101
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Murima P, Zimmermann M, Chopra T, Pojer F, Fonti G, Dal Peraro M, Alonso S, Sauer U, Pethe K, McKinney JD. A rheostat mechanism governs the bifurcation of carbon flux in mycobacteria. Nat Commun 2016; 7:12527. [PMID: 27555519 PMCID: PMC4999502 DOI: 10.1038/ncomms12527] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 07/11/2016] [Indexed: 11/30/2022] Open
Abstract
Fatty acid metabolism is an important feature of the pathogenicity of Mycobacterium tuberculosis during infection. Consumption of fatty acids requires regulation of carbon flux bifurcation between the oxidative TCA cycle and the glyoxylate shunt. In Escherichia coli, flux bifurcation is regulated by phosphorylation-mediated inhibition of isocitrate dehydrogenase (ICD), a paradigmatic example of post-translational mechanisms governing metabolic fluxes. Here, we demonstrate that, in contrast to E. coli, carbon flux bifurcation in mycobacteria is regulated not by phosphorylation but through metabolic cross-activation of ICD by glyoxylate, which is produced by the glyoxylate shunt enzyme isocitrate lyase (ICL). This regulatory circuit maintains stable partitioning of fluxes, thus ensuring a balance between anaplerosis, energy production, and precursor biosynthesis. The rheostat-like mechanism of metabolite-mediated control of flux partitioning demonstrates the importance of allosteric regulation during metabolic steady-state. The sensitivity of this regulatory mechanism to perturbations presents a potentially attractive target for chemotherapy. Microbes survive in dynamic environments by modulating their intracellular metabolism. Here, the authors reveal that mycobacteria employ a rheostat-like mechanism to regulate carbon flux between the oxidative TCA cycle and the glyoxylate shunt during glucose-acetate diauxic shift.
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Affiliation(s)
- Paul Murima
- School of Life Sciences, Swiss Federal Institute of Technology in Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Michael Zimmermann
- Institute of Molecular Systems Biology, Swiss Federal Institute of Technology in Zürich (ETHZ), CH-8093 Zürich, Switzerland
| | - Tarun Chopra
- School of Life Sciences, Swiss Federal Institute of Technology in Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Florence Pojer
- Protein Crystallography Platform, Swiss Federal Institute of Technology in Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Giulia Fonti
- School of Life Sciences, Swiss Federal Institute of Technology in Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Matteo Dal Peraro
- School of Life Sciences, Swiss Federal Institute of Technology in Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Sylvie Alonso
- Department of Microbiology, Yong Loo Lin School of Medicine and Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore
| | - Uwe Sauer
- Institute of Molecular Systems Biology, Swiss Federal Institute of Technology in Zürich (ETHZ), CH-8093 Zürich, Switzerland
| | - Kevin Pethe
- Lee Kong Chian School of Medicine and School of Biological Sciences, Nanyang Technological University, 59 Nanyang Drive, Singapore 636 921, Singapore
| | - John D McKinney
- School of Life Sciences, Swiss Federal Institute of Technology in Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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102
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Hu Y, Wang Z, Feng L, Chen Z, Mao C, Zhu Y, Chen S. σ(E) -dependent activation of RbpA controls transcription of the furA-katG operon in response to oxidative stress in mycobacteria. Mol Microbiol 2016; 102:107-20. [PMID: 27353316 DOI: 10.1111/mmi.13449] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/22/2016] [Indexed: 01/08/2023]
Abstract
Mycobacterium tuberculosis adopts various strategies to cope with oxidative stress during infection. Transcriptional regulators, including σ factors, make important contributions to this stress response, but how these proteins cooperate with each other is largely unknown. In this study, the role of RbpA and its cooperation with σ factors in response to oxidative stress are investigated. Knock down expression of rbpA in Mycobacterium smegmatis attenuated bacterial survival in the presence of H2 O2 . Additionally, transcription of the rbpA gene was induced by H2 O2 in a σ(E) -dependent manner. After induction, RbpA interacts with the principal sigma factor, σ(A) , to control the transcription of furA-katG operon, which encodes an H2 O2 scavenging enzyme. Moreover, this regulation is responsible for the role of σ(E) in oxidative response because bacterial survival was attenuated and transcription of the furA-katG operon was down-regulated with H2 O2 treatment in sigE deletion mutant (ΔsigE), and over-expression of RbpA in ΔsigE strain restored all of these phenotypes. Taken together, our study first illustrated a mechanism for σ(E) in response to oxidative stress through regulation of rbpA transcription. This study was also the first to demonstrate that RbpA is required for the full response to oxidative stress by cooperating with the principal σ(A) .
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Affiliation(s)
- Yangbo Hu
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Zhongwei Wang
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, 10086, China
| | - Lipeng Feng
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, 10086, China
| | - Zhenkang Chen
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, 10086, China
| | - Chunyou Mao
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, 10086, China
| | - Yan Zhu
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, 10086, China
| | - Shiyun Chen
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.
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103
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Guo J, Wang C, Han Y, Liu Z, Wu T, Liu Y, Liu Y, Tan Y, Cai X, Cao Y, Wang B, Zhang B, Liu C, Tan S, Zhang T. Identification of Lysine Acetylation in Mycobacterium abscessus Using LC-MS/MS after Immunoprecipitation. J Proteome Res 2016; 15:2567-78. [PMID: 27323652 DOI: 10.1021/acs.jproteome.6b00116] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Mycobacterium abscessus (MAB), which manifests in the pulmonary system, is one of the neglected causes of nontuberculous mycobacteria (NTM) infection. Treatment against MAB is difficult, characterized by its intrinsic antibiotic drug resistance. Lysine acetylation can alter the physiochemical property of proteins in living organisms. This study aimed to determine if this protein post-translational modification (PTM) exists in a clinical isolate M. abscessus GZ002. We used the antiacetyl-lysine immunoprecipitation to enrich the low-abundant PTM proteins, followed by the LC-MS/MS analysis. The lysine acetylome of M. abscessus GZ002 was determined. There were 459 lysine acetylation sites found in 289 acetylated proteins. Lysine acetylation occurred in 5.87% of the M. abscessus GZ002 proteome, and at least 25% of them were growth essential. Aerobic respiration and carbohydrate metabolic pathways of M. abscessus GZ002 were enriched with lysine acetylation. Through bioinformatics analysis, we identified four major acetyl motif logos (K(ac)Y, K(ac)F, K(ac)H, and DK(ac)). Further comparison of the reported M. tuberculosis (MTB) acetylomes and that of MAB GZ002 revealed several common features between these two species. The lysine residues of several antibiotic-resistance, virulence, and persistence-related proteins were acetylated in both MAB GZ002 and MTB. There were 51 identical acetylation sites in 37 proteins found in common between MAB GZ002 and MTB. Overall, we demonstrate a profile of lysine acetylation in MAB GZ002 proteome that shares similarities with MTB. Interventions that target at these conserved sections may be valuable as anti-NTM or anti-TB therapies.
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Affiliation(s)
- Jintao Guo
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS) , Guangzhou, China
| | - Changwei Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS) , Guangzhou, China
| | - Yi Han
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS) , Guangzhou, China
| | - Zhiyong Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS) , Guangzhou, China
| | - Tian Wu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS) , Guangzhou, China
| | - Yan Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS) , Guangzhou, China
| | - Yang Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS) , Guangzhou, China.,School of Life Sciences, University of Anhui , Hefei, China
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital , Guangzhou, China
| | - Xinshan Cai
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital , Guangzhou, China
| | - Yuanyuan Cao
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS) , Guangzhou, China.,School of Life Sciences, University of Anhui , Hefei, China
| | - Bangxing Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS) , Guangzhou, China.,School of Life Sciences, University of Anhui , Hefei, China
| | - Buchang Zhang
- School of Life Sciences, University of Anhui , Hefei, China
| | - Chunping Liu
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital , Guangzhou, China
| | - Shouyong Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital , Guangzhou, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS) , Guangzhou, China
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104
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Boutte CC, Baer CE, Papavinasasundaram K, Liu W, Chase MR, Meniche X, Fortune SM, Sassetti CM, Ioerger TR, Rubin EJ. A cytoplasmic peptidoglycan amidase homologue controls mycobacterial cell wall synthesis. eLife 2016; 5. [PMID: 27304077 PMCID: PMC4946905 DOI: 10.7554/elife.14590] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 06/14/2016] [Indexed: 01/08/2023] Open
Abstract
Regulation of cell wall assembly is essential for bacterial survival and contributes to pathogenesis and antibiotic tolerance in Mycobacterium tuberculosis (Mtb). However, little is known about how the cell wall is regulated in stress. We found that CwlM, a protein homologous to peptidoglycan amidases, coordinates peptidoglycan synthesis with nutrient availability. Surprisingly, CwlM is sequestered from peptidoglycan (PG) by localization in the cytoplasm, and its enzymatic function is not essential. Rather, CwlM is phosphorylated and associates with MurA, the first enzyme in PG precursor synthesis. Phosphorylated CwlM activates MurA ~30 fold. CwlM is dephosphorylated in starvation, resulting in lower MurA activity, decreased cell wall metabolism, and increased tolerance to multiple antibiotics. A phylogenetic analysis of cwlM implies that localization in the cytoplasm drove the evolution of this factor. We describe a system that controls cell wall metabolism in response to starvation, and show that this regulation contributes to antibiotic tolerance.
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Affiliation(s)
- Cara C Boutte
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, United States
| | - Christina E Baer
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Kadamba Papavinasasundaram
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Weiru Liu
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, United States
| | - Michael R Chase
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, United States
| | - Xavier Meniche
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Sarah M Fortune
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, United States
| | - Christopher M Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Thomas R Ioerger
- Department of Computer Science, Texas A and M University, Texas, United States
| | - Eric J Rubin
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, United States.,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, United States
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105
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Lin K, O'Brien KM, Trujillo C, Wang R, Wallach JB, Schnappinger D, Ehrt S. Mycobacterium tuberculosis Thioredoxin Reductase Is Essential for Thiol Redox Homeostasis but Plays a Minor Role in Antioxidant Defense. PLoS Pathog 2016; 12:e1005675. [PMID: 27249779 PMCID: PMC4889078 DOI: 10.1371/journal.ppat.1005675] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 05/12/2016] [Indexed: 02/06/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) must cope with exogenous oxidative stress imposed by the host. Unlike other antioxidant enzymes, Mtb's thioredoxin reductase TrxB2 has been predicted to be essential not only to fight host defenses but also for in vitro growth. However, the specific physiological role of TrxB2 and its importance for Mtb pathogenesis remain undefined. Here we show that genetic inactivation of thioredoxin reductase perturbed several growth-essential processes, including sulfur and DNA metabolism and rapidly killed and lysed Mtb. Death was due to cidal thiol-specific oxidizing stress and prevented by a disulfide reductant. In contrast, thioredoxin reductase deficiency did not significantly increase susceptibility to oxidative and nitrosative stress. In vivo targeting TrxB2 eradicated Mtb during both acute and chronic phases of mouse infection. Deliberately leaky knockdown mutants identified the specificity of TrxB2 inhibitors and showed that partial inactivation of TrxB2 increased Mtb's susceptibility to rifampicin. These studies reveal TrxB2 as essential thiol-reducing enzyme in Mtb in vitro and during infection, establish the value of targeting TrxB2, and provide tools to accelerate the development of TrxB2 inhibitors.
