, Iraq
| | - Daniela Ghisotti
- Department of Biosciences, University of Milan, Milan 20133, Italy
| | - Jad Sassine
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Anna Straatman-Iwanowska
- Electron Microscopy Facility, Core Biotechnology Services, University of Leicester, Leicester LE1 7RH, UK
| | - Andrew R Bottrill
- Protein Nucleic Acid Laboratory, University of Leicester, Leicester LE1 7RH, UK
| | - Patrick J Moynihan
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Russell Wallis
- Leicester Tuberculosis Research Group, Department of Infection, Immunity and Inflammation, University of Leicester, Leicester LE1 9HN, UK; The Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 7HB, UK
| | - Philippe Barthe
- Centre de Biochimie Structurale, CNRS, INSERM, University of Montpellier, Montpellier 34090, France
| | - Martin Cohen-Gonsaud
- Centre de Biochimie Structurale, CNRS, INSERM, University of Montpellier, Montpellier 34090, France
| | - Paul Ajuh
- Gemini Biosciences, Liverpool Science Park, Liverpool L3 5TF, UK
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Galina V Mukamolova
- Leicester Tuberculosis Research Group, Department of Infection, Immunity and Inflammation, University of Leicester, Leicester LE1 9HN, UK.
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Chawla M, Mishra S, Anand K, Parikh P, Mehta M, Vij M, Verma T, Singh P, Jakkala K, Verma HN, AjitKumar P, Ganguli M, Narain Seshasayee AS, Singh A. Redox-dependent condensation of the mycobacterial nucleoid by WhiB4. Redox Biol 2018; 19:116-133. [PMID: 30149290 PMCID: PMC6111044 DOI: 10.1016/j.redox.2018.08.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/02/2018] [Accepted: 08/11/2018] [Indexed: 12/22/2022] Open
Abstract
Oxidative stress response in bacteria is mediated through coordination between the regulators of oxidant-remediation systems (e.g. OxyR, SoxR) and nucleoid condensation (e.g. Dps, Fis). However, these genetic factors are either absent or rendered non-functional in the human pathogen Mycobacterium tuberculosis (Mtb). Therefore, how Mtb organizes genome architecture and regulates gene expression to counterbalance oxidative imbalance is unknown. Here, we report that an intracellular redox-sensor, WhiB4, dynamically links genome condensation and oxidative stress response in Mtb. Disruption of WhiB4 affects the expression of genes involved in maintaining redox homeostasis, central metabolism, and respiration under oxidative stress. Notably, disulfide-linked oligomerization of WhiB4 in response to oxidative stress activates the protein’s ability to condense DNA. Further, overexpression of WhiB4 led to hypercondensation of nucleoids, redox imbalance and increased susceptibility to oxidative stress, whereas WhiB4 disruption reversed this effect. In accordance with the findings in vitro, ChIP-Seq data demonstrated non-specific binding of WhiB4 to GC-rich regions of the Mtb genome. Lastly, data indicate that WhiB4 deletion affected the expression of ~ 30% of genes preferentially bound by the protein, suggesting both direct and indirect effects on gene expression. We propose that WhiB4 structurally couples Mtb’s response to oxidative stress with genome organization and transcription. Genome condensation is involved in the management of oxidative stress in bacteria. A relation between the genome condensation and oxidative stress is unclear in Mtb. A redox sensor WhiB4 calibrates genome-condensation and antioxidants in Mtb. Over-expression of WhiB4 hyper-condensed genome and induced killing by oxidants. WhiB4 deficiency delayed genome condensation and promoted oxidative stress survival.
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Affiliation(s)
- Manbeena Chawla
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Saurabh Mishra
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Kushi Anand
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Pankti Parikh
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Mansi Mehta
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Manika Vij
- Department of Structural Biology, CSIR-Institute of Genomics and Integrative Biology, South Campus, Mathura Road, New Delhi 110020, India; Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India
| | - Taru Verma
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India; Centre for BioSystems Science and Engineering (BSSE), Indian Institute of Science, Bangalore 560012, India
| | - Parul Singh
- National Centre for Biological Science, Bangalore 560065, India; SASTRA University, Thanjavur 613401, Tamil Nadu, India
| | - Kishor Jakkala
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - H N Verma
- Jaipur National University, Jagatpura, Jaipur 302017, India
| | - Parthasarathi AjitKumar
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Munia Ganguli
- Department of Structural Biology, CSIR-Institute of Genomics and Integrative Biology, South Campus, Mathura Road, New Delhi 110020, India; Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India
| | | | - Amit Singh
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India.
