Frequently arising ESX-1-associated phase variants influence Mycobacterium tuberculosis fitness in the presence of host and antibiotic pressures
ABSTRACT Mycobacterium tuberculosis (Mtb) exhibits an impressive ability to adapt to rapidly changing environments, despite its genome’s apparent stability. Recently, phase variation through indel formation in homopolymeric tracts (HT) has emerged as a potentially important mechanism promoting adapt...
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American Society for Microbiology
2025-03-01
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| Online Access: | https://journals.asm.org/doi/10.1128/mbio.03762-24 |
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| author | Michael J. Luna Peter O. Oluoch Jiazheng Miao Peter Culviner Kadamba Papavinasasundaram Eleni Jaecklein Scarlet S. Shell Thomas R. Ioerger Sarah M. Fortune Maha R. Farhat Christopher M. Sassetti |
| author_facet | Michael J. Luna Peter O. Oluoch Jiazheng Miao Peter Culviner Kadamba Papavinasasundaram Eleni Jaecklein Scarlet S. Shell Thomas R. Ioerger Sarah M. Fortune Maha R. Farhat Christopher M. Sassetti |
| author_sort | Michael J. Luna |
| collection | DOAJ |
| description | ABSTRACT Mycobacterium tuberculosis (Mtb) exhibits an impressive ability to adapt to rapidly changing environments, despite its genome’s apparent stability. Recently, phase variation through indel formation in homopolymeric tracts (HT) has emerged as a potentially important mechanism promoting adaptation in Mtb. This study examines the impact of common phase variants associated with the ESX-1 type VII secretion system, focusing on a highly variable HT upstream of the ESX-1 regulatory factor, espR. By engineering this frequently observed indel into an isogenic background, we demonstrate that a single nucleotide insertion in the espR 5′UTR causes post-transcriptional upregulation of EspR protein abundance and corresponding alterations in the EspR regulon. Consequently, this mutation increases the expression of ESX-1 components in the espACD operon and enhances ESX-1 substrate secretion. We find that this indel specifically increases isoniazid resistance without impacting the effectiveness of other drugs tested. Furthermore, we show that two distinct observed HT indels that regulate either espR translation or espACD transcription increase bacterial fitness in a mouse infection model. The presence of multiple ESX-1-associated HTs provides a mechanism to combinatorially tune protein secretion, drug sensitivity, and host-pathogen interactions. More broadly, these findings support emerging data that Mtb utilizes HT-mediated phase variation to direct genetic variation to certain sites across the genome in order to adapt to changing pressures.IMPORTANCEMycobacterium tuberculosis (Mtb) is responsible for more deaths worldwide than any other single infectious agent. Understanding how this pathogen adapts to the varied environmental pressures imposed by host immunity and antibiotics has important implications for the design of more effective therapies. In this work, we show that the genome of Mtb contains multiple contingency loci that control the activity of the ESX-1 secretion system, which is critical for interactions with the host. These loci consist of homopolymeric DNA tracts in gene regulatory regions that are subject to high-frequency reversible variation and act to tune the activity of ESX-1. We find that variation at these sites increases the fitness of Mtb in the presence of antibiotic and/or during infection. These findings indicate that Mtb has the ability to diversify its genome in specific sites to create subpopulations of cells that are preadapted to new conditions. |
| format | Article |
| id | doaj-art-e16237984cdc4f27af07bf07b754472e |
| institution | DOAJ |
| issn | 2150-7511 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | American Society for Microbiology |
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| series | mBio |
| spelling | doaj-art-e16237984cdc4f27af07bf07b754472e2025-08-20T02:59:06ZengAmerican Society for MicrobiologymBio2150-75112025-03-0116310.1128/mbio.03762-24Frequently arising ESX-1-associated phase variants influence Mycobacterium tuberculosis fitness in the presence of host and antibiotic pressuresMichael J. Luna0Peter O. Oluoch1Jiazheng Miao2Peter Culviner3Kadamba Papavinasasundaram4Eleni Jaecklein5Scarlet S. Shell6Thomas R. Ioerger7Sarah M. Fortune8Maha R. Farhat9Christopher M. Sassetti10Department of Microbiology, UMass Chan Medical School, Worcester, Massachusetts, USADepartment of Microbiology, UMass Chan Medical School, Worcester, Massachusetts, USADepartment of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USADepartment