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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Juárez-Cepeda J, Valenzuela O, Garibay-Valdez E, Velazquez C, Garibay-Escobar A. Gene expression during the development of Mycobacterium smegmatis biofilms on hydroxyapatite surfaces. Int Microbiol 2024; 27:257-263. [PMID: 37311924 DOI: 10.1007/s10123-023-00385-7] [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: 03/15/2023] [Revised: 05/19/2023] [Accepted: 05/31/2023] [Indexed: 06/15/2023]
Abstract
Bacterial biofilms are a consortium of bacteria that are strongly bound to each other and the surface on which they developed irreversibly. Bacteria can survive adverse environmental conditions and undergo changes when transitioning from a planktonic form to community cells. The process of mycobacteria adhesion is complex, involving characteristics and properties of bacteria, surfaces, and environmental factors; therefore, the formation of different biofilms is possible. Cell wall-, lipid-, and lipid transporter-related genes (glycopeptidolipids, GroEL1, protein kinase) are important in mycobacterial biofilm development. We investigated gene expression during in vitro development of Mycobacterium smegmatis biofilms on a hydroxyapatite (HAP) surface. Biofilm formation by M. smegmatis cells was induced for 1, 2, 3, and 5 days on the HAP surface. Mycobacteria on polystyrene generated an air-liquid interface biofilm, and on the fifth day, it increased by 35% in the presence of HAP. Six genes with key roles in biofilm formation were analyzed by real-time RT‒qPCR during the biofilm formation of M. smegmatis on both abiotic surfaces. The expression of groEL1, lsr2, mmpL11, mps, pknF, and rpoZ genes during biofilm formation on the HAP surface did not exhibit significant changes compared to the polystyrene surface. These genes involved in biofilm formation are not affected by HAP.
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Affiliation(s)
- Jacqueline Juárez-Cepeda
- Departmento de Ciencias Químico Biológicas, Universidad de Sonora, Rosales y Luis Encinas S/N, 83000, Hermosillo, Sonora, México
| | - Olivia Valenzuela
- Departmento de Ciencias Químico Biológicas, Universidad de Sonora, Rosales y Luis Encinas S/N, 83000, Hermosillo, Sonora, México
| | - Estefanía Garibay-Valdez
- Centro de Investigación en Alimentación y Desarrollo, A. C. Km 0.6 Carretera a La Victoria, Hermosillo, Sonora, México
| | - Carlos Velazquez
- Departmento de Ciencias Químico Biológicas, Universidad de Sonora, Rosales y Luis Encinas S/N, 83000, Hermosillo, Sonora, México
| | - Adriana Garibay-Escobar
- Departmento de Ciencias Químico Biológicas, Universidad de Sonora, Rosales y Luis Encinas S/N, 83000, Hermosillo, Sonora, México.
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8
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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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9
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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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10
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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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11
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Grigorov AS, Skvortsova YV, Bychenko OS, Aseev LV, Koledinskaya LS, Boni IV, Azhikina TL. Dynamic Transcriptional Landscape of Mycobacterium smegmatis under Cold Stress. Int J Mol Sci 2023; 24:12706. [PMID: 37628885 PMCID: PMC10454040 DOI: 10.3390/ijms241612706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Bacterial adaptation to cold stress requires wide transcriptional reprogramming. However, the knowledge of molecular mechanisms underlying the cold stress response of mycobacteria is limited. We conducted comparative transcriptomic analysis of Mycobacterium smegmatis subjected to cold shock. The growth of M. smegmatis cultivated at 37 °C was arrested just after exposure to cold (acclimation phase) but later (by 24 h) was resumed at a much slower rate (adaptation phase). Transcriptomic analyses revealed distinct gene expression patterns corresponding to the two phases. During the acclimation phase, differential expression was observed for genes associated with cell wall remodeling, starvation response, and osmotic pressure stress, in parallel with global changes in the expression of transcription factors and the downregulation of ribosomal genes, suggesting an energy-saving strategy to support survival. At the adaptation phase, the expression profiles were recovered, indicating restoration of the processes repressed earlier. Comparison of transcriptional responses in M. smegmatis with those in other bacteria revealed unique adaptation strategies developed by mycobacteria. Our findings shed light on the molecular mechanisms underlying M. smegmatis survival under cold stress. Further research should clarify whether the discovered transcriptional mechanisms exist in other mycobacterial species, including pathogenic Mycobacterium tuberculosis, which could be important for transmission control.
