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Hu Z, Xia J, Wu J, Zhao H, Ji P, Gu L, Gu W, Chen Z, Xu J, Huang X, Ma J, Chen A, Li J, Shu T, Fan XY. A multistage Sendai virus vaccine incorporating latency-associated antigens induces protection against acute and latent tuberculosis. Emerg Microbes Infect 2024; 13:2300463. [PMID: 38164736 PMCID: PMC10769537 DOI: 10.1080/22221751.2023.2300463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 12/24/2023] [Indexed: 01/03/2024]
Abstract
One-quarter of the world's population is infected with Mycobacterium tuberculosis (Mtb). After initial exposure, more immune-competent persons develop asymptomatic latent tuberculosis infection (LTBI) but not active diseases, creates an extensive reservoir at risk of developing active tuberculosis. Previously, we constructed a novel recombinant Sendai virus (SeV)-vectored vaccine encoding two dominant antigens of Mtb, which elicited immune protection against acute Mtb infection. In this study, nine Mtb latency-associated antigens were screened as potential supplementary vaccine candidate antigens, and three antigens (Rv2029c, Rv2028c, and Rv3126c) were selected based on their immune-therapeutic effect in mice, and their elevated immune responses in LTBI human populations. Then, a recombinant SeV-vectored vaccine, termed SeV986A, that expresses three latency-associated antigens and Ag85A was constructed. In murine models, the doses, titers, and inoculation sites of SeV986A were optimized, and its immunogenicity in BCG-primed and BCG-naive mice were determined. Enhanced immune protection against the Mtb challenge was shown in both acute-infection and latent-infection murine models. The expression levels of several T-cell exhaustion markers were significantly lower in the SeV986A-vaccinated group, suggesting that the expression of latency-associated antigens inhibited the T-cell exhaustion process in LTBI infection. Hence, the multistage quarter-antigenic SeV986A vaccine holds considerable promise as a novel post-exposure prophylaxis vaccine against tuberculosis.
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Affiliation(s)
- Zhidong Hu
- Shanghai Public Health Clinical Center & Shanghai Institute of Infectious Diseases and Biosecurity, Fudan University, Shanghai, People’s Republic of China
| | - Jingxian Xia
- Shanghai Public Health Clinical Center & Shanghai Institute of Infectious Diseases and Biosecurity, Fudan University, Shanghai, People’s Republic of China
| | - Juan Wu
- Shanghai Public Health Clinical Center & Shanghai Institute of Infectious Diseases and Biosecurity, Fudan University, Shanghai, People’s Republic of China
| | - Huimin Zhao
- Shanghai Public Health Clinical Center & Shanghai Institute of Infectious Diseases and Biosecurity, Fudan University, Shanghai, People’s Republic of China
| | - Ping Ji
- Shanghai Public Health Clinical Center & Shanghai Institute of Infectious Diseases and Biosecurity, Fudan University, Shanghai, People’s Republic of China
| | - Ling Gu
- Shanghai Public Health Clinical Center & Shanghai Institute of Infectious Diseases and Biosecurity, Fudan University, Shanghai, People’s Republic of China
| | - Wenfei Gu
- Shanghai Public Health Clinical Center & Shanghai Institute of Infectious Diseases and Biosecurity, Fudan University, Shanghai, People’s Republic of China
| | - Zhenyan Chen
- Shanghai Public Health Clinical Center & Shanghai Institute of Infectious Diseases and Biosecurity, Fudan University, Shanghai, People’s Republic of China
| | - Jinchuan Xu
- Shanghai Public Health Clinical Center & Shanghai Institute of Infectious Diseases and Biosecurity, Fudan University, Shanghai, People’s Republic of China
| | - Xuejiao Huang
- Shanghai Public Health Clinical Center & Shanghai Institute of Infectious Diseases and Biosecurity, Fudan University, Shanghai, People’s Republic of China
| | | | - Anke Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
| | | | - Xiao-Yong Fan
- Shanghai Public Health Clinical Center & Shanghai Institute of Infectious Diseases and Biosecurity, Fudan University, Shanghai, People’s Republic of China
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Johnson MP, Lauterkorn N, Lewis R, Labeed FH, Hingley-Wilson SM, Hughes MP. Dielectric properties of human macrophages are altered by Mycobacterium tuberculosis infection. Electrophoresis 2024; 45:1555-1561. [PMID: 38517249 DOI: 10.1002/elps.202300239] [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: 10/20/2023] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 03/23/2024]
Abstract
The analysis of cell electrophysiology for pathogenic samples at BSL3 can be problematic. It is virtually impossible to isolate infected from uninfected without a label, for example green fluorescent protein, which can potentially alter the cell electrical properties. Furthermore, the measurement of highly pathogenic organisms often requires equipment dedicated only for use with these organisms due to safety considerations. To address this, we have used dielectrophoresis to study the electrical properties of the human THP-1 cell line and monocyte-derived macrophages before and after infection with non-labelled Mycobacterium tuberculosis. Infection with these highly pathogenic bacilli resulted in changes including a raised surface conductance (associated with reduced zeta potential) and increased capacitance, suggesting an increase in surface roughness. We have also investigated the effect of fixation on THP-1 cells as a means to enable study on fixed samples in BSL1 or 2 laboratories, which suggests that the properties of these cells are largely unaffected by the fixation process. This advance results in a novel technique enabling the isolation of infected and non-infected cells in a sample without labelling.
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Affiliation(s)
- Matthew P Johnson
- Centre for Biomedical Engineering, University of Surrey, Guildford, Surrey, UK
| | - Nira Lauterkorn
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, Surrey, UK
| | - Rebecca Lewis
- Department of Comparative Biomedical Sciences, University of Surrey, Guildford, Surrey, UK
| | - Fatima H Labeed
- Centre for Biomedical Engineering, University of Surrey, Guildford, Surrey, UK
- Department of Biology, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Suzanne M Hingley-Wilson
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, Surrey, UK
| | - Michael Pycraft Hughes
- Centre for Biomedical Engineering, University of Surrey, Guildford, Surrey, UK
- Department of Biomedical Engineering and Biotechnology, Khalifa University, Abu Dhabi, United Arab Emirates
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3
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Chen YQ, Cao SH, Yang XY, Liu Y, Li CY. Potential biomarkers for evaluating the BCG vaccination response based on humoral immunity. Heliyon 2024; 10:e32117. [PMID: 38947452 PMCID: PMC11214448 DOI: 10.1016/j.heliyon.2024.e32117] [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: 04/01/2023] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 07/02/2024] Open
Abstract
Background The current prophylactic tuberculosis vaccine Bacille Calmette-Guérin (BCG), was derived in the 1920s, but the humoral immune responses induced by BCG vaccination have not been fully elucidated to date. In this study, our aim was to reveal the profiles of antibody responses induced by BCG vaccination in adults and identify the potential biomarkers for evaluating the BCG vaccination response. Methods Proteome microarrays were performed to reveal the serum profiles of antibody responses induced by BCG vaccination in adults. ELISA was used to validate the potential biomarkers in validation cohort (79 healthy controls and 58 BCG-vaccinated subjects). Then combined panel was established by logistic regression analysis based on OD values of potential biomarkers. Results Multiple antigens elicited stronger serum IgG or IgM antibody responses in BCG vaccinated subjects than healthy subjects at 12 weeks post BCG vaccination; among the antigens, Rv0060, Rv2026c and Rv3379c were further verified using 137 serum samples and presented the moderate performance in assessment of the BCG vaccination response by receiver operating characteristic analysis. Furthermore, a combined panel exhibited an improved AUC of 0.923, and the sensitivity and specificity were 77.59 % and 91.14 %, respectively. In addition, the antibody response against Rv0060, Rv2026c and Rv3379c was related to the clinical background to a certain extent. Conclusions The novel antigens identified in our study could offer better knowledge towards developing a more efficacious vaccine based on humoral immune responses, and they could be potential biomarkers in assessments of BCG vaccination responses.
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Affiliation(s)
- Yan-Qing Chen
- Department of Sentience and Technology, Beijing Geriatric Hospital, Beijing, China
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Shu-Hui Cao
- Department of Laboratory Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Xin-Yu Yang
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Yi Liu
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Chuan-You Li
- Beijing Center for Disease Prevention and Control, Beijing, China
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing, China
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Banerjee A, Chakraborty M, Sharma S, Chaturvedi R, Bose A, Biswas P, Singh A, Visweswariah SS. Cyclic AMP binding to a universal stress protein in Mycobacterium tuberculosis is essential for viability. J Biol Chem 2024; 300:107287. [PMID: 38636658 PMCID: PMC11107214 DOI: 10.1016/j.jbc.2024.107287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 04/20/2024] Open
Abstract
Mycobacterial genomes encode multiple adenylyl cyclases and cAMP effector proteins, underscoring the diverse ways these bacteria utilize cAMP. We identified universal stress proteins, Rv1636 and MSMEG_3811 in Mycobacterium tuberculosis and Mycobacterium smegmatis, respectively, as abundantly expressed, novel cAMP-binding proteins. Rv1636 is secreted via the SecA2 secretion system in M. tuberculosis but is not directly responsible for the efflux of cAMP from the cell. In slow-growing mycobacteria, intrabacterial concentrations of Rv1636 were equivalent to the concentrations of cAMP present in the cell. In contrast, levels of intrabacterial MSMEG_3811 in M. smegmatis were lower than that of cAMP and therefore, overexpression of Rv1636 increased levels of "bound" cAMP. While msmeg_3811 could be readily deleted from the genome of M. smegmatis, we found that the rv1636 gene is essential for the viability of M. tuberculosis and is dependent on the cAMP-binding ability of Rv1636. Therefore, Rv1636 may function to regulate cAMP signaling by direct sequestration of the second messenger. This is the first evidence of a "sponge" for any second messenger in bacterial signaling that would allow mycobacterial cells to regulate the available intrabacterial "free" pool of cAMP.
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Affiliation(s)
- Arka Banerjee
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India
| | - Moubani Chakraborty
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India
| | - Suruchi Sharma
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India
| | - Ruchi Chaturvedi
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bengaluru, India
| | - Avipsa Bose
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India
| | - Priyanka Biswas
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India
| | - Amit Singh
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bengaluru, India
| | - Sandhya S Visweswariah
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India.
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Girardo B, Schopfer LM, Yue Y, Lockridge O, Larson MA. Polyaminated, acetylated and stop codon readthrough of recombinant Francisella tularensis universal stress protein in Escherichia coli. PLoS One 2024; 19:e0299701. [PMID: 38683788 PMCID: PMC11057771 DOI: 10.1371/journal.pone.0299701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/14/2024] [Indexed: 05/02/2024] Open
Abstract
Recombinant Francisella tularensis universal stress protein with a C-terminal histidine-tag (rUsp/His6) was expressed in Escherichia coli. Endogenous F. tularensis Usp has a predicted molecular mass of 30 kDa, but rUsp/His6 had an apparent molecular weight of 33 kDa based on Western blot analyses. To determine the source of the higher molecular weight for rUsp/His6, post translational modifications were examined. Tryptic peptides of purified rUsp/His6 were subjected to liquid chromatography tandem mass spectrometry (LC-MS/MS) and fragmentation spectra were searched for acetylated lysines and polyaminated glutamines. Of the 24 lysines in rUsp/His6, 10 were acetylated (K63, K68, K72, K129, K175, K201, K208, K212, K233, and K238) and three of the four glutamines had putrescine, spermidine and spermine adducts (Q55, Q60 and Q267). The level of post-translational modification was substoichiometric, eliminating the possibility that these modifications were the sole contributor to the 3 kDa extra mass of rUsp/His6. LC-MS/MS revealed that stop codon readthrough had occurred resulting in the unexpected addition of 20 extra amino acids at the C-terminus of rUsp/His6, after the histidine tag. Further, the finding of polyaminated glutamines in rUsp/His6 indicated that E. coli is capable of transglutaminase activity.
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Affiliation(s)
- Benjamin Girardo
- Pathology and Microbiology Department, University of Nebraska Medical Center, Omaha, NE, United States of America
| | - Lawrence M. Schopfer
- Eppley Institute, University of Nebraska Medical Center, Omaha, NE, United States of America
| | - Yinshi Yue
- Pathology and Microbiology Department, University of Nebraska Medical Center, Omaha, NE, United States of America
| | - Oksana Lockridge
- Eppley Institute, University of Nebraska Medical Center, Omaha, NE, United States of America
| | - Marilynn A. Larson
- Pathology and Microbiology Department, University of Nebraska Medical Center, Omaha, NE, United States of America
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Yan T, Li M, Wang Q, Wang M, Liu L, Ma C, Xiang X, Zhou Q, Liu Z, Gong Z. Structures, functions, and regulatory networks of universal stress proteins in clinically relevant pathogenic Bacteria. Cell Signal 2024; 116:111032. [PMID: 38185228 DOI: 10.1016/j.cellsig.2023.111032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/14/2023] [Accepted: 12/30/2023] [Indexed: 01/09/2024]
Abstract
Universal stress proteins are a class of proteins widely present in bacteria, archaea, plants, and invertebrates, playing essential roles in bacterial adaptation to various environmental stresses. The functions of bacterial universal stress proteins are versatile, including resistance to oxidative stress, maintenance of cell wall integrity, DNA damage repair, regulation of cell division and growth, among others. When facing stresses such as temperature changes, pH shifts, fluctuations in oxygen concentration, and exposure to toxins, these proteins can bind to specific DNA sequences and rapidly adjust bacterial metabolic pathways and gene expression patterns to adapt to the new environment. In summary, bacterial universal stress proteins play a crucial role in bacterial adaptability and survival. A comprehensive understanding of bacterial stress response mechanisms and the development of new antibacterial strategies are of great significance. This review summarizes the research progress on the structure, function, and regulatory factors of universal stress proteins in clinically relevant bacteria, aiming to facilitate deeper investigations by clinicians and researchers into universal stress proteins.
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Affiliation(s)
- Tao Yan
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Min Li
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Qiuyan Wang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Meng Wang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Lijuan Liu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Chengcheng Ma
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xiaohong Xiang
- School of Pharmacy, Chongqing Medical and Pharmaceutical College, Chongqing, China
| | - Qiang Zhou
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Zhou Liu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.
| | - Zhen Gong
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.
