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Sun CL, Pratama AA, Gazitúa MC, Cronin D, McGivern BB, Wainaina JM, Vik DR, Zayed AA, Bolduc B, Wrighton KC, Rich VI, Sullivan MB. Virus ecology and 7-year temporal dynamics across a permafrost thaw gradient. Environ Microbiol 2024; 26:e16665. [PMID: 39101434 DOI: 10.1111/1462-2920.16665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 05/16/2024] [Indexed: 08/06/2024]
Abstract
Soil microorganisms are pivotal in the global carbon cycle, but the viruses that affect them and their impact on ecosystems are less understood. In this study, we explored the diversity, dynamics, and ecology of soil viruses through 379 metagenomes collected annually from 2010 to 2017. These samples spanned the seasonally thawed active layer of a permafrost thaw gradient, which included palsa, bog, and fen habitats. We identified 5051 virus operational taxonomic units (vOTUs), doubling the known viruses for this site. These vOTUs were largely ephemeral within habitats, suggesting a turnover at the vOTU level from year to year. While the diversity varied by thaw stage and depth-related patterns were specific to each habitat, the virus communities did not significantly change over time. The abundance ratios of virus to host at the phylum level did not show consistent trends across the thaw gradient, depth, or time. To assess potential ecosystem impacts, we predicted hosts in silico and found viruses linked to microbial lineages involved in the carbon cycle, such as methanotrophy and methanogenesis. This included the identification of viruses of Candidatus Methanoflorens, a significant global methane contributor. We also detected a variety of potential auxiliary metabolic genes, including 24 carbon-degrading glycoside hydrolases, six of which are uniquely terrestrial. In conclusion, these long-term observations enhance our understanding of soil viruses in the context of climate-relevant processes and provide opportunities to explore their role in terrestrial carbon cycling.
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Affiliation(s)
- Christine L Sun
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, USA
- National Science Foundation EMERGE Biology Integration Institute, The Ohio State University, Columbus, USA
| | - Akbar Adjie Pratama
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, USA
- National Science Foundation EMERGE Biology Integration Institute, The Ohio State University, Columbus, USA
| | | | - Dylan Cronin
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, USA
- National Science Foundation EMERGE Biology Integration Institute, The Ohio State University, Columbus, USA
| | - Bridget B McGivern
- National Science Foundation EMERGE Biology Integration Institute, The Ohio State University, Columbus, USA
- Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - James M Wainaina
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, USA
| | - Dean R Vik
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, USA
- National Science Foundation EMERGE Biology Integration Institute, The Ohio State University, Columbus, USA
| | - Ahmed A Zayed
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, USA
- National Science Foundation EMERGE Biology Integration Institute, The Ohio State University, Columbus, USA
| | - Benjamin Bolduc
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, USA
- National Science Foundation EMERGE Biology Integration Institute, The Ohio State University, Columbus, USA
| | - Kelly C Wrighton
- National Science Foundation EMERGE Biology Integration Institute, The Ohio State University, Columbus, USA
- Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Virginia I Rich
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, USA
- National Science Foundation EMERGE Biology Integration Institute, The Ohio State University, Columbus, USA
- Byrd Polar and Climate Research Center, The Ohio State University, Columbus, Ohio, USA
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, USA
- National Science Foundation EMERGE Biology Integration Institute, The Ohio State University, Columbus, USA
- Byrd Polar and Climate Research Center, The Ohio State University, Columbus, Ohio, USA
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, Ohio, USA
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2
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Szabo E, Nagy B, Czajlik A, Komlodi T, Ozohanics O, Tretter L, Ambrus A. Mitochondrial Alpha-Keto Acid Dehydrogenase Complexes: Recent Developments on Structure and Function in Health and Disease. Subcell Biochem 2024; 104:295-381. [PMID: 38963492 DOI: 10.1007/978-3-031-58843-3_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
The present work delves into the enigmatic world of mitochondrial alpha-keto acid dehydrogenase complexes discussing their metabolic significance, enzymatic operation, moonlighting activities, and pathological relevance with links to underlying structural features. This ubiquitous family of related but diverse multienzyme complexes is involved in carbohydrate metabolism (pyruvate dehydrogenase complex), the citric acid cycle (α-ketoglutarate dehydrogenase complex), and amino acid catabolism (branched-chain α-keto acid dehydrogenase complex, α-ketoadipate dehydrogenase complex); the complexes all function at strategic points and also participate in regulation in these metabolic pathways. These systems are among the largest multienzyme complexes with at times more than 100 protein chains and weights ranging up to ~10 million Daltons. Our chapter offers a wealth of up-to-date information on these multienzyme complexes for a comprehensive understanding of their significance in health and disease.