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Affiliation(s)
- Kan Lin
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
- Program in Immunology and Microbial Pathogenesis, Weill Graduate School of Medical Sciences of Cornell University, New York, New York, United States of America
| | - Kathryn M. O'Brien
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | - Carolina Trujillo
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | - Ruojun Wang
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
- Program in Immunology and Microbial Pathogenesis, Weill Graduate School of Medical Sciences of Cornell University, New York, New York, United States of America
| | - Joshua B. Wallach
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
- * E-mail: (DS); (SE)
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
- Program in Immunology and Microbial Pathogenesis, Weill Graduate School of Medical Sciences of Cornell University, New York, New York, United States of America
- * E-mail: (DS); (SE)
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106
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Chao MC, Abel S, Davis BM, Waldor MK. The design and analysis of transposon insertion sequencing experiments. Nat Rev Microbiol 2016; 14:119-28. [PMID: 26775926 DOI: 10.1038/nrmicro.2015.7] [Citation(s) in RCA: 148] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Transposon insertion sequencing (TIS) is a powerful approach that can be extensively applied to the genome-wide definition of loci that are required for bacterial growth under diverse conditions. However, experimental design choices and stochastic biological processes can heavily influence the results of TIS experiments and affect downstream statistical analysis. In this Opinion article, we discuss TIS experimental parameters and how these factors relate to the benefits and limitations of the various statistical frameworks that can be applied to the computational analysis of TIS data.
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Affiliation(s)
- Michael C Chao
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, USA; the Division of Infectious Disease, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; and the Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA
| | - Sören Abel
- Department of Pharmacy, University of Tromsø, The Arctic University of Norway, 9019 Tromsø, Norway
| | - Brigid M Davis
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, USA; the Division of Infectious Disease, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; and the Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA
| | - Matthew K Waldor
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, USA; the Division of Infectious Disease, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; and the Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA
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107
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Matarlo JS, Lu Y, Daryaee F, Daryaee T, Ruzsicska B, Walker SG, Tonge PJ. A Methyl 4-Oxo-4-phenylbut-2-enoate with in Vivo Activity against MRSA that Inhibits MenB in the Bacterial Menaquinone Biosynthesis Pathway. ACS Infect Dis 2016; 2:329-340. [PMID: 27294200 DOI: 10.1021/acsinfecdis.6b00023] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
4-Oxo-4-phenyl-but-2-enoates inhibit MenB, the 1,4-dihydroxyl-2-naphthoyl-CoA synthase in the bacterial menaquinone (MK) biosynthesis pathway, through the formation of an adduct with coenzyme A (CoA). Here, we show that the corresponding methyl butenoates have MIC values as low as 0.35-0.75 µg/mL against drug sensitive and resistant strains of Staphylococcus aureus. Mode of action studies on the most potent compound, methyl 4-(4-chlorophenyl)-4-oxobut-2-enoate (1), reveal that 1 is converted into the corresponding CoA adduct in S. aureus cells, and that this adduct binds to the S. aureus MenB (saMenB) with a Kd value of 2 µM. The antibacterial spectrum of 1 is limited to bacteria that utilize MK for respiration, and the activity of 1 can be complemented with exogenous MK or menadione. Finally, treatment of methicillin-resistant S. aureus (MRSA) with 1 results in the small colony variant phenotype and thus 1 phenocopies knockout of the menB gene. Taken together the data indicate that the antibacterial activity of 1 results from a specific effect on MK biosynthesis. We also evaluated the in vivo efficacy of 1 using two mouse models of MRSA infection. Notably, compound 1 increased survival in a systemic infection model and resulted in a dose-dependent decrease in bacterial load in a thigh infection model, validating MenB as a target for the development of new anti-MRSA candidates.
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Affiliation(s)
- Joe S. Matarlo
- Institute of Chemical Biology & Drug Discovery, Department of Chemistry, and ‡Department of Oral Biology and Pathology, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Yang Lu
- Institute of Chemical Biology & Drug Discovery, Department of Chemistry, and ‡Department of Oral Biology and Pathology, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Fereidoon Daryaee
- Institute of Chemical Biology & Drug Discovery, Department of Chemistry, and ‡Department of Oral Biology and Pathology, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Taraneh Daryaee
- Institute of Chemical Biology & Drug Discovery, Department of Chemistry, and ‡Department of Oral Biology and Pathology, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Bela Ruzsicska
- Institute of Chemical Biology & Drug Discovery, Department of Chemistry, and ‡Department of Oral Biology and Pathology, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Stephen G. Walker
- Institute of Chemical Biology & Drug Discovery, Department of Chemistry, and ‡Department of Oral Biology and Pathology, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Peter J. Tonge
- Institute of Chemical Biology & Drug Discovery, Department of Chemistry, and ‡Department of Oral Biology and Pathology, Stony Brook University, Stony Brook, New York 11794-3400, United States
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108
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Comparative analysis of metabolic machinery of Frankia along with other selected actinobacteria. Symbiosis 2016. [DOI: 10.1007/s13199-016-0410-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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109
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Influence of Conformation of M. tuberculosis RNase P Protein Subunit on Its Function. PLoS One 2016; 11:e0153798. [PMID: 27088505 PMCID: PMC4835064 DOI: 10.1371/journal.pone.0153798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 04/04/2016] [Indexed: 01/22/2023] Open
Abstract
RNase P is an essential enzyme that processes 5' end leader sequence of pre-tRNA to generate mature tRNA. The bacterial RNase Ps contain a RNA subunit and one protein subunit, where the RNA subunit contains the catalytic activity. The protein subunit which lacks any catalytic activity, relaxes the ionic requirements for holoenzyme reaction and is indispensable for pre-tRNA cleavage in vivo. In the current study, we reconstituted the M. tuberculosis RNase P holoenzyme in vitro. We prepared the RNase P protein through two different strategies that differ in the conditions under which the recombinant M. tuberculosis protein, expressed in E. coli was purified. The mycobacterial RNase P protein which was purified under native conditions subsequent to isolation from inclusion bodies and in vitro renaturation, was capable of cleaving pre-tRNA specifically without the requirement of RNase P RNA. However, the preparation that was purified under denaturing conditions and refolded subsequently lacked any inherent pre-tRNA processing activity and cleaved the substrate only as a component of the holoenzyme with the RNA subunit. We found that the two RNase P protein preparations attained alternative conformations and differed with respect to their stability as well.
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110
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Rathnaiah G, Bannantine JP, Bayles DO, Zinniel DK, Stabel JR, Gröhn YT, Barletta RG. Analysis of Mycobacterium avium subsp. paratuberculosis mutant libraries reveals loci-dependent transposition biases and strategies for novel mutant discovery. MICROBIOLOGY-SGM 2016; 162:633-641. [PMID: 26888023 DOI: 10.1099/mic.0.000258] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP), the aetiological agent of Johne's disease, is one of the most important bacterial pathogens in ruminants. A thorough understanding of MAP pathogenesis is needed to develop new vaccines and diagnostic tests. The generation of comprehensive random transposon mutant libraries is a fundamental genetic technology to determine the role of genes in physiology and pathogenesis. In this study, whole MAP genome analysis compared the insertion sites for the mycobacterial transposon Tn5367 derived from the Mycobacterium smegmatis insertion sequence IS1096 and the mariner transposon MycoMarT7 carrying the Himar1 transposase. We determined that only MycoMarT7 provides a random representation of insertions in 99 % of all MAP genes. Analysis of the MAP K-10 genome indicated that 710 of all ORFs do not possess IS1096 recognition sites, while only 37 do not have the recognition site for MycoMarT7. Thus, a significant number of MAP genes remain underrepresented in insertion libraries from IS1096-derived transposons. Analysis of MycoMarT7 and Tn5367 mutants showed that Tn5367 has a predilection to insert within intergenic regions, suggesting that MycoMarT7 is the more adequate for generating a comprehensive library. However, we uncovered the novel finding that both transposons have loci-dependent biases, with Tn5367 being the most skewed. These loci-dependent transposition biases led to an underestimation of the number of independent mutants required to generate a comprehensive mutant library, leading to an overestimation of essential genes. Herein, we also demonstrated a useful platform for gene discovery and analysis by isolating three novel mutants for each transposon.
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Affiliation(s)
- Govardhan Rathnaiah
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska, Lincoln, NE,USA
| | - John P Bannantine
- Infectious Bacterial Diseases, National Animal Disease Center, United States Department of Agriculture - Agricultural Research Service, Ames, IA, USA
| | - Darrell O Bayles
- Infectious Bacterial Diseases, National Animal Disease Center, United States Department of Agriculture - Agricultural Research Service, Ames, IA, USA
| | - Denise K Zinniel
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska, Lincoln, NE,USA
| | - Judith R Stabel
- Infectious Bacterial Diseases, National Animal Disease Center, United States Department of Agriculture - Agricultural Research Service, Ames, IA, USA
| | - Yrjö T Gröhn
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, NY, USA
| | - Raúl G Barletta
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska, Lincoln, NE,USA
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111
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Choudhary E, Lunge A, Agarwal N. Strategies of genome editing in mycobacteria: Achievements and challenges. Tuberculosis (Edinb) 2016; 98:132-8. [PMID: 27156629 DOI: 10.1016/j.tube.2016.03.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 03/14/2016] [Accepted: 03/21/2016] [Indexed: 01/07/2023]
Abstract
Tremendous amount of physiological and functional complexities acquired through decades of evolutionary pressure makes Mycobacterium tuberculosis (Mtb) one of the most dreadful microorganisms infecting humans from centuries. Astonishing advances in genomics and genome editing tools substantially grew our knowledge about Mtb as an organism but dramatically failed to completely understand it as a pathogen. Though conventional tools based on homologous recombination, antisense, controlled proteolysis, etc. have made important contributions in advancing our understanding of the pathophysiology of Mtb, yet these approaches have not accentuated our exploration of mycobacterium on account of certain technical limitations. In this review article we have compiled various approaches implemented in genome editing of mycobacteria along with the latest adaptation of clustered regularly interspaced short palindromic repeat (CRISPR)-interference (CRISPRi), emphasizing the achievements and challenges associated with these techniques.
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Affiliation(s)
- Eira Choudhary
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121001, Haryana, India; Symbiosis School of Biomedical Sciences, Symbiosis International University, Lavale, Pune 412115, Maharashtra, India
| | - Ajitesh Lunge
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121001, Haryana, India; Jawaharlal Nehru University, New Mehrauli Road, Near Munirka, New Delhi 110067, Delhi, India
| | - Nisheeth Agarwal
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121001, Haryana, India.
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112
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Abstract
Genetic strategies have yet to come into their own as tools for antibiotic development. While holding a lot of initial promise, they have only recently started to bear fruit in the quest for new drug targets. An ever-increasing body of knowledge is showing that genetics can lead to significant improvements in the success and efficiency of drug discovery. Techniques such as high-frequency transposon mutagenesis and expression modulation have matured and have been applied successfully not only to the identification and characterization of new targets, but also to their validation as tractable weaknesses of bacteria. Past experience shows that choosing targets must not rely on gene essentiality alone, but rather needs to incorporate knowledge of the system as a whole. The ability to manipulate genes and their expression is key to ensuring that we understand the entire set of processes that are affected by drug treatment. Focusing on exacerbating these perturbations, together with the identification of new targets to which resistance has not yet occurred--both enabled by genetic approaches--may point us toward the successful development of new combination therapies engineered based on underlying biology.
