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Transcriptomic and Proteomic Analysis of Gardnerella vaginalis Responding to Acidic pH and Hydrogen Peroxide Stress. Microorganisms 2023; 11:microorganisms11030695. [PMID: 36985268 PMCID: PMC10051395 DOI: 10.3390/microorganisms11030695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/07/2023] [Accepted: 03/07/2023] [Indexed: 03/11/2023] Open
Abstract
Gardnerella vaginalis is the main pathogen that causes bacterial vaginosis. In the healthy vaginal microecological environment of a woman, the lactobacilli produce lactate and hydrogen peroxide to inhibit the growth of pathogens such as G. vaginalis. The lack of lactobacilli results in a high pH and low hydrogen peroxide in the vagina which facilitate G. vaginalis growth, leading to the imbalance of the vaginal microecology. In this study, lactate and hydrogen peroxide were added to a G. vaginalis culture medium to simulate the co-culture of the lactobacilli and G. vaginalis, and then the genes related to the stress response of G. vaginalis were identified using transcriptomics and proteomics. It was indicated that, among all the upregulated genes, most of them encoded transporters associated with the efflux of harmful substances, and the majority of the downregulated genes were related to the biofilm formation and epithelial cell adhesion. This study may help find new drug targets for G. vaginalis for the development of novel therapies for bacterial vaginosis.
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Jabbari S. Unravelling microbial efflux through mathematical modelling. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36409600 DOI: 10.1099/mic.0.001264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
AbstractMathematical modelling is a useful tool that is increasingly used in the life sciences to understand and predict the behaviour of biological systems. This review looks at how this interdisciplinary approach has advanced our understanding of microbial efflux, the process by which microbes expel harmful substances. The discussion is largely in the context of antimicrobial resistance, but applications in synthetic biology are also touched upon. The goal of this paper is to spark further fruitful collaborations between modellers and experimentalists in the efflux community and beyond.
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Affiliation(s)
- Sara Jabbari
- School of Mathematics and Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
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Youlden G, McNeil HE, Blair JMA, Jabbari S, King JR. Mathematical Modelling Highlights the Potential for Genetic Manipulation as an Adjuvant to Counter Efflux-Mediated MDR in Salmonella. Bull Math Biol 2022; 84:56. [PMID: 35380320 PMCID: PMC8983579 DOI: 10.1007/s11538-022-01011-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 03/02/2022] [Indexed: 11/18/2022]
Abstract
Bacteria have developed resistance to antibiotics by various mechanisms, notable amongst these is the use of permeation barriers and the expulsion of antibiotics via efflux pumps. The resistance-nodulation-division (RND) family of efflux pumps is found in Gram-negative bacteria and a major contributor to multidrug resistance (MDR). In particular, Salmonella encodes five RND efflux pump systems: AcrAB, AcrAD, AcrEF, MdsAB and MdtAB which have different substrate ranges including many antibiotics. We produce a spatial partial differential equation (PDE) model governing the diffusion and efflux of antibiotic in Salmonella, via these RND efflux pumps. Using parameter fitting techniques on experimental data, we are able to establish the behaviour of multiple wild-type and efflux mutant Salmonella strains, which enables us to produce efflux profiles for each individual efflux pump system. By combining the model with a gene regulatory network (GRN) model of efflux regulation, we simulate how the bacteria respond to their environment. Finally, performing a parameter sensitivity analysis, we look into various different targets to inhibit the efflux pumps. The model provides an in silico framework with which to test these potential adjuvants to counter MDR.
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Affiliation(s)
- George Youlden
- School of Mathematics, University of Birmingham, Birmingham, B15 2TT, UK.