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Affiliation(s)
- Eszter Szabo
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Balint Nagy
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Andras Czajlik
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Timea Komlodi
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Oliver Ozohanics
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Laszlo Tretter
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Attila Ambrus
- Department of Biochemistry, Semmelweis University, Budapest, Hungary.
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3
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Juliano BR, Keating JW, Li HW, Anders AG, Xie Z, Ruotolo BT. Development of an Automated, High-Throughput Methodology for Native Mass Spectrometry and Collision-Induced Unfolding. Anal Chem 2023; 95:16717-16724. [PMID: 37924308 PMCID: PMC11081713 DOI: 10.1021/acs.analchem.3c03788] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2023]
Abstract
Native ion mobility mass spectrometry (nIM-MS) has emerged as a useful technology for the rapid evaluation of biomolecular structures. When combined with collisional activation in a collision-induced unfolding (CIU) experiment, nIM-MS experimentation can be leveraged to gain greater insight into biomolecular conformation and stability. However, nIM-MS and CIU remain throughput limited due to nonautomated sample preparation and introduction. Here, we explore the use of a RapidFire robotic sample handling system to develop an automated, high-throughput methodology for nMS and CIU. We describe native RapidFire-MS (nRapidFire-MS) capable of performing online desalting and sample introduction in as little as 10 s per sample. When combined with CIU, our nRapidFire-MS approach can be used to collect CIU fingerprints in 30 s following desalting by using size exclusion chromatography cartridges. When compared to nMS and CIU data collected using standard approaches, ion signals recorded by nRapidFire-MS exhibit identical ion collision cross sections, indicating that the same conformational populations are tracked by the two approaches. Our data further suggest that nRapidFire-MS can be extended to study a variety of biomolecular classes, including proteins and protein complexes ranging from 5 to 300 kDa and oligonucleotides. Furthermore, nRapidFire-MS data acquired for biotherapeutics suggest that nRapidFire-MS has the potential to enable high-throughput nMS analyses of biopharmaceutical samples. We conclude by discussing the potential of nRapidFire-MS for enabling the development of future CIU assays capable of catalyzing breakthroughs in protein engineering, inhibitor discovery, and formulation development for biotherapeutics.
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Affiliation(s)
- Brock R Juliano
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Joseph W Keating
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Henry W Li
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Anna G Anders
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Zhuoer Xie
- Attribute Sciences, Process Development, Amgen, Thousand Oaks, California 91320, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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4
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Mishra S, Saito K. Clinically encountered growth phenotypes of tuberculosis-causing bacilli and their in vitro study: A review. Front Cell Infect Microbiol 2022; 12:1029111. [PMID: 36439231 PMCID: PMC9684195 DOI: 10.3389/fcimb.2022.1029111] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/20/2022] [Indexed: 07/11/2024] Open
Abstract
The clinical manifestations of tuberculosis (TB) vary widely in severity, site of infection, and outcomes of treatment-leading to simultaneous efforts to individualize therapy safely and to search for shorter regimens that can be successfully used across the clinical spectrum. In these endeavors, clinicians and researchers alike employ mycobacterial culture in rich media. However, even within the same patient, individual bacilli among the population can exhibit substantial variability in their culturability. Bacilli in vitro also demonstrate substantial heterogeneity in replication rate and cultivation requirements, as well as susceptibility to killing by antimicrobials. Understanding parallels in clinical, ex vivo and in vitro growth phenotype diversity may be key to identifying those phenotypes responsible for treatment failure, relapse, and the reactivation of bacilli that progresses TB infection to disease. This review briefly summarizes the current role of mycobacterial culture in the care of patients with TB and the ex vivo evidence of variability in TB culturability. We then discuss current advances in in vitro models that study heterogenous subpopulations within a genetically identical bulk culture, with an emphasis on the effect of oxidative stress on bacillary cultivation requirements. The review highlights the complexity that heterogeneity in mycobacterial growth brings to the interpretation of culture in clinical settings and research. It also underscores the intricacies present in the interplay between growth phenotypes and antimicrobial susceptibility. Better understanding of population dynamics and growth requirements over time and space promises to aid both the attempts to individualize TB treatment and to find uniformly effective therapies.
