1
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Novak JK, Kennedy PG, Gardner JG. Transcriptomic analyses of bacterial growth on fungal necromass reveal different microbial community niches during degradation. Appl Environ Microbiol 2024:e0106224. [PMID: 39264205 DOI: 10.1128/aem.01062-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 08/28/2024] [Indexed: 09/13/2024] Open
Abstract
Bacteria are major drivers of organic matter decomposition and play crucial roles in global nutrient cycling. Although the degradation of dead fungal biomass (necromass) is increasingly recognized as an important contributor to soil carbon (C) and nitrogen (N) cycling, the genes and metabolic pathways involved in necromass degradation are less characterized. In particular, how bacteria degrade necromass containing different quantities of melanin, which largely control rates of necromass decomposition in situ, is largely unknown. To address this gap, we conducted a multi-timepoint transcriptomic analysis using three Gram-negative, bacterial species grown on low or high melanin necromass of Hyaloscypha bicolor. The bacterial species, Cellvibrio japonicus, Chitinophaga pinensis, and Serratia marcescens, belong to genera known to degrade necromass in situ. We found that while bacterial growth was consistently higher on low than high melanin necromass, the CAZyme-encoding gene expression response of the three species was similar between the two necromass types. Interestingly, this trend was not shared for genes encoding nitrogen utilization, which varied in C. pinensis and S. marcescens during growth on high vs low melanin necromass. Additionally, this study tested the metabolic capabilities of these bacterial species to grow on a diversity of C and N sources and found that the three bacteria have substantially different utilization patterns. Collectively, our data suggest that as necromass changes chemically over the course of degradation, certain bacterial species are favored based on their differential metabolic capacities.IMPORTANCEFungal necromass is a major component of the carbon (C) in soils as well as an important source of nitrogen (N) for plant and microbial growth. Bacteria associated with necromass represent a distinct subset of the soil microbiome and characterizing their functional capacities is the critical next step toward understanding how they influence necromass turnover. This is particularly important for necromass varying in melanin content, which has been observed to control the rate of necromass decomposition across a variety of ecosystems. Here we assessed the gene expression of three necromass-degrading bacteria grown on low or high melanin necromass and characterized their metabolic capacities to grow on different C and N substrates. These transcriptomic and metabolic studies provide the first steps toward assessing the physiological relevance of up-regulated CAZyme-encoding genes in necromass decomposition and provide foundational data for generating a predictive model of the molecular mechanisms underpinning necromass decomposition by soil bacteria.
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Affiliation(s)
- Jessica K Novak
- Department of Biological Sciences, University of Maryland-Baltimore County, Baltimore, Maryland, USA
| | - Peter G Kennedy
- Department of Plant and Microbial Biology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Jeffrey G Gardner
- Department of Biological Sciences, University of Maryland-Baltimore County, Baltimore, Maryland, USA
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2
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Franklin A, Salgueiro VC, Layton AJ, Sullivan R, Mize T, Vázquez-Iniesta L, Benedict ST, Gurcha SS, Anso I, Besra GS, Banzhaf M, Lovering AL, Williams SJ, Guerin ME, Scott NE, Prados-Rosales R, Lowe EC, Moynihan PJ. The mycobacterial glycoside hydrolase LamH enables capsular arabinomannan release and stimulates growth. Nat Commun 2024; 15:5740. [PMID: 38982040 PMCID: PMC11233589 DOI: 10.1038/s41467-024-50051-3] [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: 12/06/2023] [Accepted: 06/26/2024] [Indexed: 07/11/2024] Open
Abstract
Mycobacterial glycolipids are important cell envelope structures that drive host-pathogen interactions. Arguably, the most important are lipoarabinomannan (LAM) and its precursor, lipomannan (LM), which are trafficked from the bacterium to the host via unknown mechanisms. Arabinomannan is thought to be a capsular derivative of these molecules, lacking a lipid anchor. However, the mechanism by which this material is generated has yet to be elucidated. Here, we describe the identification of a glycoside hydrolase family 76 enzyme that we term LamH (Rv0365c in Mycobacterium tuberculosis) which specifically cleaves α-1,6-mannoside linkages within LM and LAM, driving its export to the capsule releasing its phosphatidyl-myo-inositol mannoside lipid anchor. Unexpectedly, we found that the catalytic activity of this enzyme is important for efficient exit from stationary phase cultures, potentially implicating arabinomannan as a signal for growth phase transition. Finally, we demonstrate that LamH is important for M. tuberculosis survival in macrophages.
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Affiliation(s)
- Aaron Franklin
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Vivian C Salgueiro
- Department of Preventive Medicine, Public Health and Microbiology, School of Medicine, Universidad Autonoma de Madrid, Madrid, Spain
| | | | - Rudi Sullivan
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Todd Mize
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Lucía Vázquez-Iniesta
- Department of Preventive Medicine, Public Health and Microbiology, School of Medicine, Universidad Autonoma de Madrid, Madrid, Spain
| | | | | | - Itxaso Anso
- Structural Glycobiology Laboratory, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona, Spanish National Research Council, Barcelona Science Park, c/Baldiri Reixac 10-12, Tower R, 08028, Barcelona, Catalonia, Spain
| | - Gurdyal S Besra
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Manuel Banzhaf
- School of Biosciences, University of Birmingham, Birmingham, UK
| | | | - Spencer J Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia
| | - Marcelo E Guerin
- Structural Glycobiology Laboratory, Department of Structural and Molecular Biology; Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona, Catalonia, Spain
| | - Nichollas E Scott
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Rafael Prados-Rosales
- Department of Preventive Medicine, Public Health and Microbiology, School of Medicine, Universidad Autonoma de Madrid, Madrid, Spain
| | - Elisabeth C Lowe
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne, UK.
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3
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Hu JR, Li JM, Wang HY, Sun ML, Huang CY, Wang HC. Analysis of growth dynamics in five different media and metabolic phenotypic characteristics of Piriformospora indica. Front Microbiol 2024; 14:1301743. [PMID: 38260913 PMCID: PMC10800966 DOI: 10.3389/fmicb.2023.1301743] [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: 09/25/2023] [Accepted: 12/13/2023] [Indexed: 01/24/2024] Open
Abstract
Piriformospora indica is an important endophytic fungus with broad potential for alleviating biotic and abiotic stress on host plants. This study monitored the growth dynamics of P. indica on five commonly used artificial media for microorganisms and analyzed its metabolic characteristics using Biolog Phenotype Microarray (PM) technology. The results showed that P. indica grew fastest on Potato Dextrose Agar (PDA), followed by Kidney Bean Agar (KBA), Alkyl Ester Agar (AEA), Oatmeal Agar (OA), and Luria-Bertani Agar (LB), and the most suitable medium for spore production was OA. Using Biolog PM1-10, 950 metabolic phenotypes of P. indica were obtained. P. indica could metabolize 87.89% of the tested carbon sources, 87.63% of the tested nitrogen sources, 96.61% of the tested phosphorus sources, and 100% of the tested sulfur sources. P. indica displayed 92 kinds of tested biosynthetic pathways, and it could grow under 92 kinds of tested osmotic pressures and 88 kinds of tested pH conditions. PM plates 1-2 revealed 43 efficient carbon sources, including M-Hydroxyphenyl acid, N-Acetyl-D-Glucosamine, Tyramine, Maltotrios, α-D-Glucosine, I-Erythritol, L-Valine, D-Melezitose, D-Tagatose, and Turanose. PM plates 3,6-8 indicated 170 efficient nitrogen sources, including Adenosine, Inosine Allantoin, D, L-Lactamide, Arg-Met, lle-Trp, Ala-Arg, Thr-Arg, Trp-Tyr, Val-Asn, Gly-Gly-D-Leu, Gly-Gly-Phe, and Leu-Leu-Leu. This study demonstrates that P. indica can metabolize a variety of substrates, such as carbon and nitrogen sources, and has a wide range of environmental adaptability. The growth dynamics on artificial culture media and metabolic phenotypes of P. indica can be used to investigate its biological characteristics, screen for more suitable growth and sporulation conditions, and elucidate the physiological mechanisms that enhance the stress resistance of host plants. This study provides a theoretical basis for its better application in agriculture.
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Affiliation(s)
- Jing-rong Hu
- Institute of Advanced Agricultural Science, Hubei University of Arts and Science, Xiangyang, Hubei, China
- College of Agriculture, Yangtze University, Jingzhou, China
| | - Jin-meng Li
- College of Agriculture, Yangtze University, Jingzhou, China
| | - Hai-yan Wang
- Institute of Advanced Agricultural Science, Hubei University of Arts and Science, Xiangyang, Hubei, China
| | - Mei-li Sun
- College of Agriculture, Yangtze University, Jingzhou, China
| | - Chun-yang Huang
- Guizhou Provincial Tobacco Company, Zunyi Branch, Zunyi, China
| | - Han-cheng Wang
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, Guizhou, China
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4
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Franklin A, Layton AJ, Mize T, Salgueiro VC, Sullivan R, Benedict ST, Gurcha SS, Anso I, Besra GS, Banzhaf M, Lovering AL, Williams SJ, Guerin ME, Scott NE, Prados-Rosales R, Lowe EC, Moynihan PJ. The mycobacterial glycoside hydrolase LamH enables capsular arabinomannan release and stimulates growth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.26.563968. [PMID: 37961452 PMCID: PMC10634837 DOI: 10.1101/2023.10.26.563968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Mycobacterial glycolipids are important cell envelope structures that drive host-pathogen interactions. Arguably, the most important amongst these are lipoarabinomannan (LAM) and its precursor, lipomannan (LM), which are both trafficked out of the bacterium to the host via unknown mechanisms. An important class of exported LM/LAM is the capsular derivative of these molecules which is devoid of its lipid anchor. Here, we describe the identification of a glycoside hydrolase family 76 enzyme that we term LamH which specifically cleaves α-1,6-mannoside linkages within LM and LAM, driving its export to the capsule releasing its phosphatidyl-myo-inositol mannoside lipid anchor. Unexpectedly, we found that the catalytic activity of this enzyme is important for efficient exit from stationary phase cultures where arabinomannan acts as a signal for growth phase transition. Finally, we demonstrate that LamH is important for Mycobacterium tuberculosis survival in macrophages. These data provide a new framework for understanding the biological role of LAM in mycobacteria.