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Diao J, Gu W, Jiang Z, Wang J, Zou H, Zong C, Ma L. Comprehensive Analysis of Universal Stress Protein Family Genes and Their Expression in Fusarium oxysporum Response of Populus davidiana × P. alba var. pyramidalis Louche Based on the Transcriptome. Int J Mol Sci 2023; 24:ijms24065405. [PMID: 36982480 PMCID: PMC10049587 DOI: 10.3390/ijms24065405] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 02/24/2023] [Accepted: 03/07/2023] [Indexed: 03/14/2023] Open
Abstract
Universal stress proteins (USPs) are typical stress-inducible proteins that function directly in a variety of biotic or abiotic stresses and effectively protect plants from complex, adverse environments. However, the expression patterns of USP genes under pathogen stress and their molecular mechanisms in stress resistance have not been reported in detail. In this study, 46 USP genes were identified from Populus trichocarpa (PtrUSPs), and their biological characteristics were comprehensively analyzed based on phylogeny, physicochemical properties of proteins, and gene structures. The promoter regions of PtrUSPs contain a variety of cis-acting elements related to hormone and stress response. The results of a collinearity analysis showed that PtsrUSPs were highly conserved with homologous genes from four other representative species (Arabidopsis thaliana, Eucalyptus grandis, Glycine max, and Solanum lycopersicum). Furthermore, RNA-Seq analysis showed that the expression of 46 USPs from P. davidiana × P. alba var. pyramidalis Louche (PdpapUSPs) was significantly induced by Fusarium oxysporum. The co-expression network and gene ontology analysis of PtrUSPs showed that they participated in the response to stress and response to stimulus through precise coordination. The results of this paper systematically revealed the biological characteristics of PtrUSPs and the characteristics of their response to F. oxysporum stress, which will lay a theoretical foundation for improving genetic traits and the breeding of poplar disease-resistant varieties in subsequent studies.
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Affiliation(s)
- Jian Diao
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Wei Gu
- College of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Zhehui Jiang
- College of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Jiaqi Wang
- College of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Hongfei Zou
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Cheng Zong
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- Correspondence: (C.Z.); (L.M.)
| | - Ling Ma
- College of Forestry, Northeast Forestry University, Harbin 150040, China
- Correspondence: (C.Z.); (L.M.)
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O'Connor A, Jurado‐Martín I, Mysior MM, Manzira AL, Drabinska J, Simpson JC, Lucey M, Schaffer K, Berisio R, McClean S. A universal stress protein upregulated by hypoxia has a role in Burkholderia cenocepacia intramacrophage survival: Implications for chronic infection in cystic fibrosis. Microbiologyopen 2023; 12:e1311. [PMID: 36825886 PMCID: PMC9733578 DOI: 10.1002/mbo3.1311] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 07/29/2022] [Accepted: 07/29/2022] [Indexed: 12/13/2022] Open
Abstract
Universal stress proteins (USPs) are ubiquitously expressed in bacteria, archaea, and eukaryotes and play a lead role in adaptation to environmental conditions. They enable adaptation of bacterial pathogens to the conditions encountered in the human niche, including hypoxia, oxidative stress, osmotic stress, nutrient deficiency, or acid stress, thereby facilitating colonization. We previously reported that all six USP proteins encoded within a low-oxygen activated (lxa) locus in Burkholderia cenocepacia showed increased abundance during chronic colonization of the cystic fibrosis (CF) lung. However, the role of USPs in chronic cystic fibrosis infection is not well understood. Structural modeling identified surface arginines on one lxa-encoded USP, USP76, which suggested it mediated interactions with heparan sulfate. Using mutants derived from the B. cenocepacia strain, K56-2, we show that USP76 is involved in host cell attachment. Pretreatment of lung epithelial cells with heparanase reduced the binding of the wild-type and complement strains but not the Δusp76 mutant strain, indicating that USP76 is directly or indirectly involved in receptor recognition on the surface of epithelial cells. We also show that USP76 is required for growth and survival in many conditions associated with the CF lung, including acidic conditions and oxidative stress. Moreover, USP76 also has a role in survival in macrophages isolated from people with CF. Overall, while further elucidation of the exact mechanism(s) is required, we can conclude that USP76, which is upregulated during chronic infection, is involved in bacterial survival within CF macrophages, a hallmark of Burkholderia infection.
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Affiliation(s)
- Andrew O'Connor
- School of Biomolecular and Biomedical SciencesUniversity College DublinBelfieldDublinIreland
| | - Irene Jurado‐Martín
- School of Biomolecular and Biomedical SciencesUniversity College DublinBelfieldDublinIreland
- UCD Conway Institute of Biomolecular and Biomedical ScienceBefieldDublinIreland
| | - Margaritha M. Mysior
- UCD Conway Institute of Biomolecular and Biomedical ScienceBefieldDublinIreland
- Cell Screening Laboratory, School of Biology and Environmental ScienceUniversity College DublinBelfieldDublinIreland
| | - Anotidaishe L. Manzira
- School of Biomolecular and Biomedical SciencesUniversity College DublinBelfieldDublinIreland
- UCD Conway Institute of Biomolecular and Biomedical ScienceBefieldDublinIreland
| | - Joanna Drabinska
- School of Biomolecular and Biomedical SciencesUniversity College DublinBelfieldDublinIreland
- UCD Conway Institute of Biomolecular and Biomedical ScienceBefieldDublinIreland
| | - Jeremy C. Simpson
- UCD Conway Institute of Biomolecular and Biomedical ScienceBefieldDublinIreland
- Cell Screening Laboratory, School of Biology and Environmental ScienceUniversity College DublinBelfieldDublinIreland
| | - Mary Lucey
- Department of MicrobiologySt. Vincent's University HospitalElm ParkDublinIreland
| | - Kirsten Schaffer
- Department of MicrobiologySt. Vincent's University HospitalElm ParkDublinIreland
| | - Rita Berisio
- Institute of Biostructures and BioimagingNational Research CouncilNaplesItaly
| | - Siobhán McClean
- School of Biomolecular and Biomedical SciencesUniversity College DublinBelfieldDublinIreland
- UCD Conway Institute of Biomolecular and Biomedical ScienceBefieldDublinIreland
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Contreras Á, Díaz G, Mendoza SN, Canto M, Agosín E. Metabolic behavior for a mutant Oenococcus oeni strain with high resistance to ethanol to survive under oenological multi-stress conditions. Front Microbiol 2023; 14:1100501. [PMID: 36970676 PMCID: PMC10033693 DOI: 10.3389/fmicb.2023.1100501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 02/09/2023] [Indexed: 03/29/2023] Open
Abstract
Malolactic fermentation (MLF) positively influences the quality of the wine, and it occurs as a result of a lactic acid bacteria's metabolism, mainly of the Oenococcus oeni species. However, delays and halting of MLF are frequent problems in the wine industry. This is mainly because O. oeni's development is inhibited by different kinds of stress. Even though the sequencing of the genome of the PSU-1 strain of O. oeni, as well as other strains, has made it possible to identify genes involved in the resistance to some types of stress, all of the factors that could be involved are still unknown. With the aim of contributing to this knowledge, the random mutagenesis technique was used in this study as a strategy for genetic improvement of strains of the O. oeni species. The technique proved to be capable of generating a different and improved strain when compared to the PSU-1 strain (the parent from which it descends). Then, we evaluated the metabolic behavior of both strains in three different wines. We used synthetic MaxOeno wine (pH 3.5; 15% v/v ethanol), red wine (Cabernet Sauvignon), and white wine (Chardonnay). Furthermore, we compared the transcriptome of both strains, grown in MaxOeno synthetic wine. The specific growth rate of the E1 strain was on average 39% higher in comparison to the PSU-1 strain. Interestingly, E1 strain showed an overexpression of the OEOE_1794 gene, which encodes a UspA-like protein, which has been described as promoting growth. We observed that the E1 strain was able to convert, on average, 34% more malic acid into lactate than the PSU-1 strain, regardless of the wine being used. On the other hand, the E1 strain showed a flux rate of fructose-6-phosphate production that was 86% higher than the mannitol production rate, and the internal flux rates increase in the direction of pyruvate production. This coincides with the higher number of OEOE_1708 gene transcripts observed in the E1 strain grown in MaxOeno. This gene encodes for an enzyme fructokinase (EC 2.7.1.4) involved in the transformation of fructose to fructose-6-phosphate.
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Affiliation(s)
- Ángela Contreras
- Applied Microbiology Laboratory, Center for Biotechnology of Natural Resources, Faculty of Agricultural and Forestry Sciences, School of Biotechnology, Universidad Católica del Maule, Talca, Chile
- *Correspondence: Angela Contreras,
| | - Gabriela Díaz
- Laboratory of Biotechnology, Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Sebastián N. Mendoza
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Mauricio Canto
- Applied Microbiology Laboratory, Center for Biotechnology of Natural Resources, Faculty of Agricultural and Forestry Sciences, School of Biotechnology, Universidad Católica del Maule, Talca, Chile
| | - Eduardo Agosín
- Laboratory of Biotechnology, Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
- Eduardo Agosin,
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10
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Singh N, Sharma N, Singh P, Pandey M, Ilyas M, Sisodiya L, Choudhury T, Gosain TP, Singh R, Atmakuri K. HupB, a nucleoid-associated protein, is critical for survival of Mycobacterium tuberculosis under host-mediated stresses and for enhanced tolerance to key first-line antibiotics. Front Microbiol 2022; 13:937970. [PMID: 36071978 PMCID: PMC9441915 DOI: 10.3389/fmicb.2022.937970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/12/2022] [Indexed: 11/30/2022] Open
Abstract
To survive and establish its niche, Mycobacterium tuberculosis (Mtb) engages in a steady battle against an array of host defenses and a barrage of antibiotics. Here, we demonstrate that Mtb employs HupB, a nucleoid-associated protein (NAP) as its key player to simultaneously battle and survive in these two stress-inducing fronts. Typically, NAPs are key to bacterial survival under a wide array of environmental or host-mediated stresses. Here, we report that for Mtb to survive under different macrophage-induced assaults including acidic pH, nutrient depletion, oxidative and nitrosative stresses, HupB presence is critical. As expected, the hupB knockout mutant is highly sensitive to these host-mediated stresses. Furthermore, Mtb aptly modulates HupB protein levels to overcome these stresses. We also report that HupB aids Mtb to gain tolerance to high levels of rifampicin (RIF) and isoniazid (INH) exposure. Loss of hupB makes Mtb highly susceptible to even short exposures to reduced amounts of RIF and INH. Overexpressing hupB in Mtb or complementing hupB in the hupB knockout mutant triggers enhanced survival of Mtb under these stresses. We also find that upon loss of hupB, Mtb significantly enhances the permeability of its cell wall by modulating the levels of several surface lipids including phthiocerol dimycocerosates (PDIMs), thus possibly influencing overall susceptibility to host-mediated stresses. Loss of hupB also downregulates efflux pump expression possibly influencing increased susceptibility to INH and RIF. Finally, we find that therapeutic targeting of HupB with SD1, a known small molecule inhibitor, significantly enhances Mtb susceptibility to INH and THP-1 macrophages and significantly reduces MIC to INH. Thus, our data strongly indicate that HupB is a highly promising therapeutic target especially for potential combinatorial shortened therapy with reduced INH and RIF doses.
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Affiliation(s)
- Niti Singh
- Infection and Immunology Group, Translational Health Science and Technology Institute, Faridabad, Haryana, India
- Manipal University, Manipal, Karnataka, India
| | - Nishant Sharma
- Infection and Immunology Group, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Padam Singh
- Infection and Immunology Group, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Manitosh Pandey
- Infection and Immunology Group, Translational Health Science and Technology Institute, Faridabad, Haryana, India
- Department of Life Sciences, ITM University, Gwalior, Madhya Pradesh, India
| | - Mohd Ilyas
- Infection and Immunology Group, Translational Health Science and Technology Institute, Faridabad, Haryana, India
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Lovely Sisodiya
- Infection and Immunology Group, Translational Health Science and Technology Institute, Faridabad, Haryana, India
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Tejaswini Choudhury
- Infection and Immunology Group, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Tannu Priya Gosain
- Infection and Immunology Group, Translational Health Science and Technology Institute, Faridabad, Haryana, India
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Ramandeep Singh
- Infection and Immunology Group, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Krishnamohan Atmakuri
- Infection and Immunology Group, Translational Health Science and Technology Institute, Faridabad, Haryana, India
- *Correspondence: Krishnamohan Atmakuri
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Mechanistic Insight into the Enzymatic Inhibition of β-Amyrin against Mycobacterial Rv1636: In Silico and In Vitro Approaches. BIOLOGY 2022; 11:biology11081214. [PMID: 36009841 PMCID: PMC9405466 DOI: 10.3390/biology11081214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 08/02/2022] [Accepted: 08/08/2022] [Indexed: 12/05/2022]
Abstract
Simple Summary Rv1636 is a mycobacterial universal stress protein whose expression level increases in different type of stress conditions. This protein promotes the growth of Mycobacterium tuberculosis in the host derived stress conditions generated during infection. Therefore in this manuscipt, we are trying to target Rv1636 using natural inhibitor. Targeting essential Mycobacterial protein using natural prodect was hypothesized to generate a molecule with low toxic effects and high inhibitory activity. It was found that Rv1636 contains ATPase activity and its ATPase activity gets disturbed by addition of β-Amyrin in the reaction. β-Amyrin was forund to interfere with the ATP binding site of Rv1636 which was confirmed by molecular docking anad dynamic studies. In addition to the ATPase activity, Rv1636 was also contain the cAMP binding capacity and also involved in balancing the cAMP levels inside cells. So, targeting Rv1636 using β-Amyrin disrupts its ATPase activity and cAMP regulatory activity and these conditions might make Mycobacterium tuberculosis more susceptible to the host derived stress conditions. Abstract Mycobacterium tuberculosis has seen tremendous success as it has developed defenses to reside in host alveoli despite various host-related stress circumstances. Rv1636 is a universal stress protein contributing to mycobacterial survival in different host-derived stress conditions. Both ATP and cAMP can be bound with the Rv1636, and their binding actions are independent of one another. β-Amyrin, a triterpenoid compound, is abundant in medicinal plants and has many pharmacological properties and broad therapeutic potential. The current study uses biochemical, biophysical, and computational methods to define the binding of Rv1636 with β-Amyrin. A substantial interaction between β-Amyrin and Rv1636 was discovered by molecular docking studies, which helped decipher the critical residues involved in the binding process. VAL60 is a crucial residue found in the complexes of both Rv1636_β-Amyrin and Rv1636-ATP. Additionally, the Rv1636_β-Amyrin complex was shown to be stable by molecular dynamics simulation studies (MD), with minimal changes observed during the simulation. In silico observations were further complemented by in vitro assays. Successful cloning, expression, and purification of Rv1636 were accomplished using Ni-NTA affinity chromatography. The results of the ATPase activity assay indicated that Rv1636’s ATPase activity was inhibited in the presence of various β-Amyrin concentrations. Additionally, circular dichroism spectroscopy (CD) was used to examine modifications to Rv1636 secondary structure upon binding of β-Amyrin. Finally, isothermal titration calorimetry (ITC) advocated spontaneous binding of β-Amyrin with Rv1636 elucidating the thermodynamics of the Rv1636_β-Amyrin complex. Thus, the study establishes that β-Amyrin binds to Rv1636 with a significant affinity forming a stable complex and inhibiting its ATPase activity. The present study suggests that β-Amyrin might affect the functioning of Rv1636, which makes the bacterium vulnerable to different stress conditions.