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Affiliation(s)
- Saurabh Mishra
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, United States
| | - Kohta Saito
- Department of Medicine, Weill Cornell Medicine, New York, NY, United States
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5
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Romano GE, Silva-Pereira TT, de Melo FM, Sisco MC, Banari AC, Zimpel CK, Soler-Camargo NC, Guimarães AMDS. Unraveling the metabolism of Mycobacterium caprae using comparative genomics. Tuberculosis (Edinb) 2022; 136:102254. [PMID: 36126496 DOI: 10.1016/j.tube.2022.102254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 08/01/2022] [Accepted: 08/25/2022] [Indexed: 11/19/2022]
Abstract
In our laboratory, Mycobacterium caprae has poor growth in standard medium (SM) 7H9-OADC supplemented with pyruvate and Tween-80. Our objectives were to identify mutations affecting M. caprae metabolism and use this information to design a culture medium to improve its growth. We selected 77 M. caprae genomes and sequenced M. caprae NLA000201913 used in our experiments. Mutations present in >95% of the strains compared to Mycobacterium tuberculosis H37Rv were analyzed in silico for their deleterious effects on proteins of metabolic pathways. Apart from the known defect in the pyruvate kinase, M. caprae has important lesions in enzymes of the TCA cycle, methylmalonyl cycle, B12 metabolism, and electron-transport chain. We provide evidence of enzymatic redundancy elimination and epistatic mutations, and possible production of toxic metabolites hindering M. caprae growth in vitro. A newly designed SM supplemented with l-glutamate allowed faster growth and increased final microbial mass of M. caprae. However, possible accumulation of metabolic waste-products and/or nutritional limitations halted M. caprae growth prior to a M. tuberculosis-like stationary phase. Our findings suggest that M. caprae relies on GABA and/or glyoxylate shunts for in vitro growth in routine media. The newly developed medium will improve experiments with this bacterium by allowing faster growth in vitro.
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Affiliation(s)
- Giovanni Emiddio Romano
- Laboratory of Applied Research in Mycobacteria (LaPAM), Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, 1374 Prof Lineu Prestes Avenue, Room 229, São Paulo, SP, 05508-000, Brazil.
| | - Taiana Tainá Silva-Pereira
- Laboratory of Applied Research in Mycobacteria (LaPAM), Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, 1374 Prof Lineu Prestes Avenue, Room 229, São Paulo, SP, 05508-000, Brazil.
| | - Filipe Menegatti de Melo
- Laboratory of Applied Research in Mycobacteria (LaPAM), Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, 1374 Prof Lineu Prestes Avenue, Room 229, São Paulo, SP, 05508-000, Brazil.
| | - Maria Carolina Sisco
- Laboratory of Applied Research in Mycobacteria (LaPAM), Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, 1374 Prof Lineu Prestes Avenue, Room 229, São Paulo, SP, 05508-000, Brazil.
| | - Alexandre Campos Banari
- Laboratory of Applied Research in Mycobacteria (LaPAM), Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, 1374 Prof Lineu Prestes Avenue, Room 229, São Paulo, SP, 05508-000, Brazil; Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, 87 Prof Dr Orlando Marques de Paiva Avenue, São Paulo, SP, 05508-270, Brazil.
