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Stupar M, Tan L, Kerr ED, De Voss CJ, Forde BM, Schulz BL, West NP. TcrXY is an acid-sensing two-component transcriptional regulator of Mycobacterium tuberculosis required for persistent infection. Nat Commun 2024; 15:1615. [PMID: 38388565 PMCID: PMC10883919 DOI: 10.1038/s41467-024-45343-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 01/22/2024] [Indexed: 02/24/2024] Open
Abstract
The ability of Mycobacterium tuberculosis (Mtb) to persist in the host complicates and prolongs tuberculosis (TB) patient chemotherapy. Here we demonstrate that a neglected two-component system (TCS) of Mtb, TcrXY, is an autoregulated acid-sensing TCS that controls a functionally diverse 70-gene regulon required for bacterial persistence. Characterisation of two representatives of this regulon, Rv3706c and Rv3705A, implicate these genes as key determinants for the survival of Mtb in vivo by serving as important effectors to mitigate redox stress at acidic pH. We show that genetic silencing of the response regulator tcrX using CRISPR interference attenuates the persistence of Mtb during chronic mouse infection and improves treatment with the two front-line anti-TB drugs, rifampicin and isoniazid. We propose that targeting TcrXY signal transduction blocks the ability of Mtb to sense and respond to acid stress, resulting in a disordered program of persistence to render the organism vulnerable to existing TB chemotherapy.
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Affiliation(s)
- Miljan Stupar
- School of Chemistry and Molecular Biosciences, Australian Infectious Disease Research Centre, The University of Queensland, Brisbane, Australia
| | - Lendl Tan
- School of Chemistry and Molecular Biosciences, Australian Infectious Disease Research Centre, The University of Queensland, Brisbane, Australia
| | - Edward D Kerr
- School of Chemistry and Molecular Biosciences, Australian Infectious Disease Research Centre, The University of Queensland, Brisbane, Australia
| | - Christopher J De Voss
- School of Chemistry and Molecular Biosciences, Australian Infectious Disease Research Centre, The University of Queensland, Brisbane, Australia
| | - Brian M Forde
- Faculty of Medicine, UQ Centre for Clinical Research, The University of Queensland, Brisbane, Australia
| | - Benjamin L Schulz
- School of Chemistry and Molecular Biosciences, Australian Infectious Disease Research Centre, The University of Queensland, Brisbane, Australia
| | - Nicholas P West
- School of Chemistry and Molecular Biosciences, Australian Infectious Disease Research Centre, The University of Queensland, Brisbane, Australia.
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Patil RS, Sharma S, Bhaskarwar AV, Nambiar S, Bhat NA, Koppolu MK, Bhukya H. TetR and OmpR family regulators in natural product biosynthesis and resistance. Proteins 2023. [PMID: 37874037 DOI: 10.1002/prot.26621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 08/30/2023] [Accepted: 10/06/2023] [Indexed: 10/25/2023]
Abstract
This article provides a comprehensive review and sequence-structure analysis of transcription regulator (TR) families, TetR and OmpR/PhoB, involved in specialized secondary metabolite (SSM) biosynthesis and resistance. Transcription regulation is a fundamental process, playing a crucial role in orchestrating gene expression to confer a survival advantage in response to frequent environmental stress conditions. This process, coupled with signal sensing, enables bacteria to respond to a diverse range of intra and extracellular signals. Thus, major bacterial signaling systems use a receptor domain to sense chemical stimuli along with an output domain responsible for transcription regulation through DNA-binding. Sensory and output domains on a single polypeptide chain (one component system, OCS) allow response to stimuli by allostery, that is, DNA-binding affinity modulation upon signal presence/absence. On the other hand, two component systems (TCSs) allow cross-talk between the sensory and output domains as they are disjoint and transmit information by phosphorelay to mount a response. In both cases, however, TRs play a central role. Biosynthesis of SSMs, which includes antibiotics, is heavily regulated by TRs as it diverts the cell's resources towards the production of these expendable compounds, which also have clinical applications. These TRs have evolved to relay information across specific signals and target genes, thus providing a rich source of unique mechanisms to explore towards addressing the rapid escalation in antimicrobial resistance (AMR). Here, we focus on the TetR and OmpR family TRs, which belong to OCS and TCS, respectively. These TR families are well-known examples of regulators in secondary metabolism and are ubiquitous across different bacteria, as they also participate in a myriad of cellular processes apart from SSM biosynthesis and resistance. As a result, these families exhibit higher sequence divergence, which is also evident from our bioinformatic analysis of 158 389 and 77 437 sequences from TetR and OmpR family TRs, respectively. The analysis of both sequence and structure allowed us to identify novel motifs in addition to the known motifs responsible for TR function and its structural integrity. Understanding the diverse mechanisms employed by these TRs is essential for unraveling the biosynthesis of SSMs. This can also help exploit their regulatory role in biosynthesis for significant pharmaceutical, agricultural, and industrial applications.