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12
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Kim H, Kim M, Kim S, Lee YM, Shin SC. Characterization of antimicrobial resistance genes and virulence factor genes in an Arctic permafrost region revealed by metagenomics. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 294:118634. [PMID: 34875269 DOI: 10.1016/j.envpol.2021.118634] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 11/29/2021] [Accepted: 12/03/2021] [Indexed: 06/13/2023]
Abstract
Antimicrobial resistance genes (ARGs) and virulence factor genes (VFGs) constitute a serious threat to public health, and climate change has been predicted to affect the increase in bacterial pathogens harboring ARGs and VFGs. However, studies on bacterial pathogens and their ARGs and VFGs in permafrost region have received limited attention. In this study, a metagenomic approach was applied to a comprehensive survey to detect potential ARGs, VFGs, and pathogenic antibiotic resistant bacteria (PARB) carrying both ARGs and VFGs in the active layer and permafrost. Overall, 70 unique ARGs against 18 antimicrobial drug classes and 599 VFGs classified as 38 virulence factors were detected in the Arctic permafrost region. Eight genes with mobile genetic elements (MGEs) carrying ARGs were identified; most MGEs were classified as phages. In the metagenome-assembled genomes, the presence of 15 PARB was confirmed. The soil profile showed that the transcripts per million (TPM) values of ARGs and VFGs in the sub-soil horizon were significantly lower than those in the top soil horizon. Based on the TPM value of each gene, major ARGs, VFGs, and these genes in PARB from the Arctic permafrost region were identified and their distribution was confirmed. The major host bacteria for ARGs and VFGs and PARB were identified. A comparison of the percentage identity distribution of ARGs and VFGs to reference databases indicated that ARGs and VFGs in the Arctic soils differ from previously identified genes. Our results may help understand the characteristics and distribution of ARGs, VFGs, and these genes in PARB in the Arctic permafrost region. This findings suggest that the Arctic permafrost region may serve as potential reservoirs for ARGs, VFGs, and PARB. These genes could pose a new threat to human health if they are released by permafrost thawing owing to global warming and propagate to other regions.
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Affiliation(s)
- Heesoo Kim
- Division of Life Sciences, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Mincheol Kim
- Division of Life Sciences, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Sanghee Kim
- Division of Life Sciences, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Yung Mi Lee
- Division of Life Sciences, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Seung Chul Shin
- Division of Life Sciences, Korea Polar Research Institute, Incheon, 21990, Republic of Korea.
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13
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Masamba P, Weber BW, Sewell BT, Kappo AP. Crystallization and preliminary structural determination of the universal stress G4LZI3 protein from Schistosoma mansoni. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2022.101057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022] Open
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14
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Vilchèze C, Yan B, Casey R, Hingley-Wilson S, Ettwiller L, Jacobs WR. Commonalities of Mycobacterium tuberculosis Transcriptomes in Response to Defined Persisting Macrophage Stresses. Front Immunol 2022; 13:909904. [PMID: 35844560 PMCID: PMC9283954 DOI: 10.3389/fimmu.2022.909904] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/06/2022] [Indexed: 12/03/2022] Open
Abstract
As the goal of a bacterium is to become bacteria, evolution has imposed continued selections for gene expression. The intracellular pathogen Mycobacterium tuberculosis, the causative agent of tuberculosis, has adopted a fine-tuned response to survive its host's methods to aggressively eradicate invaders. The development of microarrays and later RNA sequencing has led to a better understanding of biological processes controlling the relationship between host and pathogens. In this study, RNA-seq was performed to detail the transcriptomes of M. tuberculosis grown in various conditions related to stresses endured by M. tuberculosis during host infection and to delineate a general stress response incurring during persisting macrophage stresses. M. tuberculosis was subjected to long-term growth, nutrient starvation, hypoxic and acidic environments. The commonalities between these stresses point to M. tuberculosis maneuvering to exploit propionate metabolism for lipid synthesis or to withstand propionate toxicity whilst in the intracellular environment. While nearly all stresses led to a general shutdown of most biological processes, up-regulation of pathways involved in the synthesis of amino acids, cofactors, and lipids were observed only in hypoxic M. tuberculosis. This data reveals genes and gene cohorts that are specifically or exclusively induced during all of these persisting stresses. Such knowledge could be used to design novel drug targets or to define possible M. tuberculosis vulnerabilities for vaccine development. Furthermore, the disruption of specific functions from this gene set will enhance our understanding of the evolutionary forces that have caused the tubercle bacillus to be a highly successful pathogen.
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Affiliation(s)
- Catherine Vilchèze
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Bo Yan
- Research Department, Genome Biology Division, New England Biolabs Inc., Ipswich, MA, United States
| | - Rosalyn Casey
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Suzie Hingley-Wilson
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Laurence Ettwiller
- Research Department, Genome Biology Division, New England Biolabs Inc., Ipswich, MA, United States
| | - William R. Jacobs
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States
- *Correspondence: William R. Jacobs Jr,
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15
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Masamba P, Kappo AP. Parasite Survival and Disease Persistence in Cystic Fibrosis, Schistosomiasis and Pathogenic Bacterial Diseases: A Role for Universal Stress Proteins? Int J Mol Sci 2021; 22:10878. [PMID: 34639223 PMCID: PMC8509486 DOI: 10.3390/ijms221910878] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/15/2021] [Accepted: 09/28/2021] [Indexed: 12/16/2022] Open
Abstract
Universal stress proteins (USPs) were originally discovered in Escherichia coli over two decades ago and since then their presence has been detected in various organisms that include plants, archaea, metazoans, and bacteria. As their name suggests, they function in a series of various cellular responses in both abiotic and biotic stressful conditions such as oxidative stress, exposure to DNA damaging agents, nutrient starvation, high temperature and acidic stress, among others. Although a highly conserved group of proteins, the molecular and biochemical aspects of their functions are largely evasive. This is concerning, as it was observed that USPs act as essential contributors to the survival/persistence of various infectious pathogens. Their ubiquitous nature in various organisms, as well as their augmentation during conditions of stress, is a clear indication of their direct or indirect importance in providing resilience against such conditions. This paper seeks to clarify what has already been reported in the literature on the proposed mechanism of action of USPs in pathogenic organisms.
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Affiliation(s)
- Priscilla Masamba
- Molecular Biophysics and Structural Biology (MBSB) Group, Department of Biochemistry, Kingsway Campus, University of Johannesburg, Auckland Park 2006, South Africa;
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16
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Isokpehi RD, McInnis DS, Destefano AM, Johnson GS, Walker AD, Hall YA, Mapp BW, Johnson MO, Simmons SS. Bioinformatics Investigations of Universal Stress Proteins from Mercury-Methylating Desulfovibrionaceae. Microorganisms 2021; 9:microorganisms9081780. [PMID: 34442859 PMCID: PMC8401546 DOI: 10.3390/microorganisms9081780] [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: 06/16/2021] [Revised: 07/30/2021] [Accepted: 08/06/2021] [Indexed: 11/26/2022] Open
Abstract
The presence of methylmercury in aquatic environments and marine food sources is of global concern. The chemical reaction for the addition of a methyl group to inorganic mercury occurs in diverse bacterial taxonomic groups including the Gram-negative, sulfate-reducing Desulfovibrionaceae family that inhabit extreme aquatic environments. The availability of whole-genome sequence datasets for members of the Desulfovibrionaceae presents opportunities to understand the microbial mechanisms that contribute to methylmercury production in extreme aquatic environments. We have applied bioinformatics resources and developed visual analytics resources to categorize a collection of 719 putative universal stress protein (USP) sequences predicted from 93 genomes of Desulfovibrionaceae. We have focused our bioinformatics investigations on protein sequence analytics by developing interactive visualizations to categorize Desulfovibrionaceae universal stress proteins by protein domain composition and functionally important amino acids. We identified 651 Desulfovibrionaceae universal stress protein sequences, of which 488 sequences had only one USP domain and 163 had two USP domains. The 488 single USP domain sequences were further categorized into 340 sequences with ATP-binding motif and 148 sequences without ATP-binding motif. The 163 double USP domain sequences were categorized into (1) both USP domains with ATP-binding motif (3 sequences); (2) both USP domains without ATP-binding motif (138 sequences); and (3) one USP domain with ATP-binding motif (21 sequences). We developed visual analytics resources to facilitate the investigation of these categories of datasets in the presence or absence of the mercury-methylating gene pair (hgcAB). Future research could utilize these functional categories to investigate the participation of universal stress proteins in the bacterial cellular uptake of inorganic mercury and methylmercury production, especially in anaerobic aquatic environments.
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Affiliation(s)
- Raphael D. Isokpehi
- College of Science, Engineering and Mathematics, Bethune-Cookman University, Daytona Beach, FL 32114, USA; (D.S.M.); (A.M.D.); (G.S.J.); (A.D.W.); (Y.A.H.); (B.W.M.)
- Correspondence:
| | - Dominique S. McInnis
- College of Science, Engineering and Mathematics, Bethune-Cookman University, Daytona Beach, FL 32114, USA; (D.S.M.); (A.M.D.); (G.S.J.); (A.D.W.); (Y.A.H.); (B.W.M.)
| | - Antoinette M. Destefano
- College of Science, Engineering and Mathematics, Bethune-Cookman University, Daytona Beach, FL 32114, USA; (D.S.M.); (A.M.D.); (G.S.J.); (A.D.W.); (Y.A.H.); (B.W.M.)
| | - Gabrielle S. Johnson
- College of Science, Engineering and Mathematics, Bethune-Cookman University, Daytona Beach, FL 32114, USA; (D.S.M.); (A.M.D.); (G.S.J.); (A.D.W.); (Y.A.H.); (B.W.M.)
| | - Akimio D. Walker
- College of Science, Engineering and Mathematics, Bethune-Cookman University, Daytona Beach, FL 32114, USA; (D.S.M.); (A.M.D.); (G.S.J.); (A.D.W.); (Y.A.H.); (B.W.M.)
| | - Yessenia A. Hall
- College of Science, Engineering and Mathematics, Bethune-Cookman University, Daytona Beach, FL 32114, USA; (D.S.M.); (A.M.D.); (G.S.J.); (A.D.W.); (Y.A.H.); (B.W.M.)
| | - Baraka W. Mapp
- College of Science, Engineering and Mathematics, Bethune-Cookman University, Daytona Beach, FL 32114, USA; (D.S.M.); (A.M.D.); (G.S.J.); (A.D.W.); (Y.A.H.); (B.W.M.)
| | - Matilda O. Johnson
- College of Nursing and Health Sciences, Bethune-Cookman University, Daytona Beach, FL 32114, USA;
| | - Shaneka S. Simmons
- Department of Science and Mathematics, Jarvis Christian College, Hawkins, TX 75765, USA;
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17
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Durán D, Albareda M, García C, Marina AI, Ruiz-Argüeso T, Palacios JM. Proteome Analysis Reveals a Significant Host-Specific Response in Rhizobium leguminosarum bv. viciae Endosymbiotic Cells. Mol Cell Proteomics 2020; 20:100009. [PMID: 33214187 PMCID: PMC7950203 DOI: 10.1074/mcp.ra120.002276] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/15/2020] [Accepted: 11/19/2020] [Indexed: 11/06/2022] Open
Abstract
The Rhizobium-legume symbiosis is a beneficial interaction in which the bacterium converts atmospheric nitrogen into ammonia and delivers it to the plant in exchange for carbon compounds. This symbiosis implies the adaptation of bacteria to live inside host plant cells. In this work, we apply RP-LC-MS/MS and isobaric tags as relative and absolute quantitation techniques to study the proteomic profile of endosymbiotic cells (bacteroids) induced by Rhizobium leguminosarum bv viciae strain UPM791 in legume nodules. Nitrogenase subunits, tricarboxylic acid cycle enzymes, and stress-response proteins are among the most abundant from over 1000 rhizobial proteins identified in pea (Pisum sativum) bacteroids. Comparative analysis of bacteroids induced in pea and in lentil (Lens culinaris) nodules revealed the existence of a significant host-specific differential response affecting dozens of bacterial proteins, including stress-related proteins, transcriptional regulators, and proteins involved in the carbon and nitrogen metabolisms. A mutant affected in one of these proteins, homologous to a GntR-like transcriptional regulator, showed a symbiotic performance significantly impaired in symbiosis with pea but not with lentil plants. Analysis of the proteomes of bacteroids isolated from both hosts also revealed the presence of different sets of plant-derived nodule-specific cysteine-rich peptides, indicating that the endosymbiotic bacteria find a host-specific cocktail of chemical stressors inside the nodule. By studying variations of the bacterial response to different plant cell environments, we will be able to identify specific limitations imposed by the host that might give us clues for the improvement of rhizobial performance.
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Affiliation(s)
- David Durán
- Centro de Biotecnología y Genómica de Plantas (C.B.G.P.) UPM-INIA, Campus de Montegancedo, Universidad Politécnica de Madrid, Madrid, Spain; Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Marta Albareda
- Centro de Biotecnología y Genómica de Plantas (C.B.G.P.) UPM-INIA, Campus de Montegancedo, Universidad Politécnica de Madrid, Madrid, Spain; Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Carlos García
- Servicio de Proteómica, Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC Campus Cantoblanco, Madrid, Spain
| | - Ana-Isabel Marina
- Servicio de Proteómica, Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC Campus Cantoblanco, Madrid, Spain
| | - Tomás Ruiz-Argüeso
- Centro de Biotecnología y Genómica de Plantas (C.B.G.P.) UPM-INIA, Campus de Montegancedo, Universidad Politécnica de Madrid, Madrid, Spain; Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Jose-Manuel Palacios
- Centro de Biotecnología y Genómica de Plantas (C.B.G.P.) UPM-INIA, Campus de Montegancedo, Universidad Politécnica de Madrid, Madrid, Spain; Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain.