of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, Massachusetts, USADepartment of Microbiology, UMass Chan Medical School, Worcester, Massachusetts, USADepartment of Microbiology, UMass Chan Medical School, Worcester, Massachusetts, USADepartment of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts, USADepartment of Computer Science and Engineering, Texas A&M University, College Station, Texas, USADepartment of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, Massachusetts, USADepartment of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USADepartment of Microbiology, UMass Chan Medical School, Worcester, Massachusetts, USAABSTRACT Mycobacterium tuberculosis (Mtb) exhibits an impressive ability to adapt to rapidly changing environments, despite its genome’s apparent stability. Recently, phase variation through indel formation in homopolymeric tracts (HT) has emerged as a potentially important mechanism promoting adaptation in Mtb. This study examines the impact of common phase variants associated with the ESX-1 type VII secretion system, focusing on a highly variable HT upstream of the ESX-1 regulatory factor, espR. By engineering this frequently observed indel into an isogenic background, we demonstrate that a single nucleotide insertion in the espR 5′UTR causes post-transcriptional upregulation of EspR protein abundance and corresponding alterations in the EspR regulon. Consequently, this mutation increases the expression of ESX-1 components in the espACD operon and enhances ESX-1 substrate secretion. We find that this indel specifically increases isoniazid resistance without impacting the effectiveness of other drugs tested. Furthermore, we show that two distinct observed HT indels that regulate either espR translation or espACD transcription increase bacterial fitness in a mouse infection model. The presence of multiple ESX-1-associated HTs provides a mechanism to combinatorially tune protein secretion, drug sensitivity, and host-pathogen interactions. More broadly, these findings support emerging data that Mtb utilizes HT-mediated phase variation to direct genetic variation to certain sites across the genome in order to adapt to changing pressures.IMPORTANCEMycobacterium tuberculosis (Mtb) is responsible for more deaths worldwide than any other single infectious agent. Understanding how this pathogen adapts to the varied environmental pressures imposed by host immunity and antibiotics has important implications for the design of more effective therapies. In this work, we show that the genome of Mtb contains multiple contingency loci that control the activity of the ESX-1 secretion system, which is critical for interactions with the host. These loci consist of homopolymeric DNA tracts in gene regulatory regions that are subject to high-frequency reversible variation and act to tune the activity of ESX-1. We find that variation at these sites increases the fitness of Mtb in the presence of antibiotic and/or during infection. These findings indicate that Mtb has the ability to diversify its genome in specific sites to create subpopulations of cells that are preadapted to new conditions.https://journals.asm.org/doi/10.1128/mbio.03762-24tuberculosisbacterial geneticsphase variation |
| spellingShingle | Michael J. Luna Peter O. Oluoch Jiazheng Miao Peter Culviner Kadamba Papavinasasundaram Eleni Jaecklein Scarlet S. Shell Thomas R. Ioerger Sarah M. Fortune Maha R. Farhat Christopher M. Sassetti Frequently arising ESX-1-associated phase variants influence Mycobacterium tuberculosis fitness in the presence of host and antibiotic pressures mBio tuberculosis bacterial genetics phase variation |
| title | Frequently arising ESX-1-associated phase variants influence Mycobacterium tuberculosis fitness in the presence of host and antibiotic pressures |
| title_full | Frequently arising ESX-1-associated phase variants influence Mycobacterium tuberculosis fitness in the presence of host and antibiotic pressures |
| title_fullStr | Frequently arising ESX-1-associated phase variants influence Mycobacterium tuberculosis fitness in the presence of host and antibiotic pressures |
| title_full_unstemmed | Frequently arising ESX-1-associated phase variants influence Mycobacterium tuberculosis fitness in the presence of host and antibiotic pressures |
| title_short | Frequently arising ESX-1-associated phase variants influence Mycobacterium tuberculosis fitness in the presence of host and antibiotic pressures |
| title_sort | frequently arising esx 1 associated phase variants influence mycobacterium tuberculosis fitness in the presence of host and antibiotic pressures |
| topic | tuberculosis bacterial genetics phase variation |
| url | https://journals.asm.org/doi/10.1128/mbio.03762-24 |
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