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Affiliation(s)
- Rachit S Patil
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Siddhant Sharma
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Aditya V Bhaskarwar
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Souparnika Nambiar
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Niharika A Bhat
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Mani Kanta Koppolu
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Hussain Bhukya
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
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Park HT, Lee SM, Ko S, Kim S, Park HE, Shin MK, Kim D, Yoo HS. Delineating transcriptional crosstalk between Mycobacterium avium subsp. paratuberculosis and human THP-1 cells at the early stage of infection via dual RNA-seq analysis. Vet Res 2022; 53:71. [PMID: 36100945 PMCID: PMC9469519 DOI: 10.1186/s13567-022-01089-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/13/2022] [Indexed: 12/02/2022] Open
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of Johne’s disease, a chronic debilitating disease in ruminants. To control this disease, it is crucial to understand immune evasion and the mechanism of persistence by analyzing the early phase interplays of the intracellular pathogens and their hosts. In the present study, host–pathogen interactions at the transcriptomic level were investigated in an in vitro macrophage infection model. When differentiated human THP-1 cells were infected with MAP, the expression of various genes associated with stress responses and metabolism was altered in both host and MAP at 3 h post-infection. MAP upregulates stress-responsive global gene regulators, such as two-component systems and sigma factors, in response to oxidative and cell wall stress. Downstream genes involved in type VII secretion systems, cell wall synthesis (polyketide biosynthesis proteins), and iron uptake were changed in response to the intracellular environment of macrophages. On the host side, upregulation of inflammatory cytokine genes was observed along with pattern recognition receptor genes. Notably, alterations in gene sets involved in arginine metabolism were observed in both the host and MAP, along with significant downregulation of NOS2 expression. These observations suggest that the utilization of metabolites such as arginine by intracellular MAP might affect host NO production. Our dual RNA-seq data can provide novel insights by capturing the global transcriptome with higher resolution, especially in MAP, thus enabling a more systematic understanding of host–pathogen interactions.
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Affiliation(s)
- Hong-Tae Park
- Department of Infectious Diseases, College of Veterinary Medicine, Seoul National University, Seoul, 08826, Korea
| | - Sang-Mok Lee
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Korea
| | - Seyoung Ko
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Korea
| | - Suji Kim
- Department of Infectious Diseases, College of Veterinary Medicine, Seoul National University, Seoul, 08826, Korea
| | - Hyun-Eui Park
- Department of Microbiology, College of Medicine, Research Institute of Life Science, Gyeongsang National University, Jinju, 52828, Korea
| | - Min-Kyoung Shin
- Department of Microbiology, College of Medicine, Research Institute of Life Science, Gyeongsang National University, Jinju, 52828, Korea
| | - Donghyuk Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Korea.
| | - Han Sang Yoo
- Department of Infectious Diseases, College of Veterinary Medicine, Seoul National University, Seoul, 08826, Korea.
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Zhang Z, Yu YX, Wang YG, Liu X, Wang LF, Zhang H, Liao MJ, Li B. Complete genome analysis of a virulent Vibrio scophthalmi strain VSc190401 isolated from diseased marine fish half-smooth tongue sole, Cynoglossus semilaevis. BMC Microbiol 2020; 20:341. [PMID: 33176689 PMCID: PMC7661262 DOI: 10.1186/s12866-020-02028-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 10/30/2020] [Indexed: 12/12/2022] Open
Abstract
Background Vibrio scophthalmi is an opportunistic bacterial pathogen, which is widely distributed in the marine environment. Earlier studies have suggested that it is a normal microorganism in the turbot gut. However, recent studies have confirmed that this bacterial strain can cause diseases in many different marine animals. Therefore, it is necessary to investigate its whole genome for better understanding its physiological and pathogenic mechanisms. Results In the present study, we obtained a pathogenic strain of V. scophthalmi from diseased half-smooth tongue sole (Cynoglossus semilaevis) and sequenced its whole genome. Its genome contained two circular chromosomes and two plasmids with a total size of 3,541,838 bp, which harbored 3185 coding genes. Among these genes, 2648, 2298, and 1915 genes could be found through annotation information in COG, Blast2GO, and KEGG databases, respectively. Moreover, 10 genomic islands were predicted to exist in the chromosome I through IslandViewer online system. Comparison analysis in VFDB and PHI databases showed that this strain had 334 potential virulence-related genes and 518 pathogen-host interaction-related genes. Although it contained genes related to four secretion systems of T1SS, T2SS, T4SS, and T6SS, there was only one complete T2SS secretion system. Based on CARD database blast results, 180 drug resistance genes belonging to 27 antibiotic resistance categories were found in the whole genome of such strain. However, there were many differences between the phenotype and genotype of drug resistance. Conclusions Based on the whole genome analysis, the pathogenic V. scophthalmi strain contained many types of genes related to pathogenicity and drug resistance. Moreover, it showed inconsistency between phenotype and genotype on drug resistance. These results suggested that the physiological mechanism seemed to be complex. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-020-02028-7.