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18
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The ATP-Binding Cassette (ABC) Transport Systems in Mycobacterium tuberculosis: Structure, Function, and Possible Targets for Therapeutics. BIOLOGY 2020; 9:biology9120443. [PMID: 33291531 PMCID: PMC7761784 DOI: 10.3390/biology9120443] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/06/2020] [Accepted: 11/12/2020] [Indexed: 12/22/2022]
Abstract
Simple Summary Mycobacterium tuberculosis is a bacterium of great medical importance because it causes tuberculosis, a disease that affects millions of people worldwide. Two important features are related to this bacterium: its ability to infect and survive inside the host, minimizing the immune response, and the burden of clinical isolates that are highly resistant to antibiotics treatment. These two phenomena are directly affected by cell envelope proteins, such as proteins from the ATP-Binding Cassette (ABC transporters) superfamily. In this review, we have compiled information on all the M. tuberculosis ABC transporters described so far, both from a functional and structural point of view, and show their relevance for the bacillus and the potential targets for studies aiming to control the microorganism and structural features. Abstract Mycobacterium tuberculosis is the etiological agent of tuberculosis (TB), a disease that affects millions of people in the world and that is associated with several human diseases. The bacillus is highly adapted to infect and survive inside the host, mainly because of its cellular envelope plasticity, which can be modulated to adapt to an unfriendly host environment; to manipulate the host immune response; and to resist therapeutic treatment, increasing in this way the drug resistance of TB. The superfamily of ATP-Binding Cassette (ABC) transporters are integral membrane proteins that include both importers and exporters. Both types share a similar structural organization, yet only importers have a periplasmic substrate-binding domain, which is essential for substrate uptake and transport. ABC transporter-type importers play an important role in the bacillus physiology through the transport of several substrates that will interfere with nutrition, pathogenesis, and virulence. Equally relevant, exporters have been involved in cell detoxification, nutrient recycling, and antibiotics and drug efflux, largely affecting the survival and development of multiple drug-resistant strains. Here, we review known ABC transporters from M. tuberculosis, with particular focus on the diversity of their structural features and relevance in infection and drug resistance.
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Matarredona L, Camacho M, Zafrilla B, Bonete MJ, Esclapez J. The Role of Stress Proteins in Haloarchaea and Their Adaptive Response to Environmental Shifts. Biomolecules 2020; 10:biom10101390. [PMID: 33003558 PMCID: PMC7601130 DOI: 10.3390/biom10101390] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/18/2020] [Accepted: 09/24/2020] [Indexed: 12/26/2022] Open
Abstract
Over the years, in order to survive in their natural environment, microbial communities have acquired adaptations to nonoptimal growth conditions. These shifts are usually related to stress conditions such as low/high solar radiation, extreme temperatures, oxidative stress, pH variations, changes in salinity, or a high concentration of heavy metals. In addition, climate change is resulting in these stress conditions becoming more significant due to the frequency and intensity of extreme weather events. The most relevant damaging effect of these stressors is protein denaturation. To cope with this effect, organisms have developed different mechanisms, wherein the stress genes play an important role in deciding which of them survive. Each organism has different responses that involve the activation of many genes and molecules as well as downregulation of other genes and pathways. Focused on salinity stress, the archaeal domain encompasses the most significant extremophiles living in high-salinity environments. To have the capacity to withstand this high salinity without losing protein structure and function, the microorganisms have distinct adaptations. The haloarchaeal stress response protects cells against abiotic stressors through the synthesis of stress proteins. This includes other heat shock stress proteins (Hsp), thermoprotectants, survival proteins, universal stress proteins, and multicellular structures. Gene and family stress proteins are highly conserved among members of the halophilic archaea and their study should continue in order to develop means to improve for biotechnological purposes. In this review, all the mechanisms to cope with stress response by haloarchaea are discussed from a global perspective, specifically focusing on the role played by universal stress proteins.
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Mycobacterium tuberculosis Rv2005c Induces Dendritic Cell Maturation and Th1 Responses and Exhibits Immunotherapeutic Activity by Fusion with the Rv2882c Protein. Vaccines (Basel) 2020; 8:vaccines8030370. [PMID: 32664238 PMCID: PMC7564171 DOI: 10.3390/vaccines8030370] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/02/2020] [Accepted: 07/06/2020] [Indexed: 01/06/2023] Open
Abstract
Immunotherapy represents a promising approach for improving current antibiotic treatments through the engagement of the host’s immune system. Latency-associated antigens have been included as components of multistage subunit tuberculosis vaccines. We first identified Rv2005c, a DosR regulon-encoded protein, as a seroreactive protein. In this study, we found that Rv2005c induced dendritic cell (DC) maturation and Th1 responses, and its expression by Mycobacterium tuberculosis (Mtb) within macrophages was enhanced by treatment with CoCl2, a hypoxia-mimetic agent. T cells activated by Rv2005c-matured DCs induced antimycobacterial activity in macrophages under hypoxic conditions but not under normoxic conditions. However, Rv2005c alone did not exhibit any significant vaccine efficacy in our mouse model. The fusion of Rv2005c to the macrophage-activating protein Rv2882c resulted in significant activation of DCs and antimycobacterial activity in macrophages, which were enhanced under hypoxic conditions. Furthermore, the Rv2882c-Rv2005c fusion protein showed significant adjunctive immunotherapeutic effects and led to the generation of long-lasting, antigen-specific, multifunctional CD4+ T cells that coproduced TNF-α, IFN-γ and IL-2 in the lungs of our established mouse model. Overall, these results provide a novel fusion protein with immunotherapeutic potential as adjunctive chemotherapy for tuberculosis.
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Lopez Quezada L, Smith R, Lupoli TJ, Edoo Z, Li X, Gold B, Roberts J, Ling Y, Park SW, Nguyen Q, Schoenen FJ, Li K, Hugonnet JE, Arthur M, Sacchettini JC, Nathan C, Aubé J. Activity-Based Protein Profiling Reveals That Cephalosporins Selectively Active on Non-replicating Mycobacterium tuberculosis Bind Multiple Protein Families and Spare Peptidoglycan Transpeptidases. Front Microbiol 2020; 11:1248. [PMID: 32655524 PMCID: PMC7324553 DOI: 10.3389/fmicb.2020.01248] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 05/15/2020] [Indexed: 11/13/2022] Open
Abstract
As β-lactams are reconsidered for the treatment of tuberculosis (TB), their targets are assumed to be peptidoglycan transpeptidases, as verified by adduct formation and kinetic inhibition of Mycobacterium tuberculosis (Mtb) transpeptidases by carbapenems active against replicating Mtb. Here, we investigated the targets of recently described cephalosporins that are selectively active against non-replicating (NR) Mtb. NR-active cephalosporins failed to inhibit recombinant Mtb transpeptidases. Accordingly, we used alkyne analogs of NR-active cephalosporins to pull down potential targets through unbiased activity-based protein profiling and identified over 30 protein binders. None was a transpeptidase. Several of the target candidates are plausibly related to Mtb's survival in an NR state. However, biochemical tests and studies of loss of function mutants did not identify a unique target that accounts for the bactericidal activity of these beta-lactams against NR Mtb. Instead, NR-active cephalosporins appear to kill Mtb by collective action on multiple targets. These results highlight the ability of these β-lactams to target diverse classes of proteins.
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Affiliation(s)
- Landys Lopez Quezada
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Robert Smith
- Chemical Methodologies & Library Development Center, The University of Kansas, Lawrence, KS, United States
| | - Tania J. Lupoli
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Zainab Edoo
- Sorbonne Université, Sorbonne Paris Cité, Université de Paris, INSERM, Centre de Recherche des Cordeliers, CRC, Paris, France
| | - Xiaojun Li
- Departments of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Ben Gold
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Julia Roberts
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Yan Ling
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Sae Woong Park
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Quyen Nguyen
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Frank J. Schoenen
- Chemical Methodologies & Library Development Center, The University of Kansas, Lawrence, KS, United States
| | - Kelin Li
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jean-Emmanuel Hugonnet
- Sorbonne Université, Sorbonne Paris Cité, Université de Paris, INSERM, Centre de Recherche des Cordeliers, CRC, Paris, France
| | - Michel Arthur
- Sorbonne Université, Sorbonne Paris Cité, Université de Paris, INSERM, Centre de Recherche des Cordeliers, CRC, Paris, France
| | - James C. Sacchettini
- Departments of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Carl Nathan
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Jeffrey Aubé
- Chemical Methodologies & Library Development Center, The University of Kansas, Lawrence, KS, United States
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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Samanta S, Biswas P, Banerjee A, Bose A, Siddiqui N, Nambi S, Saini DK, Visweswariah SS. A universal stress protein in Mycobacterium smegmatis sequesters the cAMP-regulated lysine acyltransferase and is essential for biofilm formation. J Biol Chem 2020; 295:1500-1516. [PMID: 31882539 PMCID: PMC7008380 DOI: 10.1074/jbc.ra119.011373] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 12/19/2019] [Indexed: 01/08/2023] Open
Abstract
Universal stress proteins (USPs) are present in many bacteria, and their expression is enhanced under various environmental stresses. We have previously identified a USP in Mycobacterium smegmatis that is a product of the msmeg_4207 gene and is a substrate for a cAMP-regulated protein lysine acyltransferase (KATms; MSMEG_5458). Here, we explored the role of this USP (USP4207) in M. smegmatis and found that its gene is present in an operon that also contains genes predicted to encode a putative tripartite tricarboxylate transporter (TTT). Transcription of the TTT-usp4207 operon was induced in the presence of citrate and tartrate, perhaps by the activity of a divergent histidine kinase-response regulator gene pair. A usp4207-deleted strain had rough colony morphology and reduced biofilm formation compared with the WT strain; however, both normal colony morphology and biofilm formation were restored in a Δusp4207Δkatms strain. We identified several proteins whose acetylation was lost in the Δkatms strain, and whose transcript levels increased in M. smegmatis biofilms along with that of USP4207, suggesting that USP4207 insulates KATms from its other substrates in the cell. We propose that USP4207 sequesters KATms from diverse substrates whose activities are down-regulated by acylation but are required for biofilm formation, thus providing a defined role for this USP in mycobacterial physiology and stress responses.
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Affiliation(s)
- Sintu Samanta
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Priyanka Biswas
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Arka Banerjee
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Avipsa Bose
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Nida Siddiqui
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Subhalaxmi Nambi
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Deepak Kumar Saini
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Sandhya S Visweswariah
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, Karnataka 560012, India.
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Havis S, Rangel J, Mali S, Bodunrin A, Housammy Z, Zimmerer R, Murphy J, Widger WR, Bark SJ. A color-based competition assay for studying bacterial stress responses in Micrococcus luteus. FEMS Microbiol Lett 2019; 366:5379281. [PMID: 30865770 DOI: 10.1093/femsle/fnz054] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/12/2019] [Indexed: 12/30/2022] Open
Abstract
Competition assays measure differences between populations of bacteria after stress adaptation, populations of different bacteria and mutations in antibiotic resistance genes. We have developed a competition-based assay to evaluate if genes upregulated under starvation are important for bacterial survival. Stress responses are critical for survival in non-pathogenic and pathogenic bacteria alike including Mycobacterium tuberculosis, Enterococcus fecaelis, Escherichia coli and Staphylococcus aureus. Unfortunately, most stress-survival proteins are poorly understood because suitable model bacteria and techniques are limited. To address this problem, we have engineered Micrococcus luteus NCTC 2665 (M. luteus) for competition assays by inactivating the sarcinaxanthin biosynthesis gene crtE (ΔcrtE), changing M. luteus colonies from yellow to white. This change allows easy identification in mixed cultures. The crtE knockout is relatively neutral for growth in complex and minimal acetate media and shows a measured fitness of one in competition with yellow wild-type bacteria. The ΔcrtE M. luteus competition assay identified a competition defect in a M. luteus strain when a specific universal stress protein was inactivated, suggesting a negative survival phenotype for this protein. We anticipate this competition assay can identify defects in other gene knockouts and mutational studies in M. luteus and will enhance our understanding of bacterial survival mechanisms.
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Affiliation(s)
- Spencer Havis
- Department of Biology and Biochemistry, The University of Houston, Houston, TX, USA
| | - Jonathan Rangel
- Department of Biology and Biochemistry, The University of Houston, Houston, TX, USA
| | - Sujina Mali
- Department of Biology, Washington University, St. Louis, MO, USA
| | - Abiodun Bodunrin
- Department of Biology and Biochemistry, The University of Houston, Houston, TX, USA
| | - Zina Housammy
- University of North Texas Health Sciences Center, Fort Worth, TX, USA
| | - Rene Zimmerer
- Department of Biology and Biochemistry, The University of Houston, Houston, TX, USA
| | - Jesse Murphy
- Department of Biology and Biochemistry, The University of Houston, Houston, TX, USA
| | - William R Widger
- Department of Biology and Biochemistry, The University of Houston, Houston, TX, USA
| | - Steven J Bark
- Department of Biology and Biochemistry, The University of Houston, Houston, TX, USA
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Fang QJ, Han YX, Shi YJ, Huang HQ, Fang ZG, Hu YH. Universal stress proteins contribute Edwardsiella piscicida adversity resistance and pathogenicity and promote blocking host immune response. FISH & SHELLFISH IMMUNOLOGY 2019; 95:248-258. [PMID: 31654767 DOI: 10.1016/j.fsi.2019.10.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 10/02/2019] [Accepted: 10/19/2019] [Indexed: 06/10/2023]
Abstract
Universal stress proteins (Usps) exist ubiquitously in bacteria and other organisms. Usps play an important role in adaptation of bacteria to a variety of environmental stresses. There is increasing evidence that Usps facilitate pathogens to adapt host environment and are involved in pathogenicity. Edwardsiella piscicida (formerly included in E. tarda) is a severe fish pathogen and infects various important economic fish including tilapia (Oreochromis niloticus). In E. piscicida, a number of systems and factors that are involved in stress resistance and pathogenesis were identified. However, the function of Usps in E. piscicida is totally unknown. In this study, we examined the expressions of 13 usp genes in E. piscicida and found that most of these usp genes were up-regulated expression under high temperature, oxidative stress, acid stress, and host serum stress. Particularly, among these usp genes, usp13, exhibited dramatically high expression level upon several stress conditions. To investigate the biological role of usp13, a markerless usp13 in-frame mutant strain, TX01Δusp13, was constructed. Compared to the wild type TX01, TX01Δusp13 exhibited markedly compromised tolerance to high temperature, hydrogen peroxide, and low pH. Deletion of usp13 significantly retarded bacterial biofilm growth and decreased resistance against serum killing. Pathogenicity analysis showed that the inactivation of usp13 significantly impaired the ability of E. piscicida to invade into host cell and infect host tissue. Introduction of a trans-expressed usp13 gene restored the lost virulence of TX01Δusp13. In support of these results, host immune response induced by TX01 and TX01Δusp13 was examined, and the results showed reactive oxygen species (ROS) levels in TX01Δusp13-infected macrophages were significantly higher than those in TX01-infected cells. The expression level of several cytokines (IL-6, IL-8, IL-10, TNF-α, and CC2) in TX01Δusp13-infected fish was significantly higher than that in TX01-infected fish. These results suggested that the deletion of usp13 attenuated the ability of bacteria to overcome the host immune response to pathogen infection. Taken together, our study indicated Usp13 of E. piscicida was not only important participant in adversity resistance, but also was essential for E. piscicida pathogenicity and contributed to block host immune response to pathogen infection.