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Affiliation(s)
- Aaron Franklin
- School of Biosciences, University of Birmingham, Birmingham, U.K., B15 2TT
| | - Abigail J. Layton
- School of Biosciences, University of Birmingham, Birmingham, U.K., B15 2TT
| | - Todd Mize
- School of Biosciences, University of Birmingham, Birmingham, U.K., B15 2TT
| | - Vivian C. Salgueiro
- Department of Preventive Medicine, Public Health and Microbiology. School of Medicine. Universidad Autonoma de Madrid, 28029 Madrid, Spain
| | - Rudi Sullivan
- School of Biosciences, University of Birmingham, Birmingham, U.K., B15 2TT
| | - Samuel T. Benedict
- School of Biosciences, University of Birmingham, Birmingham, U.K., B15 2TT
| | - Sudagar S. Gurcha
- School of Biosciences, University of Birmingham, Birmingham, U.K., B15 2TT
| | - Itxaso Anso
- Structural Glycobiology Laboratory, Biocruces Health Research Institute, Barakaldo, Bizkaia, 48903, Spain
| | - Gurdyal S. Besra
- School of Biosciences, University of Birmingham, Birmingham, U.K., B15 2TT
| | - Manuel Banzhaf
- School of Biosciences, University of Birmingham, Birmingham, U.K., B15 2TT
| | - Andrew L. Lovering
- School of Biosciences, University of Birmingham, Birmingham, U.K., B15 2TT
| | - Spencer J. Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Marcelo E. Guerin
- Structural Glycobiology Laboratory, Department of Structural and Molecular Biology; Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona Science Park, c/Baldiri Reixac 4-8, Tower R, 08028 Barcelona, Catalonia, Spain
| | - Nichollas E. Scott
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Rafael Prados-Rosales
- Department of Preventive Medicine, Public Health and Microbiology. School of Medicine. Universidad Autonoma de Madrid, 28029 Madrid, Spain
| | - Elisabeth C. Lowe
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne, U.K., NE2 4HH
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5
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Cunningham SA, Mandrekar JN, Suh G, Patel R. Preliminary Reproducibility Evaluation of a Phage Susceptibility Testing Method Using a Collection of Escherichia coli and Staphylococcus aureus Phages. J Appl Lab Med 2022; 7:1468-1475. [DOI: 10.1093/jalm/jfac051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 05/03/2022] [Indexed: 11/14/2022]
Abstract
Abstract
Background
Increasing antimicrobial resistance combined with a lagging pipeline of novel antimicrobial compounds have resulted in a resurgence of interest in phage therapy. To select optimal phage or phage combinations for patients for whom phage therapy is considered, assessment of activity of a panel of phages against the patients’ bacterial isolate(s) should ideally be performed. Classical phage susceptibility testing methods (i.e., agar overlay) may be laborious, with expertise outside of normal training and competency of medical laboratory science staff needed.
Content
Adaptive Phage Therapeutics™ leveraged a commercially available phenotyping system (Biolog OmniLog®) to generate the PhageBank Susceptibility Test™, which uses a custom data analysis pipeline (PhageSelect™) to measure the delay in reaching log-phase metabolic activity (“hold time”) when a given isolate is challenged with a specific phage. The goal of this study was to preliminarily assess reproducibility of this approach by testing 2 bacterial species at 2 sites, APT and an academic site. Nineteen Escherichia coli phages were tested against 18 bacterial isolates, and 21 Staphylococcus aureus phages, against 11 bacterial isolates. Result comparisons were statistically excellent for E. coli (κ = 0.7990) and good/fair for S. aureus (κ = 0.6360).
Summary
The described method provides good/fair to excellent statistical reproducibility for assessment of phage susceptibility of 2 commonly encountered bacterial species.
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Affiliation(s)
- Scott A Cunningham
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic , Rochester, MN , USA
| | - Jayawant N Mandrekar
- Division of Biomedical Statistics and Informatics, Mayo Clinic , Rochester, MN , USA
| | - Gina Suh
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic , Rochester, MN , USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic , Rochester, MN , USA
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic , Rochester, MN , USA
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6
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Anand P, Akhter Y. A review on enzyme complexes of electron transport chain from Mycobacterium tuberculosis as promising drug targets. Int J Biol Macromol 2022; 212:474-494. [PMID: 35613677 DOI: 10.1016/j.ijbiomac.2022.05.124] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/05/2022] [Accepted: 05/17/2022] [Indexed: 12/20/2022]
Abstract
Energy metabolism is a universal process occurring in all life forms. In Mycobacterium tuberculosis (Mtb), energy production is carried out in two possible ways, oxidative phosphorylation (OxPhos) and substrate-level phosphorylation. Mtb is an obligate aerobic bacterium, making it dependent on OxPhos for ATP synthesis and growth. Mtb inhabits varied micro-niches during the infection cycle, outside and within the host cells, which alters its primary metabolic pathways during the pathogenesis. In this review, we discuss cellular respiration in the context of the mechanism and structural importance of the proteins and enzyme complexes involved. These protein-protein complexes have been proven to be essential for Mtb virulence as they aid the bacteria's survival during aerobic and hypoxic conditions. ATP synthase, a crucial component of the electron transport chain, has been in the limelight, as a prominent drug target against tuberculosis. Likewise, in this review, we have explored other protein-protein complexes of the OxPhos pathway, their functional essentiality, and their mechanism in Mtb's diverse lifecycle. The review summarises crucial target proteins and reported inhibitors of the electron transport chain pathway of Mtb.
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Affiliation(s)
- Pragya Anand
- Department of Biotechnology, School of Life Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Lucknow, Uttar Pradesh 226025, India
| | - Yusuf Akhter
- Department of Biotechnology, School of Life Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Lucknow, Uttar Pradesh 226025, India.
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7
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Karlikowska M, Singh A, Bhatt A, Ott S, Bottrill AR, Besra GS, Fullam E. Biochemical and phenotypic characterisation of the Mycobacterium smegmatis transporter UspABC. Cell Surf 2021; 7:100052. [PMID: 34296047 PMCID: PMC8281650 DOI: 10.1016/j.tcsw.2021.100052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/02/2021] [Accepted: 04/03/2021] [Indexed: 11/08/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) is an intracellular human pathogen that has evolved to survive in a nutrient limited environment within the host for decades. Accordingly, Mtb has developed strategies to acquire scarce nutrients and the mycobacterial transporter systems provide an important route for the import of key energy sources. However, the physiological role of the Mtb transporters and their substrate preference(s) are poorly characterised. Previous studies have established that the Mtb UspC solute-binding domain recognises amino- and phosphorylated-sugars, indicating that the mycobacterial UspABC transporter plays a key role in the import of peptidoglycan precursors. Herein, we have used a wide array of approaches to investigate the role of UspABC in Mycobacterium smegmatis by analysis of mutant strains that either lack the solute binding domain: ΔuspC or the entire transport complex: ΔuspABC. Analysis of mycobacterial transcripts shows that the uspABC system is functionally expressed in mycobacteria as a contiguous reading frame. Topology mapping confirms an Nin-Cin orientation of the UspAB integral membrane spanning domains. Phenotypic microarray profiling of commercially available sugars suggests, unexpectedly, that the uspC and ΔuspABC mutants had different carbon utilisation profiles and that neither strain utilised glucose-1-phosphate. Furthermore, proteomics analysis showed an alteration in the abundance of proteins involved in sugar and lipid metabolism, crucial for cell envelope synthesis, and we propose that UspABC has an important role in determining the interplay between these pathways.
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Affiliation(s)
| | - Albel Singh
- Institute of Microbiology & Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Apoorva Bhatt
- Institute of Microbiology & Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Sascha Ott
- Warwick Medical School, University of Warwick, CV4 7AL, UK
- Bioinformatics Research Technology Platform, University of Warwick, Coventry CV4 7AL, UK
| | | | - Gurdyal S. Besra
- Institute of Microbiology & Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Elizabeth Fullam
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
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8
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Tsai NC, Hsu TS, Kuo SC, Kao CT, Hung TH, Lin DG, Yeh CS, Chu CC, Lin JS, Lin HH, Ko CY, Chang TH, Su JC, Lin YCJ. Large-scale data analysis for robotic yeast one-hybrid platforms and multi-disciplinary studies using GateMultiplex. BMC Biol 2021; 19:214. [PMID: 34560855 PMCID: PMC8461970 DOI: 10.1186/s12915-021-01140-y] [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: 03/03/2021] [Accepted: 09/03/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Yeast one-hybrid (Y1H) is a common technique for identifying DNA-protein interactions, and robotic platforms have been developed for high-throughput analyses to unravel the gene regulatory networks in many organisms. Use of these high-throughput techniques has led to the generation of increasingly large datasets, and several software packages have been developed to analyze such data. We previously established the currently most efficient Y1H system, meiosis-directed Y1H; however, the available software tools were not designed for processing the additional parameters suggested by meiosis-directed Y1H to avoid false positives and required programming skills for operation. RESULTS We developed a new tool named GateMultiplex with high computing performance using C++. GateMultiplex incorporated a graphical user interface (GUI), which allows the operation without any programming skills. Flexible parameter options were designed for multiple experimental purposes to enable the application of GateMultiplex even beyond Y1H platforms. We further demonstrated the data analysis from other three fields using GateMultiplex, the identification of lead compounds in preclinical cancer drug discovery, the crop line selection in precision agriculture, and the ocean pollution detection from deep-sea fishery. CONCLUSIONS The user-friendly GUI, fast C++ computing speed, flexible parameter setting, and applicability of GateMultiplex facilitate the feasibility of large-scale data analysis in life science fields.