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Abstract
Mycobacteria inhabit a wide range of intracellular and extracellular environments. Many of these environments are highly dynamic and therefore mycobacteria are faced with the constant challenge of redirecting their metabolic activity to be commensurate with either replicative growth or a non-replicative quiescence. A fundamental feature in this adaptation is the ability of mycobacteria to respire, regenerate reducing equivalents and generate ATP via oxidative phosphorylation. Mycobacteria harbor multiple primary dehydrogenases to fuel the electron transport chain and two terminal respiratory oxidases, an aa3 -type cytochrome c oxidase and cytochrome bd-type menaquinol oxidase, are present for dioxygen reduction coupled to the generation of a protonmotive force. Hypoxia leads to the downregulation of key respiratory complexes, but the molecular mechanisms regulating this expression are unknown. Despite being obligate aerobes, mycobacteria have the ability to metabolize in the absence of oxygen and a number of reductases are present to facilitate the turnover of reducing equivalents under these conditions (e.g. nitrate reductase, succinate dehydrogenase/fumarate reductase). Hydrogenases and ferredoxins are also present in the genomes of mycobacteria suggesting the ability of these bacteria to adapt to an anaerobic-type of metabolism in the absence of oxygen. ATP synthesis by the membrane-bound F1FO-ATP synthase is essential for growing and non-growing mycobacteria and the enzyme is able to function over a wide range of protonmotive force values (aerobic to hypoxic). The discovery of lead compounds that target respiration and oxidative phosphorylation in Mycobacterium tuberculosis highlights the importance of this area for the generation of new front line drugs to combat tuberculosis.
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114
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Liu F, Wang C, Wu Z, Zhang Q, Liu P. A zero-inflated Poisson model for insertion tolerance analysis of genes based on Tn-seq data. Bioinformatics 2016; 32:1701-8. [PMID: 26833344 DOI: 10.1093/bioinformatics/btw061] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 01/25/2016] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Transposon insertion sequencing (Tn-seq) is an emerging technology that combines transposon mutagenesis with next-generation sequencing technologies for the identification of genes related to bacterial survival. The resulting data from Tn-seq experiments consist of sequence reads mapped to millions of potential transposon insertion sites and a large portion of insertion sites have zero mapped reads. Novel statistical method for Tn-seq data analysis is needed to infer functions of genes on bacterial growth. RESULTS In this article, we propose a zero-inflated Poisson model for analyzing the Tn-seq data that are high-dimensional and with an excess of zeros. Maximum likelihood estimates of model parameters are obtained using an expectation-maximization (EM) algorithm, and pseudogenes are utilized to construct appropriate statistical tests for the transposon insertion tolerance of normal genes of interest. We propose a multiple testing procedure that categorizes genes into each of the three states, hypo-tolerant, tolerant and hyper-tolerant, while controlling the false discovery rate. We evaluate the proposed method with simulation studies and apply the proposed method to a real Tn-seq data from an experiment that studied the bacterial pathogen, Campylobacter jejuniAvailability and implementation: We provide R code for implementing our proposed method at http://github.com/ffliu/TnSeq A user's guide with example data analysis is also available there. CONTACT pliu@iastate.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Chong Wang
- Department of Statistics, Iowa State University, Department of Veterinary Diagnostic and Production Animal Medicine and
| | - Zuowei Wu
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50010, USA
| | - Qijing Zhang
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50010, USA
| | - Peng Liu
- Department of Statistics, Iowa State University
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115
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DeJesus MA, Ioerger TR. Normalization of transposon-mutant library sequencing datasets to improve identification of conditionally essential genes. J Bioinform Comput Biol 2016; 14:1642004. [PMID: 26932272 DOI: 10.1142/s021972001642004x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Sequencing of transposon-mutant libraries using next-generation sequencing (TnSeq) has become a popular method for determining which genes and non-coding regions are essential for growth under various conditions in bacteria. For methods that rely on quantitative comparison of counts of reads at transposon insertion sites, proper normalization of TnSeq datasets is vitally important. Real TnSeq datasets are often noisy and exhibit a significant skew that can be dominated by high counts at a small number of sites (often for non-biological reasons). If two datasets that are not appropriately normalized are compared, it might cause the artifactual appearance of Differentially Essential (DE) genes in a statistical test, constituting type I errors (false positives). In this paper, we propose a novel method for normalization of TnSeq datasets that corrects for the skew of read-count distributions by fitting them to a Beta-Geometric distribution. We show that this read-count correction procedure reduces the number of false positives when comparing replicate datasets grown under the same conditions (for which no genuine differences in essentiality are expected). We compare these results to results obtained with other normalization procedures, and show that it results in greater reduction in the number of false positives. In addition we investigate the effects of normalization on the detection of DE genes.
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Affiliation(s)
- Michael A DeJesus
- 1 Department of Computer Science, Texas A&M University, College Station, Texas 77843, USA
| | - Thomas R Ioerger
- 1 Department of Computer Science, Texas A&M University, College Station, Texas 77843, USA
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116
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Mycobacterial Metabolic Syndrome: LprG and Rv1410 Regulate Triacylglyceride Levels, Growth Rate and Virulence in Mycobacterium tuberculosis. PLoS Pathog 2016; 12:e1005351. [PMID: 26751071 PMCID: PMC4709180 DOI: 10.1371/journal.ppat.1005351] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 11/30/2015] [Indexed: 11/19/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) mutants lacking rv1411c, which encodes the lipoprotein LprG, and rv1410c, which encodes a putative efflux pump, are dramatically attenuated for growth in mice. Here we show that loss of LprG-Rv1410 in Mtb leads to intracellular triacylglyceride (TAG) accumulation, and overexpression of the locus increases the levels of TAG in the culture medium, demonstrating a role of this locus in TAG transport. LprG binds TAG within a large hydrophobic cleft and is sufficient to transfer TAG from donor to acceptor membranes. Further, LprG-Rv1410 is critical for broadly regulating bacterial growth and metabolism in vitro during carbon restriction and in vivo during infection of mice. The growth defect in mice is due to disrupted bacterial metabolism and occurs independently of key immune regulators. The in vivo essentiality of this locus suggests that this export system and other regulators of metabolism should be considered as targets for novel therapeutics. Of the estimated 2 billion people worldwide currently infected with Mycobacterium tuberculosis (Mtb), surprisingly few go on to develop active tuberculosis (TB) disease. The vast majority, 95 percent, of infected individuals develop latent TB, remaining infected but without disease. Despite its importance in global health, the question of what determines whether an infected individual will develop active or latent TB remains largely unanswered. Changes in how Mtb grows in response to stressors presented by the host environment likely play an important role in this process. In particular, the manifold ways in which Mtb synthesizes, degrades, and transports lipids dictates its growth in an infected host. Here, we show that lipid transport is an important function of two TB genes known to be required for Mtb’s ability to cause disease in the mouse model of infection. Using a variety of genetic and biochemical techniques, we found that the products of these genes prevent the cytosolic accumulation of a lipid associated with non-growing Mtb under the metabolic conditions it encounters during infection. Our results indicate an important role for the metabolism of Mtb in its ability to orchestrate a productive infection and cause disease.
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117
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Iron Acquisition in Mycobacterium avium subsp. paratuberculosis. J Bacteriol 2015; 198:857-66. [PMID: 26712939 PMCID: PMC4810606 DOI: 10.1128/jb.00922-15] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Accepted: 12/18/2015] [Indexed: 01/26/2023] Open
Abstract
Mycobacterium avium subsp. paratuberculosis is a host-adapted pathogen that evolved from the environmental bacterium M. avium subsp. hominissuis through gene loss and gene acquisition. Growth of M. avium subsp. paratuberculosis in the laboratory is enhanced by supplementation of the media with the iron-binding siderophore mycobactin J. Here we examined the production of mycobactins by related organisms and searched for an alternative iron uptake system in M. avium subsp. paratuberculosis. Through thin-layer chromatography and radiolabeled iron-uptake studies, we showed that M. avium subsp. paratuberculosis is impaired for both mycobactin synthesis and iron acquisition. Consistent with these observations, we identified several mutations, including deletions, in M. avium subsp. paratuberculosis genes coding for mycobactin synthesis. Using a transposon-mediated mutagenesis screen conditional on growth without myobactin, we identified a potential mycobactin-independent iron uptake system on a M. avium subsp. paratuberculosis-specific genomic island, LSPP15. We obtained a transposon (Tn) mutant with a disruption in the LSPP15 gene MAP3776c for targeted study. The mutant manifests increased iron uptake as well as intracellular iron content, with genes downstream of the transposon insertion (MAP3775c to MAP3772c [MAP3775-2c]) upregulated as the result of a polar effect. As an independent confirmation, we observed the same iron uptake phenotypes by overexpressing MAP3775-2c in wild-type M. avium subsp. paratuberculosis. These data indicate that the horizontally acquired LSPP15 genes contribute to iron acquisition by M. avium subsp. paratuberculosis, potentially allowing the subsequent loss of siderophore production by this pathogen. IMPORTANCE Many microbes are able to scavenge iron from their surroundings by producing iron-chelating siderophores. One exception is Mycobacterium avium subsp. paratuberculosis, a fastidious, slow-growing animal pathogen whose growth needs to be supported by exogenous mycobacterial siderophore (mycobactin) in the laboratory. Data presented here demonstrate that, compared to other closely related M. avium subspecies, mycobactin production and iron uptake are different in M. avium subsp. paratuberculosis, and these phenotypes may be caused by numerous deletions in its mycobactin biosynthesis pathway. Using a genomic approach, supplemented by targeted genetic and biochemical studies, we identified that LSPP15, a horizontally acquired genomic island, may encode an alternative iron uptake system. These findings shed light on the potential physiological consequence of horizontal gene transfer in M. avium subsp. paratuberculosis evolution.
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118
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Jamet S, Slama N, Domingues J, Laval F, Texier P, Eynard N, Quémard A, Peixoto A, Lemassu A, Daffé M, Cam K. The Non-Essential Mycolic Acid Biosynthesis Genes hadA and hadC Contribute to the Physiology and Fitness of Mycobacterium smegmatis. PLoS One 2015; 10:e0145883. [PMID: 26701652 PMCID: PMC4689354 DOI: 10.1371/journal.pone.0145883] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 12/09/2015] [Indexed: 12/11/2022] Open
Abstract
Gram positive mycobacteria with a high GC content, such as the etiological agent of tuberculosis Mycobacterium tuberculosis, possess an outer membrane mainly composed of mycolic acids (MAs), the so-called mycomembrane, which is essential for the cell. About thirty genes are involved in the biosynthesis of MAs, which include the hadA, hadB and hadC genes that encode the dehydratases Fatty Acid Synthase type II (FAS-II) known to function as the heterodimers HadA-HadB and HadB-HadC. The present study shows that M. smegmatis cells remain viable in the absence of either HadA and HadC or both. Inactivation of HadC has a dramatic effect on the physiology and fitness of the mutant strains whereas that of HadA exacerbates the phenotype of a hadC deletion. The hadC mutants exhibit a novel MA profile, display a distinct colony morphology, are less aggregated, are impaired for sliding motility and biofilm development and are more resistant to detergent. Conversely, the hadC mutants are significantly more susceptible to low- and high-temperature and to selective toxic compounds, including several current anti-tubercular drugs.