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Affiliation(s)
- Qing-Jian Fang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, College of Marine Science, Hainan University, Haikou, 570228, China; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Yue-Xin Han
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Yan-Jie Shi
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Hui-Qin Huang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China; Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bio-resources, Haikou, 571101, China
| | - Zai-Guang Fang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, College of Marine Science, Hainan University, Haikou, 570228, China.
| | - Yong-Hua Hu
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), China; Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bio-resources, Haikou, 571101, China.
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25
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A Universal Stress Protein That Controls Bacterial Stress Survival in Micrococcus luteus. J Bacteriol 2019; 201:JB.00497-19. [PMID: 31548273 DOI: 10.1128/jb.00497-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 09/05/2019] [Indexed: 12/14/2022] Open
Abstract
Bacteria have remarkable mechanisms to survive severe external stresses, and one of the most enigmatic is the nonreplicative persistent (NRP) state. Practically, NRP bacteria are difficult to treat, and so inhibiting the proteins underlying this survival state may render such bacteria more susceptible to external stresses, including antibiotics. Unfortunately, we know little about the proteins and mechanisms conferring survival through the NRP state. Here, we report that a universal stress protein (Usp) is a primary regulator of bacterial survival through the NRP state in Micrococcus luteus NCTC 2665, a biosafety level 1 (BSL1) mycobacterial relative. Usps are widely conserved, and bacteria, including Mycobacterium tuberculosis, Mycobacterium smegmatis, and Escherichia coli, have multiple paralogs with overlapping functions that have obscured their functional roles. A kanamycin resistance cassette inserted into the M. luteus universal stress protein A 616 gene (ΔuspA616::kan M. luteus) ablates the UspA616 protein and drastically impairs M. luteus survival under even short-term starvation (survival, 83% wild type versus 32% ΔuspA616::kan M. luteus) and hypoxia (survival, 96% wild type versus 48% ΔuspA616::kan M. luteus). We observed no detrimental UspA616 knockout phenotype in logarithmic growth. Proteomics demonstrated statistically significant log-phase upregulation of glyoxylate pathway enzymes isocitrate lyase and malate synthase in ΔuspA616::kan M. luteus We note that these enzymes and the M. tuberculosis UspA616 homolog (Rv2623) are important in M. tuberculosis virulence and chronic infection, suggesting that Usps are important stress proteins across diverse bacterial species. We propose that UspA616 is a metabolic switch that controls survival by regulating the glyoxylate shunt.IMPORTANCE Bacteria tolerate severe external stresses, including antibiotics, through a nonreplicative persistent (NRP) survival state, yet the proteins regulating this survival state are largely unknown. We show a specific universal stress protein (UspA616) controls the NRP state in Micrococcus luteus Usps are widely conserved across bacteria, but their biological function(s) has remained elusive. UspA616 inactivation renders M. luteus susceptible to stress: bacteria die instead of adapting through the NRP state. UspA616 regulates malate synthase and isocitrate lyase, glyoxylate pathway enzymes important for chronic Mycobacterium tuberculosis infection. These data show that UspA616 regulates NRP stress survival in M. luteus and suggest a function for homologous proteins in other bacteria. Importantly, inhibitors of UspA616 and homologs may render NRP bacteria more susceptible to stresses, including current antibiotics.
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26
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Ganguli G, Mukherjee U, Sonawane A. Peroxisomes and Oxidative Stress: Their Implications in the Modulation of Cellular Immunity During Mycobacterial Infection. Front Microbiol 2019; 10:1121. [PMID: 31258517 PMCID: PMC6587667 DOI: 10.3389/fmicb.2019.01121] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 05/03/2019] [Indexed: 12/12/2022] Open
Abstract
Host redox dependent physiological responses play crucial roles in the determination of mycobacterial infection process. Mtb explores oxygen rich lung microenvironments to initiate infection process, however, later on the bacilli adapt to oxygen depleted conditions and become non-replicative and unresponsive toward anti-TB drugs to enter in the latency stage. Mtb is equipped with various sensory mechanisms and a battery of pro- and anti-oxidant enzymes to protect themselves from the host oxidative stress mechanisms. After host cell invasion, mycobacteria induces the expression of NADPH oxidase 2 (NOX2) to generate superoxide radicals (O 2 - ), which are then converted to more toxic hydrogen peroxide (H2O2) by superoxide dismutase (SOD) and subsequently reduced to water by catalase. However, the metabolic cascades and their key regulators associated with cellular redox homeostasis are poorly understood. Phagocytosed mycobacteria en route through different subcellular organelles, where the local environment generated during infection determines the outcome of disease. For a long time, mitochondria were considered as the key player in the redox regulation, however, accumulating evidences report vital role for peroxisomes in the maintenance of cellular redox equilibrium in eukaryotic cells. Deletion of peroxisome-associated peroxin genes impaired detoxification of reactive oxygen species and peroxisome turnover post-infection, thereby leading to altered synthesis of transcription factors, various cell-signaling cascades in favor of the bacilli. This review focuses on how mycobacteria would utilize host peroxisomes to alter redox balance and metabolic regulatory mechanisms to support infection process. Here, we discuss implications of peroxisome biogenesis in the modulation of host responses against mycobacterial infection.
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Affiliation(s)
- Geetanjali Ganguli
- School of Biotechnology, KIIT (deemed to be University), Bhubaneswar, India
| | - Utsav Mukherjee
- School of Biotechnology, KIIT (deemed to be University), Bhubaneswar, India
| | - Avinash Sonawane
- School of Biotechnology, KIIT (deemed to be University), Bhubaneswar, India
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
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27
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Song N, Li Z, Cui Z, Chen L, Cui Y, Dang G, Li Z, Li H, Liu S. The prominent alteration in transcriptome and metabolome of Mycobacterium bovis BCG str. Tokyo 172 induced by vitamin B 1. BMC Microbiol 2019; 19:104. [PMID: 31117936 PMCID: PMC6530141 DOI: 10.1186/s12866-019-1492-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 05/14/2019] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Vitamin B1 (VB1) is a crucial dietary nutrient and essential cofactor for several key enzymes in the regulation of cellular and metabolic processes, and more importantly in the activation of immune system. To date, the precise role of VB1 in Mycobacterium tuberculosis remains to be fully understood. RESULTS In this study, the transcriptional and metabolic profiles of VB1-treated Mycobacterium. bovis BCG were analyzed by RNA-sequencing and LC-MS (Liquid chromatography coupled to mass spectrometry). The selection of BCG strain was based on its common physiological features shared with M. tuberculosis. The results of cell growth assays demonstrated that VB1 inhibited the BCG growth rate in vitro. Transcriptomic analysis revealed that the expression levels of genes related to fatty acid metabolism, cholesterol metabolism, glycolipid catabolism, DNA replication, protein translation, cell division and cell wall formation were significantly downregulated in M. bovis BCG treated with VB1. In addition, the metabolomics LC-MS data indicated that most of the amino acids and adenosine diphosphate (ADP) were decreased in M. bovis BCG strain after VB1 treatment. CONCLUSIONS This study provides the molecular and metabolic bases to understand the impacts of VB1 on M.bovis BCG.
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Affiliation(s)
- Ningning Song
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Zhaoli Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Ziyin Cui
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Liping Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yingying Cui
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Guanghui Dang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Zhe Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - He Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Siguo Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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Sharma D, Lata M, Faheem M, Khan AU, Joshi B, Venkatesan K, Shukla S, Bisht D. Role of M.tuberculosis protein Rv2005c in the aminoglycosides resistance. Microb Pathog 2019; 132:150-155. [PMID: 31059757 DOI: 10.1016/j.micpath.2019.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/02/2019] [Accepted: 05/02/2019] [Indexed: 10/26/2022]
Abstract
Tuberculosis is an airborne infectious disease caused by Mycobacterium tuberculosis which threatens the globe. Aminoglycosides {Amikacin (AK) & Kanamycin (KM)} are WHO recommended second-line anti-TB drugs used against the treatment of drug-resistant tuberculosis. Aminoglycosides target the steps of protein translation machinery of M.tuberculosis. Several mechanisms have been put forward to elucidate the phenomena of aminoglycosides resistance but our knowledge is still insufficient. The aim of the study was to understand the involvement of Mycobacterium tuberculosis universal stress protein (Rv2005c) in aminoglycosides resistance and virulence. To establish the relationship of universal stress protein Rv2005c with AK & KM resistance, Rv2005c was cloned, expressed in E.coli BL21 using pQE2 expression vector and antimicrobial drug susceptibility testing (DST) was carried out. STRING-10 was also used to predict the interacting protein partners of Rv2005c. DST showed that the minimum inhibitory concentration of induced recombinant cells (Rv2005c) were five and four folds shifted with AK and KM E-strips, respectively. STRING-10 showed the interacting protein partners of Rv2005c. Overexpression of Rv2005c leads to shifting in MIC which might be signifying its involvement in the survival/resistance of Mycobacteria by inhibiting/modulating the effects of AK and KM released from the E-strips. Interactome also suggests that Rv2005c and its interacting protein partners are cumulatively involved in M.tuberculosis resistance, stresses, and latency.
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Affiliation(s)
- Divakar Sharma
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra, 282004, India; Interdisciplinary Biotechnology Unit, Aligarh Muslim University Aligarh, 202002, India.
| | - Manju Lata
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra, 282004, India
| | - Mohammad Faheem
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University Aligarh, 202002, India
| | - Asad Ullah Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University Aligarh, 202002, India
| | - Beenu Joshi
- Department of Immunology, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra, 282004, India
| | - Krishnamurthy Venkatesan
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra, 282004, India
| | - Sangeeta Shukla
- School of Studies (SOS) Zoology, Jiwaji University, Gwalior, 474011, India
| | - Deepa Bisht
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra, 282004, India.
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29
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Miryala SK, Anbarasu A, Ramaiah S. Impact of bedaquiline and capreomycin on the gene expression patterns of multidrug‐resistant
Mycobacterium tuberculosis
H37Rv strain and understanding the molecular mechanism of antibiotic resistance. J Cell Biochem 2019; 120:14499-14509. [DOI: 10.1002/jcb.28711] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 03/06/2019] [Accepted: 03/15/2019] [Indexed: 01/03/2023]
Affiliation(s)
- Sravan Kumar Miryala
- Department of Bio‐Sciences, Medical and Biological Computing Laboratory, School of Bio Sciences and Technology Vellore Institute of Technology Vellore Tamil Nadu India
| | - Anand Anbarasu
- Department of Bio‐Sciences, Medical and Biological Computing Laboratory, School of Bio Sciences and Technology Vellore Institute of Technology Vellore Tamil Nadu India
| | - Sudha Ramaiah
- Department of Bio‐Sciences, Medical and Biological Computing Laboratory, School of Bio Sciences and Technology Vellore Institute of Technology Vellore Tamil Nadu India
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30
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Aruleba RT, Adekiya TA, Oyinloye BE, Masamba P, Mbatha LS, Pretorius A, Kappo AP. PZQ Therapy: How Close are we in the Development of Effective Alternative Anti-schistosomal Drugs? Infect Disord Drug Targets 2019; 19:337-349. [PMID: 30599112 PMCID: PMC7046992 DOI: 10.2174/1871526519666181231153139] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/24/2018] [Accepted: 12/25/2018] [Indexed: 11/22/2022]
Abstract
Today schistosomiasis, caused mainly by the three major schistosome species (S. mansoni, S. haematobium and S. japonicum), has for many decades and still continues to be on a rapid and swift rise globally, claiming thousands of lives every year and leaving 800 million people at the risk of infection. Due to the high prevalence of this disease and the steady increase in the infection rates, praziquantel (PZQ) remains the only effective drug against this acute disease although it has no effect on the juvenile schistosome parasite. However, no significant approaches have been made in recent years in the discovery of new or alternative drugs and unfortunately, resistance to this drug has been reported in some parts of the world. Therefore, it is imperative to develop a new drug for this debilitating disease. In this review, a brief history of past, present, and new promising anti-schistosomal drugs is presented.
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Affiliation(s)
- Raphael Taiwo Aruleba
- Biotechnology and Structural Biology (BSB) Group, Department of Biochemistry and Microbiology, University of Zululand, KwaDlangezwa 3886, South Africa
| | - Tayo Alex Adekiya
- Biotechnology and Structural Biology (BSB) Group, Department of Biochemistry and Microbiology, University of Zululand, KwaDlangezwa 3886, South Africa
| | - Babatunji Emmanuel Oyinloye
- Biotechnology and Structural Biology (BSB) Group, Department of Biochemistry and Microbiology, University of Zululand, KwaDlangezwa 3886, South Africa
- Department of Biochemistry, Afe Babalola University, PMB 5454, Ado-Ekiti 360001, Nigeria
| | - Priscilla Masamba
- Biotechnology and Structural Biology (BSB) Group, Department of Biochemistry and Microbiology, University of Zululand, KwaDlangezwa 3886, South Africa
| | - Londiwe Simphiwe Mbatha
- Biotechnology and Structural Biology (BSB) Group, Department of Biochemistry and Microbiology, University of Zululand, KwaDlangezwa 3886, South Africa
| | - Ashley Pretorius
- Bioinformatics Research Group (BRG), DST/Mintek Nanotechnology Innovation Centre, Biolabels Node, Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa
| | - Abidemi Paul Kappo
- Biotechnology and Structural Biology (BSB) Group, Department of Biochemistry and Microbiology, University of Zululand, KwaDlangezwa 3886, South Africa
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Zhao HM, Du R, Li CL, Ji P, Li HC, Wu K, Hu Z, Lu SH, Lowrie DB, Fan XY. Differential T cell responses against DosR-associated antigen Rv2028c in BCG-vaccinated populations with tuberculosis infection. J Infect 2018; 78:275-280. [PMID: 30528871 DOI: 10.1016/j.jinf.2018.10.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 10/30/2018] [Accepted: 10/31/2018] [Indexed: 02/07/2023]
Abstract
The IFN-γ release assays (IGRAs) based on region of difference 1 (RD1) antigens have improved diagnosis of Mycobacterium tuberculosis (Mtb) infection. However, IGRAs with these antigens could not distinguish latent tuberculosis infection (LTBI) from active tuberculosis (ATB). DosR regulon genes are thought to be important for Mtb dormancy, and their products have higher immunogenicity in LTBI than ATB individuals, suggesting protective immunity mediated by DosR regulon-encoded antigens and potential utility of them for differential diagnostics of Mtb-infected populations or development of therapeutic vaccines against tuberculosis (TB). Among them, Rv2028c is a dormancy-related antigen that has demonstrated potential use in TB control, but its immunological characteristics in the BCG-vaccinated Chinese population are unknown. In this study, a total of 148 individuals, including 98 patients with ATB, 20 cases with LTBI and 30 healthy controls, were tested for Rv2028c-specific T cell responses by using an IFN-γ ELISA assay. The results showed that the T-cell responses in LTBI individuals were almost always higher than those in ATB patients, regardless of the site of infection or the results of bacteriological examination in the patients. This allowed for good differentiation between these two groups of Mtb-infected individuals even in the BCG-vaccinated high TB-incidence setting that pertains in China. In addition, the diagnostic efficacy for ATB was enhanced by combining the results from Rv2028c and RD1 antigen-based IFN-γ ELISA assays. In conclusion, Rv2028c-specific T-cell responses might contribute to natural protection against dormant Mtb infection, and the determination of these responses can aid discrimination between healthy LTBI individuals and ATB patients in the Mtb-infected populations.