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Affiliation(s)
- Ni-Chiao Tsai
- Department of Life Science and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Tzu-Shu Hsu
- Department of Pharmacy, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
| | - Shang-Che Kuo
- Department of Pharmacy, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, 10617, Taiwan
| | - Chung-Ting Kao
- Department of Life Science and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Tzu-Huan Hung
- Biotechnology Division, Taiwan Agricultural Research Institute, Taichung, 41362, Taiwan
| | - Da-Gin Lin
- Biotechnology Division, Taiwan Agricultural Research Institute, Taichung, 41362, Taiwan
| | - Chung-Shu Yeh
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Chia-Chen Chu
- Department of Life Science and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Jeng-Shane Lin
- Department of Life Sciences, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Hsin-Hung Lin
- Department of Horticulture and Biotechnology, Chinese Culture University, Taipei, 11114, Taiwan
| | - Chia-Ying Ko
- Department of Life Sciences and Institute of Fisheries Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Tien-Hsien Chang
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan.
| | - Jung-Chen Su
- Department of Pharmacy, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan.
| | - Ying-Chung Jimmy Lin
- Department of Life Science and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, 10617, Taiwan.
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, 10617, Taiwan.
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9
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Costantini PE, Firrincieli A, Fedi S, Parolin C, Viti C, Cappelletti M, Vitali B. Insight into phenotypic and genotypic differences between vaginal Lactobacillus crispatus BC5 and Lactobacillus gasseri BC12 to unravel nutritional and stress factors influencing their metabolic activity. Microb Genom 2021; 7. [PMID: 34096840 PMCID: PMC8461478 DOI: 10.1099/mgen.0.000575] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The vaginal microbiota, normally characterized by lactobacilli presence, is crucial for vaginal health. Members belonging to L. crispatus and L. gasseri species exert crucial protective functions against pathogens, although a total comprehension of factors that influence their dominance in healthy women is still lacking. Here we investigated the complete genome sequence and comprehensive phenotypic profile of L. crispatus strain BC5 and L. gasseri strain BC12, two vaginal strains featured by anti-bacterial and anti-viral activities. Phenotype microarray (PM) results revealed an improved capacity of BC5 to utilize different carbon sources as compared to BC12, although some specific carbon sources that can be associated to the human diet were only metabolized by BC12, i.e. uridine, amygdalin, tagatose. Additionally, the two strains were mostly distinct in the capacity to utilize the nitrogen sources under analysis. On the other hand, BC12 showed tolerance/resistance towards twice the number of stressors (i.e. antibiotics, toxic metals etc.) with respect to BC5. The divergent phenotypes observed in PM were supported by the identification in either BC5 or BC12 of specific genetic determinants that were found to be part of the core genome of each species. The PM results in combination with comparative genome data provide insights into the possible environmental factors and genetic traits supporting the predominance of either L. crispatus BC5 or L. gasseri BC12 in the vaginal niche, giving also indications for metabolic predictions at the species level.
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Affiliation(s)
| | - Andrea Firrincieli
- Department of Pharmacy and Biotechnology (FaBit), University of Bologna, Bologna, Italy
| | - Stefano Fedi
- Department of Pharmacy and Biotechnology (FaBit), University of Bologna, Bologna, Italy
| | - Carola Parolin
- Department of Pharmacy and Biotechnology (FaBit), University of Bologna, Bologna, Italy
| | - Carlo Viti
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Florence, Italy
| | - Martina Cappelletti
- Department of Pharmacy and Biotechnology (FaBit), University of Bologna, Bologna, Italy
| | - Beatrice Vitali
- Department of Pharmacy and Biotechnology (FaBit), University of Bologna, Bologna, Italy
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10
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López-Agudelo VA, Mendum TA, Laing E, Wu H, Baena A, Barrera LF, Beste DJV, Rios-Estepa R. A systematic evaluation of Mycobacterium tuberculosis Genome-Scale Metabolic Networks. PLoS Comput Biol 2020; 16:e1007533. [PMID: 32542021 PMCID: PMC7316355 DOI: 10.1371/journal.pcbi.1007533] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 06/25/2020] [Accepted: 05/08/2020] [Indexed: 01/06/2023] Open
Abstract
Metabolism underpins the pathogenic strategy of the causative agent of TB, Mycobacterium tuberculosis (Mtb), and therefore metabolic pathways have recently re-emerged as attractive drug targets. A powerful approach to study Mtb metabolism as a whole, rather than just individual enzymatic components, is to use a systems biology framework, such as a Genome-Scale Metabolic Network (GSMN) that allows the dynamic interactions of all the components of metabolism to be interrogated together. Several GSMNs networks have been constructed for Mtb and used to study the complex relationship between the Mtb genotype and its phenotype. However, the utility of this approach is hampered by the existence of multiple models, each with varying properties and performances. Here we systematically evaluate eight recently published metabolic models of Mtb-H37Rv to facilitate model choice. The best performing models, sMtb2018 and iEK1011, were refined and improved for use in future studies by the TB research community.
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Affiliation(s)
- Víctor A. López-Agudelo
- Grupo de Bioprocesos, Departamento de Ingeniería Química, Universidad de Antioquia UdeA, Medellín, Colombia
- Grupo de Inmunología Celular e Inmunogenética (GICIG), Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Tom A. Mendum
- Department of Microbial Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Emma Laing
- Department of Microbial Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - HuiHai Wu
- Department of Microbial Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Andres Baena
- Grupo de Inmunología Celular e Inmunogenética (GICIG), Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Luis F. Barrera
- Grupo de Inmunología Celular e Inmunogenética (GICIG), Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
- Instituto de Investigaciones Médicas, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Dany J. V. Beste
- Department of Microbial Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Rigoberto Rios-Estepa
- Grupo de Bioprocesos, Departamento de Ingeniería Química, Universidad de Antioquia UdeA, Medellín, Colombia
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11
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Ng SW, Selvarajah GT, Cheah YK, Mustaffa Kamal F, Omar AR. Cellular Metabolic Profiling of CrFK Cells Infected with Feline Infectious Peritonitis Virus Using Phenotype Microarrays. Pathogens 2020; 9:E412. [PMID: 32466289 PMCID: PMC7281222 DOI: 10.3390/pathogens9050412] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/13/2020] [Accepted: 05/18/2020] [Indexed: 02/07/2023] Open
Abstract
Feline infectious peritonitis (FIP) is a fatal feline immune-mediated disease caused by feline infectious peritonitis virus (FIPV). Little is known about the biological pathways associated in FIP pathogenesis. This is the first study aiming to determine the phenotypic characteristics on the cellular level in relation to specific metabolic pathways of importance to FIP pathogenesis. METHODS The internalization of type II FIPV WSU 79-1146 in Crandell-Rees Feline Kidney (CrFK) cells was visualized using a fluorescence microscope, and optimization prior to phenotype microarray (PM) study was performed. Then, four types of Biolog Phenotype MicroArray™ plates (PM-M1 to PM-M4) precoated with different carbon and nitrogen sources were used to determine the metabolic profiles in FIPV-infected cells. RESULTS The utilization of palatinose was significantly low in FIPV-infected cells; however, there were significant increases in utilizing melibionic acid, L-glutamine, L-glutamic acid and alanyl-glutamine (Ala-Gln) compared to non-infected cells. CONCLUSION This study has provided the first insights into the metabolic profiling of a feline coronavirus infection in vitro using PMs and deduced that glutamine metabolism is one of the essential metabolic pathways for FIPV infection and replication. Further studies are necessary to develop strategies to target the glutamine metabolic pathway in FIPV infection.
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Affiliation(s)
- Shing Wei Ng
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia;
- Institute of Bioscience, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia
| | - Gayathri Thevi Selvarajah
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia;
- Institute of Bioscience, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia
| | - Yoke Kqueen Cheah
- Department of Biomedical Sciences, Faculty of Medicine and Biomedical Health Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia;
| | - Farina Mustaffa Kamal
- Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (F.M.K.); (A.R.O.)
| | - Abdul Rahman Omar
- Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (F.M.K.); (A.R.O.)
- Institute of Bioscience, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia
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12
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Loukil A, Bouzid F, Osman DA, Drancourt M. Decrypting the environmental sources of Mycobacterium canettii by high-throughput biochemical profiling. PLoS One 2019; 14:e0222078. [PMID: 31479485 PMCID: PMC6719871 DOI: 10.1371/journal.pone.0222078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 08/21/2019] [Indexed: 12/31/2022] Open
Abstract
Mycobacterium canettii is a smooth bacillus related to the Mycobacterium tuberculosis complex. It causes lymph nodes and pulmonary tuberculosis in patients living in countries of the Horn of Africa, including Djibouti. The environmental reservoirs of M. canettii are still unknown. We aimed to further decrypt these potential reservoirs by using an original approach of High-Throughput Carbon and Azote Substrate Profiling. The Biolog Phenotype profiling was performed on six clinical strains of M. canettii and one M. tuberculosis strain was used as a positive control. The experiments were duplicated and authenticated by negative controls. While M. tuberculosis metabolized 22/190 (11%) carbon substrates and 3/95 (3%) nitrogen substrates, 17/190 (8.9%) carbon substrates and three nitrogen substrates were metabolized by the six M. canettii strains forming the so-called corebiologome. A total at 16 carbon substrates and three nitrogen substrates were metabolized in common by M. tuberculosis and the six M. canettii strains. Moreover, at least one M. canettii strain metabolized 36/190 (19%) carbon substrates and 3/95 (3%) nitrogen substrates for a total of 39/285 (13%) substrates. Classifying these carbon and nitrogen substrates into ten potential environmental sources (plants, fruits and vegetables, bacteria, algae, fungi, nematodes, mollusks, mammals, insects and inanimate environment) significantly associated carbon and nitrogen substrates metabolized by at least one M. canettii strain with plants (p = 0.006). These results suggest that some plants endemic in the Horn of Africa may serve as ecological niches for M. canettii. Further ethnobotanical studies will indicate plant usages by local populations, then guiding field microbiological investigations in order to prove the definite environmental reservoirs of this opportunistic tuberculous pathogen.