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Affiliation(s)
- Stevie Jamet
- Centre National de la Recherche Scientifique, IPBS, UMR 5089, F-31077 Toulouse, France
- Univ. Toulouse, UPS, F-31000 Toulouse, France
| | - Nawel Slama
- Centre National de la Recherche Scientifique, IPBS, UMR 5089, F-31077 Toulouse, France
- Univ. Toulouse, UPS, F-31000 Toulouse, France
| | - Joana Domingues
- Centre National de la Recherche Scientifique, IPBS, UMR 5089, F-31077 Toulouse, France
- Univ. Toulouse, UPS, F-31000 Toulouse, France
| | - Françoise Laval
- Centre National de la Recherche Scientifique, IPBS, UMR 5089, F-31077 Toulouse, France
- Univ. Toulouse, UPS, F-31000 Toulouse, France
| | - Pauline Texier
- Centre National de la Recherche Scientifique, IPBS, UMR 5089, F-31077 Toulouse, France
- Univ. Toulouse, UPS, F-31000 Toulouse, France
| | - Nathalie Eynard
- Centre National de la Recherche Scientifique, IPBS, UMR 5089, F-31077 Toulouse, France
- Univ. Toulouse, UPS, F-31000 Toulouse, France
| | - Annaik Quémard
- Centre National de la Recherche Scientifique, IPBS, UMR 5089, F-31077 Toulouse, France
- Univ. Toulouse, UPS, F-31000 Toulouse, France
| | - Antonio Peixoto
- Centre National de la Recherche Scientifique, IPBS, UMR 5089, F-31077 Toulouse, France
- Univ. Toulouse, UPS, F-31000 Toulouse, France
| | - Anne Lemassu
- Centre National de la Recherche Scientifique, IPBS, UMR 5089, F-31077 Toulouse, France
- Univ. Toulouse, UPS, F-31000 Toulouse, France
| | - Mamadou Daffé
- Centre National de la Recherche Scientifique, IPBS, UMR 5089, F-31077 Toulouse, France
- Univ. Toulouse, UPS, F-31000 Toulouse, France
| | - Kaymeuang Cam
- Centre National de la Recherche Scientifique, IPBS, UMR 5089, F-31077 Toulouse, France
- Univ. Toulouse, UPS, F-31000 Toulouse, France
- * E-mail:
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119
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Majlessi L, Prados-Rosales R, Casadevall A, Brosch R. Release of mycobacterial antigens. Immunol Rev 2015; 264:25-45. [PMID: 25703550 DOI: 10.1111/imr.12251] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Mycobacterium tuberculosis has evolved from a Mycobacterium canettii-like progenitor pool into one of the most successful and widespread human pathogens. The pathogenicity of M. tuberculosis is linked to its ability to secrete/export/release selected mycobacterial proteins, and it is also established that active release of mycobacterial antigens is a prerequisite for strong immune recognition. Recent research has enabled mycobacterial secretion systems and vesicle-based release of mycobacterial antigens to be elucidated, which together with host-related specificities constitute key variables that determine the outcome of infection. Here, we discuss recently discovered, novel aspects on the nature and the regulation of antigen release of the tuberculosis agent with particular emphasis on the biological characterization of mycobacteria-specific ESX/type VII secretion systems and their secreted proteins, belonging to the Esx, PE, and PPE categories. The importance of specific mycobacterial antigen release is probably best exemplified by the striking differences observed between the cellular events during infection with the ESX-1-deficient, attenuated Mycobacterium bovis BCG compared to the virulent M. tuberculosis, which are clearly important for design of more specific diagnostics and more efficient vaccines.
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Affiliation(s)
- Laleh Majlessi
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
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120
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Ehrt S, Rhee K, Schnappinger D. Mycobacterial genes essential for the pathogen's survival in the host. Immunol Rev 2015; 264:319-26. [PMID: 25703569 DOI: 10.1111/imr.12256] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Mycobacterium tuberculosis (Mtb) has evolved within the human immune system as both host and reservoir. The study of genes required for its growth and persistence in vivo thus offers linked insights into its pathogenicity and host immunity. Studies of Mtb mutants have implicated metabolic adaptation (consisting of carbon, nitrogen, vitamin, and cofactor metabolism), intrabacterial pH homeostasis, and defense against reactive oxygen and reactive nitrogen species, as key determinants of its pathogenicity. However, the mechanisms of host immunity are complex and often combinatorial. Growing evidence has thus begun to reveal that the determinants of Mtb's pathogenicity may serve a broader and more complex array of functions than the isolated experimental settings in which they were initially found. Here, we review select examples, which exemplify this complexity, highlighting the distinct phases of Mtb's life cycle and the diverse microenvironments encountered therein.
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Affiliation(s)
- Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
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121
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Yunck R, Cho H, Bernhardt TG. Identification of MltG as a potential terminase for peptidoglycan polymerization in bacteria. Mol Microbiol 2015; 99:700-18. [PMID: 26507882 DOI: 10.1111/mmi.13258] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/12/2015] [Indexed: 12/27/2022]
Abstract
Bacterial cells are fortified against osmotic lysis by a cell wall made of peptidoglycan (PG). Synthases called penicillin-binding proteins (PBPs), the targets of penicillin and related antibiotics, polymerize the glycan strands of PG and crosslink them into the cell wall meshwork via attached peptides. The average length of glycan chains inserted into the matrix by the PBPs is thought to play an important role in bacterial morphogenesis, but polymerization termination factors controlling this process have yet to be discovered. Here, we report the identification of Escherichia coli MltG (YceG) as a potential terminase for glycan polymerization that is broadly conserved in bacteria. A clone containing mltG was initially isolated in a screen for multicopy plasmids generating a lethal phenotype in cells defective for the PG synthase PBP1b. Biochemical studies revealed that MltG is an inner membrane enzyme with endolytic transglycosylase activity capable of cleaving at internal positions within a glycan polymer. Radiolabeling experiments further demonstrated MltG-dependent nascent PG processing in vivo, and bacterial two-hybrid analysis identified an MltG-PBP1b interaction. Mutants lacking MltG were also shown to have longer glycans in their PG relative to wild-type cells. Our combined results are thus consistent with a model in which MltG associates with PG synthetic complexes to cleave nascent polymers and terminate their elongation.
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Affiliation(s)
- Rachel Yunck
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Hongbaek Cho
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Thomas G Bernhardt
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA
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122
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Comparative Genome and Network Centrality Analysis to Identify Drug Targets of Mycobacterium tuberculosis H37Rv. BIOMED RESEARCH INTERNATIONAL 2015; 2015:212061. [PMID: 26618166 PMCID: PMC4651637 DOI: 10.1155/2015/212061] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 09/09/2015] [Accepted: 09/27/2015] [Indexed: 12/01/2022]
Abstract
Potential drug targets of Mycobacterium tuberculosis H37Rv were identified through systematically integrated comparative genome and network centrality analysis. The comparative analysis of the complete genome of Mycobacterium tuberculosis H37Rv against Database of Essential Genes (DEG) yields a list of proteins which are essential for the growth and survival of the pathogen. Those proteins which are nonhomologous with human were selected. The resulting proteins were then prioritized by using the four network centrality measures: degree, closeness, betweenness, and eigenvector. Proteins whose centrality value is close to the centre of gravity of the interactome network were proposed as a final list of potential drug targets for the pathogen. The use of an integrated approach is believed to increase the success of the drug target identification process. For the purpose of validation, selective comparisons have been made among the proposed targets and previously identified drug targets by various other methods. About half of these proteins have been already reported as potential drug targets. We believe that the identified proteins will be an important input to experimental study which in the way could save considerable amount of time and cost of drug target discovery.
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Soni V, Upadhayay S, Suryadevara P, Samla G, Singh A, Yogeeswari P, Sriram D, Nandicoori VK. Depletion of M. tuberculosis GlmU from Infected Murine Lungs Effects the Clearance of the Pathogen. PLoS Pathog 2015; 11:e1005235. [PMID: 26489015 PMCID: PMC4619583 DOI: 10.1371/journal.ppat.1005235] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 09/27/2015] [Indexed: 01/06/2023] Open
Abstract
M. tuberculosis N-acetyl-glucosamine-1-phosphate uridyltransferase (GlmUMtb) is a bi-functional enzyme engaged in the synthesis of two metabolic intermediates N-acetylglucosamine-1-phosphate (GlcNAc-1-P) and UDP-GlcNAc, catalyzed by the C- and N-terminal domains respectively. UDP-GlcNAc is a key metabolite essential for the synthesis of peptidoglycan, disaccharide linker, arabinogalactan and mycothiols. While glmUMtb was predicted to be an essential gene, till date the role of GlmUMtb in modulating the in vitro growth of Mtb or its role in survival of pathogen ex vivo / in vivo have not been deciphered. Here we present the results of a comprehensive study dissecting the role of GlmUMtb in arbitrating the survival of the pathogen both in vitro and in vivo. We find that absence of GlmUMtb leads to extensive perturbation of bacterial morphology and substantial reduction in cell wall thickness under normoxic as well as hypoxic conditions. Complementation studies show that the acetyl- and uridyl- transferase activities of GlmUMtb are independently essential for bacterial survival in vitro, and GlmUMtb is also found to be essential for mycobacterial survival in THP-1 cells as well as in guinea pigs. Depletion of GlmUMtb from infected murine lungs, four weeks post infection, led to significant reduction in the bacillary load. The administration of Oxa33, a novel oxazolidine derivative that specifically inhibits GlmUMtb, to infected mice resulted in significant decrease in the bacillary load. Thus our study establishes GlmUMtb as a strong candidate for intervention measures against established tuberculosis infections. The synthesis of the Mtb cell wall involves a cascade of reactions catalyzed by cytosolic and cell membrane-bound enzymes. The reaction catalyzed by GlmUMtb (an enzyme with acetyltransferase and uridyltransferase activities) generates UDP-GlcNAc, a central nucleotide-sugar building block of the cell wall. Apart from cell wall synthesis UDP-GlcNAc is an essential metabolite participating in other cellular processes including disaccharide linker and mycothiol biosynthesis. GlmUMtb shares very little sequence similarity with eukaryotic acetyltransferase and uridyltransferase enzymes. Many pathogens have alternative pathway(s) for foraging GlcNAc from the host. The present study was undertaken to see the effects of depleting GlmUMtb on pathogen survival in the host animal. We have generated a conditional gene replacement mutant of glmUMtb and find that depletion of GlmUMtb at any stage of bacterial growth or in mice infected with Mtb including a well-established infection, results in irreversible bacterial death due to perturbation of cell wall synthesis. We have developed a novel anti-GlmUMtb inhibitor (Oxa33), identified its binding site on GlmUMtb, and shown its specificity for GlmUMtb. The study demonstrates that GlmUMtb is a promising target for therapeutic intervention and Oxa33 can be pursued as a lead molecule.
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Affiliation(s)
- Vijay Soni
- National Institute of Immunology, New Delhi, India
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Hyderabad, India
| | | | - Priyanka Suryadevara
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Hyderabad, India
| | - Ganesh Samla
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Hyderabad, India
| | - Archana Singh
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Perumal Yogeeswari
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Hyderabad, India
| | - Dharmarajan Sriram
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Hyderabad, India
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Maksymiuk C, Ioerger T, Balakrishnan A, Bryk R, Rhee K, Sacchettini J, Nathan C. Comparison of transposon and deletion mutants in Mycobacterium tuberculosis: The case of rv1248c, encoding 2-hydroxy-3-oxoadipate synthase. Tuberculosis (Edinb) 2015; 95:689-694. [PMID: 26547230 DOI: 10.1016/j.tube.2015.08.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 08/27/2015] [Accepted: 08/31/2015] [Indexed: 11/30/2022]
Abstract
We compared phenotypes of five strains of Mycobacterium tuberculosis (Mtb) differing in their expression of rv1248c and its product, 2-hydroxy-3-oxoadipate synthase (HOAS), with a focus on carbon source-dependent growth rates and attenuation in mice. Surprisingly, an rv1248c transposon mutant on a CDC1551 background grew differently than an rv1248c deletion mutant on the same background. Moreover, the same rv1248c deletion in two different yet genetically similar strain backgrounds (CDC1551 and H37Rv) gave different phenotypes, though each could be complemented. Whole genome re-sequencing did not provide an obvious explanation for these discrepancies. These observations offer a cautionary lesson about the strength of inference from complementation and sequence analysis, and commend consideration of more complex phenomena than usually contemplated in Mtb, such as epigenetic control.