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Affiliation(s)
- Zheng Zhang
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academic of Fishery Sciences, Qingdao, Shandong, 266071, PR China. .,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, Shandong, 266237, PR China.
| | - Yong-Xiang Yu
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academic of Fishery Sciences, Qingdao, Shandong, 266071, PR China
| | - Yin-Geng Wang
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academic of Fishery Sciences, Qingdao, Shandong, 266071, PR China. .,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, Shandong, 266237, PR China.
| | - Xiao Liu
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academic of Fishery Sciences, Qingdao, Shandong, 266071, PR China
| | - Li-Fang Wang
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academic of Fishery Sciences, Qingdao, Shandong, 266071, PR China
| | - Hao Zhang
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academic of Fishery Sciences, Qingdao, Shandong, 266071, PR China
| | - Mei-Jie Liao
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academic of Fishery Sciences, Qingdao, Shandong, 266071, PR China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, Shandong, 266237, PR China
| | - Bin Li
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academic of Fishery Sciences, Qingdao, Shandong, 266071, PR China
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Singh KK, Bhardwaj N, Sankhe GD, Udaykumar N, Singh R, Malhotra V, Saini DK. Acetylation of Response Regulator Proteins, TcrX and MtrA in M. tuberculosis Tunes their Phosphotransfer Ability and Modulates Two-Component Signaling Crosstalk. J Mol Biol 2019; 431:777-793. [DOI: 10.1016/j.jmb.2019.01.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 01/01/2019] [Accepted: 01/03/2019] [Indexed: 01/31/2023]
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Del Portillo P, García-Morales L, Menéndez MC, Anzola JM, Rodríguez JG, Helguera-Repetto AC, Ares MA, Prados-Rosales R, Gonzalez-y-Merchand JA, García MJ. Hypoxia Is Not a Main Stress When Mycobacterium tuberculosis Is in a Dormancy-Like Long-Chain Fatty Acid Environment. Front Cell Infect Microbiol 2019; 8:449. [PMID: 30687646 PMCID: PMC6333855 DOI: 10.3389/fcimb.2018.00449] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 12/18/2018] [Indexed: 12/12/2022] Open
Abstract
The capacity of Mycobacterium tuberculosis (Mtb) to sense, respond and adapt to a variable and hostile environment within the host makes it one of the most successful human pathogens. During different stages of infection, Mtb is surrounded by a plethora of lipid molecules and current evidence points out the relevance of fatty acids during the infectious process. In this study, we have compared the transcriptional response of Mtb to hypoxia in cultures supplemented with a mix of even long-chain fatty acids or dextrose as main carbon sources. Using RNA sequencing, we have identified differential expressed genes in early and late hypoxia, defined according to the in vitro Wayne and Hayes model, and compared the results with the exponential phase of growth in both carbon sources. We show that the number of genes over-expressed in the lipid medium was quite low in both, early and late hypoxia, relative to conditions including dextrose, with the exception of transcripts of stable and non-coding RNAs, which were more expressed in the fatty acid medium. We found that sigB and sigE were over-expressed in the early phase of hypoxia, confirming their pivotal role in early adaptation to low oxygen concentration independently of the carbon source. A drastic contrast was found with the transcriptional regulatory factors at early hypoxia. Only 2 transcriptional factors were over-expressed in early hypoxia in the lipid medium compared to 37 that were over-expressed in the dextrose medium. Instead of Rv0081, known to be the central regulator of hypoxia in dextrose, Rv2745c (ClgR), seems to play a main role in hypoxia in the fatty acid medium. The low level of genes associated to the stress-response during their adaptation to hypoxia in fatty acids, suggests that this lipid environment makes hypoxia a less stressful condition for the tubercle bacilli. Taken all together, these results indicate that the presence of lipid molecules shapes the metabolic response of Mtb to an adaptive state for different stresses within the host, including hypoxia. This fact could explain the success of Mtb to establish long-term survival during latent infection.