| | - Cristina Kraemer Zimpel
- Laboratory of Applied Research in Mycobacteria (LaPAM), Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, 1374 Prof Lineu Prestes Avenue, Room 229, São Paulo, SP, 05508-000, Brazil; Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, 87 Prof Dr Orlando Marques de Paiva Avenue, São Paulo, SP, 05508-270, Brazil.
| | - Naila Cristina Soler-Camargo
- Laboratory of Applied Research in Mycobacteria (LaPAM), Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, 1374 Prof Lineu Prestes Avenue, Room 229, São Paulo, SP, 05508-000, Brazil; Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, 87 Prof Dr Orlando Marques de Paiva Avenue, São Paulo, SP, 05508-270, Brazil.
| | - Ana Marcia de Sá Guimarães
- Laboratory of Applied Research in Mycobacteria (LaPAM), Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, 1374 Prof Lineu Prestes Avenue, Room 229, São Paulo, SP, 05508-000, Brazil; Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University. 625 Harrison Street, West Lafayette, IN, 47907, USA.
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6
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Meireles DA, da Silva Neto JF, Domingos RM, Alegria TGP, Santos LCM, Netto LES. Ohr - OhrR, a neglected and highly efficient antioxidant system: Structure, catalysis, phylogeny, regulation, and physiological roles. Free Radic Biol Med 2022; 185:6-24. [PMID: 35452809 DOI: 10.1016/j.freeradbiomed.2022.04.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 03/09/2022] [Accepted: 04/02/2022] [Indexed: 12/24/2022]
Abstract
Ohrs (organic hydroperoxide resistance proteins) are antioxidant enzymes that play central roles in the response of microorganisms to organic peroxides. Here, we describe recent advances in the structure, catalysis, phylogeny, regulation, and physiological roles of Ohr proteins and of its transcriptional regulator, OhrR, highlighting their unique features. Ohr is extremely efficient in reducing fatty acid peroxides and peroxynitrite, two oxidants relevant in host-pathogen interactions. The highly reactive Cys residue of Ohr, named peroxidatic Cys (Cp), composes together with an arginine and a glutamate the catalytic triad. The catalytic cycle of Ohrs involves a condensation between a sulfenic acid (Cp-SOH) and the thiol of the second conserved Cys, leading to the formation of an intra-subunit disulfide bond, which is then reduced by dihydrolipoamide or lipoylated proteins. A structural switch takes place during catalysis, with the opening and closure of the active site by the so-called Arg-loop. Ohr is part of the Ohr/OsmC super-family that also comprises OsmC and Ohr-like proteins. Members of the Ohr, OsmC and Ohr-like subgroups present low sequence similarities among themselves, but share a high structural conservation, presenting two Cys residues in their active site. The pattern of gene expression is also distinct among members of the Ohr/OsmC subfamilies. The expression of ohr genes increases upon organic hydroperoxides treatment, whereas the signals for the upregulation of osmC are entry into the stationary phase and/or osmotic stress. For many ohr genes, the upregulation by organic hydroperoxides is mediated by OhrR, a Cys-based transcriptional regulator that only binds to its target DNAs in its reduced state. Since Ohrs and OhrRs are involved in virulence of some microorganisms and are absent in vertebrate and vascular plants, they may represent targets for novel therapeutic approaches based on the disruption of this key bacterial organic peroxide defense system.
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Affiliation(s)
- Diogo A Meireles
- Laboratório de Fisiologia e Bioquímica de Microrganismos (LFBM) da Universidade Estadual do Norte Fluminense Darcy Ribeiro, Brazil
| | - José F da Silva Neto
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos da Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo (FMRP-USP), Brazil
| | | | - Thiago G P Alegria
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, Brazil
| | - Lene Clara M Santos
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, Brazil
| | - Luis Eduardo S Netto
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, Brazil.