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Affiliation(s)
- Ahmed Loukil
- Aix-Marseille Univ., IRD, MEPHI, IHU Méditerranée-Infection, Marseille, France
| | - Fériel Bouzid
- Aix-Marseille Univ., IRD, MEPHI, IHU Méditerranée-Infection, Marseille, France
- Université de Gafsa, Faculté des Sciences de Gafsa, Gafsa, Tunisia
| | - Djaltou Aboubaker Osman
- Institut de Recherche Médicinale, Centre d’Etudes et de Recherche de Djibouti (CERD), Djibouti, République de Djibouti
| | - Michel Drancourt
- Aix-Marseille Univ., IRD, MEPHI, IHU Méditerranée-Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- * E-mail:
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13
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The hydrolase LpqI primes mycobacterial peptidoglycan recycling. Nat Commun 2019; 10:2647. [PMID: 31201321 PMCID: PMC6572805 DOI: 10.1038/s41467-019-10586-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 05/14/2019] [Indexed: 12/26/2022] Open
Abstract
Growth and division by most bacteria requires remodelling and cleavage of their cell wall. A byproduct of this process is the generation of free peptidoglycan (PG) fragments known as muropeptides, which are recycled in many model organisms. Bacteria and hosts can harness the unique nature of muropeptides as a signal for cell wall damage and infection, respectively. Despite this critical role for muropeptides, it has long been thought that pathogenic mycobacteria such as Mycobacterium tuberculosis do not recycle their PG. Herein we show that M. tuberculosis and Mycobacterium bovis BCG are able to recycle components of their PG. We demonstrate that the core mycobacterial gene lpqI, encodes an authentic NagZ β-N-acetylglucosaminidase and that it is essential for PG-derived amino sugar recycling via an unusual pathway. Together these data provide a critical first step in understanding how mycobacteria recycle their peptidoglycan. Bacterial growth and division require remodelling of the cell wall, which generates free peptidoglycan fragments. Here, Moynihan et al. show that Mycobacterium tuberculosis can recycle components of their peptidoglycan, and characterise a crucial enzyme required for this process.
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14
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Deng Y, Su Y, Liu S, Guo Z, Cheng C, Ma H, Wu J, Feng J, Chen C. Identification of a Novel Small RNA srvg23535 in Vibrio alginolyticus ZJ-T and Its Characterization With Phenotype MicroArray Technology. Front Microbiol 2018; 9:2394. [PMID: 30349521 PMCID: PMC6186989 DOI: 10.3389/fmicb.2018.02394] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Accepted: 09/18/2018] [Indexed: 01/28/2023] Open
Abstract
Small non-coding RNAs (sRNAs) are important modulators of gene expression and are involved in the pathogenesis and survival of prokaryotes. However, few studies have been conducted with Vibrio alginolyticus, which limits our ability to probe the regulation of virulence and environmental adaptation by sRNAs in this opportunistic pathogen. In this study, the sRNA candidate srvg23535 was identified in V. alginolyticus ZJ-T. The precise transcript end, secondary structure, and sequence conservation were determined. A srvg23535 null mutant was constructed and characterized by using Phenotype MicroArray (PM) technology. In silico target prediction was conducted by IntaRNA and TargetRNA2. Subsequently, a 107 nt transcript was validated with a sigma70 promoter at the 5' end and a Rho-independent terminator at the 3' end. The sRNA srvg23535 had four stem-loop structures and was conserved among Vibrio harveyi, Vibrio parahaemolyticus, and Vibrio splendidus. Deletion of srvg23535 in V. alginolyticus ZJ-T led to a weaker utilization of D-mannose, D-melibiose, lactulose, and inosine as carbon sources but stronger utilization of L-cysteine as nitrogen source. Moreover, the srvg2353 mutant showed stronger resistance to osmotic stress but weaker resistance to pH stress. Additionally, a total of 22 common targets were identified and several were related to the observed phenotype of the mutant. This study indicated that the novel sRNA, srvg23535, is conserved and restricted to Vibrio spp., affecting the utilization of several carbon and nitrogen sources and the response to osmotic and pH stress. These results extend our understanding of sRNA regulation in V. alginolyticus and provide a significant resource for the further study of the precise target mRNAs of srvg23535, which may provide targets for antibacterial therapeutic or attenuated vaccines against Vibrio spp.
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Affiliation(s)
- Yiqin Deng
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.,Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Youlu Su
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Songlin Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Zhixun Guo
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Changhong Cheng
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Hongling Ma
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Jinjun Wu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Juan Feng
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Chang Chen
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Xisha/Nansha Ocean Observation and Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
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15
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Nahid P, Jarlsberg LG, Kato-Maeda M, Segal MR, Osmond DH, Gagneux S, Dobos K, Gold M, Hopewell PC, Lewinsohn DM. Interplay of strain and race/ethnicity in the innate immune response to M. tuberculosis. PLoS One 2018; 13:e0195392. [PMID: 29787561 PMCID: PMC5963792 DOI: 10.1371/journal.pone.0195392] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 03/21/2018] [Indexed: 11/19/2022] Open
Abstract
Background The roles of host and pathogen factors in determining innate immune responses to M. tuberculosis are not fully understood. In this study, we examined host macrophage immune responses of 3 race/ethnic groups to 3 genetically and geographically diverse M. tuberculosis lineages. Methods Monocyte-derived macrophages from healthy Filipinos, Chinese and non-Hispanic White study participants (approximately 45 individuals/group) were challenged with M. tuberculosis whole cell lysates of clinical strains Beijing HN878 (lineage 2), Manila T31 (lineage 1), CDC1551 (lineage 4), the reference strain H37Rv (lineage 4), as well as with Toll-like receptor 2 agonist lipoteichoic acid (TLR2/LTA) and TLR4 agonist lipopolysaccharide (TLR4/LPS). Following overnight incubation, multiplex assays for nine cytokines: IL-1β, IL-2, IL-6, IL-8, IL-10, IL-12p70, IFNγ, TNFα, and GM-CSF, were batch applied to supernatants. Results Filipino macrophages produced less IL-1, IL-6, and more IL-8, compared to macrophages from Chinese and Whites. Race/ethnicity had only subtle effects or no impact on the levels of IL-10, IL-12p70, TNFα and GM-CSF. In response to the Toll-like receptor 2 agonist lipoteichoic acid (TLR2/LTA), Filipino macrophages again had lower IL-1 and IL-6 responses and a higher IL-8 response, compared to Chinese and Whites. The TLR2/LTA-stimulated Filipino macrophages also produced lower amounts of IL-10, TNFα and GM-CSF. Race/ethnicity had no impact on IL-12p70 levels released in response to TLR2/LTA. The responses to TLR4 agonist lipopolysaccharide (TLR4/LPS) were similar to the TLR2/LTA responses, for IL-1, IL-6, IL-8, and IL-10. However, TLR4/LPS triggered the release of less IL-12p70 from Filipino macrophages, and less TNFα from White macrophages. Conclusions Both host race/ethnicity and pathogen strain influence the innate immune response. Such variation may have implications for the development of new tools across TB therapeutics, immunodiagnostics and vaccines.
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Affiliation(s)
- P. Nahid
- Division of Pulmonary and Critical Care Medicine, San Francisco General Hospital, University of California, San Francisco, United States of America
- * E-mail: (PN); (DML)
| | - L. G. Jarlsberg
- Division of Pulmonary and Critical Care Medicine, San Francisco General Hospital, University of California, San Francisco, United States of America
| | - M. Kato-Maeda
- Division of Pulmonary and Critical Care Medicine, San Francisco General Hospital, University of California, San Francisco, United States of America
| | - M. R. Segal
- Department of Epidemiology & Biostatistics, University of California, San Francisco, United States of America
| | - D. H. Osmond
- Department of Epidemiology & Biostatistics, University of California, San Francisco, United States of America
| | - S. Gagneux
- Swiss Tropical and Public Health Institute, Department of Medical Parasitology and Infection Biology, University of Basel, Basel, Switzerland
| | - K. Dobos
- Colorado State University, Department of Microbiology, Immunology & Pathology, Fort Collins, CO, United States of America
| | - M. Gold
- Department of Research, Veterans Affairs Portland Health Care Center, Portland, Oregon, United States of America
| | - P. C. Hopewell
- Division of Pulmonary and Critical Care Medicine, San Francisco General Hospital, University of California, San Francisco, United States of America
| | - D. M. Lewinsohn
- Department of Pulmonary and Critical Care Medicine, Oregon Health and Sciences University, Portland, Oregon
- Department of Research, Veterans Affairs Portland Health Care Center, Portland, Oregon, United States of America
- * E-mail: (PN); (DML)
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16
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Chong TM, Chen JW, See-Too WS, Yu CY, Ang GY, Lim YL, Yin WF, Grandclément C, Faure D, Dessaux Y, Chan KG. Phenotypic and genomic survey on organic acid utilization profile of Pseudomonas mendocina strain S5.2, a vineyard soil isolate. AMB Express 2017; 7:138. [PMID: 28655216 PMCID: PMC5484659 DOI: 10.1186/s13568-017-0437-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 06/19/2017] [Indexed: 12/30/2022] Open
Abstract
Root exudates are chemical compounds that are released from living plant roots and provide significant energy, carbon, nitrogen and phosphorus sources for microbes inhabiting the rhizosphere. The exudates shape the microflora associated with the plant, as well as influences the plant health and productivity. Therefore, a better understanding of the trophic link that is established between the plant and the associated bacteria is necessary. In this study, a comprehensive survey on the utilization of grapevine and rootstock related organic acids were conducted on a vineyard soil isolate which is Pseudomonas mendocina strain S5.2. Phenotype microarray analysis has demonstrated that this strain can utilize several organic acids including lactic acid, succinic acid, malic acid, citric acid and fumaric acid as sole growth substrates. Complete genome analysis using single molecule real-time technology revealed that the genome consists of a 5,120,146 bp circular chromosome and a 252,328 bp megaplasmid. A series of genetic determinants associated with the carbon utilization signature of the strain were subsequently identified in the chromosome. Of note, the coexistence of genes encoding several iron-sulfur cluster independent isoenzymes in the genome indicated the importance of these enzymes in the events of iron deficiency. Synteny and comparative analysis have also unraveled the unique features of D-lactate dehydrogenase of strain S5.2 in the study. Collective information of this work has provided insights on the metabolic role of this strain in vineyard soil rhizosphere.