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Affiliation(s)
- Patricia Del Portillo
- Departamento de Biotecnología Molecular y Biología Computacional y Bioinformática, Corporación CorpoGen, Bogotá, Colombia
| | - Lázaro García-Morales
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Ciudad de México, Mexico
| | - María Carmen Menéndez
- Departamento de Medicina Preventiva, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
| | - Juan Manuel Anzola
- Departamento de Biotecnología Molecular y Biología Computacional y Bioinformática, Corporación CorpoGen, Bogotá, Colombia
| | - Juan Germán Rodríguez
- Departamento de Biotecnología Molecular y Biología Computacional y Bioinformática, Corporación CorpoGen, Bogotá, Colombia
| | - Addy Cecilia Helguera-Repetto
- Departamento de Inmunobioquímica, Torre de Investigación, Instituto Nacional de Perinatología Isidro Espinosa de los Reyes, Ciudad de México, Mexico
| | - Miguel A. Ares
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
| | - Rafael Prados-Rosales
- Departamento de Medicina Preventiva, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
- Center for Cooperative Research bioGUNE (CICbioGUNE), Bizkaia Technology Park, Derio, Spain
| | - Jorge A. Gonzalez-y-Merchand
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - María Jesús García
- Departamento de Medicina Preventiva, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
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Chawla M, Mishra S, Anand K, Parikh P, Mehta M, Vij M, Verma T, Singh P, Jakkala K, Verma HN, AjitKumar P, Ganguli M, Narain Seshasayee AS, Singh A. Redox-dependent condensation of the mycobacterial nucleoid by WhiB4. Redox Biol 2018; 19:116-133. [PMID: 30149290 PMCID: PMC6111044 DOI: 10.1016/j.redox.2018.08.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/02/2018] [Accepted: 08/11/2018] [Indexed: 12/22/2022] Open
Abstract
Oxidative stress response in bacteria is mediated through coordination between the regulators of oxidant-remediation systems (e.g. OxyR, SoxR) and nucleoid condensation (e.g. Dps, Fis). However, these genetic factors are either absent or rendered non-functional in the human pathogen Mycobacterium tuberculosis (Mtb). Therefore, how Mtb organizes genome architecture and regulates gene expression to counterbalance oxidative imbalance is unknown. Here, we report that an intracellular redox-sensor, WhiB4, dynamically links genome condensation and oxidative stress response in Mtb. Disruption of WhiB4 affects the expression of genes involved in maintaining redox homeostasis, central metabolism, and respiration under oxidative stress. Notably, disulfide-linked oligomerization of WhiB4 in response to oxidative stress activates the protein’s ability to condense DNA. Further, overexpression of WhiB4 led to hypercondensation of nucleoids, redox imbalance and increased susceptibility to oxidative stress, whereas WhiB4 disruption reversed this effect. In accordance with the findings in vitro, ChIP-Seq data demonstrated non-specific binding of WhiB4 to GC-rich regions of the Mtb genome. Lastly, data indicate that WhiB4 deletion affected the expression of ~ 30% of genes preferentially bound by the protein, suggesting both direct and indirect effects on gene expression. We propose that WhiB4 structurally couples Mtb’s response to oxidative stress with genome organization and transcription. Genome condensation is involved in the management of oxidative stress in bacteria. A relation between the genome condensation and oxidative stress is unclear in Mtb. A redox sensor WhiB4 calibrates genome-condensation and antioxidants in Mtb. Over-expression of WhiB4 hyper-condensed genome and induced killing by oxidants. WhiB4 deficiency delayed genome condensation and promoted oxidative stress survival.