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Affiliation(s)
- Hui-Min Zhao
- Shanghai Public Health Clinical Center, Key Laboratory of Medical Molecular Virology of MOE/MOH, Fudan University, 2901 Caolang Rd., Shanghai 201508, China; School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325035, China
| | - Rui Du
- School of Laboratory Medicine and Life Science, Jinlin Agriculture University, Changchun 130033, China
| | - Chun-Ling Li
- Shanghai Public Health Clinical Center, Key Laboratory of Medical Molecular Virology of MOE/MOH, Fudan University, 2901 Caolang Rd., Shanghai 201508, China; School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325035, China
| | - Ping Ji
- Shanghai Public Health Clinical Center, Key Laboratory of Medical Molecular Virology of MOE/MOH, Fudan University, 2901 Caolang Rd., Shanghai 201508, China
| | - Hai-Cong Li
- Shanghai Public Health Clinical Center, Key Laboratory of Medical Molecular Virology of MOE/MOH, Fudan University, 2901 Caolang Rd., Shanghai 201508, China
| | - Kang Wu
- Shanghai Public Health Clinical Center, Key Laboratory of Medical Molecular Virology of MOE/MOH, Fudan University, 2901 Caolang Rd., Shanghai 201508, China
| | - Zhidong Hu
- Shanghai Public Health Clinical Center, Key Laboratory of Medical Molecular Virology of MOE/MOH, Fudan University, 2901 Caolang Rd., Shanghai 201508, China
| | - Shui-Hua Lu
- Shanghai Public Health Clinical Center, Key Laboratory of Medical Molecular Virology of MOE/MOH, Fudan University, 2901 Caolang Rd., Shanghai 201508, China
| | - Douglas B Lowrie
- Shanghai Public Health Clinical Center, Key Laboratory of Medical Molecular Virology of MOE/MOH, Fudan University, 2901 Caolang Rd., Shanghai 201508, China
| | - Xiao-Yong Fan
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325035, China; Shanghai Public Health Clinical Center, Key Laboratory of Medical Molecular Virology of MOE/MOH, Fudan University, 2901 Caolang Rd., Shanghai 201508, China; School of Laboratory Medicine and Life Science, Jinlin Agriculture University, Changchun 130033, China.
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Akgul A, Nho SW, Kalindamar S, Tekedar HC, Abdalhamed H, Lawrence ML, Karsi A. Universal Stress Proteins Contribute Edwardsiella ictaluri Virulence in Catfish. Front Microbiol 2018; 9:2931. [PMID: 30546354 PMCID: PMC6279896 DOI: 10.3389/fmicb.2018.02931] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 11/14/2018] [Indexed: 11/21/2022] Open
Abstract
Edwardsiella ictaluri is an intracellular Gram-negative facultative pathogen causing enteric septicemia of catfish (ESC), a common disease resulting in substantial economic losses in the U.S. catfish industry. Previously, we demonstrated that several universal stress proteins (USPs) are highly expressed under in vitro and in vivo stress conditions, indicating their importance for E. ictaluri survival. However, the roles of these USPs in E. ictaluri virulence is not known yet. In this work, 10 usp genes of E. ictaluri were in-frame deleted and characterized in vitro and in vivo. Results show that all USP mutants were sensitive to acidic condition (pH 5.5), and EiΔusp05 and EiΔusp08 were very sensitive to oxidative stress (0.1% H2O2). Virulence studies indicated that EiΔusp05, EiΔusp07, EiΔusp08, EiΔusp09, EiΔusp10, and EiΔusp13 were attenuated significantly compared to E. ictaluri wild-type (EiWT; 20, 45, 20, 20, 55, and 10% vs. 74.1% mortality, respectively). Efficacy experiments showed that vaccination of catfish fingerlings with EiΔusp05, EiΔusp07, EiΔusp08, EiΔusp09, EiΔusp10, and EiΔusp13 provided complete protection against EiWT compared to sham-vaccinated fish (0% vs. 58.33% mortality). Our results support that USPs contribute E. ictaluri virulence in catfish.
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Affiliation(s)
- Ali Akgul
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, MS, United States
| | - Seong Won Nho
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, MS, United States
| | - Safak Kalindamar
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, MS, United States
| | - Hasan C Tekedar
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, MS, United States
| | - Hossam Abdalhamed
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, MS, United States
| | - Mark L Lawrence
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, MS, United States
| | - Attila Karsi
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, MS, United States
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Chen Y, Cao S, Liu Y, Zhang X, Wang W, Li C. Potential role for Rv2026c- and Rv2421c- specific antibody responses in diagnosing active tuberculosis. Clin Chim Acta 2018; 487:369-376. [PMID: 30195451 DOI: 10.1016/j.cca.2018.09.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/04/2018] [Accepted: 09/05/2018] [Indexed: 10/28/2022]
Abstract
The current diagnostic methods for tuberculosis (TB) have several limitations. Although commercial serological tests based on antibody detection are available, their variable accuracies limit their roles in the clinic. The aim of this study was to discover the improved biomarkers for TB disease by investigating the serum profiles of IgG and IgM antibodies against nearly all Mycobacterium tuberculosis (MTB) antigens in 36 active TB patients and 18 healthy controls (HCs) using proteome microarrays. Our results revealed that multiple antigens could induce stronger serum IgG or IgM responses in TB patients compared to HCs, among them, Rv2026c and Rv2421c were further validated by ELISA with sera from 221 samples and showed the moderate performance in diagnosing TB by receiver operating characteristic analysis. Moreover, logistic regression analysis was performed to establish a combined panel that provided better sensitivity and specificity at 82.5% and 88.12%, respectively, than single antigens in the diagnosis of active TB. Furthermore, the antibody reactivity against Rv2026c and Rv2421c was correlated with clinical backgrounds. These results suggest that the combination of different antigens and classes of antibodies could provide promise and encouragement in developing an efficient serological test for the diagnosis of active TB.
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Affiliation(s)
- Yanqing Chen
- Institute for Geriatrics and Rehabilitation, Beijing Geriatric Hospital, Beijing University of Chinese Medicine, Beijing 100095, China.; Department of Laboratory Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Shuhui Cao
- Institute for Geriatrics and Rehabilitation, Beijing Geriatric Hospital, Beijing University of Chinese Medicine, Beijing 100095, China.; Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Yi Liu
- Institute for Geriatrics and Rehabilitation, Beijing Geriatric Hospital, Beijing University of Chinese Medicine, Beijing 100095, China
| | - Xuxia Zhang
- Institute for Geriatrics and Rehabilitation, Beijing Geriatric Hospital, Beijing University of Chinese Medicine, Beijing 100095, China
| | - Wei Wang
- Institute for Geriatrics and Rehabilitation, Beijing Geriatric Hospital, Beijing University of Chinese Medicine, Beijing 100095, China
| | - Chuanyou Li
- Institute for Geriatrics and Rehabilitation, Beijing Geriatric Hospital, Beijing University of Chinese Medicine, Beijing 100095, China..
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Akgul A, Akgul A, Lawrence ML, Karsi A. Stress-related genes promote Edwardsiella ictaluri pathogenesis. PLoS One 2018; 13:e0194669. [PMID: 29554143 PMCID: PMC5858854 DOI: 10.1371/journal.pone.0194669] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 03/07/2018] [Indexed: 12/22/2022] Open
Abstract
Edwardsiella ictaluri is a Gram-negative facultative anaerobic rod and the causative agent of enteric septicemia of channel catfish (ESC), which is one of the most prevalent diseases of catfish, causing significant economic losses in the catfish industry. E. ictaluri is resistant to complement system and macrophage killing, which results in rapid systemic septicemia. However, mechanisms of E. ictaluri stress responses under conditions of host environment are not studied well. Therefore, in this work, we report E. ictaluri stress responses during hydrogen peroxide, low pH, and catfish serum stresses as well as during catfish invasion. E. ictaluri stress responses were characterized by identifying expression of 13 universal stress protein (USP) genes (usp01-usp13) and seven USP-interacting protein genes (groEL, groES, dnaK, grpE, and clpB, grpE, relA). Data indicated that three usp genes (usp05, usp07, and usp13) were highly expressed in all stress conditions. Similarly, E. ictaluri heat shock proteins groEL, groES, dnaK, grpE, and clpB were highly expressed in oxidative stress. Also, E. ictaluri grpE and relA were highly expressed in catfish spleen and head kidney. These findings contribute to our understanding of stress response mechanisms in E. ictaluri stress response, and stress-related proteins that are essential for E. ictaluri could be potential targets for live attenuated vaccine development against ESC.
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Affiliation(s)
- Ali Akgul
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, United States of America
| | - Ayfer Akgul
- Department of Clinical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, United States of America
| | - Mark L. Lawrence
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, United States of America
| | - Attila Karsi
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, United States of America
- * E-mail:
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Espinola SM, Cancela MP, Brisolara Corrêa L, Zaha A. Evolutionary fates of universal stress protein paralogs in Platyhelminthes. BMC Evol Biol 2018; 18:10. [PMID: 29390964 PMCID: PMC5793430 DOI: 10.1186/s12862-018-1129-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 01/23/2018] [Indexed: 11/16/2022] Open
Abstract
Background Universal stress proteins (USPs) are present in all domains of life. Their expression is upregulated in response to a large variety of stress conditions. The functional diversity found in this protein family, paired with the sequence degeneration of the characteristic ATP-binding motif, suggests a complex evolutionary pattern for the paralogous USP-encoding genes. In this work, we investigated the origin, genomic organization, expression patterns and evolutionary history of the USP gene family in species of the phylum Platyhelminthes. Results Our data showed a cluster organization, a lineage-specific distribution, and the presence of several pseudogenes among the USP gene copies identified. The absence of a well conserved -CCAATCA- motif in the promoter region was positively correlated with low or null levels of gene expression, and with amino acid changes within the ligand binding motifs. Despite evidence of the pseudogenization of various USP genes, we detected an important functional divergence at several residues, mostly located near sites that are critical for ligand interaction. Conclusions Our results provide a broad framework for the evolution of the USP gene family, based on the emergence of new paralogs that face very contrasting fates, including pseudogenization, subfunctionalization or neofunctionalization. This framework aims to explain the sequence and functional diversity of this gene family, providing a foundation for future studies in other taxa in which USPs occur. Electronic supplementary material The online version of this article (10.1186/s12862-018-1129-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sergio Martin Espinola
- Programa de Pós Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Martin Pablo Cancela
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Programa de Pós Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Lauís Brisolara Corrêa
- Programa de Pós Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Arnaldo Zaha
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil. .,Programa de Pós Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.
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Vollmer AC, Bark SJ. Twenty-Five Years of Investigating the Universal Stress Protein: Function, Structure, and Applications. ADVANCES IN APPLIED MICROBIOLOGY 2017; 102:1-36. [PMID: 29680123 DOI: 10.1016/bs.aambs.2017.10.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Since the initial discovery of universal stress protein A (UspA) 25 years ago, remarkable advances in molecular and biochemical technologies have revolutionized our understanding of biology. Many studies using these technologies have focused on characterization of the uspA gene and Usp-type proteins. These studies have identified the conservation of Usp-like proteins across bacteria, archaea, plants, and even some invertebrate animals. Regulation of these proteins under diverse stresses has been associated with different stress-response genes including spoT and relA in the stringent response and the dosR two-component signaling pathways. These and other foundational studies suggest Usps serve regulatory and protective roles to enable adaptation and survival under external stresses. Despite these foundational studies, many bacterial species have multiple paralogs of genes encoding these proteins and ablation of the genes does not provide a distinct phenotype. This outcome has limited our understanding of the biochemical functions of these proteins. Here, we summarize the current knowledge of Usps in general and UspA in particular across different genera as well as conclusions about their functions from seminal studies in diverse organisms. Our objective has been to organize the foundational studies in this field to identify the significant impediments to further understanding of Usp functions at the molecular level. We propose ideas and experimental approaches that may overcome these impediments and drive future development of molecular approaches to understand and target Usps as central regulators of stress adaptation and survival. Despite the fact that the full functions of Usps are still not known, creative many applications have already been proposed, tested, and used. The complementary approaches of basic research and applications, along with new technology and analytic tools, may yield the elusive yet critical functions of universal stress proteins in diverse systems.
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Garcia-Morales L, Leon-Solis L, Monroy-Muñoz IE, Talavera-Paulin M, Serafin-López J, Estrada-Garcia I, Rivera-Gutierrez S, Cerna-Cortes JF, Helguera-Repetto AC, Gonzalez-Y-Merchand JA. Comparative proteomic profiles reveal characteristic Mycobacterium tuberculosis proteins induced by cholesterol during dormancy conditions. MICROBIOLOGY-SGM 2017; 163:1237-1247. [PMID: 28771131 DOI: 10.1099/mic.0.000512] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Cholesterol has been reported to play an important role during Mycobacterium tuberculosis infection and during its dormant state inside the host. We present the determination of proteomic profiles of M. tuberculosis H37Rv in the presence of cholesterol as the sole carbon source under exponential growth and in two in vitro dormancy phases (NRP1 and NRP2). Using 2D-PAGE, we detected that M. tuberculosis expressed a high diversity of proteins in both exponential and non-replicative phases. We also found that cholesterol was involved in the overexpression of some proteins related to sulfur metabolism (CysA2), electron transport (FixB), cell wall synthesis (Ald), iron storage (BfrB), protein synthesis (Tig and EF-Tu) and dormancy maintenance (HspX and TB 31.7). According to our results we propose that proteins Ald, BfrB, FadA5 and TB31.7 are likely to play a fundamental role during in vitro dormancy of M. tuberculosis in the presence of cholesterol, helping to counteract its intracellular hostile microenvironment.