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Affiliation(s)
- Christina Maksymiuk
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Thomas Ioerger
- Department of Computer Science and Engineering, Texas A&M University, USA
| | - Anand Balakrishnan
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Ruslana Bryk
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Kyu Rhee
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - James Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, USA
| | - Carl Nathan
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10065, USA.
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125
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Kwon YM, Ricke SC, Mandal RK. Transposon sequencing: methods and expanding applications. Appl Microbiol Biotechnol 2015; 100:31-43. [DOI: 10.1007/s00253-015-7037-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 09/15/2015] [Accepted: 09/20/2015] [Indexed: 12/26/2022]
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126
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Matarlo JS, Evans CE, Sharma I, Lavaud LJ, Ngo SC, Shek R, Rajashankar KR, French JB, Tan DS, Tonge PJ. Mechanism of MenE inhibition by acyl-adenylate analogues and discovery of novel antibacterial agents. Biochemistry 2015; 54:6514-6524. [PMID: 26394156 DOI: 10.1021/acs.biochem.5b00966] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
MenE is an o-succinylbenzoyl-CoA (OSB-CoA) synthetase in the bacterial menaquinone biosynthesis pathway and is a promising target for the development of novel antibacterial agents. The enzyme catalyzes CoA ligation via an acyl-adenylate intermediate, and we have previously reported tight-binding inhibitors of MenE based on stable acyl-sulfonyladenosine analogues of this intermediate, including OSB-AMS (1), which has an IC50 value of ≤25 nM for Escherichia coli MenE. Herein, we show that OSB-AMS reduces menaquinone levels in Staphylococcus aureus, consistent with its proposed mechanism of action, despite the observation that the antibacterial activity of OSB-AMS is ∼1000-fold lower than the IC50 for enzyme inhibition. To inform the synthesis of MenE inhibitors with improved antibacterial activity, we have undertaken a structure-activity relationship (SAR) study stimulated by the knowledge that OSB-AMS can adopt two isomeric forms in which the OSB side chain exists either as an open-chain keto acid or a cyclic lactol. These studies revealed that negatively charged analogues of the keto acid form bind, while neutral analogues do not, consistent with the hypothesis that the negatively charged keto acid form of OSB-AMS is the active isomer. X-ray crystallography and site-directed mutagenesis confirm the importance of a conserved arginine for binding the OSB carboxylate. Although most lactol isomers tested were inactive, a novel difluoroindanediol inhibitor (11) with improved antibacterial activity was discovered, providing a pathway toward the development of optimized MenE inhibitors in the future.
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Affiliation(s)
- Joe S Matarlo
- Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY 11794-3400.,Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-3400
| | - Christopher E Evans
- Pharmacology Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Indrajeet Sharma
- Chemical Biology Program and Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Lubens J Lavaud
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400
| | - Stephen C Ngo
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400
| | - Roger Shek
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-3400
| | - Kanagalaghatta R Rajashankar
- NE-CAT and Department of Chemistry and Chemical Biology, Building 436E, Argonne National Laboratory, Argonne, IL 60439
| | - Jarrod B French
- Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY 11794-3400.,Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400.,Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-3400
| | - Derek S Tan
- Pharmacology Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065.,Chemical Biology Program and Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Peter J Tonge
- Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY 11794-3400.,Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400
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127
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DeJesus MA, Ambadipudi C, Baker R, Sassetti C, Ioerger TR. TRANSIT--A Software Tool for Himar1 TnSeq Analysis. PLoS Comput Biol 2015; 11:e1004401. [PMID: 26447887 PMCID: PMC4598096 DOI: 10.1371/journal.pcbi.1004401] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 06/10/2015] [Indexed: 02/07/2023] Open
Abstract
TnSeq has become a popular technique for determining the essentiality of genomic regions in bacterial organisms. Several methods have been developed to analyze the wealth of data that has been obtained through TnSeq experiments. We developed a tool for analyzing Himar1 TnSeq data called TRANSIT. TRANSIT provides a graphical interface to three different statistical methods for analyzing TnSeq data. These methods cover a variety of approaches capable of identifying essential genes in individual datasets as well as comparative analysis between conditions. We demonstrate the utility of this software by analyzing TnSeq datasets of M. tuberculosis grown on glycerol and cholesterol. We show that TRANSIT can be used to discover genes which have been previously implicated for growth on these carbon sources. TRANSIT is written in Python, and thus can be run on Windows, OSX and Linux platforms. The source code is distributed under the GNU GPL v3 license and can be obtained from the following GitHub repository: https://github.com/mad-lab/transit.
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Affiliation(s)
- Michael A. DeJesus
- Department of Computer Science, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
| | - Chaitra Ambadipudi
- Department of Computer Science, Texas A&M University, College Station, Texas, United States of America
| | - Richard Baker
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Christopher Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Thomas R. Ioerger
- Department of Computer Science, Texas A&M University, College Station, Texas, United States of America
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128
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Evolution of Mycolic Acid Biosynthesis Genes and Their Regulation during Starvation in Mycobacterium tuberculosis. J Bacteriol 2015; 197:3797-811. [PMID: 26416833 DOI: 10.1128/jb.00433-15] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 09/22/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Mycobacterium tuberculosis, the etiological agent of tuberculosis, is a Gram-positive bacterium with a unique cell envelope composed of an essential outer membrane. Mycolic acids, which are very-long-chain (up to C100) fatty acids, are the major components of this mycomembrane. The enzymatic pathways involved in the biosynthesis and transport of mycolates are fairly well documented and are the targets of the major antituberculous drugs. In contrast, only fragmented information is available on the expression and regulation of the biosynthesis genes. In this study, we report that the hadA, hadB, and hadC genes, which code for the mycolate biosynthesis dehydratase enzymes, are coexpressed with three genes that encode proteins of the translational apparatus. Consistent with the well-established control of the translation potential by nutrient availability, starvation leads to downregulation of the hadABC genes along with most of the genes required for the synthesis, modification, and transport of mycolates. The downregulation of a subset of the biosynthesis genes is partially dependent on RelMtb, the key enzyme of the stringent response. We also report the phylogenetic evolution scenario that has shaped the current genetic organization, characterized by the coregulation of the hadABC operon with genes of the translational apparatus and with genes required for the modification of the mycolates. IMPORTANCE Mycobacterium tuberculosis infects one-third of the human population worldwide, and despite the available therapeutic arsenal, it continues to kill millions of people each year. There is therefore an urgent need to identify new targets and develop a better understanding of how the bacterium is adapting itself to host defenses during infection. A prerequisite of this understanding is knowledge of how this adaptive skill has been implanted by evolution. Nutrient scarcity is an environmental condition the bacterium has to cope with during infection. In many bacteria, adaptation to starvation relies partly on the stringent response. M. tuberculosis's unique outer membrane layer, the mycomembrane, is crucial for its viability and virulence. Despite its being the target of the major antituberculosis drugs, only scattered information exists on how the genes required for biosynthesis of the mycomembrane are expressed and regulated during starvation. This work has addressed this issue as a step toward the identification of new targets in the fight against M. tuberculosis.
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129
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Abstract
Human cytomegalovirus (HCMV) exhibits surprisingly high genomic diversity during natural infection although little is known about the limits or patterns of HCMV diversity among humans. To address this deficiency, we analyzed genomic diversity among congenitally infected infants. We show that there is an upper limit to HCMV genomic diversity in these patient samples, with ∼ 25% of the genome being devoid of polymorphisms. These low diversity regions were distributed across 26 loci that were preferentially located in DNA-processing genes. Furthermore, by developing, to our knowledge, the first genome-wide mutation and recombination rate maps for HCMV, we show that genomic diversity is positively correlated with these two rates. In contrast, median levels of viral genomic diversity did not vary between putatively single or mixed strain infections. We also provide evidence that HCMV populations isolated from vascular compartments of hosts from different continents are genetically similar and that polymorphisms in glycoproteins and regulatory proteins are enriched in these viral populations. This analysis provides the most highly detailed map of HCMV genomic diversity in human hosts to date and informs our understanding of the distribution of HCMV genomic diversity within human hosts.
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130
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Speer A, Sun J, Danilchanka O, Meikle V, Rowland JL, Walter K, Buck BR, Pavlenok M, Hölscher C, Ehrt S, Niederweis M. Surface hydrolysis of sphingomyelin by the outer membrane protein Rv0888 supports replication of Mycobacterium tuberculosis in macrophages. Mol Microbiol 2015; 97:881-97. [PMID: 26036301 DOI: 10.1111/mmi.13073] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2015] [Indexed: 12/19/2022]
Abstract
Sphingomyelinases secreted by pathogenic bacteria play important roles in host-pathogen interactions ranging from interfering with phagocytosis and oxidative burst to iron acquisition. This study shows that the Mtb protein Rv0888 possesses potent sphingomyelinase activity cleaving sphingomyelin, a major lipid in eukaryotic cells, into ceramide and phosphocholine, which are then utilized by Mtb as carbon, nitrogen and phosphorus sources, respectively. An Mtb rv0888 deletion mutant did not grow on sphingomyelin as a sole carbon source anymore and replicated poorly in macrophages indicating that Mtb utilizes sphingomyelin during infection. Rv0888 is an unusual membrane protein with a surface-exposed C-terminal sphingomyelinase domain and a putative N-terminal channel domain that mediated glucose and phosphocholine uptake across the outer membrane in an M. smegmatis porin mutant. Hence, we propose to name Rv0888 as SpmT (sphingomyelinase of Mycobacterium tuberculosis). Erythrocyte membranes contain up to 27% sphingomyelin. The finding that Rv0888 accounts for half of Mtb's hemolytic activity is consistent with its sphingomyelinase activity and the observation that Rv0888 levels are increased in the presence of erythrocytes and sphingomyelin by 5- and 100-fold, respectively. Thus, Rv0888 is a novel outer membrane protein that enables Mtb to utilize sphingomyelin as a source of several essential nutrients during intracellular growth.