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Affiliation(s)
- Teik Min Chong
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Jian-Woon Chen
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
- UM Omics Centre, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Wah-Seng See-Too
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Choo-Yee Yu
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA, 40450 Shah Alam, Selangor Malaysia
| | - Geik-Yong Ang
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA, 40450 Shah Alam, Selangor Malaysia
| | - Yan Lue Lim
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Catherine Grandclément
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-Sur-Yvette, France
| | - Denis Faure
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-Sur-Yvette, France
| | - Yves Dessaux
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-Sur-Yvette, France
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
- UM Omics Centre, University of Malaya, 50603 Kuala Lumpur, Malaysia
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López-Agudelo VA, Baena A, Ramirez-Malule H, Ochoa S, Barrera LF, Ríos-Estepa R. Metabolic adaptation of two in silico mutants of Mycobacterium tuberculosis during infection. BMC SYSTEMS BIOLOGY 2017; 11:107. [PMID: 29157227 PMCID: PMC5697012 DOI: 10.1186/s12918-017-0496-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 11/13/2017] [Indexed: 12/16/2022]
Abstract
BACKGROUND Up to date, Mycobacterium tuberculosis (Mtb) remains as the worst intracellular killer pathogen. To establish infection, inside the granuloma, Mtb reprograms its metabolism to support both growth and survival, keeping a balance between catabolism, anabolism and energy supply. Mtb knockouts with the faculty of being essential on a wide range of nutritional conditions are deemed as target candidates for tuberculosis (TB) treatment. Constraint-based genome-scale modeling is considered as a promising tool for evaluating genetic and nutritional perturbations on Mtb metabolic reprogramming. Nonetheless, few in silico assessments of the effect of nutritional conditions on Mtb's vulnerability and metabolic adaptation have been carried out. RESULTS A genome-scale model (GEM) of Mtb, modified from the H37Rv iOSDD890, was used to explore the metabolic reprogramming of two Mtb knockout mutants (pfkA- and icl-mutants), lacking key enzymes of central carbon metabolism, while exposed to changing nutritional conditions (oxygen, and carbon and nitrogen sources). A combination of shadow pricing, sensitivity analysis, and flux distributions patterns allowed us to identify metabolic behaviors that are in agreement with phenotypes reported in the literature. During hypoxia, at high glucose consumption, the Mtb pfkA-mutant showed a detrimental growth effect derived from the accumulation of toxic sugar phosphate intermediates (glucose-6-phosphate and fructose-6-phosphate) along with an increment of carbon fluxes towards the reductive direction of the tricarboxylic acid cycle (TCA). Furthermore, metabolic reprogramming of the icl-mutant (icl1&icl2) showed the importance of the methylmalonyl pathway for the detoxification of propionyl-CoA, during growth at high fatty acid consumption rates and aerobic conditions. At elevated levels of fatty acid uptake and hypoxia, we found a drop in TCA cycle intermediate accumulation that might create redox imbalance. Finally, findings regarding Mtb-mutant metabolic adaptation associated with asparagine consumption and acetate, succinate and alanine production, were in agreement with literature reports. CONCLUSIONS This study demonstrates the potential application of genome-scale modeling, flux balance analysis (FBA), phenotypic phase plane (PhPP) analysis and shadow pricing to generate valuable insights about Mtb metabolic reprogramming in the context of human granulomas.
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Affiliation(s)
- Víctor A. López-Agudelo
- Grupo de Bioprocesos, Departamento de Ingeniería Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
- Grupo de Inmunología Celular e Inmunogenética (GICIG), Facultad de Medicina, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | - Andres Baena
- Grupo de Inmunología Celular e Inmunogenética (GICIG), Facultad de Medicina, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | | | - Silvia Ochoa
- Grupo de investigación en Simulación, Diseño, Control y Optimización de Procesos (SIDCOP), Departamento de Ingeniería Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | - Luis F. Barrera
- Grupo de Inmunología Celular e Inmunogenética (GICIG), Facultad de Medicina, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
- Instituto de Investigaciones Médicas, Facultad de Medicina, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | - Rigoberto Ríos-Estepa
- Grupo de Bioprocesos, Departamento de Ingeniería Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
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Dadura K, Płocińska R, Rumijowska-Galewicz A, Płociński P, Żaczek A, Dziadek B, Zaborowski A, Dziadek J. PdtaS Deficiency Affects Resistance of Mycobacteria to Ribosome Targeting Antibiotics. Front Microbiol 2017; 8:2145. [PMID: 29163430 PMCID: PMC5676007 DOI: 10.3389/fmicb.2017.02145] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 10/19/2017] [Indexed: 11/13/2022] Open
Abstract
Two-component regulatory systems (TCSSs) are key regulatory elements responsible for the adaptation of bacteria to environmental stresses. A classical TCSS is typically comprised of a sensory histidine kinase and a corresponding response regulator. Here, we used homologous recombination to construct a Mycobacterium smegmatis mutant defective in the synthesis of cytosolic histidine kinase PdtaS (Msmeg_1918). The resulting ΔpdtaS mutant strain was tested in the Phenotype Microarray screening system, which allowed us to identify aminoglycoside antibiotic sensitivity, tetracyclines antibiotic resistance as well as membrane transport and respiration, as the main processes affected by removal of pdtaS. The antibiotic sensitivity profiles were confirmed by survival assessment and complementation studies. To gain insight into the molecular mechanisms responsible for the observed phenotype, we compared ribosomal RNA and protein profiles of the mutant and wild-type strains. We carried out Northern blotting and qRT-PCR to compare rRNA levels and analyzed ribosome sedimentation patterns of the wild-type and mutant strains on sucrose gradients. Isolated ribosomes were further used to estimate relative abundance of individual proteins in the ribosomal subunits using label free mass spectrometry analysis. Additionally, the ΔpdtaS mutant revealed lower activity of the respiratory chain as measured by the rate of TTC (triphenyltetrazolium chloride) reduction, while at the same time showing only insignificant changes in the uptake of aminoglycosides. We postulate that deficiency of PdtaS affects the oxidative respiration rates and ribosomal composition causing relevant changes to intrinsic resistance or susceptibility to antibiotics targeting ribosomes, which are commonly used to treat mycobacterial infections.
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Affiliation(s)
- Karolina Dadura
- Institute for Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Renata Płocińska
- Institute for Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | | | | | - Anna Żaczek
- Department of Biochemistry and Cell Biology, University of Rzeszów, Rzeszów, Poland
| | - Bożena Dziadek
- Department of Immunoparasitology, University of Łódź, Łódź, Poland
| | | | - Jarosław Dziadek
- Institute for Medical Biology, Polish Academy of Sciences, Łódź, Poland
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19
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Nouioui I, Carro L, Teramoto K, Igual JM, Jando M, Del Carmen Montero-Calasanz M, Sutcliffe I, Sangal V, Goodfellow M, Klenk HP. Mycobacterium eburneum sp. nov., a non-chromogenic, fast-growing strain isolated from sputum. Int J Syst Evol Microbiol 2017; 67:3174-3181. [PMID: 28869002 DOI: 10.1099/ijsem.0.002033] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A polyphasic study was undertaken to establish the taxonomic position of a non-chromogenic, rapidly growing Mycobacterium strain that had been isolated from sputum. The strain, CECT 8775T, has chemotaxonomic and cultural properties consistent with its classification in the genus Mycobacterium and was distinguished from the type strains of closely related mycobacterial species, notably from Mycobacterium paraense DSM 46749T, its nearest phylogenetic neighbour, based on 16S rRNA, hsp65 and rpoB gene sequence data. These organisms were also distinguished by a broad range of chemotaxonomic and phenotypic features and by a digital DNA-DNA relatedness value of 22.8 %. Consequently, the strain is considered to represent a novel species of Mycobacterium for which the name Mycobacterium eburneum sp. nov is proposed; the type strain is X82T (CECT 8775T=DSM 44358T).
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Affiliation(s)
- Imen Nouioui
- School of Biology, Ridley Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Lorena Carro
- School of Biology, Ridley Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Kanae Teramoto
- Advanced and Fundamental Technology Center, JEOL Ltd., 3-1-2 Musashino, Akishima, Tokyo 196-8558, Japan
| | - José M Igual
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), c/Cordel de Merinas 40-52, 37008 Salamanca, Spain
| | - Marlen Jando
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | | | - Iain Sutcliffe
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Vartul Sangal
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Michael Goodfellow
- School of Biology, Ridley Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Hans-Peter Klenk
- School of Biology, Ridley Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
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Shigatoxin encoding Bacteriophage ϕ24 B modulates bacterial metabolism to raise antimicrobial tolerance. Sci Rep 2017; 7:40424. [PMID: 28106081 PMCID: PMC5247750 DOI: 10.1038/srep40424] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 12/07/2016] [Indexed: 01/15/2023] Open
Abstract
How temperate bacteriophages play a role in microbial infection and disease progression is not fully understood. They do this in part by carrying genes that promote positive evolutionary selection for the lysogen. Using Biolog phenotype microarrays and comparative metabolite profiling we demonstrate the impact of the well-characterised Shiga toxin-prophage ϕ24B on its Escherichia coli host MC1061. As a lysogen, the prophage alters the bacterial physiology by increasing the rates of respiration and cell proliferation. This is the first reported study detailing phage-mediated control of the E. coli biotin and fatty acid synthesis that is rate limiting to cell growth. Through ϕ24B conversion the lysogen also gains increased antimicrobial tolerance to chloroxylenol and 8-hydroxyquinoline. Distinct metabolite profiles discriminate between MC1061 and the ϕ24B lysogen in standard culture, and when treated with 2 antimicrobials. This is also the first reported use of metabolite profiling to characterise the physiological impact of lysogeny under antimicrobial pressure. We propose that temperate phages do not need to carry antimicrobial resistance genes to play a significant role in tolerance to antimicrobials.