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Affiliation(s)
- Lazaro Garcia-Morales
- Departamento de Microbiologia, Escuela Nacional de Ciencias Biologicas (ENCB), Instituto Politecnico Nacional (IPN), Prolongacion Carpio y Plan de Ayala s/n, Ciudad de Mexico, 11340, Mexico
| | - Lizbel Leon-Solis
- Laboratorios de Biologicos y Reactivos de México S.A. de C.V., Birmex. Instituto Nacional de Virologia. Prolongacion Manuel Carpio No. 492, Delegacion Miguel Hidalgo 11340, Ciudad de Mexico, Mexico
| | - Irma E Monroy-Muñoz
- Departamento de Genetica y Genomica Humana, Torre de Investigacion, Instituto Nacional de Perinatologia Isidro Espinosa de los Reyes, SSA. Montes Urales 800, Lomas de Chapultepec, Ciudad de Mexico, 11000, Mexico
| | - Moises Talavera-Paulin
- Departamento de Inmunologia, Escuela Nacional de Ciencias Biologicas (ENCB), Instituto Politecnico Nacional (IPN), Prolongacion Carpio y Plan de Ayala s/n, Ciudad de Mexico, 11340, Mexico
| | - Jeanet Serafin-López
- Departamento de Inmunologia, Escuela Nacional de Ciencias Biologicas (ENCB), Instituto Politecnico Nacional (IPN), Prolongacion Carpio y Plan de Ayala s/n, Ciudad de Mexico, 11340, Mexico
| | - Iris Estrada-Garcia
- Departamento de Inmunologia, Escuela Nacional de Ciencias Biologicas (ENCB), Instituto Politecnico Nacional (IPN), Prolongacion Carpio y Plan de Ayala s/n, Ciudad de Mexico, 11340, Mexico
| | - Sandra Rivera-Gutierrez
- Departamento de Microbiologia, Escuela Nacional de Ciencias Biologicas (ENCB), Instituto Politecnico Nacional (IPN), Prolongacion Carpio y Plan de Ayala s/n, Ciudad de Mexico, 11340, Mexico
| | - Jorge F Cerna-Cortes
- Departamento de Microbiologia, Escuela Nacional de Ciencias Biologicas (ENCB), Instituto Politecnico Nacional (IPN), Prolongacion Carpio y Plan de Ayala s/n, Ciudad de Mexico, 11340, Mexico
| | - Addy C Helguera-Repetto
- Departamento de Inmunobioquimica, Torre de Investigacion, Instituto Nacional de Perinatologia Isidro Espinosa de los Reyes, SSA. Montes Urales 800, Lomas de Chapultepec, Ciudad de Mexico, 11000, Mexico
| | - Jorge A Gonzalez-Y-Merchand
- Departamento de Microbiologia, Escuela Nacional de Ciencias Biologicas (ENCB), Instituto Politecnico Nacional (IPN), Prolongacion Carpio y Plan de Ayala s/n, Ciudad de Mexico, 11340, Mexico
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A Proteomic Signature of Dormancy in the Actinobacterium Micrococcus luteus. J Bacteriol 2017; 199:JB.00206-17. [PMID: 28484042 DOI: 10.1128/jb.00206-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 04/24/2017] [Indexed: 12/13/2022] Open
Abstract
Dormancy is a protective state in which diverse bacteria, including Mycobacterium tuberculosis, Staphylococcus aureus, Treponema pallidum (syphilis), and Borrelia burgdorferi (Lyme disease), curtail metabolic activity to survive external stresses, including antibiotics. Evidence suggests dormancy consists of a continuum of interrelated states, including viable but nonculturable (VBNC) and persistence states. VBNC and persistence contribute to antibiotic tolerance, reemergence from latent infections, and even quorum sensing and biofilm formation. Previous studies indicate that the protein mechanisms regulating persistence and VBNC states are not well understood. We have queried the VBNC state of Micrococcus luteus NCTC 2665 (MI-2665) by quantitative proteomics combining gel electrophoresis, high-performance liquid chromatography, and tandem mass spectrometry to elucidate some of these mechanisms. MI-2665 is a nonpathogenic actinobacterium containing a small (2.5-Mb), high-GC-content genome which exhibits a well-defined VBNC state induced by nutrient deprivation. The MI-2665 VBNC state demonstrated a loss of protein diversity accompanied by increased levels of 18 proteins that are conserved across actinobacteria, 14 of which have not been previously identified in VNBC. These proteins implicate an anaplerotic strategy in the transition to VBNC, including changes in the glyoxylate shunt, redox and amino acid metabolism, and ribosomal regulatory processes. Our data suggest that MI-2665 is a viable model for dissecting the protein mechanisms underlying the VBNC stress response and provide the first protein-level signature of this state. We expect that this protein signature will enable future studies deciphering the protein mechanisms of dormancy and identify novel therapeutic strategies effective against antibiotic-tolerant bacterial infections.IMPORTANCE Dormancy is a protective state enabling bacteria to survive antibiotics, starvation, and the immune system. Dormancy is comprised of different states, including persistent and viable but nonculturable (VBNC) states that contribute to the spread of bacterial infections. Therefore, it is imperative to identify how bacteria utilize these different dormancy states to survive antibiotic treatment. The objective of our research is to eliminate dormancy as a route to antibiotic tolerance by understanding the proteins that control dormancy in Micrococcus luteus NCTC 2665. This bacterium has unique advantages for studying dormancy, including a small genome and a well-defined and reproducible VBNC state. Our experiments implicate four previously identified and 14 novel proteins upregulated in VBNC that may regulate this critical survival mechanism.
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Tremonte P, Succi M, Coppola R, Sorrentino E, Tipaldi L, Picariello G, Pannella G, Fraternali F. Homology-Based Modeling of Universal Stress Protein from Listeria innocua Up-Regulated under Acid Stress Conditions. Front Microbiol 2016; 7:1998. [PMID: 28066336 PMCID: PMC5168468 DOI: 10.3389/fmicb.2016.01998] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 11/29/2016] [Indexed: 01/31/2023] Open
Abstract
An Universal Stress Protein (USP) expressed under acid stress condition by Listeria innocua ATCC 33090 was investigated. The USP was up-regulated not only in the stationary phase but also during the exponential growth phase. The three dimensional (3D) structure of USP was predicted using a combined proteomic and bioinformatics approach. Phylogenetic analysis showed that the USP from Listeria detected in our study was distant from the USPs of other bacteria (such as Pseudomonas spp., Escherichia coli, Salmonella spp.) and clustered in a separate and heterogeneous class including several USPs from Listeria spp. and Lactobacillus spp. An important information on the studied USP was obtained from the 3D-structure established through the homology modeling procedure. In detail, the Model_USP-691 suggested that the investigated USP had a homo-tetrameric quaternary structure. Each monomer presented an architecture analogous to the Rossmann-like α/β-fold with five parallel β-strands, and four α-helices. The analysis of monomer-monomer interfaces and quality of the structure alignments confirmed the model reliability. In fact, the structurally and sequentially conserved hydrophobic residues of the β-strand 5 (in particular the residues V146 and V148) were involved in the inter-chains contact. Moreover, the highly conserved residues I139 and H141 in the region α4 were involved in the dimer association and functioned as hot spots into monomer–monomer interface assembly. The hypothetical assembly of dimers was also supported by the large interface area and by the negative value of solvation free energy gain upon interface interaction. Finally, the structurally conserved ATP-binding motif G-2X-G-9X-G(S/T-N) suggested for a putative role of ATP in stabilizing the tetrameric assembly of the USP. Therefore, the results obtained from a multiple approach, consisting in the application of kinetic, proteomic, phylogenetic and modeling analyses, suggest that Listeria USP could be considered a new type of ATP-binding USP involved in the response to acid stress condition during the exponential growth phase.
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Affiliation(s)
- Patrizio Tremonte
- Department of Agricultural, Environmental and Food Sciences (DiAAA), University of Molise Campobasso, Italy
| | - Mariantonietta Succi
- Department of Agricultural, Environmental and Food Sciences (DiAAA), University of Molise Campobasso, Italy
| | - Raffaele Coppola
- Department of Agricultural, Environmental and Food Sciences (DiAAA), University of Molise Campobasso, Italy
| | - Elena Sorrentino
- Department of Agricultural, Environmental and Food Sciences (DiAAA), University of Molise Campobasso, Italy
| | - Luca Tipaldi
- Department of Agricultural, Environmental and Food Sciences (DiAAA), University of Molise Campobasso, Italy
| | - Gianluca Picariello
- Institute of Food Science, National Research Council (ISA-CNR) Avellino, Italy
| | - Gianfranco Pannella
- Department of Agricultural, Environmental and Food Sciences (DiAAA), University of Molise Campobasso, Italy
| | - Franca Fraternali
- Randall Division of Cellular and Molecular Biophysics, New Hunt's House King's College London, UK
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Jia Q, Hu X, Shi D, Zhang Y, Sun M, Wang J, Mi K, Zhu G. Universal stress protein Rv2624c alters abundance of arginine and enhances intracellular survival by ATP binding in mycobacteria. Sci Rep 2016; 6:35462. [PMID: 27762279 PMCID: PMC5071874 DOI: 10.1038/srep35462] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 09/30/2016] [Indexed: 01/05/2023] Open
Abstract
The universal stress protein family is a family of stress-induced proteins. Universal stress proteins affect latency and antibiotic resistance in mycobacteria. Here, we showed that Mycobacterium smegmatis overexpressing M. tuberculosis universal stress protein Rv2624c exhibits increased survival in human monocyte THP-1 cells. Transcriptome analysis suggested that Rv2624c affects histidine metabolism, and arginine and proline metabolism. LC-MS/MS analysis showed that Rv2624c affects the abundance of arginine, a modulator of both mycobacteria and infected THP-1 cells. Biochemical analysis showed that Rv2624c is a nucleotide-binding universal stress protein, and an Rv2624c mutant incapable of binding ATP abrogated the growth advantage in THP-1 cells. Rv2624c may therefore modulate metabolic pathways in an ATP-dependent manner, changing the abundance of arginine and thus increasing survival in THP-1 cells.
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Affiliation(s)
- Qiong Jia
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Xinling Hu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, CAS, Beijing 100101, China.,The Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Dawei Shi
- Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing 100050, China
| | - Yan Zhang
- Zhangjiakou Center for Adverse Drug Reaction and Drug Abuse, Hebei 075000, China
| | - Meihao Sun
- College of Chemistry and Life Sciences, Zhejiang Normal University, Zhejiang 321004, China
| | - Jianwei Wang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Kaixia Mi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, CAS, Beijing 100101, China
| | - Guofeng Zhu
- Shanghai Municipal Center for Disease Control &Prevention, Shanghai 200336, China
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41
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Devasundaram S, Gopalan A, Das SD, Raja A. Proteomics Analysis of Three Different Strains of Mycobacterium tuberculosis under In vitro Hypoxia and Evaluation of Hypoxia Associated Antigen's Specific Memory T Cells in Healthy Household Contacts. Front Microbiol 2016; 7:1275. [PMID: 27667981 PMCID: PMC5017210 DOI: 10.3389/fmicb.2016.01275] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 08/02/2016] [Indexed: 01/08/2023] Open
Abstract
In vitro mimicking conditions are thought to reflect the environment experienced by Mycobacterium tuberculosis inside the host granuloma. The majority of in vitro dormancy experimental models use laboratory-adapted strains H37Rv or Erdman instead of prevalent clinical strains involved during disease outbreaks. Thus, we included the most prevalent clinical strains (S7 and S10) of M. tuberculosis from south India in addition to H37Rv for our in vitro oxygen depletion (hypoxia) experimental model. Cytosolic proteins were prepared from hypoxic cultures, resolved by two-dimensional electrophoresis and protein spots were characterized by mass spectrometry. In total, 49 spots were characterized as over-expressed or newly emergent between the three strains. Two antigens (ESAT-6, Lpd) out of the 49 characterized spots were readily available in recombinant form in our lab. Hence, these two genes were overexpressed, purified and used for in vitro stimulation of whole blood collected from healthy household contacts (HHC) and active pulmonary tuberculosis patients (PTB). Multicolor flow cytometry analysis showed high levels of antigen specific CD4(+) central memory T cells in the circulation of HHC compared to PTB (p < 0.005 for ESAT-6 and p < 0.0005 for Lpd). This shows proteins that are predicted to be up regulated during in vitro hypoxia in most prevalent clinical strains would indicate possible potential immunogens. In vitro hypoxia experiments with most prevalent clinical strains would also elucidate the probable true representative antigens involved in adaptive mechanisms.
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Affiliation(s)
- Santhi Devasundaram
- Department of Immunology, National Institute for Research in Tuberculosis (ICMR) Chennai, India
| | - Akilandeswari Gopalan
- Department of Immunology, National Institute for Research in Tuberculosis (ICMR) Chennai, India
| | - Sulochana D Das
- Department of Immunology, National Institute for Research in Tuberculosis (ICMR) Chennai, India
| | - Alamelu Raja
- Department of Immunology, National Institute for Research in Tuberculosis (ICMR) Chennai, India
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Trindade RV, Pinto AFM, Santos DS, Bizarro CV. Pulse Proteolysis and Precipitation for Target Identification. J Proteome Res 2016; 15:2236-45. [DOI: 10.1021/acs.jproteome.6b00214] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rogério V. Trindade
- Centro
de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto
Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), 6681/92-A. Av. Ipiranga-TECNOPUC-Prédio 92A 90619-900, Porto Alegre, Rio Grande do Sul, Brazil
| | - Antônio F. M. Pinto
- Centro
de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto
Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), 6681/92-A. Av. Ipiranga-TECNOPUC-Prédio 92A 90619-900, Porto Alegre, Rio Grande do Sul, Brazil
| | - Diógenes S. Santos
- Centro
de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto
Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), 6681/92-A. Av. Ipiranga-TECNOPUC-Prédio 92A 90619-900, Porto Alegre, Rio Grande do Sul, Brazil
| | - Cristiano V. Bizarro
- Centro
de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto
Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), 6681/92-A. Av. Ipiranga-TECNOPUC-Prédio 92A 90619-900, Porto Alegre, Rio Grande do Sul, Brazil
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Differential roles of the hemerythrin-like proteins of Mycobacterium smegmatis in hydrogen peroxide and erythromycin susceptibility. Sci Rep 2015; 5:16130. [PMID: 26607739 PMCID: PMC4660385 DOI: 10.1038/srep16130] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 10/08/2015] [Indexed: 11/09/2022] Open
Abstract
Hemerythrin-like proteins are oxygen-carrying non-heme di-iron binding proteins and their functions have effect on oxidation-reduction regulation and antibiotic resistance. Recent studies using bioinformatic analyses suggest that multiple hemerythrin-like protein coding sequences might have been acquired by lateral gene transfer and the number of hemerythrin-like proteins varies amongst different species. Mycobacterium smegmatis contains three hemerythrin-like proteins, MSMEG_3312, MSMEG_2415 and MSMEG_6212. In this study, we have systematically analyzed all three hemerythrin-like proteins in M. smegmatis and our results identified and characterized two functional classes: MSMEG_2415 plays an important role in H2O2 susceptibility, and MSMEG_3312 and MSMEG_6212 are associated with erythromycin susceptibility. Phylogenetic analysis indicated that these three proteins have different evolutionary origins, possibly explaining their different physiological functions. Here, combined with biological and phylogenetic analyses, our results provide new insights into the evolutionary divergence of the hemerythrin-like proteins in M. smegmatis.