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45
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Bose T, Das C, Dutta A, Mahamkali V, Sadhu S, Mande SS. Understanding the role of interactions between host and Mycobacterium tuberculosis under hypoxic condition: an in silico approach. BMC Genomics 2018; 19:555. [PMID: 30053801 PMCID: PMC6064076 DOI: 10.1186/s12864-018-4947-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 07/19/2018] [Indexed: 01/17/2023] Open
Abstract
Background Mycobacterium tuberculosis infection in humans is often associated with extended period of latency. To adapt to the hostile hypoxic environment inside a macrophage, M. tuberculosis cells undergo several physiological and metabolic changes. Previous studies have mostly focused on inspecting individual facets of this complex process. In order to gain deeper insights into the infection process and to understand the coordination among different regulatory/ metabolic pathways in the pathogen, the current in silico study investigates three aspects, namely, (i) host-pathogen interactions (HPIs) between human and M. tuberculosis proteins, (ii) gene regulatory network pertaining to adaptation of M. tuberculosis to hypoxia and (iii) alterations in M. tuberculosis metabolism under hypoxic condition. Subsequently, cross-talks between these components have been probed to evaluate possible gene-regulatory events as well as HPIs which are likely to drive metabolic changes during pathogen’s adaptation to the intra-host hypoxic environment. Results The newly identified HPIs suggest the pathogen’s ability to subvert host mediated reactive oxygen intermediates/ reactive nitrogen intermediates (ROI/ RNI) stress as well as their potential role in modulating host cell cycle and cytoskeleton structure. The results also indicate a significantly pronounced effect of HPIs on hypoxic metabolism of M. tuberculosis. Findings from the current study underscore the necessity of investigating the infection process from a systems-level perspective incorporating different facets of intra-cellular survival of the pathogen. Conclusions The comprehensive host-pathogen interaction network, a Boolean model of M. tuberculosis H37Rv (Mtb) hypoxic gene-regulation, as well as a genome scale metabolic model of Mtb, built for this study are expected to be useful resources for future studies on tuberculosis infection. Electronic supplementary material The online version of this article (10.1186/s12864-018-4947-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tungadri Bose
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Limited, Pune, India.,Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Chandrani Das
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Limited, Pune, India.,Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Anirban Dutta
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Limited, Pune, India.
| | - Vishnuvardhan Mahamkali
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Limited, Pune, India.,Present Address: Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Australia
| | - Sudipta Sadhu
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Limited, Pune, India
| | - Sharmila S Mande
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Limited, Pune, India.
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46
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Chen YE, Fischbach MA, Belkaid Y. Skin microbiota-host interactions. Nature 2018; 553:427-436. [PMID: 29364286 DOI: 10.1038/nature25177] [Citation(s) in RCA: 375] [Impact Index Per Article: 62.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 11/28/2017] [Indexed: 12/23/2022]
Abstract
The skin is a complex and dynamic ecosystem that is inhabited by bacteria, archaea, fungi and viruses. These microbes-collectively referred to as the skin microbiota-are fundamental to skin physiology and immunity. Interactions between skin microbes and the host can fall anywhere along the continuum between mutualism and pathogenicity. In this Review, we highlight how host-microbe interactions depend heavily on context, including the state of immune activation, host genetic predisposition, barrier status, microbe localization, and microbe-microbe interactions. We focus on how context shapes the complex dialogue between skin microbes and the host, and the consequences of this dialogue for health and disease.
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Affiliation(s)
- Y Erin Chen
- Department of Dermatology, University of California San Francisco, San Francisco, California, USA.,Department of Bioengineering and ChEM-H, Stanford University, Stanford, California, USA
| | - Michael A Fischbach
- Department of Bioengineering and ChEM-H, Stanford University, Stanford, California, USA
| | - Yasmine Belkaid
- NIAID Microbiome Program, National Institute of Allergy and Infectious Disease, NIH, Bethesda, Maryland, USA.,Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Disease, NIH, Bethesda, Maryland, USA
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47
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Kriel NL, Gallant J, van Wyk N, van Helden P, Sampson SL, Warren RM, Williams MJ. Mycobacterial nucleoid associated proteins: An added dimension in gene regulation. Tuberculosis (Edinb) 2018. [DOI: 10.1016/j.tube.2017.12.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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48
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Anaerobic Mycobacterium tuberculosis Cell Death Stems from Intracellular Acidification Mitigated by the DosR Regulon. J Bacteriol 2017; 199:JB.00320-17. [PMID: 28874407 DOI: 10.1128/jb.00320-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 08/23/2017] [Indexed: 01/28/2023] Open
Abstract