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Affiliation(s)
- Alexander Speer
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jim Sun
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Olga Danilchanka
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Virginia Meikle
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jennifer L Rowland
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Kerstin Walter
- Infection Immunology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Borstel, Germany
| | - Bradford R Buck
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Mikhail Pavlenok
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Christoph Hölscher
- Infection Immunology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Borstel, Germany.,Cluster of Excellence 'Inflammation at Interfaces', Christian-Albrechts-University, Kiel, Germany
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
| | - Michael Niederweis
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
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131
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Kieser KJ, Boutte CC, Kester JC, Baer CE, Barczak AK, Meniche X, Chao MC, Rego EH, Sassetti CM, Fortune SM, Rubin EJ. Phosphorylation of the Peptidoglycan Synthase PonA1 Governs the Rate of Polar Elongation in Mycobacteria. PLoS Pathog 2015; 11:e1005010. [PMID: 26114871 PMCID: PMC4483258 DOI: 10.1371/journal.ppat.1005010] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 06/07/2015] [Indexed: 01/11/2023] Open
Abstract
Cell growth and division are required for the progression of bacterial infections. Most rod-shaped bacteria grow by inserting new cell wall along their mid-section. However, mycobacteria, including the human pathogen Mycobacterium tuberculosis, produce new cell wall material at their poles. How mycobacteria control this different mode of growth is incompletely understood. Here we find that PonA1, a penicillin binding protein (PBP) capable of transglycosylation and transpeptidation of cell wall peptidoglycan (PG), is a major governor of polar growth in mycobacteria. PonA1 is required for growth of Mycobacterium smegmatis and is critical for M. tuberculosis during infection. In both cases, PonA1’s catalytic activities are both required for normal cell length, though loss of transglycosylase activity has a more pronounced effect than transpeptidation. Mutations that alter the amount or the activity of PonA1 result in abnormal formation of cell poles and changes in cell length. Moreover, altered PonA1 activity results in dramatic differences in antibiotic susceptibility, suggesting that a balance between the two enzymatic activities of PonA1 is critical for survival. We also find that phosphorylation of a cytoplasmic region of PonA1 is required for normal activity. Mutations in a critical phosphorylated residue affect transglycosylase activity and result in abnormal rates of cell elongation. Together, our data indicate that PonA1 is a central determinant of polar growth in mycobacteria, and its governance of cell elongation is required for robust cell fitness during both host-induced and antibiotic stress. Bacterial infections rely on continued bacterial growth. Studying cell growth is particularly important for pathogens such as Mycobacterium tuberculosis that grow differently than model organisms. Unlike Escherichia coli or Bacillus subtilis, which grow by incorporating cell wall material along their body, mycobacteria grow from the pole. It remains unclear how mycobacteria construct and extend their poles. Our work identifies a cell wall synthase, PonA1, as a key determinant of mycobacterial polar growth. PonA1 governs polar growth through two enzymatic activities that build the cell wall’s peptidoglycan (PG); both of these activities are required for normal cell growth. Changes in the amount or activity of PonA1 leads to misplaced cell poles and inhibition of cell proliferation. PonA1 is phosphorylated, an unusual modification for PG synthases. This phosphorylation tunes the rate of cell elongation. Changing PonA1’s regulatory or enzymatic activity impacts the survival of cells in the host or when treated with antibiotics. Our work shows how mycobacterial cell pole construction and cell fitness is governed by a major cell wall synthase; these findings may have implications for other bacteria that elongate from their poles.
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Affiliation(s)
- Karen J. Kieser
- Department of Immunology and Infectious Disease, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Cara C. Boutte
- Department of Immunology and Infectious Disease, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Jemila C. Kester
- Department of Immunology and Infectious Disease, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Christina E. Baer
- Department of Microbiology and Physiological Systems, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Amy K. Barczak
- Division of Infectious Disease, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Xavier Meniche
- Department of Microbiology and Physiological Systems, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Michael C. Chao
- Department of Immunology and Infectious Disease, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - E. Hesper Rego
- Department of Immunology and Infectious Disease, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Christopher M. Sassetti
- Department of Microbiology and Physiological Systems, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Sarah M. Fortune
- Department of Immunology and Infectious Disease, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Eric J. Rubin
- Department of Immunology and Infectious Disease, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
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132
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A Genome-Wide Screen Reveals that the Vibrio cholerae Phosphoenolpyruvate Phosphotransferase System Modulates Virulence Gene Expression. Infect Immun 2015; 83:3381-95. [PMID: 26056384 DOI: 10.1128/iai.00411-15] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 06/05/2015] [Indexed: 12/21/2022] Open
Abstract
Diverse environmental stimuli and a complex network of regulatory factors are known to modulate expression of Vibrio cholerae's principal virulence factors. However, there is relatively little known about how metabolic factors impinge upon the pathogen's well-characterized cascade of transcription factors that induce expression of cholera toxin and the toxin-coregulated pilus (TCP). Here, we used a transposon insertion site (TIS) sequencing-based strategy to identify new factors required for expression of tcpA, which encodes the major subunit of TCP, the organism's chief intestinal colonization factor. Besides identifying most of the genes known to modulate tcpA expression, the screen yielded ptsI and ptsH, which encode the enzyme I (EI) and Hpr components of the V. cholerae phosphoenolpyruvate phosphotransferase system (PTS). In addition to reduced expression of TcpA, strains lacking EI, Hpr, or the associated EIIA(Glc) protein produced less cholera toxin (CT) and had a diminished capacity to colonize the infant mouse intestine. The PTS modulates virulence gene expression by regulating expression of tcpPH and aphAB, which themselves control expression of toxT, the central activator of virulence gene expression. One mechanism by which PTS promotes virulence gene expression appears to be by modulating the amounts of intracellular cyclic AMP (cAMP). Our findings reveal that the V. cholerae PTS is an additional modulator of the ToxT regulon and demonstrate the potency of loss-of-function TIS sequencing screens for defining regulatory networks.
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133
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Characterization of DNA substrate specificities of apurinic/apyrimidinic endonucleases from Mycobacterium tuberculosis. DNA Repair (Amst) 2015; 33:1-16. [PMID: 26043425 DOI: 10.1016/j.dnarep.2015.05.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 04/19/2015] [Accepted: 05/18/2015] [Indexed: 11/24/2022]
Abstract
Apurinic/apyrimidinic (AP) endonucleases are key enzymes involved in the repair of abasic sites and DNA strand breaks. Pathogenic bacteria Mycobacterium tuberculosis contains two AP endonucleases: MtbXthA and MtbNfo members of the exonuclease III and endonuclease IV families, which are exemplified by Escherichia coli Xth and Nfo, respectively. It has been shown that both MtbXthA and MtbNfo contain AP endonuclease and 3'→5' exonuclease activities. However, it remains unclear whether these enzymes hold 3'-repair phosphodiesterase and nucleotide incision repair (NIR) activities. Here, we report that both mycobacterial enzymes have 3'-repair phosphodiesterase and 3'-phosphatase, and MtbNfo contains in addition a very weak NIR activity. Interestingly, depending on pH, both enzymes require different concentrations of divalent cations: 0.5mM MnCl2 at pH 7.6 and 10 mM at pH 6.5. MtbXthA requires a low ionic strength and 37 °C, while MtbNfo requires high ionic strength (200 mM KCl) and has a temperature optimum at 60 °C. Point mutation analysis showed that D180 and N182 in MtbXthA and H206 and E129 in MtbNfo are critical for enzymes activities. The steady-state kinetic parameters indicate that MtbXthA removes 3'-blocking sugar-phosphate and 3'-phosphate moieties at DNA strand breaks with an extremely high efficiency (kcat/KM=440 and 1280 μM(-1)∙min(-1), respectively), while MtbNfo exhibits much lower 3'-repair activities (kcat/KM=0.26 and 0.65 μM(-1)∙min(-1), respectively). Surprisingly, both MtbXthA and MtbNfo exhibited very weak AP site cleavage activities, with kinetic parameters 100- and 300-fold lower, respectively, as compared with the results reported previously. Expression of MtbXthA and MtbNfo reduced the sensitivity of AP endonuclease-deficient E. coli xth nfo strain to methylmethanesulfonate and H2O2 to various degrees. Taken together, these data establish the DNA substrate specificity of M. tuberculosis AP endonucleases and suggest their possible role in the repair of oxidative DNA damage generated by endogenous and host- imposed factors.
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134
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Alumasa JN, Keiler KC. Clicking on trans-translation drug targets. Front Microbiol 2015; 6:498. [PMID: 26042115 PMCID: PMC4436901 DOI: 10.3389/fmicb.2015.00498] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 05/06/2015] [Indexed: 11/20/2022] Open
Affiliation(s)
- John N Alumasa
- Department of Biochemistry and Molecular Biology, Pennsylvania State University University Park, PA, USA
| | - Kenneth C Keiler
- Department of Biochemistry and Molecular Biology, Pennsylvania State University University Park, PA, USA
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135
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Prisic S, Hwang H, Dow A, Barnaby O, Pan TS, Lonzanida JA, Chazin WJ, Steen H, Husson RN. Zinc regulates a switch between primary and alternative S18 ribosomal proteins in Mycobacterium tuberculosis. Mol Microbiol 2015; 97:263-80. [PMID: 25858183 DOI: 10.1111/mmi.13022] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/02/2015] [Indexed: 12/21/2022]
Abstract
The Mycobacterium tuberculosis genome encodes five putative 'alternative' ribosomal proteins whose expression is repressed at high Zn(2+) concentration. Each alternative protein has a primary homologue that is predicted to bind Zn(2+). We hypothesized that zinc triggers a switch between these paired homologous proteins and therefore chose one of these pairs, S18-1/S18-2, to study mechanisms of the predicted competition for their incorporation into ribosomes. Our data show that Zn(2+)-depletion causes accumulation of both S18-2 mRNA and protein. In contrast, S18-1 mRNA levels are unchanged to slightly elevated under Zn(2+)-limited conditions. However, the amount of S18-1 protein is markedly decreased. We further demonstrate that both S18 proteins interact with ribosomal protein S6, a committed step in ribosome biogenesis. Zn(2+) is absolutely required for the S18-1/S6 interaction while it is dispensable for S18-2/S6 dimer formation. These data suggest a model in which S18-1 is the dominant ribosome constituent in high zinc conditions, e.g. inside of phagosomes, but that it can be replaced by S18-2 when zinc is deficient, e.g. in the extracellular milieu. Consequently, Zn(2+)-depletion may serve as a signal for building alternative ribosomes when M. tuberculosis is released from macrophages, to allow survival in the extracellular environment.
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Affiliation(s)
- Sladjana Prisic
- Division of Infectious Diseases, Boston Children's Hospital/Harvard Medical School, Boston, MA.,Department of Microbiology, University of Hawaii at Manoa, Honolulu, HI
| | - Hyonson Hwang
- Department of Pathology, Boston Children's Hospital/Harvard Medical School, Boston, MA
| | - Allexa Dow
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, HI
| | - Omar Barnaby
- Department of Pathology, Boston Children's Hospital/Harvard Medical School, Boston, MA
| | - Tenny S Pan
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, HI
| | | | - Walter J Chazin
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Hanno Steen
- Department of Pathology, Boston Children's Hospital/Harvard Medical School, Boston, MA
| | - Robert N Husson
- Division of Infectious Diseases, Boston Children's Hospital/Harvard Medical School, Boston, MA
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136
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Mendum TA, Wu H, Kierzek AM, Stewart GR. Lipid metabolism and Type VII secretion systems dominate the genome scale virulence profile of Mycobacterium tuberculosis in human dendritic cells. BMC Genomics 2015; 16:372. [PMID: 25956932 PMCID: PMC4425887 DOI: 10.1186/s12864-015-1569-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 04/23/2015] [Indexed: 12/20/2022] Open
Abstract
Background Mycobacterium tuberculosis continues to kill more people than any other bacterium. Although its archetypal host cell is the macrophage, it also enters, and survives within, dendritic cells (DCs). By modulating the behaviour of the DC, M. tuberculosis is able to manipulate the host’s immune response and establish an infection. To identify the M. tuberculosis genes required for survival within DCs we infected primary human DCs with an M. tuberculosis transposon library and identified mutations with a reduced ability to survive. Results Parallel sequencing of the transposon inserts of the surviving mutants identified a large number of genes as being required for optimal intracellular fitness in DCs. Loci whose mutation attenuated intracellular survival included those involved in synthesising cell wall lipids, not only the well-established virulence factors, pDIM and cord factor, but also sulfolipids and PGL, which have not previously been identified as having a direct virulence role in cells. Other attenuated loci included the secretion systems ESX-1, ESX-2 and ESX-4, alongside many PPE genes, implicating a role for ESX-5. In contrast the canonical ESAT-6 family of ESX substrates did not have intra-DC fitness costs suggesting an alternative ESX-1 associated virulence mechanism. With the aid of a gene-nutrient interaction model, metabolic processes such as cholesterol side chain catabolism, nitrate reductase and cysteine-methionine metabolism were also identified as important for survival in DCs. Conclusion We conclude that many of the virulence factors required for survival in DC are shared with macrophages, but that survival in DCs also requires several additional functions, such as cysteine-methionine metabolism, PGLs, sulfolipids, ESX systems and PPE genes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1569-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tom A Mendum
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK.
| | - Huihai Wu
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK.
| | - Andrzej M Kierzek
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK.
| | - Graham R Stewart
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK.