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Affiliation(s)
- Artem S. Grigorov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | | | | | | | | | | | - Tatyana L. Azhikina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
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12
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Hołówka J, Łebkowski T, Feddersen H, Giacomelli G, Drużka K, Makowski Ł, Trojanowski D, Broda N, Bramkamp M, Zakrzewska-Czerwińska J. Mycobacterial IHF is a highly dynamic nucleoid-associated protein that assists HupB in organizing chromatin. Front Microbiol 2023; 14:1146406. [PMID: 36960278 PMCID: PMC10028186 DOI: 10.3389/fmicb.2023.1146406] [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: 01/17/2023] [Accepted: 02/20/2023] [Indexed: 03/09/2023] Open
Abstract
Nucleoid-associated proteins (NAPs) crucially contribute to organizing bacterial chromatin and regulating gene expression. Among the most highly expressed NAPs are the HU and integration host factor (IHF) proteins, whose functional homologues, HupB and mycobacterial integration host factor (mIHF), are found in mycobacteria. Despite their importance for the pathogenicity and/or survival of tubercle bacilli, the role of these proteins in mycobacterial chromosome organization remains unknown. Here, we used various approaches, including super-resolution microscopy, to perform a comprehensive analysis of the roles of HupB and mIHF in chromosome organization. We report that HupB is a structural agent that maintains chromosome integrity on a local scale, and that the lack of this protein alters chromosome morphology. In contrast, mIHF is a highly dynamic protein that binds DNA only transiently, exhibits susceptibility to the chromosomal DNA topology changes and whose depletion leads to the growth arrest of tubercle bacilli. Additionally, we have shown that depletion of Mycobacterium smegmatis integration host factor (msIHF) leads to chromosome shrinkage and replication inhibition.
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Affiliation(s)
- Joanna Hołówka
- Department of Molecular Microbiology, University of Wrocław, Wrocław, Poland
- *Correspondence: Joanna Hołówka,
| | - Tomasz Łebkowski
- Department of Molecular Microbiology, University of Wrocław, Wrocław, Poland
| | - Helge Feddersen
- Institute for General Microbiology, Christian-Albrechts-University, Kiel, Germany
| | - Giacomo Giacomelli
- Institute for General Microbiology, Christian-Albrechts-University, Kiel, Germany
| | - Karolina Drużka
- Department of Molecular Microbiology, University of Wrocław, Wrocław, Poland
| | - Łukasz Makowski
- Department of Molecular Microbiology, University of Wrocław, Wrocław, Poland
| | - Damian Trojanowski
- Department of Molecular Microbiology, University of Wrocław, Wrocław, Poland
| | - Natalia Broda
- Department of Molecular Microbiology, University of Wrocław, Wrocław, Poland
| | - Marc Bramkamp
- Institute for General Microbiology, Christian-Albrechts-University, Kiel, Germany
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Elimination of PknL and MSMEG_4242 in Mycobacterium smegmatis alters the character of the outer cell envelope and selects for mutations in Lsr2. ACTA ACUST UNITED AC 2021; 7:100060. [PMID: 34485766 PMCID: PMC8408660 DOI: 10.1016/j.tcsw.2021.100060] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 11/23/2022]
Abstract
Elimination of pknL and adjacent gene MSMEG_4242 in M. smegmatis produces rough & smooth colonies. All smooth colony mutants have inactivated lsr2 genes. Inactivated lsr2 leads to high expression of MSMEG_4727 and increased synthesis of LOS. Smooth mutants don’t form biofilms, have longer bacilli and increased sliding motility. Rough strains deleted for pknL and MSMEG_4242 form biofilms but have aberrant sliding motility. We propose a phosphorylation cascade of PknB phosphorylating PknL that then phosphorylates Lsr2.
Four serine/threonine kinases are present in all mycobacteria: PknA, PknB, PknG and PknL. PknA and PknB are essential for growth and replication, PknG regulates metabolism, but little is known about PknL. Inactivation of pknL and adjacent regulator MSMEG_4242 in rough colony M. smegmatis mc2155 produced both smooth and rough colonies. Upon restreaking rough colonies, smooth colonies appeared at a frequency of ~ 1/250. Smooth mutants did not form biofilms, showed increased sliding motility and anomalous lipids on thin-layer chromatography, identified by mass spectrometry as lipooligosaccharides and perhaps also glycopeptidolipids. RNA-seq and Sanger sequencing revealed that all smooth mutants had inactivated lsr2 genes due to mutations and different IS1096 insertions. When complemented with lsr2, the colonies became rough, anomalous lipids disappeared and sliding motility decreased. Smooth mutants showed increased expression of IS1096 transposase TnpA and MSMEG_4727, which encodes a protein similar to PKS5. When MSMEG_4727 was deleted, smooth pknL/MSMEG_4242/lsr2 mutants reverted to rough, formed good biofilms, their motility decreased slightly and their anomalous lipids disappeared. Rough delpknL/del4242 mutants formed poor biofilms and showed decreased, aberrant sliding motility and both phenotypes were complemented with the two deleted genes. Inactivation of lsr2 changes colony morphology from rough to smooth, augments sliding motility and increases expression of MSMEG_4727 and other enzymes synthesizing lipooligosaccharides, apparently preventing biofilm formation. Similar morphological phase changes occur in other mycobacteria, likely reflecting environmental adaptations. PknL and MSMEG_4242 regulate lipid components of the outer cell envelope and their absence selects for lsr2 inactivation. A regulatory, phosphorylation cascade model is proposed.
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