Mycobacterium tuberculosis is a strict aerobe capable of prolonged survival in the absence of oxygen. We investigated the ability of anaerobic M. tuberculosis to counter challenges to internal pH homeostasis in the absence of aerobic respiration, the primary mechanism of proton efflux for aerobic bacilli. Anaerobic M. tuberculosis populations were markedly impaired for survival under a mildly acidic pH relative to standard culture conditions. An acidic environmental pH greatly increased the susceptibilities of anaerobic bacilli to the collapse of the proton motive force by protonophores, to antimicrobial compounds that target entry into the electron transport system, and to small organic acids with uncoupling activity. However, anaerobic bacilli exhibited high tolerance against these challenges at a near-neutral pH. At a slightly alkaline pH, which was near the optimum intracellular pH, the addition of protonophores even improved the long-term survival of bacilli. Although anaerobic M. tuberculosis bacilli under acidic conditions maintained 40% lower ATP levels than those of bacilli under standard culture conditions, ATP loss alone could not explain the drop in viability. Protonophores decreased ATP levels by more than 90% regardless of the extracellular pH but were bactericidal only under acidic conditions, indicating that anaerobic bacilli could survive an extreme ATP loss provided that the external pH was within viable intracellular parameters. Acidic conditions drastically decreased the anaerobic survival of a DosR mutant, while an alkaline environment improved the survival of the DosR mutant. Together, these findings indicate that intracellular acidification is a primary challenge for the survival of anaerobic M. tuberculosis and that the DosR regulon plays a critical role in sustaining internal pH homeostasis.IMPORTANCE During infection, M. tuberculosis bacilli are prevalent in environments largely devoid of oxygen, yet the factors that influence the survival of these severely growth-limited and metabolically limited bacilli remain poorly understood. We determined how anaerobic bacilli respond to fluctuations in environmental pH and observed that these bacilli were highly susceptible to stresses that promoted internal acidic stress, whereas conditions that promoted an alkaline internal pH promoted long-term survival even during severe ATP depletion. The DosR regulon, a major regulator of general hypoxic stress, played an important role in maintaining internal pH homeostasis under anaerobic conditions. Together, these findings indicate that in the absence of aerobic respiration, protection from internal acidification is crucial for long-term M. tuberculosis survival.
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Ghosh S, Chatterji D. Two zinc finger proteins from Mycobacterium smegmatis: DNA binding and activation of transcription. Genes Cells 2017. [PMID: 28639742 DOI: 10.1111/gtc.12507] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Single zinc finger domain containing proteins are very few in number. Of numerous zinc finger proteins in eukaryotes, only three of them like GAGA, Superman and DNA binding by one finger (Dof) have single zinc finger domain. Although few zinc finger proteins have been described in eubacteria, no protein with single C4 zinc finger has been described in details in anyone of them. In this article, we are describing two novel C-terminal C4 zinc finger proteins-Msmeg_0118 and Msmeg_3613 from Mycobacterium smegmatis. We have named these proteins as Mszfp1 (Mycobacterial Single Zinc Finger Protein 1) and Mszfp2 (Mycobacterial Single Zinc Finger Protein 2). Both the proteins are expressed constitutively, can bind to DNA and regulate transcription. It appears that Mszfp1 and Mszfp2 may activate transcription by interacting with RNA polymerase.
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Affiliation(s)
- Subho Ghosh
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
| | - Dipankar Chatterji
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
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50
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Wang J, Guo J, Wang S, Zeng Z, Zheng D, Yao X, Yu H, Ruan L. The global strategy employed by Xanthomonas oryzae pv. oryzae to conquer low-oxygen tension. J Proteomics 2017; 161:68-77. [PMID: 28412528 DOI: 10.1016/j.jprot.2017.04.006] [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: 08/04/2016] [Revised: 03/21/2017] [Accepted: 04/09/2017] [Indexed: 10/19/2022]
Abstract
Xanthomonas oryzae pv. oryzae (Xoo) is a notorious rice pathogen that causes bacterial leaf blight (BLB), a destructive rice disease. Low-oxygen tension in the xylem vessels of rice stresses Xoo during infection. In this study, differentially expressed proteins under normoxic and hypoxic conditions were identified using high-performance liquid chromatography (HPLC) coupled with LC-MS/MS to investigate the global effects of low oxygen environment on Xoo PXO99A. A statistically validated list of 187 (normoxia) and 140 (hypoxia) proteins with functional assignments was generated, allowing the reconstruction of central metabolic pathways. Ten proteins involved in aromatic amino acid biosynthesis, glycolysis, butanoate metabolism, propanoate metabolism and biological adhesion were significantly modulated under low-oxygen tension. The genes encoded by these proteins were in-frame deleted, and three of them were determined to be required for full virulence in Xoo. The contributions of these three genes to important virulence-associated functions, including extracellular polysaccharide, cell motility and antioxidative ability, are presented. BIOLOGICAL SIGNIFICANCE To study how Xanthomonas oryzae pv. oryzae (Xoo) conquers low-oxygen tension in the xylem of rice, we identified differentially expressed proteins under normoxic and hypoxia. We found 140 proteins that uniquely expressed under the hypoxia were involved in 33 metabolism pathways. We identified 3 proteins were required for full virulence in Xoo and related to the ability of extracellular polysaccharide, cell motility, and antioxidative. This study is helpful for broadening our knowledge of the metabolism processed of Xoo in the xylem of rice.
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Affiliation(s)
- Jianliang Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jing Guo
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Shasha Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhiyong Zeng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Dehong Zheng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaoyan Yao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Haoquan Yu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lifang Ruan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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