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Kaneene JB, Hattey JA, Bolin CA, Averill J, Miller R. Survivability of Mycobacterium bovis on salt and salt-mineral blocks fed to cattle. Am J Vet Res 2017; 78:57-62. [PMID: 28029286 DOI: 10.2460/ajvr.78.1.57] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To determine the survivability of Mycobacterium bovis on salt and salt-mineral blocks in typical weather conditions in Michigan over two 12-day periods at the height of summer and winter. SAMPLE 4 salt (NaCl) and 4 salt-mineral blocks inoculated with pure cultures of a strain of M bovis currently circulating in Michigan livestock and wildlife. PROCEDURES In the summer and again in the winter, inoculated blocks were placed in secured outdoor facilities where equal numbers of each block type (2/type/season) were exposed to shade or sunlight. Samples were collected from randomly selected areas on the surface of each block beginning within 1 hour after placement (day 0) twice a day for the first 4 days and once a day from days 7 through 11. Bacterial culture of samples was performed to detect viable M bovis. RESULTS Depending on the exposure conditions, salt blocks yielded viable M bovis for up to 2 days after inoculation and salt-mineral blocks yielded viable M bovis for > 3 days. Survival time was greatest on salt-mineral blocks kept outdoors in the shade during the winter. The odds of recovering viable M bovis from salt-mineral block samples were 4.9 times as great during the winter (vs the summer) and 3.0 times as great with exposure to shade (vs sunlight). CONCLUSIONS AND CLINICAL RELEVANCE Results from this study indicated that salt and salt-mineral blocks should be considered potential sources of bovine tuberculosis when designing risk mitigation programs for cattle herds in areas with wildlife reservoirs of M bovis.
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Sanchini A, Dematheis F, Semmler T, Lewin A. Metabolic phenotype of clinical and environmental Mycobacterium avium subsp. hominissuis isolates. PeerJ 2017; 5:e2833. [PMID: 28070460 PMCID: PMC5214758 DOI: 10.7717/peerj.2833] [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: 09/07/2016] [Accepted: 11/27/2016] [Indexed: 11/29/2022] Open
Abstract
Background Mycobacterium avium subsp. hominissuis (MAH) is an emerging opportunistic human pathogen. It can cause pulmonary infections, lymphadenitis and disseminated infections in immuno-compromised patients. In addition, MAH is widespread in the environment, since it has been isolated from water, soil or dust. In recent years, knowledge on MAH at the molecular level has increased substantially. In contrast, knowledge of the MAH metabolic phenotypes remains limited. Methods In this study, for the first time we analyzed the metabolic substrate utilization of ten MAH isolates, five from a clinical source and five from an environmental source. We used BIOLOG Phenotype MicroarrayTM technology for the analysis. This technology permits the rapid and global analysis of metabolic phenotypes. Results The ten MAH isolates tested showed different metabolic patterns pointing to high intra-species diversity. Our MAH isolates preferred to use fatty acids such as Tween, caproic, butyric and propionic acid as a carbon source, and L-cysteine as a nitrogen source. Environmental MAH isolates resulted in being more metabolically active than clinical isolates, since the former metabolized more strongly butyric acid (p = 0.0209) and propionic acid (p = 0.00307). Discussion Our study provides new insight into the metabolism of MAH. Understanding how bacteria utilize substrates during infection might help the developing of strategies to fight such infections.
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Affiliation(s)
- Andrea Sanchini
- Division 16, Mycotic and Parasitic Agents and Mycobacteria, Robert Koch Institute , Berlin , Germany
| | - Flavia Dematheis
- Institute of Microbiology and Epizootics, Free University Berlin , Berlin , Germany
| | - Torsten Semmler
- NG 1 Microbial Genomics, Robert Koch Institute , Berlin , Germany
| | - Astrid Lewin
- Division 16, Mycotic and Parasitic Agents and Mycobacteria, Robert Koch Institute , Berlin , Germany
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Zingue D, Bouam A, Militello M, Drancourt M. High-Throughput Carbon Substrate Profiling of Mycobacterium ulcerans Suggests Potential Environmental Reservoirs. PLoS Negl Trop Dis 2017; 11:e0005303. [PMID: 28095422 PMCID: PMC5271411 DOI: 10.1371/journal.pntd.0005303] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 01/27/2017] [Accepted: 01/04/2017] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Mycobacterium ulcerans is a close derivative of Mycobacterium marinum and the agent of Buruli ulcer in some tropical countries. Epidemiological and environmental studies pointed towards stagnant water ecosystems as potential sources of M. ulcerans, yet the ultimate reservoirs remain elusive. We hypothesized that carbon substrate determination may help elucidating the spectrum of potential reservoirs. METHODOLOGY/PRINCIPAL FINDINGS In a first step, high-throughput phenotype microarray Biolog was used to profile carbon substrates in one M. marinum and five M. ulcerans strains. A total of 131/190 (69%) carbon substrates were metabolized by at least one M. ulcerans strain, including 28/190 (15%) carbon substrates metabolized by all five M. ulcerans strains of which 21 substrates were also metabolized by M. marinum. In a second step, 131 carbon substrates were investigated, through a bibliographical search, for their known environmental sources including plants, fruits and vegetables, bacteria, algae, fungi, nematodes, mollusks, mammals, insects and the inanimate environment. This analysis yielded significant association of M. ulcerans with bacteria (p = 0.000), fungi (p = 0.001), algae (p = 0.003) and mollusks (p = 0.007). In a third step, the Medline database was cross-searched for bacteria, fungi, mollusks and algae as potential sources of carbon substrates metabolized by all tested M. ulcerans; it indicated that 57% of M. ulcerans substrates were associated with bacteria, 18% with alga, 11% with mollusks and 7% with fungi. CONCLUSIONS This first report of high-throughput carbon substrate utilization by M. ulcerans would help designing media to isolate and grow this pathogen. Furthermore, the presented data suggest that potential M. ulcerans environmental reservoirs might be related to micro-habitats where bacteria, fungi, algae and mollusks are abundant. This should be followed by targeted investigations in Buruli ulcer endemic regions.
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Affiliation(s)
- Dezemon Zingue
- Aix Marseille Univ, INSERM, CNRS, IRD, URMITE, Marseille, France
| | - Amar Bouam
- Aix Marseille Univ, INSERM, CNRS, IRD, URMITE, Marseille, France
| | - Muriel Militello
- Aix Marseille Univ, INSERM, CNRS, IRD, URMITE, Marseille, France
| | - Michel Drancourt
- Aix Marseille Univ, INSERM, CNRS, IRD, URMITE, Marseille, France
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Shubin M, Schaufler K, Tedin K, Vehkala M, Corander J. Identifying Multiple Potential Metabolic Cycles in Time-Series from Biolog Experiments. PLoS One 2016; 11:e0162276. [PMID: 27676629 PMCID: PMC5038949 DOI: 10.1371/journal.pone.0162276] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 08/20/2016] [Indexed: 11/26/2022] Open
Abstract
Biolog Phenotype Microarray (PM) is a technology allowing simultaneous screening of the metabolic behaviour of bacteria under a large number of different conditions. Bacteria may often undergo several cycles of metabolic activity during a Biolog experiment. We introduce a novel algorithm to identify these metabolic cycles in PM experimental data, thus increasing the potential of PM technology in microbiology. Our method is based on a statistical decomposition of the time-series measurements into a set of growth models. We show that the method is robust to measurement noise and captures accurately the biologically relevant signals from the data. Our implementation is made freely available as a part of an R package for PM data analysis and can be found at www.helsinki.fi/bsg/software/Biolog_Decomposition.
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Affiliation(s)
- Mikhail Shubin
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- * E-mail:
| | - Katharina Schaufler
- Institute of Microbiology and Epizootics, Freie Univerität Berlin, Berlin, Germany
| | - Karsten Tedin
- Institute of Microbiology and Epizootics, Freie Univerität Berlin, Berlin, Germany
| | - Minna Vehkala
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Jukka Corander
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- Faculty of Medicine, University of Oslo, Oslo, Norway
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Asmar S, Sassi M, Phelippeau M, Drancourt M. Inverse correlation between salt tolerance and host-adaptation in mycobacteria. BMC Res Notes 2016; 9:249. [PMID: 27129386 PMCID: PMC4850692 DOI: 10.1186/s13104-016-2054-y] [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: 11/18/2015] [Accepted: 04/20/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The genus Mycobacterium includes host-adapted organisms regarded as obligate and opportunistic pathogens and environmental organisms. Factors contributing to this wide range of adaptations are poorly known. RESULTS We studied the salt tolerance of 46 Mycobacterium species of medical interest. Representative strains of the Mycobacterium tuberculosis complex, Mycobacterium avium complex, Mycobacterium chelonae-abscessus complex, Mycobacterium ulcerans, Mycobacterium marinum, Mycobacterium lentiflavum, Mycobacterium fortuitum and Mycobacterium conceptionense were inoculated on Middlebrook 7H10 medium supplemented with 0-10% sodium chloride. Colonies were counted after 2-4 week incubation at the appropriate 30-37 °C temperature depending on the tested strain. Further comparative genomics was done on 15 Mycobacterium strains representing the spectrum of salt-tolerance of mycobacteria. Based on the results the different species were grouped according to their salt tolerance into a "salt-sensitive" group (growth up to ≤3% salt) containing the M. tuberculosis complex, Mycobacterium chelonae, Mycobacterium lentiflavum, Mycobacterium ulcerans and Mycobacterium marinum; a "salt-intermediate" group (growth between 4 and 6% salt) comprising Mycobacterium avium, Mycobacterium intracellulare, Mycobacterium chimaera and a "salt-resistant" group (growth up to >6%) comprising Mycobacterium homonissuis, Mycobacterium bolettii, Mycobacterium fortuitum and Mycobacterium conceptionense. Genomic analysis revealed that 290 genes were unique to species belonging to the salt-sensitive group; and that 15% were annotated as being functionally associated with the ESX secretion systems Pro-Glu and Pro-Pro-Glu family proteins. CONCLUSIONS In this work we found an inverse correlation between salt tolerance and host adaptation. We thus propose that salinity is one of the multiple factors determining the ecological niches of mycobacteria.