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Affiliation(s)
- Manbeena Chawla
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Saurabh Mishra
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Kushi Anand
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Pankti Parikh
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Mansi Mehta
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Manika Vij
- Department of Structural Biology, CSIR-Institute of Genomics and Integrative Biology, South Campus, Mathura Road, New Delhi 110020, India; Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India
| | - Taru Verma
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India; Centre for BioSystems Science and Engineering (BSSE), Indian Institute of Science, Bangalore 560012, India
| | - Parul Singh
- National Centre for Biological Science, Bangalore 560065, India; SASTRA University, Thanjavur 613401, Tamil Nadu, India
| | - Kishor Jakkala
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - H N Verma
- Jaipur National University, Jagatpura, Jaipur 302017, India
| | - Parthasarathi AjitKumar
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Munia Ganguli
- Department of Structural Biology, CSIR-Institute of Genomics and Integrative Biology, South Campus, Mathura Road, New Delhi 110020, India; Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India
| | | | - Amit Singh
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India.
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Duncan C, Jamieson FB, Troudt J, Izzo L, Bielefeldt-Ohmann H, Izzo A, Mehaffy C. Whole transcriptomic and proteomic analyses of an isogenic M. tuberculosis clinical strain with a naturally occurring 15 Kb genomic deletion. PLoS One 2017; 12:e0179996. [PMID: 28650996 PMCID: PMC5484546 DOI: 10.1371/journal.pone.0179996] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 06/07/2017] [Indexed: 11/19/2022] Open
Abstract
Tuberculosis remains one of the most difficult to control infectious diseases in the world. Many different factors contribute to the complexity of this disease. These include the ability of the host to control the infection which may directly relate to nutritional status, presence of co-morbidities and genetic predisposition. Pathogen factors, in particular the ability of different Mycobacterium tuberculosis strains to respond to the harsh environment of the host granuloma, which includes low oxygen and nutrient availability and the presence of damaging radical oxygen and nitrogen species, also play an important role in the success of different strains to cause disease. In this study we evaluated the impact of a naturally occurring 12 gene 15 Kb genomic deletion on the physiology and virulence of M. tuberculosis. The strains denominated ON-A WT (wild type) and ON-A NM (natural mutant) were isolated from a previously reported TB outbreak in an inner city under-housed population in Toronto, Canada. Here we subjected these isogenic strains to transcriptomic (via RNA-seq) and proteomic analyses and identified several gene clusters with differential expression in the natural mutant, including the DosR regulon and the molybdenum cofactor biosynthesis genes, both of which were found in lower abundance in the natural mutant. We also demonstrated lesser virulence of the natural mutant in the guinea pig animal model. Overall, our findings suggest that the ON-A natural mutant is less fit to cause disease, but nevertheless has the potential to cause extended transmission in at-risk populations.
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Affiliation(s)
| | - Frances B. Jamieson
- Public Health Ontario, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - JoLynn Troudt
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States of America
| | - Linda Izzo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States of America
| | - Helle Bielefeldt-Ohmann
- School of Veterinary Science, University of Queensland, Gatton, QLD, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
- Australian Infectious Diseases Research Centre, University of Queensland, St Lucia, QLD, Australia
| | - Angelo Izzo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States of America
| | - Carolina Mehaffy
- Public Health Ontario, Toronto, ON, Canada
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States of America
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9
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Mashruwala AA, Boyd JM. The Staphylococcus aureus SrrAB Regulatory System Modulates Hydrogen Peroxide Resistance Factors, Which Imparts Protection to Aconitase during Aerobic Growth. PLoS One 2017; 12:e0170283. [PMID: 28099473 PMCID: PMC5242492 DOI: 10.1371/journal.pone.0170283] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 01/03/2017] [Indexed: 01/09/2023] Open
Abstract
The SrrAB two-component regulatory system (TCRS) positively influences the transcription of genes involved in aerobic respiration in response to changes in respiratory flux. Hydrogen peroxide (H2O2) can arise as a byproduct of spontaneous interactions between dioxygen and components of respiratory pathways. H2O2 damages cellular factors including protein associated iron-sulfur cluster prosthetic groups. We found that a Staphylococcus aureus strain lacking the SrrAB two-component regulatory system (TCRS) is sensitive to H2O2 intoxication. We tested the hypothesis that SrrAB manages the mutually inclusive expression of genes required for aerobic respiration and H2O2 resistance. Consistent with our hypothesis, a ΔsrrAB strain had decreased transcription of genes encoding for H2O2 resistance factors (kat, ahpC, dps). SrrAB was not required for the inducing the transcription of these genes in cells challenged with H2O2. Purified SrrA bound to the promoter region for dps suggesting that SrrA directly influences dps transcription. The H2O2 sensitivity of the ΔsrrAB strain was alleviated by iron chelation or deletion of the gene encoding for the peroxide regulon repressor (PerR). The positive influence of SrrAB upon H2O2 metabolism bestowed protection upon the solvent accessible iron-sulfur (FeS) cluster of aconitase from H2O2 poisoning. SrrAB also positively influenced transcription of scdA (ytfE), which encodes for a FeS cluster repair protein. Finally, we found that SrrAB positively influences H2O2 resistance only during periods of high dioxygen-dependent respiratory activity. SrrAB did not influence H2O2 resistance when cellular respiration was diminished as a result of decreased dioxygen availability, and negatively influenced it in the absence of respiration (fermentative growth). We propose a model whereby SrrAB-dependent regulatory patterns facilitate the adaptation of cells to changes in dioxygen concentrations, and thereby aids in the prevention of H2O2 intoxication during respiratory growth upon dixoygen.