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137
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Uhía I, Williams KJ, Shahrezaei V, Robertson BD. Mycobacterial Growth. Cold Spring Harb Perspect Med 2015; 5:cshperspect.a021097. [PMID: 25957314 DOI: 10.1101/cshperspect.a021097] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
In this work, we review progress made in understanding the molecular underpinnings of growth and division in mycobacteria, concentrating on work published since the last comprehensive review ( Hett and Rubin 2008). We have focused on exciting work making use of new time-lapse imaging technologies coupled with reporter-gene fusions and antimicrobial treatment to generate insights into how mycobacteria grow and divide in a heterogeneous manner. We try to reconcile the different observations reported, providing a model of how they might fit together. We also review the topic of mycobacterial spores, which has generated considerable discussion during the last few years. Resuscitation promoting factors, and regulation of growth and division, have also been actively researched, and we summarize progress in these areas.
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Affiliation(s)
- Iria Uhía
- Department of Medicine, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Kerstin J Williams
- Department of Medicine, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Vahid Shahrezaei
- Department of Mathematics, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Brian D Robertson
- Department of Medicine, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, United Kingdom
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138
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Tn-seq explorer: a tool for analysis of high-throughput sequencing data of transposon mutant libraries. PLoS One 2015; 10:e0126070. [PMID: 25938432 PMCID: PMC4418687 DOI: 10.1371/journal.pone.0126070] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 03/28/2015] [Indexed: 11/28/2022] Open
Abstract
Tn-seq is a high throughput technique for analysis of transposon mutant libraries. Tn-seq Explorer was developed as a convenient and easy-to-use package of tools for exploration of the Tn-seq data. In a typical application, the user will have obtained a collection of sequence reads adjacent to transposon insertions in a reference genome. The reads are first aligned to the reference genome using one of the tools available for this task. Tn-seq Explorer reads the alignment and the gene annotation, and provides the user with a set of tools to investigate the data and identify possibly essential or advantageous genes as those that contain significantly low counts of transposon insertions. Emphasis is placed on providing flexibility in selecting parameters and methodology most appropriate for each particular dataset. Tn-seq Explorer is written in Java as a menu-driven, stand-alone application. It was tested on Windows, Mac OS, and Linux operating systems. The source code is distributed under the terms of GNU General Public License. The program and the source code are available for download at http://www.cmbl.uga.edu/downloads/programs/Tn_seq_Explorer/ and https://github.com/sina-cb/Tn-seqExplorer.
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139
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Periwal V, Patowary A, Vellarikkal SK, Gupta A, Singh M, Mittal A, Jeyapaul S, Chauhan RK, Singh AV, Singh PK, Garg P, Katoch VM, Katoch K, Chauhan DS, Sivasubbu S, Scaria V. Comparative whole-genome analysis of clinical isolates reveals characteristic architecture of Mycobacterium tuberculosis pangenome. PLoS One 2015; 10:e0122979. [PMID: 25853708 PMCID: PMC4390332 DOI: 10.1371/journal.pone.0122979] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 02/26/2015] [Indexed: 11/18/2022] Open
Abstract
The tubercle complex consists of closely related mycobacterium species which appear to be variants of a single species. Comparative genome analysis of different strains could provide useful clues and insights into the genetic diversity of the species. We integrated genome assemblies of 96 strains from Mycobacterium tuberculosis complex (MTBC), which included 8 Indian clinical isolates sequenced and assembled in this study, to understand its pangenome architecture. We predicted genes for all the 96 strains and clustered their respective CDSs into homologous gene clusters (HGCs) to reveal a hard-core, soft-core and accessory genome component of MTBC. The hard-core (HGCs shared amongst 100% of the strains) was comprised of 2,066 gene clusters whereas the soft-core (HGCs shared amongst at least 95% of the strains) comprised of 3,374 gene clusters. The change in the core and accessory genome components when observed as a function of their size revealed that MTBC has an open pangenome. We identified 74 HGCs that were absent from reference strains H37Rv and H37Ra but were present in most of clinical isolates. We report PCR validation on 9 candidate genes depicting 7 genes completely absent from H37Rv and H37Ra whereas 2 genes shared partial homology with them accounting to probable insertion and deletion events. The pangenome approach is a promising tool for studying strain specific genetic differences occurring within species. We also suggest that since selecting appropriate target genes for typing purposes requires the expected target gene be present in all isolates being typed, therefore estimating the core-component of the species becomes a subject of prime importance.
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Affiliation(s)
- Vinita Periwal
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi—110007, India
- Academy of Scientific & Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi 110001, India
| | - Ashok Patowary
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi—110007, India
| | - Shamsudheen Karuthedath Vellarikkal
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi—110007, India
- Academy of Scientific & Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi 110001, India
| | - Anju Gupta
- Open Source Drug Discovery Unit, Council of Scientific and Industrial Research (CSIR), Anusandhan Bhavan, 2 Rafi Marg, New Delhi 110001, India
| | - Meghna Singh
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi—110007, India
- Academy of Scientific & Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi 110001, India
| | - Ashish Mittal
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi—110007, India
| | - Shamini Jeyapaul
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi—110007, India
| | - Rajendra Kumar Chauhan
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi—110007, India
| | - Ajay Vir Singh
- National JALMA Institute of Leprosy and other Mycobacterial Diseases, Post Box No.101,Tajganj, Agra-282001, India
| | - Pravin Kumar Singh
- National JALMA Institute of Leprosy and other Mycobacterial Diseases, Post Box No.101,Tajganj, Agra-282001, India
| | - Parul Garg
- National JALMA Institute of Leprosy and other Mycobacterial Diseases, Post Box No.101,Tajganj, Agra-282001, India
| | - Viswa Mohan Katoch
- National JALMA Institute of Leprosy and other Mycobacterial Diseases, Post Box No.101,Tajganj, Agra-282001, India
| | - Kiran Katoch
- National JALMA Institute of Leprosy and other Mycobacterial Diseases, Post Box No.101,Tajganj, Agra-282001, India
| | - Devendra Singh Chauhan
- National JALMA Institute of Leprosy and other Mycobacterial Diseases, Post Box No.101,Tajganj, Agra-282001, India
| | - Sridhar Sivasubbu
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi—110007, India
- * E-mail: (VS); (SS)
| | - Vinod Scaria
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi—110007, India
- * E-mail: (VS); (SS)
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140
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Yu G, Cui Z, Sun X, Peng J, Jiang J, Wu W, Huang W, Chu K, Zhang L, Ge B, Li Y. Gene expression analysis of two extensively drug-resistant tuberculosis isolates show that two-component response systems enhance drug resistance. Tuberculosis (Edinb) 2015; 95:303-14. [PMID: 25869645 DOI: 10.1016/j.tube.2015.03.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 03/21/2015] [Indexed: 10/23/2022]
Abstract
Global analysis of expression profiles using DNA microarrays was performed between a reference strain H37Rv and two clinical extensively drug-resistant isolates in response to three anti-tuberculosis drug exposures (isoniazid, capreomycin, and rifampicin). A deep analysis was then conducted using a combination of genome sequences of the resistant isolates, resistance information, and related public microarray data. Certain known resistance-associated gene sets were significantly overrepresented in upregulated genes in the resistant isolates relative to that observed in H37Rv, which suggested a link between resistance and expression levels of particular genes. In addition, isoniazid and capreomycin response genes, but not rifampicin, either obtained from published works or our data, were highly consistent with the differentially expressed genes of resistant isolates compared to those of H37Rv, indicating a strong association between drug resistance of the isolates and genes differentially regulated by isoniazid and capreomycin exposures. Based on these results, 92 genes of the studied isolates were identified as candidate resistance genes, 10 of which are known resistance-related genes. Regulatory network analysis of candidate resistance genes using published networks and literature mining showed that three two-component regulatory systems and regulator CRP play significant roles in the resistance of the isolates by mediating the production of essential envelope components. Finally, drug sensitivity testing indicated strong correlations between expression levels of these regulatory genes and sensitivity to multiple anti-tuberculosis drugs in Mycobacterium tuberculosis. These findings may provide novel insights into the mechanism underlying the emergence and development of drug resistance in resistant tuberculosis isolates and useful clues for further studies on this issue.
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Affiliation(s)
- Guohua Yu
- State Key Lab of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, College of Life Sciences, Fudan University, Shanghai 200433, PR China
| | - Zhenling Cui
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Medical School, Tongji University, Shanghai 200433, PR China
| | - Xian Sun
- State Key Lab of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, College of Life Sciences, Fudan University, Shanghai 200433, PR China
| | - Jinfu Peng
- State Key Lab of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, College of Life Sciences, Fudan University, Shanghai 200433, PR China
| | - Jun Jiang
- State Key Lab of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, College of Life Sciences, Fudan University, Shanghai 200433, PR China
| | - Wei Wu
- State Key Lab of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, College of Life Sciences, Fudan University, Shanghai 200433, PR China
| | - Wenhua Huang
- State Key Lab of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, College of Life Sciences, Fudan University, Shanghai 200433, PR China
| | - Kaili Chu
- State Key Lab of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, College of Life Sciences, Fudan University, Shanghai 200433, PR China
| | - Lu Zhang
- State Key Lab of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, College of Life Sciences, Fudan University, Shanghai 200433, PR China
| | - Baoxue Ge
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Medical School, Tongji University, Shanghai 200433, PR China.
| | - Yao Li
- State Key Lab of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, College of Life Sciences, Fudan University, Shanghai 200433, PR China.
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141
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Gene silencing by CRISPR interference in mycobacteria. Nat Commun 2015; 6:6267. [PMID: 25711368 DOI: 10.1038/ncomms7267] [Citation(s) in RCA: 182] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 01/12/2015] [Indexed: 11/08/2022] Open
Abstract
Recombination-based tools for introducing targeted genomic mutations in Mycobacterium tuberculosis are not efficient due to higher rate of illegitimate recombination compared with homologous DNA exchange. Moreover, involvement of multiple steps and specialized reagents make these tools cost ineffective. Here we introduce a novel clustered regularly interspaced short palindromic repeat (CRISPR) interference (CRISPRi) approach that efficiently represses expression of target genes in mycobacteria. CRISPRi system involves co-expression of the catalytically dead form of RNA-guided DNA endonuclease from the type II CRISPR system known as dCas9 and the small guide RNA specific to a target sequence, resulting in the DNA recognition complex that interferes with the transcription of corresponding DNA sequence. We show that co-expression of the codon-optimized dCas9 of S. pyogenes with sequence-specific guide RNA results in complete repression of individual or multiple targets in mycobacteria. CRISPRi thus offers a simple, rapid and cost-effective tool for selective control of gene expression in mycobacteria.
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142
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Abstract
Very few chemically novel agents have been approved for antibacterial chemotherapies during the last 50 yr. Yet new antibacterial drugs are needed to reduce the impact on global health of an increasing number of drug-resistant infections, including highly drug-resistant forms of tuberculosis. This review discusses how genetic approaches can be used to study the mechanism of action of whole-cell screening hits and facilitate target-driven strategies for antimicrobial drug development.