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Affiliation(s)
- Shady Asmar
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS, UMR 7278, IRD 198, Faculté de Médecine, Aix-Marseille Université, 27, Boulevard Jean Moulin, 13385, Marseille Cedex 5, France
| | | | - Michael Phelippeau
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS, UMR 7278, IRD 198, Faculté de Médecine, Aix-Marseille Université, 27, Boulevard Jean Moulin, 13385, Marseille Cedex 5, France
| | - Michel Drancourt
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS, UMR 7278, IRD 198, Faculté de Médecine, Aix-Marseille Université, 27, Boulevard Jean Moulin, 13385, Marseille Cedex 5, France.
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Dinarelli S, Girasole M, Kasas S, Longo G. Nanotools and molecular techniques to rapidly identify and fight bacterial infections. J Microbiol Methods 2016; 138:72-81. [PMID: 26806415 DOI: 10.1016/j.mimet.2016.01.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 01/13/2016] [Accepted: 01/13/2016] [Indexed: 12/22/2022]
Abstract
Reducing the emergence and spread of antibiotic-resistant bacteria is one of the major healthcare issues of our century. In addition to the increased mortality, infections caused by multi-resistant bacteria drastically enhance the healthcare costs, mainly because of the longer duration of illness and treatment. While in the last 20years, bacterial identification has been revolutionized by the introduction of new molecular techniques, the current phenotypic techniques to determine the susceptibilities of common Gram-positive and Gram-negative bacteria require at least two days from collection of clinical samples. Therefore, there is an urgent need for the development of new technologies to determine rapidly drug susceptibility in bacteria and to achieve faster diagnoses. These techniques would also lead to a better understanding of the mechanisms that lead to the insurgence of the resistance, greatly helping the quest for new antibacterial systems and drugs. In this review, we describe some of the tools most currently used in clinical and microbiological research to study bacteria and to address the challenge of infections. We discuss the most interesting advancements in the molecular susceptibility testing systems, with a particular focus on the many applications of the MALDI-TOF MS system. In the field of the phenotypic characterization protocols, we detail some of the most promising semi-automated commercial systems and we focus on some emerging developments in the field of nanomechanical sensors, which constitute a step towards the development of rapid and affordable point-of-care testing devices and techniques. While there is still no innovative technique that is capable of completely substituting for the conventional protocols and clinical practices, many exciting new experimental setups and tools could constitute the basis of the standard testing package of future microbiological tests.
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Affiliation(s)
- S Dinarelli
- Istituto di Struttura della Materia, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - M Girasole
- Istituto di Struttura della Materia, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - S Kasas
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Physique de la Matière Vivante, Lausanne, Switzerland; Département des Neurosciences Fondamentales, Université de Lausanne, Lausanne, Switzerland
| | - G Longo
- Istituto di Struttura della Materia, Consiglio Nazionale delle Ricerche, Rome, Italy.
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Orro A, Cappelletti M, D'Ursi P, Milanesi L, Di Canito A, Zampolli J, Collina E, Decorosi F, Viti C, Fedi S, Presentato A, Zannoni D, Di Gennaro P. Genome and Phenotype Microarray Analyses of Rhodococcus sp. BCP1 and Rhodococcus opacus R7: Genetic Determinants and Metabolic Abilities with Environmental Relevance. PLoS One 2015; 10:e0139467. [PMID: 26426997 PMCID: PMC4591350 DOI: 10.1371/journal.pone.0139467] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 09/14/2015] [Indexed: 11/17/2022] Open
Abstract
In this paper comparative genome and phenotype microarray analyses of Rhodococcus sp. BCP1 and Rhodococcus opacus R7 were performed. Rhodococcus sp. BCP1 was selected for its ability to grow on short-chain n-alkanes and R. opacus R7 was isolated for its ability to grow on naphthalene and on o-xylene. Results of genome comparison, including BCP1, R7, along with other Rhodococcus reference strains, showed that at least 30% of the genome of each strain presented unique sequences and only 50% of the predicted proteome was shared. To associate genomic features with metabolic capabilities of BCP1 and R7 strains, hundreds of different growth conditions were tested through Phenotype Microarray, by using Biolog plates and plates manually prepared with additional xenobiotic compounds. Around one-third of the surveyed carbon sources was utilized by both strains although R7 generally showed higher metabolic activity values compared to BCP1. Moreover, R7 showed broader range of nitrogen and sulphur sources. Phenotype Microarray data were combined with genomic analysis to genetically support the metabolic features of the two strains. The genome analysis allowed to identify some gene clusters involved in the metabolism of the main tested xenobiotic compounds. Results show that R7 contains multiple genes for the degradation of a large set of aromatic and PAHs compounds, while a lower variability in terms of genes predicted to be involved in aromatic degradation was found in BCP1. This genetic feature can be related to the strong genetic pressure exerted by the two different environment from which the two strains were isolated. According to this, in the BCP1 genome the smo gene cluster involved in the short-chain n-alkanes degradation, is included in one of the unique regions and it is not conserved in the Rhodococcus strains compared in this work. Data obtained underline the great potential of these two Rhodococcus spp. strains for biodegradation and environmental decontamination processes.
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Affiliation(s)
- Alessandro Orro
- Institute of Biomedical Technology, CNR, Segrate, Milano, Italy
| | - Martina Cappelletti
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | | | | | - Alessandra Di Canito
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy
| | - Jessica Zampolli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy; Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milano, Italy
| | - Elena Collina
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milano, Italy
| | - Francesca Decorosi
- Department of Agrifood Production and Environmental Sciences, University of Firenze, Firenze, Italy
| | - Carlo Viti
- Department of Agrifood Production and Environmental Sciences, University of Firenze, Firenze, Italy
| | - Stefano Fedi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | | | - Davide Zannoni
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Patrizia Di Gennaro
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy
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Correlation of Lactobacillus rhamnosus Genotypes and Carbohydrate Utilization Signatures Determined by Phenotype Profiling. Appl Environ Microbiol 2015; 81:5458-70. [PMID: 26048937 DOI: 10.1128/aem.00851-15] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 05/28/2015] [Indexed: 12/17/2022] Open
Abstract
Lactobacillus rhamnosus is a bacterial species commonly colonizing the gastrointestinal (GI) tract of humans and also frequently used in food products. While some strains have been studied extensively, physiological variability among isolates of the species found in healthy humans or their diet is largely unexplored. The aim of this study was to characterize the diversity of carbohydrate utilization capabilities of human isolates and food-derived strains of L. rhamnosus in relation to their niche of isolation and genotype. We investigated the genotypic and phenotypic diversity of 25 out of 65 L. rhamnosus strains from various niches, mainly human feces and fermented dairy products. Genetic fingerprinting of the strains by amplified fragment length polymorphism (AFLP) identified 11 distinct subgroups at 70% similarity and suggested niche enrichment within particular genetic clades. High-resolution carbohydrate utilization profiling (OmniLog) identified 14 carbon sources that could be used by all of the strains tested for growth, while the utilization of 58 carbon sources differed significantly between strains, enabling the stratification of L. rhamnosus strains into three metabolic clusters that partially correlate with the genotypic clades but appear uncorrelated with the strain's origin of isolation. Draft genome sequences of 8 strains were generated and employed in a gene-trait matching (GTM) analysis together with the publicly available genomes of L. rhamnosus GG (ATCC 53103) and HN001 for several carbohydrates that were distinct for the different metabolic clusters: l-rhamnose, cellobiose, l-sorbose, and α-methyl-d-glucoside. From the analysis, candidate genes were identified that correlate with l-sorbose and α-methyl-d-glucoside utilization, and the proposed function of these genes could be confirmed by heterologous expression in a strain lacking the genes. This study expands our insight into the phenotypic and genotypic diversity of the species L. rhamnosus and explores the relationships between specific carbohydrate utilization capacities and genotype and/or niche adaptation of this species.
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Novel functions of (p)ppGpp and Cyclic di-GMP in mycobacterial physiology revealed by phenotype microarray analysis of wild-type and isogenic strains of Mycobacterium smegmatis. Appl Environ Microbiol 2015; 81:2571-8. [PMID: 25636840 DOI: 10.1128/aem.03999-14] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The bacterial second messengers (p)ppGpp and bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) regulate important functions, such as transcription, virulence, biofilm formation, and quorum sensing. In mycobacteria, they regulate long-term survival during starvation, pathogenicity, and dormancy. Recently, a Pseudomonas aeruginosa strain lacking (p)ppGpp was shown to be sensitive to multiple classes of antibiotics and defective in biofilm formation. We were interested to find out whether Mycobacterium smegmatis strains lacking the gene for either (p)ppGpp synthesis (ΔrelMsm) or c-di-GMP synthesis (ΔdcpA) would display similar phenotypes. We used phenotype microarray technology to compare the growth of the wild-type and the knockout strains in the presence of several antibiotics. Surprisingly, the ΔrelMsm and ΔdcpA strains showed enhanced survival in the presence of many antibiotics, but they were defective in biofilm formation. These strains also displayed altered surface properties, like impaired sliding motility, rough colony morphology, and increased aggregation in liquid cultures. Biofilm formation and surface properties are associated with the presence of glycopeptidolipids (GPLs) in the cell walls of M. smegmatis. Thin-layer chromatography analysis of various cell wall fractions revealed that the levels of GPLs and polar lipids were reduced in the knockout strains. As a result, the cell walls of the knockout strains were significantly more hydrophobic than those of the wild type and the complemented strains. We hypothesize that reduced levels of GPLs and polar lipids may contribute to the antibiotic resistance shown by the knockout strains. Altogether, our data suggest that (p)ppGpp and c-di-GMP may be involved in the metabolism of glycopeptidolipids and polar lipids in M. smegmatis.