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Banerjee A, Adolph RS, Gopalakrishnapai J, Kleinboelting S, Emmerich C, Steegborn C, Visweswariah SS. A universal stress protein (USP) in mycobacteria binds cAMP. J Biol Chem 2015; 290:12731-43. [PMID: 25802331 DOI: 10.1074/jbc.m115.644856] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Indexed: 11/06/2022] Open
Abstract
Mycobacteria are endowed with rich and diverse machinery for the synthesis, utilization, and degradation of cAMP. The actions of cyclic nucleotides are generally mediated by binding of cAMP to conserved and well characterized cyclic nucleotide binding domains or structurally distinct cGMP-specific and -regulated cyclic nucleotide phosphodiesterase, adenylyl cyclase, and E. coli transcription factor FhlA (GAF) domain-containing proteins. Proteins with cyclic nucleotide binding and GAF domains can be identified in the genome of mycobacterial species, and some of them have been characterized. Here, we show that a significant fraction of intracellular cAMP is bound to protein in mycobacterial species, and by using affinity chromatography techniques, we identify specific universal stress proteins (USP) as abundantly expressed cAMP-binding proteins in slow growing as well as fast growing mycobacteria. We have characterized the biochemical and thermodynamic parameters for binding of cAMP, and we show that these USPs bind cAMP with a higher affinity than ATP, an established ligand for other USPs. We determined the structure of the USP MSMEG_3811 bound to cAMP, and we confirmed through structure-guided mutagenesis, the residues important for cAMP binding. This family of USPs is conserved in all mycobacteria, and we suggest that they serve as "sinks" for cAMP, making this second messenger available for downstream effectors as and when ATP levels are altered in the cell.
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Affiliation(s)
- Arka Banerjee
- From the Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore 560012, India and
| | - Ramona S Adolph
- the Department of Biochemistry, University of Bayreuth, 95440 Bayreuth, Germany
| | - Jayashree Gopalakrishnapai
- From the Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore 560012, India and
| | - Silke Kleinboelting
- the Department of Biochemistry, University of Bayreuth, 95440 Bayreuth, Germany
| | - Christiane Emmerich
- the Department of Biochemistry, University of Bayreuth, 95440 Bayreuth, Germany
| | - Clemens Steegborn
- the Department of Biochemistry, University of Bayreuth, 95440 Bayreuth, Germany
| | - Sandhya S Visweswariah
- From the Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore 560012, India and
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45
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Hu X, Li X, Huang L, Chan J, Chen Y, Deng H, Mi K. Quantitative proteomics reveals novel insights into isoniazid susceptibility in mycobacteria mediated by a universal stress protein. J Proteome Res 2015; 14:1445-54. [PMID: 25664397 DOI: 10.1021/pr5011058] [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: 11/29/2022]
Abstract
Tuberculosis (TB) is caused by the ancient pathogen, Mycobacterium tuberculosis, and is one of the most serious infectious diseases in the world. Isoniazid (INH) is an important first-line drug for the treatment of active and latent TB. INH resistance is an increasing problem in the treatment of TB. Phenotypic resistance to INH, however, is poorly understood. In this study, we constructed a strain of Mycobacterium bovis BCG that overexpresses the latency-related universal stress protein (USP), BCG_2013, and designated this strain BCG-2013. BCG_2013 overexpression increased susceptibility to INH compared with that of the wild-type strain, BCG-pMV261. Quantitative proteomic analysis revealed that BCG_2013 overexpression resulted in the upregulation of 50 proteins and the downregulation of 26 proteins among the 1500 proteins identified. Upregulation of catalase-peroxidase KatG expression in BCG-2013 was observed and confirmed by qPCR, whereas expression of other INH resistance-related proteins did not change. In addition, differential expression of the mycobacterial persistence regulator MprA and its regulatory proteins was observed. BCG_2013 and katG mRNA levels increased in a Wayne dormancy model, whereas MprA mRNA levels decreased. Taken together, our results suggest that the increase in KatG levels induced by increased BCG_2013 levels underlies the phenotypic susceptibility of mycobacteria to INH.
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Affiliation(s)
- Xinling Hu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, CAS , Beijing 100101, China
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46
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Aanandhi MV, Bhattacherjee D, George PSG, Ray A. Natural polyphenols down-regulate universal stress protein in Mycobacterium tuberculosis: An in-silico approach. J Adv Pharm Technol Res 2014; 5:171-8. [PMID: 25364695 PMCID: PMC4215480 DOI: 10.4103/2231-4040.143036] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Universal stress protein (USP) is a novel target to overcome the tuberculosis resistance. Our present study enlightens the possibilities of some natural polyphenols as an antioxidant for USP. The study has shown some molecular simulations of some selected natural antioxidants with USP. We have considered USP (Rv1636) strain for homology modeling and the selected template was taken for the docking study. Curcumin, catechin, reservetrol has shown ARG 136 (1.8Å) hydrogen bonding and two ionic bonding with carboxyl group of curcumin with LEU 130 (3.3Å) and ASN 144 (3.4Å) respectively. INH was taken for the standard molecule to perform molecular simulation. It showed poor binding interaction with the target, that is, -5.18 kcal, and two hydrogen bonding with SER 140 (1.887Å), ARG 147 (2.064Å) respectively. The study indicates possible new generation curcumin analogue for future therapy to down-regulate USP.
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Affiliation(s)
- M Vijey Aanandhi
- Department of Pharmaceutical Chemistry and Pharmacy Practice, School of Pharmaceutical Sciences, Vels University (VISTAS), Chennai, Tamil Nadu, India
| | - Debojit Bhattacherjee
- Department of Pharmaceutical Chemistry and Pharmacy Practice, School of Pharmaceutical Sciences, Vels University (VISTAS), Chennai, Tamil Nadu, India
| | - P Samuel Gideon George
- Department of Pharmaceutical Chemistry and Pharmacy Practice, School of Pharmaceutical Sciences, Vels University (VISTAS), Chennai, Tamil Nadu, India
| | - Anirban Ray
- Department of Pharmacology, Roland Institute of Pharmaceutical Sciences, Khodasingi, Berhampur, Odisha, India
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47
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Lougheed KEA, Bennett MH, Williams HD. An in vivo crosslinking system for identifying mycobacterial protein-protein interactions. J Microbiol Methods 2014; 105:67-71. [PMID: 25034228 PMCID: PMC4169665 DOI: 10.1016/j.mimet.2014.07.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 07/03/2014] [Accepted: 07/07/2014] [Indexed: 11/29/2022]
Abstract
The analysis of protein-protein interactions in Mycobacterium tuberculosis has the potential to shed light on the functions of the large number of predicted open-reading frames annotated as conserved hypothetical proteins. We have developed a formaldehyde crosslinking system to detect in vivo interactions in mycobacteria. Our Gateway-adapted vector system uses three promoter strengths, including constitutive and regulatable versions, for the expression of target proteins with either an N- or C-terminal His-Strep-Strep tag. Tandem affinity purification using the His- and Strep-tags is well-suited to the isolation of protein complexes with a high purity and no detectable background. We have validated this approach using the well-described pyruvate dehydrogenase complex.
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Affiliation(s)
| | - Mark H Bennett
- Department of Life Sciences, Imperial College London, SW7 2AZ, United Kingdom
| | - Huw D Williams
- Department of Life Sciences, Imperial College London, SW7 2AZ, United Kingdom.
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48
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Jain RK, Nayak AR, Husain AA, Panchbhai MS, Chandak N, Purohit HJ, Taori GM, Daginawala HF, Kashyap RS. Mycobacterial dormancy regulon protein Rv2623 as a novel biomarker for the diagnosis of latent and active tuberculous meningitis. DISEASE MARKERS 2013; 35:311-6. [PMID: 24167379 PMCID: PMC3787564 DOI: 10.1155/2013/309816] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 08/28/2013] [Accepted: 08/29/2013] [Indexed: 01/15/2023]
Abstract
The present study was designed to investigate Rv2623 antigen, a major dormancy regulon protein of Mycobacterium tuberculosis (MTB) in CSF of suspected latent and active tuberculous meningitis (TBM) patients. A total of 100 CSF samples from TBM (n = 31), suspected latent TBM (n = 22), and suitable noninfectious control subjects (n = 47) were collected and evaluated for Rv2623 antigen level using ELISA protocol. A significantly high (P < 0.05) mean absorbance was observed in samples of suspected latent TBM and active TBM patients as compared to non-TBM control patients. However, no significant difference in Rv2623 level was observed between suspected latent TBM and TBM patients. Our preliminary findings suggest that Rv2623 may be useful as a potential biomarker for the diagnosis of the latent as well as active TBM infection. Futher evaluation of this biomarker in large number of samples is therefore needed to confirm the result.
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Affiliation(s)
- Ruchika K. Jain
- Biochemistry Research Laboratory, Central India Institute of Medical Sciences, Bajaj Nagar, Nagpur 440010, India
| | - Amit R. Nayak
- Biochemistry Research Laboratory, Central India Institute of Medical Sciences, Bajaj Nagar, Nagpur 440010, India
| | - Aliabbas A. Husain
- Biochemistry Research Laboratory, Central India Institute of Medical Sciences, Bajaj Nagar, Nagpur 440010, India
| | - Milind S. Panchbhai
- Biochemistry Research Laboratory, Central India Institute of Medical Sciences, Bajaj Nagar, Nagpur 440010, India
| | - Nitin Chandak
- Biochemistry Research Laboratory, Central India Institute of Medical Sciences, Bajaj Nagar, Nagpur 440010, India
| | - Hemant J. Purohit
- Environmental Genomics Unit, National Environmental Engineering Research Institute, Nehru Marg, Nagpur 440020, India
| | - Girdhar M. Taori
- Biochemistry Research Laboratory, Central India Institute of Medical Sciences, Bajaj Nagar, Nagpur 440010, India
| | - Hatim F. Daginawala
- Biochemistry Research Laboratory, Central India Institute of Medical Sciences, Bajaj Nagar, Nagpur 440010, India
| | - Rajpal S. Kashyap
- Biochemistry Research Laboratory, Central India Institute of Medical Sciences, Bajaj Nagar, Nagpur 440010, India
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Mbah AN, Mahmud O, Awofolu OR, Isokpehi RD. Inferences on the biochemical and environmental regulation of universal stress proteins from Schistosomiasis parasites. Adv Appl Bioinform Chem 2013; 6:15-27. [PMID: 23696708 PMCID: PMC3656623 DOI: 10.2147/aabc.s37191] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Human schistosomiasis is a freshwater snail-transmitted disease caused by parasitic flatworms of the Schistosoma genus. Schistosoma haematobium, Schistosoma mansoni, and Schistosoma japonicum are the three major species infecting humans. These parasites undergo a complex developmental life cycle, in which they encounter a plethora of environmental signals. The presence of genes encoding the universal stress protein (USP) domain in the genomes of Schistosoma spp. suggests these flatworms are equipped to respond to unfavorable conditions. Though data on gene expression is available for USP genes, their biochemical and environmental regulation are incompletely understood. The identification of additional regulatory molecules for Schistosoma. USPs, which may be present in the human, snail, or water environments, could also be useful for schistosomiasis interventions. METHODS We developed a protocol that includes a visual analytics stage to facilitate integration, visualization, and decision making, from the results of sequence analyses and data collection on a set of 13 USPs from S. mansoni and S. japonicum. RESULTS Multiple sequence alignment identified conserved sites that could be key residues regulating the function of USPs of the Schistosoma spp. Based on the consistency and completeness of sequence annotation, we prioritized for further research the gene for a 184-amino-acid-long USP that is present in the genomes of the three human-infecting Schistosoma spp. Calcium, zinc, and magnesium ions were predicted to interact with the protein product of the gene. CONCLUSION Given that the initial effects of praziquantel on schistosomes include the influx of calcium ions, additional investigations are required to (1) functionally characterize the interactions of calcium ions with the amino acid residues of Schistosoma USPs; and (2) determine the transcriptional response of Schistosoma. USP genes to praziquantel. The data sets produced, and the visual analytics views that were developed, can be easily reused to develop new hypotheses.
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Affiliation(s)
- Andreas N Mbah
- Center for Bioinformatics and Computational Biology, Department of Biology, Jackson State University, Jackson, MS, USA ; Department of Environmental Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Pretoria, South Africa
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Chen T, He L, Deng W, Xie J. The Mycobacterium DosR regulon structure and diversity revealed by comparative genomic analysis. J Cell Biochem 2013; 114:1-6. [PMID: 22833514 DOI: 10.1002/jcb.24302] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Accepted: 07/17/2012] [Indexed: 11/12/2022]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), which claims approximately two million people annually, remains a global health concern. The non-replicating or dormancy like state of this pathogen which is impervious to anti-tuberculosis drugs is widely recognized as the culprit for this scenario. The dormancy survival regulator (DosR) regulon, composed of 48 co-regulated genes, is held as essential for Mtb persistence. The DosR regulon is regulated by a two-component regulatory system consisting of two sensor kinases-DosS (Rv3132c) and DosT (Rv2027c), and a response regulator DosR (Rv3133c). The underlying regulatory mechanism of DosR regulon expression is very complex. Many factors are involved, particularly the oxygen tension. The DosR regulon enables the pathogen to persist during lengthy hypoxia. Comparative genomic analysis demonstrated that the DosR regulon is widely distributed among the mycobacterial genomes, ranging from the pathogenic strains to the environmental strains. In-depth studies on the DosR response should provide insights into its role in TB latency in vivo and shape new measures to combat this exceeding recalcitrant pathogen.
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Affiliation(s)
- Tian Chen
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, School of Life Sciences, Southwest University, Chongqing 400715, China
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