- School of Mathematical Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Helen E McNeil
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Jessica M A Blair
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Sara Jabbari
- School of Mathematics, University of Birmingham, Birmingham, B15 2TT, UK
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - John R King
- School of Mathematical Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
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Zhang Q, Huang R, Hu H, Yu L, Tang Q, Tao Y, Liu Z, Li J, Wang G. Integrative Analysis of Hypoxia-Associated Signature in Pan-Cancer. iScience 2020; 23:101460. [PMID: 32861996 PMCID: PMC7476856 DOI: 10.1016/j.isci.2020.101460] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/18/2020] [Accepted: 08/12/2020] [Indexed: 02/06/2023] Open
Abstract
Hypoxia is serving crucial roles in cancers. This study aims to comprehensively analyze the molecular features and clinical relevance of a well-defined hypoxia-associated signature in pan-cancer using multi-omics data. Data were acquired from TCGA, CCLE, GDSC, and GEO. RNA expression pattern, copy number variation (CNV), methylation, and mutation of the signature were analyzed. The majority of the 15 genes were upregulated in cancer tissues compared with normal tissue, and RNA expression was negatively associated with methylation level. CNV occurred in almost all the cancers, whereas mutation frequency was low across different cancer types. The signature was also closely related to cancer hallmarks and cancer-related metabolism pathways. NDRG1 was upregulated in kidney cancer tissues as indicated by immunohistochemistry. Besides, most of the 15 genes were risk factors for patients' overall survival. Our results provide a valuable resource that will guide both mechanistic and therapeutic analyses of the hypoxia signature in cancers.
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Affiliation(s)
- Qian Zhang
- Department of Colorectal Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province 150086, China
| | - Rui Huang
- Department of Colorectal Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province 150086, China
| | - Hanqing Hu
- Department of Colorectal Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province 150086, China
| | - Lei Yu
- Department of Colorectal Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province 150086, China
| | - Qingchao Tang
- Department of Colorectal Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province 150086, China
| | - Yangbao Tao
- Department of Colorectal Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province 150086, China
| | - Zheng Liu
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100000, China
| | - Jiaying Li
- Department of Colorectal Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province 150086, China
| | - Guiyu Wang
- Department of Colorectal Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province 150086, China
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The Potential for Convergence between Synthetic Biology and Bioelectronics. Cell Syst 2018; 7:231-244. [DOI: 10.1016/j.cels.2018.08.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 05/30/2018] [Accepted: 08/13/2018] [Indexed: 01/20/2023]
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Perez AM, Gomez MM, Kalvapalle P, O'Brien-Gilbert E, Bennett MR, Shamoo Y. Using cellular fitness to map the structure and function of a major facilitator superfamily effluxer. Mol Syst Biol 2017; 13:964. [PMID: 29273640 PMCID: PMC5740499 DOI: 10.15252/msb.20177635] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The major facilitator superfamily (MFS) effluxers are prominent mediators of antimicrobial resistance. The biochemical characterization of MFS proteins is hindered by their complex membrane environment that makes in vitro biochemical analysis challenging. Since the physicochemical properties of proteins drive the fitness of an organism, we posed the question of whether we could reverse that relationship and derive meaningful biochemical parameters for a single protein simply from fitness changes it confers under varying strengths of selection. Here, we present a physiological model that uses cellular fitness as a proxy to predict the biochemical properties of the MFS tetracycline efflux pump, TetB, and a family of single amino acid variants. We determined two lumped biochemical parameters roughly describing Km and Vmax for TetB and variants. Including in vivo protein levels into our model allowed for more specified prediction of pump parameters relating to substrate binding affinity and pumping efficiency for TetB and variants. We further demonstrated the general utility of our model by solely using fitness to assay a library of tet(B) variants and estimate their biochemical properties.
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Affiliation(s)
- Anisha M Perez
- Department of Biosciences, Rice University, Houston, TX, USA
| | - Marcella M Gomez
- Department of Applied Mathematics & Statistics, University of California, Santa Cruz, CA, USA
| | - Prashant Kalvapalle
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, TX, USA
| | | | - Matthew R Bennett
- Department of Biosciences, Rice University, Houston, TX, USA.,Department of Bioengineering, Rice University, Houston, TX, USA
| | - Yousif Shamoo
- Department of Biosciences, Rice University, Houston, TX, USA
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