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Abstract
Metabolism underpins the physiology and pathogenesis of Mycobacterium tuberculosis. However, although experimental mycobacteriology has provided key insights into the metabolic pathways that are essential for survival and pathogenesis, determining the metabolic status of bacilli during different stages of infection and in different cellular compartments remains challenging. Recent advances-in particular, the development of systems biology tools such as metabolomics-have enabled key insights into the biochemical state of M. tuberculosis in experimental models of infection. In addition, their use to elucidate mechanisms of action of new and existing antituberculosis drugs is critical for the development of improved interventions to counter tuberculosis. This review provides a broad summary of mycobacterial metabolism, highlighting the adaptation of M. tuberculosis as specialist human pathogen, and discusses recent insights into the strategies used by the host and infecting bacillus to influence the outcomes of the host-pathogen interaction through modulation of metabolic functions.
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Affiliation(s)
- Digby F Warner
- Medical Research Council/National Health Laboratory Services/University of Cape Town Molecular Mycobacteriology Research Unit and Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine and Division of Medical Microbiology, University of Cape Town, Rondebosch 7700, South Africa
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Coscolla M, Gagneux S. Consequences of genomic diversity in Mycobacterium tuberculosis. Semin Immunol 2014; 26:431-44. [PMID: 25453224 PMCID: PMC4314449 DOI: 10.1016/j.smim.2014.09.012] [Citation(s) in RCA: 291] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 09/29/2014] [Accepted: 09/30/2014] [Indexed: 11/29/2022]
Abstract
The causative agent of human tuberculosis, Mycobacterium tuberculosis complex (MTBC), comprises seven phylogenetically distinct lineages associated with different geographical regions. Here we review the latest findings on the nature and amount of genomic diversity within and between MTBC lineages. We then review recent evidence for the effect of this genomic diversity on mycobacterial phenotypes measured experimentally and in clinical settings. We conclude that overall, the most geographically widespread Lineage 2 (includes Beijing) and Lineage 4 (also known as Euro-American) are more virulent than other lineages that are more geographically restricted. This increased virulence is associated with delayed or reduced pro-inflammatory host immune responses, greater severity of disease, and enhanced transmission. Future work should focus on the interaction between MTBC and human genetic diversity, as well as on the environmental factors that modulate these interactions.
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Affiliation(s)
- Mireia Coscolla
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland; University of Basel, Petersplatz 1, Basel 4003, Switzerland
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland; University of Basel, Petersplatz 1, Basel 4003, Switzerland.
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Baloni P, Padiadpu J, Singh A, Gupta KR, Chandra N. Identifying feasible metabolic routes in Mycobacterium smegmatis and possible alterations under diverse nutrient conditions. BMC Microbiol 2014; 14:276. [PMID: 25403821 PMCID: PMC4248442 DOI: 10.1186/s12866-014-0276-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 10/24/2014] [Indexed: 11/29/2022] Open
Abstract
Background Many studies on M. tuberculosis have emerged from using M. smegmatis MC2155 (Msm), since they share significant similarities and yet Msm is non-pathogenic and faster growing. Although several individual molecules have been studied from Msm, many questions remain open about its metabolism as a whole and its capability to be versatile. Adaptability and versatility are emergent properties of a system, warranting a molecular systems perspective to understand them. Results We identify feasible metabolic pathways in Msm in reference condition with transcriptome, phenotypic microarray, along with functional annotation of the genome. Together with transcriptome data, specific genes from a set of alternatives have been mapped onto different pathways. About 257 metabolic pathways can be considered to be feasible in Msm. Next, we probe cellular metabolism with an array of alternative carbon and nitrogen sources and identify those that are utilized and favour growth as well as those that do not support growth. In all, about 135 points in the entire metabolic map are probed. Analyzing growth patterns under these conditions, lead us to hypothesize different pathways that can become active in various conditions and possible alternate routes that may be induced, thus explaining the observed physiological adaptations. Conclusions The study provides the first detailed analysis of feasible pathways towards adaptability. We obtain mechanistic insights that explain observed phenotypic behaviour by studying gene-expression profiles and pathways inferred from the genome sequence. Comparison of transcriptome and phenome analysis of Msm and Mtb provides a rationale for understanding commonalities in metabolic adaptability. Electronic supplementary material The online version of this article (doi:10.1186/s12866-014-0276-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Priyanka Baloni
- Molecular Biophysics Unit, IISc, Bangalore, 560012, India. .,Department of Biochemistry, IISc, Bangalore, 560012, India.
| | - Jyothi Padiadpu
- Supercomputer Education and Research Centre, IISc, Bangalore, 560012, India. .,Department of Biochemistry, IISc, Bangalore, 560012, India.
| | - Anupam Singh
- Department of Biochemistry, IISc, Bangalore, 560012, India.
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Quereda JJ, Pucciarelli MG. Deletion of the membrane protein Lmo0412 increases the virulence of Listeria monocytogenes. Microbes Infect 2014; 16:623-32. [PMID: 25051038 DOI: 10.1016/j.micinf.2014.07.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 07/04/2014] [Accepted: 07/08/2014] [Indexed: 01/17/2023]
Abstract
Listeria monocytogenes is a facultative intracellular pathogen that causes gastroenteritis, meningitis, encephalitis and maternofetal infections. 20-30% of eubacterial ORFs are predicted to encode membrane proteins. The bacterial cytoplasmic membrane is a macromolecular structure, which plays a key role for the pathogenesis. Despite this, little knowledge exists regarding the function of cytoplasmic membrane proteins of Listeria during infection. Here, we investigated a predicted membrane protein of the pathogen L. monocytogenes, Lmo0412, of unknown function. Lmo0412 is only present in the Listeria genus and low conserved in the non-pathogenic species L. innocua. Bacterial fractionation and western blot analyses showed that Lmo0412 was only detectable in the membrane of L. monocytogenes EGDe during logarithmic growth phase. lmo0412 expression in L. monocytogenes was down-regulated during in vitro infection of JEG-3 epithelial cells. An L. monocytogenes mutant deficient in this membrane protein showed increased invasion of Caco-2 and NRK-49F host cells using in vitro infection models. Moreover, the lack of Lmo0412 in this deletion mutant increased the viable bacteria counts in the spleen and liver of mice compared to the wild type strain. Taken together, these data suggest a selective advantage conferred by the absence of Lmo0412 for the virulence of L. monocytogenes.
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Affiliation(s)
- Juan José Quereda
- Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain
| | - María Graciela Pucciarelli
- Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain; Departamento de Biología Molecular, Universidad Autónoma de Madrid. Centro de Biología Molecular 'Severo Ochoa'-Consejo Superior de Investigaciones Científicas (CBMSO-CSIC), 28049 Madrid, Spain.
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Lofthouse EK, Wheeler PR, Beste DJV, Khatri BL, Wu H, Mendum T, Kierzek AM, McFadden J. Systems-based approaches to probing metabolic variation within the Mycobacterium tuberculosis complex. PLoS One 2013; 8:e75913. [PMID: 24098743 PMCID: PMC3783153 DOI: 10.1371/journal.pone.0075913] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 08/16/2013] [Indexed: 01/11/2023] Open
Abstract
The Mycobacterium tuberculosis complex includes bovine and human strains of the tuberculosis bacillus, including Mycobacterium tuberculosis, Mycobacterium bovis and the Mycobacterium bovis BCG vaccine strain. M. bovis has evolved from a M. tuberculosis-like ancestor and is the ancestor of the BCG vaccine. The pathogens demonstrate distinct differences in virulence, host range and metabolism, but the role of metabolic differences in pathogenicity is poorly understood. Systems biology approaches have been used to investigate the metabolism of M. tuberculosis, but not to probe differences between tuberculosis strains. In this study genome scale metabolic networks of M. bovis and M. bovis BCG were constructed and interrogated, along with a M. tuberculosis network, to predict substrate utilisation, gene essentiality and growth rates. The models correctly predicted 87-88% of high-throughput phenotype data, 75-76% of gene essentiality data and in silico-predicted growth rates matched measured rates. However, analysis of the metabolic networks identified discrepancies between in silico predictions and in vitro data, highlighting areas of incomplete metabolic knowledge. Additional experimental studies carried out to probe these inconsistencies revealed novel insights into the metabolism of these strains. For instance, that the reduction in metabolic capability observed in bovine tuberculosis strains, as compared to M. tuberculosis, is not reflected by current genetic or enzymatic knowledge. Hence, the in silico networks not only successfully simulate many aspects of the growth and physiology of these mycobacteria, but also provide an invaluable tool for future metabolic studies.
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Affiliation(s)
- Emma K. Lofthouse
- Animal Health and Veterinary Laboratories Agency (Weybridge), Department for Bovine Tuberculosis, New Haw, Surrey, United Kingdom
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, Stag Hill, Guildford, Surrey, United Kingdom
| | - Paul R. Wheeler
- Animal Health and Veterinary Laboratories Agency (Weybridge), Department for Bovine Tuberculosis, New Haw, Surrey, United Kingdom
| | - Dany J. V. Beste
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, Stag Hill, Guildford, Surrey, United Kingdom
| | - Bhagwati L. Khatri
- Animal Health and Veterinary Laboratories Agency (Weybridge), Department for Bovine Tuberculosis, New Haw, Surrey, United Kingdom
| | - Huihai Wu
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, Stag Hill, Guildford, Surrey, United Kingdom
| | - Tom A. Mendum
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, Stag Hill, Guildford, Surrey, United Kingdom
| | - Andrzej M. Kierzek
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, Stag Hill, Guildford, Surrey, United Kingdom
| | - Johnjoe McFadden
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, Stag Hill, Guildford, Surrey, United Kingdom
- * E-mail:
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