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Affiliation(s)
- Ameya A. Mashruwala
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Jeffrey M. Boyd
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, United States of America
- * E-mail:
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10
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Abstract
Two-component regulatory systems (2CRSs) are widely used by bacteria to sense and respond to environmental stimuli with coordinated changes in gene expression. Systems are normally comprised of a sensory kinase protein that activates a transcriptional regulator by phosphorylation. Mycobacteria have few 2CRSs, but they are of key importance for bacterial survival and play important roles in pathogenicity. Mycobacterium tuberculosis has 12 paired two-component regulatory systems (which include a system with two regulators and one sensor, and a split sensor system), as well as four orphan regulators. Several systems are involved in virulence, and disruption of different systems leads to attenuation or hypervirulence. PhoPR plays a major role in regulating cell wall composition, and its inactivation results in sufficient attenuation of M. tuberculosis that deletion strains are live vaccine candidates. MprAB controls the stress response and is required for persistent infections. SenX3-RegX3 is required for control of aerobic respiration and phosphate uptake, and PrrAB is required for adaptation to intracellular infection. MtrAB is an essential system that controls DNA replication and cell division. The remaining systems (KdpDE, NarL, TrcRS, TcrXY, TcrA, PdtaRS, and four orphan regulators) are less well understood. The structure and binding motifs for several regulators have been characterized, revealing variations in function and operation. The sensors are less well characterized, and stimuli for many remain to be confirmed. This chapter reviews our current understanding of the role of two-component systems in mycobacteria, in particular M. tuberculosis.
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Ye C, Ji G, Li L, Liang C. detectIR: a novel program for detecting perfect and imperfect inverted repeats using complex numbers and vector calculation. PLoS One 2014; 9:e113349. [PMID: 25409465 PMCID: PMC4237412 DOI: 10.1371/journal.pone.0113349] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 10/22/2014] [Indexed: 11/19/2022] Open
Abstract
Inverted repeats are present in abundance in both prokaryotic and eukaryotic genomes and can form DNA secondary structures--hairpins and cruciforms that are involved in many important biological processes. Bioinformatics tools for efficient and accurate detection of inverted repeats are desirable, because existing tools are often less accurate and time consuming, sometimes incapable of dealing with genome-scale input data. Here, we present a MATLAB-based program called detectIR for the perfect and imperfect inverted repeat detection that utilizes complex numbers and vector calculation and allows genome-scale data inputs. A novel algorithm is adopted in detectIR to convert the conventional sequence string comparison in inverted repeat detection into vector calculation of complex numbers, allowing non-complementary pairs (mismatches) in the pairing stem and a non-palindromic spacer (loop or gaps) in the middle of inverted repeats. Compared with existing popular tools, our program performs with significantly higher accuracy and efficiency. Using genome sequence data from HIV-1, Arabidopsis thaliana, Homo sapiens and Zea mays for comparison, detectIR can find lots of inverted repeats missed by existing tools whose outputs often contain many invalid cases. detectIR is open source and its source code is freely available at: https://sourceforge.net/projects/detectir.
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Affiliation(s)
- Congting Ye
- Department of Automation, Xiamen University, Xiamen, Fujian 361005, China; Department of Biology, Miami University, Oxford, Ohio 45056, United States of America
| | - Guoli Ji
- Department of Automation, Xiamen University, Xiamen, Fujian 361005, China; Innovation Center for Cell Biology, Xiamen University, Xiamen, Fujian 361005, China
| | - Lei Li
- Department of Automation, Xiamen University, Xiamen, Fujian 361005, China; Department of Biology, Miami University, Oxford, Ohio 45056, United States of America
| | - Chun Liang
- Department of Biology, Miami University, Oxford, Ohio 45056, United States of America; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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