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Affiliation(s)
- Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065
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143
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A novel antimycobacterial compound acts as an intracellular iron chelator. Antimicrob Agents Chemother 2015; 59:2256-64. [PMID: 25645825 DOI: 10.1128/aac.05114-14] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Efficient iron acquisition is crucial for the pathogenesis of Mycobacterium tuberculosis. Mycobacterial iron uptake and metabolism are therefore attractive targets for antitubercular drug development. Resistance mutations against a novel pyrazolopyrimidinone compound (PZP) that is active against M. tuberculosis have been identified within the gene cluster encoding the ESX-3 type VII secretion system. ESX-3 is required for mycobacterial iron acquisition through the mycobactin siderophore pathway, which could indicate that PZP restricts mycobacterial growth by targeting ESX-3 and thus iron uptake. Surprisingly, we show that ESX-3 is not the cellular target of the compound. We demonstrate that PZP indeed targets iron metabolism; however, we found that instead of inhibiting uptake of iron, PZP acts as an iron chelator, and we present evidence that the compound restricts mycobacterial growth by chelating intrabacterial iron. Thus, we have unraveled the unexpected mechanism of a novel antimycobacterial compound.
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144
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Mdluli K, Kaneko T, Upton A. The tuberculosis drug discovery and development pipeline and emerging drug targets. Cold Spring Harb Perspect Med 2015; 5:a021154. [PMID: 25635061 PMCID: PMC4448709 DOI: 10.1101/cshperspect.a021154] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The recent accelerated approval for use in extensively drug-resistant and multidrug-resistant-tuberculosis (MDR-TB) of two first-in-class TB drugs, bedaquiline and delamanid, has reinvigorated the TB drug discovery and development field. However, although several promising clinical development programs are ongoing to evaluate new TB drugs and regimens, the number of novel series represented is few. The global early-development pipeline is also woefully thin. To have a chance of achieving the goal of better, shorter, safer TB drug regimens with utility against drug-sensitive and drug-resistant disease, a robust and diverse global TB drug discovery pipeline is key, including innovative approaches that make use of recently acquired knowledge on the biology of TB. Fortunately, drug discovery for TB has resurged in recent years, generating compounds with varying potential for progression into developable leads. In parallel, advances have been made in understanding TB pathogenesis. It is now possible to apply the lessons learned from recent TB hit generation efforts and newly validated TB drug targets to generate the next wave of TB drug leads. Use of currently underexploited sources of chemical matter and lead-optimization strategies may also improve the efficiency of future TB drug discovery. Novel TB drug regimens with shorter treatment durations must target all subpopulations of Mycobacterium tuberculosis existing in an infection, including those responsible for the protracted TB treatment duration. This review summarizes the current TB drug development pipeline and proposes strategies for generating improved hits and leads in the discovery phase that could help achieve this goal.
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Affiliation(s)
- Khisimuzi Mdluli
- Global Alliance for TB Drug Development, New York, New York 10005
| | - Takushi Kaneko
- Global Alliance for TB Drug Development, New York, New York 10005
| | - Anna Upton
- Global Alliance for TB Drug Development, New York, New York 10005
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145
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Abstract
The database of essential genes (DEG, available at http://www.essentialgene.org), constructed in 2003, has been timely updated to harbor essential-gene records of bacteria, archaea, and eukaryotes. DEG 10, the current release, includes not only essential protein-coding genes determined by genome-wide gene essentiality screens but also essential noncoding RNAs, promoters, regulatory sequences, and replication origins. Therefore, DEG 10 includes essential genomic elements under different conditions in three domains of life, with customizable BLAST tools. Based on the analysis of DEG 10, we show that the percentage of essential genes in bacterial genomes exhibits an exponential decay with increasing genome sizes. The functions, ATP binding (GO:0005524), GTP binding (GO:0005525), and DNA-directed RNA polymerase activity (GO:0003899), are likely required for organisms across life domains.
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146
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DeJesus MA, Ioerger TR. Capturing Uncertainty by Modeling Local Transposon Insertion Frequencies Improves Discrimination of Essential Genes. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2015; 12:92-102. [PMID: 26357081 DOI: 10.1109/tcbb.2014.2326857] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Transposon mutagenesis experiments enable the identification of essential genes in bacteria. Deep-sequencing of mutant libraries provides a large amount of high-resolution data on essentiality. Statistical methods developed to analyze this data have traditionally assumed that the probability of observing a transposon insertion is the same across the genome. This assumption, however, is inconsistent with the observed insertion frequencies from transposon mutant libraries of M. tuberculosis. We propose a modified Binomial model of essentiality that can characterize the insertion probability of individual genes in which we allow local variation in the background insertion frequency in different non-essential regions of the genome. Using the Metropolis-Hastings algorithm, samples of the posterior insertion probabilities were obtained for each gene, and the probability of each gene being essential is estimated. We compared our predictions to those of previous methods and show that, by taking into consideration local insertion frequencies, our method is capable of making more conservative predictions that better match what is experimentally known about essential and non-essential genes.
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147
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Long JE, DeJesus M, Ward D, Baker RE, Ioerger T, Sassetti CM. Identifying essential genes in Mycobacterium tuberculosis by global phenotypic profiling. Methods Mol Biol 2015; 1279:79-95. [PMID: 25636614 DOI: 10.1007/978-1-4939-2398-4_6] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Transposon sequencing (TnSeq) is a next-generation deep sequencing-based method to quantitatively assess the composition of complex mutant transposon libraries after pressure from selection. Although this method can be used for any organism in which transposon mutagenesis is possible, this chapter describes its use in Mycobacterium tuberculosis. More specifically, the methods for generating complex libraries through transposon mutagenesis, design of selective pressure, extraction of genomic DNA, amplification and quantification of transposon insertions through next-generation deep sequencing are covered. Determining gene essentiality and statistical analysis on data collected are also discussed.
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Affiliation(s)
- Jarukit E Long
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01655, USA
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148
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Abstract
Metabolism underpins the physiology and pathogenesis of Mycobacterium tuberculosis. However, although experimental mycobacteriology has provided key insights into the metabolic pathways that are essential for survival and pathogenesis, determining the metabolic status of bacilli during different stages of infection and in different cellular compartments remains challenging. Recent advances-in particular, the development of systems biology tools such as metabolomics-have enabled key insights into the biochemical state of M. tuberculosis in experimental models of infection. In addition, their use to elucidate mechanisms of action of new and existing antituberculosis drugs is critical for the development of improved interventions to counter tuberculosis. This review provides a broad summary of mycobacterial metabolism, highlighting the adaptation of M. tuberculosis as specialist human pathogen, and discusses recent insights into the strategies used by the host and infecting bacillus to influence the outcomes of the host-pathogen interaction through modulation of metabolic functions.
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Affiliation(s)
- Digby F Warner
- Medical Research Council/National Health Laboratory Services/University of Cape Town Molecular Mycobacteriology Research Unit and Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine and Division of Medical Microbiology, University of Cape Town, Rondebosch 7700, South Africa
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149
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Perry BJ, Yost CK. Construction of a mariner-based transposon vector for use in insertion sequence mutagenesis in selected members of the Rhizobiaceae. BMC Microbiol 2014; 14:298. [PMID: 25433486 PMCID: PMC4255674 DOI: 10.1186/s12866-014-0298-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Accepted: 11/18/2014] [Indexed: 12/11/2022] Open
Abstract
Background The Rhizobiaceae family of Gram-negative bacteria often engage in symbiosis with plants of economic importance. Historically, genetic studies to identify the function of individual genes, and characterize the biology of these bacteria have relied on the use of classical transposon mutagenesis. To increase the rate of scientific discovery in the Rhizobiaceae there is a need to adapt high-throughput genetic screens like insertion sequencing for use in this family of bacteria. Here we describe a Rhizobiaceae compatible MmeI-adapted mariner transposon that can be used with insertion sequencing for high-throughput genetic screening. Results The newly constructed mariner transposon pSAM_Rl mutagenized R. leguminosarum, S. meliloti, and A. tumefaciens at a high frequency. In R. leguminosarum, mutant pools were generated that saturated 88% of potential mariner insertions sites in the genome. Analysis of the R. leguminosarum transposon insertion sequencing data with a previously described hidden Markov model-based method resulted in assignment of the contribution of all annotated genes in the R. leguminosarum 3841 genome for growth on a complex medium. Good concordance was observed between genes observed to be required for growth on the complex medium, and previous studies. Conclusions The newly described Rhizobiaceaee compatible mariner transposon insertion sequencing vector pSAM_Rl has been shown to mutagenize at a high frequency and to be an effective tool for use in high-throughput genetic screening. The construction and validation of this transposon insertion sequencing tool for use in the Rhizobiziaceae will provide an opportunity for researchers in the Rhizobiaceae community to use high-throughput genetic screening, allowing for significant increase in the rate of genetic discovery, particularly given the recent release of genome sequences from many Rhizobiaceae strains. Electronic supplementary material The online version of this article (doi:10.1186/s12866-014-0298-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Benjamin J Perry
- Department of Biology, University of Regina, 3737 Wascana Parkway, Regina, SK, S4S 0A2, Canada.
| | - Christopher K Yost
- Department of Biology, University of Regina, 3737 Wascana Parkway, Regina, SK, S4S 0A2, Canada.
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150
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Succinate dehydrogenase is the regulator of respiration in Mycobacterium tuberculosis. PLoS Pathog 2014; 10:e1004510. [PMID: 25412183 PMCID: PMC4239112 DOI: 10.1371/journal.ppat.1004510] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 10/09/2014] [Indexed: 12/24/2022] Open
Abstract
In chronic infection, Mycobacterium tuberculosis bacilli are thought to enter a metabolic program that provides sufficient energy for maintenance of the protonmotive force, but is insufficient to meet the demands of cellular growth. We sought to understand this metabolic downshift genetically by targeting succinate dehydrogenase, the enzyme which couples the growth processes controlled by the TCA cycle with the energy production resulting from the electron transport chain. M. tuberculosis contains two operons which are predicted to encode succinate dehydrogenase enzymes (sdh-1 and sdh-2); we found that deletion of Sdh1 contributes to an inability to survive long term stationary phase. Stable isotope labeling and mass spectrometry revealed that Sdh1 functions as a succinate dehydrogenase during aerobic growth, and that Sdh2 is dispensable for this catalysis, but partially overlapping activities ensure that the loss of one enzyme can incompletely compensate for loss of the other. Deletion of Sdh1 disturbs the rate of respiration via the mycobacterial electron transport chain, resulting in an increased proportion of reduced electron carrier (menaquinol) which leads to increased oxygen consumption. The loss of respiratory control leads to an inability to recover from stationary phase. We propose a model in which succinate dehydrogenase is a governor of cellular respiration in the adaptation to low oxygen environments. This work establishes the principle that Mycobacterium tuberculosis undergoes a metabolic remodeling as oxygen concentrations fall that serves to decrease its rate of oxygen consumption and therefore oxidative phosphorylation. Furthermore, cells can be stimulated to respire, even in low oxygen conditions, by providing reducing equivalents to the respiratory chain by either genetic manipulation (deletion of succinate dehydrogenase) or by exogenous addition of reducing agents such as DTT. Thus, activation of persister cells may be accomplished by increasing their respiration rate in low oxygen conditions. These findings will inform the design of novel drug screens which should seek enhancers of cellular respiration to find compounds which will serve to shorten the duration of TB chemotherapy.
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