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7
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Harold LK, Jinich A, Hards K, Cordeiro A, Keighley LM, Cross A, McNeil MB, Rhee K, Cook GM. Deciphering functional redundancy and energetics of malate oxidation in mycobacteria. J Biol Chem 2022; 298:101859. [PMID: 35337802 PMCID: PMC9062433 DOI: 10.1016/j.jbc.2022.101859] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 03/20/2022] [Accepted: 03/21/2022] [Indexed: 02/07/2023] Open
Abstract
Oxidation of malate to oxaloacetate, catalyzed by either malate dehydrogenase (Mdh) or malate quinone oxidoreductase (Mqo), is a critical step of the tricarboxylic acid cycle. Both Mqo and Mdh are found in most bacterial genomes, but the level of functional redundancy between these enzymes remains unclear. A bioinformatic survey revealed that Mqo was not as widespread as Mdh in bacteria but that it was highly conserved in mycobacteria. We therefore used mycobacteria as a model genera to study the functional role(s) of Mqo and its redundancy with Mdh. We deleted mqo from the environmental saprophyte Mycobacterium smegmatis, which lacks Mdh, and found that Mqo was essential for growth on nonfermentable carbon sources. On fermentable carbon sources, the Δmqo mutant exhibited delayed growth and lowered oxygen consumption and secreted malate and fumarate as terminal end products. Furthermore, heterologous expression of Mdh from the pathogenic species Mycobacterium tuberculosis shortened the delayed growth on fermentable carbon sources and restored growth on nonfermentable carbon sources at a reduced growth rate. In M. tuberculosis, CRISPR interference of either mdh or mqo expression resulted in a slower growth rate compared to controls, which was further inhibited when both genes were knocked down simultaneously. These data reveal that exergonic Mqo activity powers mycobacterial growth under nonenergy limiting conditions and that endergonic Mdh activity complements Mqo activity, but at an energetic cost for mycobacterial growth. We propose Mdh is maintained in slow-growing mycobacterial pathogens for use under conditions such as hypoxia that require reductive tricarboxylic acid cycle activity.
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Affiliation(s)
- Liam K Harold
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand.
| | - Adrian Jinich
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Kiel Hards
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
| | - Alexandra Cordeiro
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Laura M Keighley
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Alec Cross
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Matthew B McNeil
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
| | - Kyu Rhee
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Gregory M Cook
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand.
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Abstract
There are many reactive intermediates found in metabolic pathways. Could these potentially toxic molecules be exploited for an organism's benefit? We propose that during certain microbial infections, the production of inherently reactive aldehydes by an infected host is a previously unappreciated innate immune defence mechanism. While there has been a significant focus on the effects of aldehydes on mammalian physiology, the idea that they might be exploited or purposefully induced to kill pathogens is new. Given that aldehydes are made as parts of metabolic programmes that accompany immune cell activation by the cytokine interferon-gamma (IFN-γ) during infections, we hypothesize that aldehydes are among the arsenal of IFN-γ-inducible effectors needed for pathogen control.
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Affiliation(s)
- K. Heran Darwin
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, USA
| | - Sarah A. Stanley
- Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, Berkeley, CA, USA,Division of Infectious Disease and Vaccinology, School of Public Health, University of California, Berkeley, CA, USA
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9
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CRISPR Interference Reveals That All- Trans-Retinoic Acid Promotes Macrophage Control of Mycobacterium tuberculosis by Limiting Bacterial Access to Cholesterol and Propionyl Coenzyme A. mBio 2022; 13:e0368321. [PMID: 35038923 PMCID: PMC8764544 DOI: 10.1128/mbio.03683-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Macrophages are a protective replicative niche for Mycobacterium tuberculosis (Mtb) but can kill the infecting bacterium when appropriately activated. To identify mechanisms of clearance, we compared levels of bacterial restriction by human macrophages after treatment with 26 compounds, including some currently in clinical trials for tuberculosis. All-trans-retinoic acid (ATRA), an active metabolite of vitamin A, drove the greatest increase in Mtb control. Bacterial clearance was transcriptionally and functionally associated with changes in macrophage cholesterol trafficking and lipid metabolism. To determine how these macrophage changes affected bacterial control, we performed the first Mtb CRISPR interference screen in an infection model, identifying Mtb genes specifically required to survive in ATRA-activated macrophages. These data showed that ATRA treatment starves Mtb of cholesterol and the downstream metabolite propionyl coenzyme A (propionyl-CoA). Supplementation with sources of propionyl-CoA, including cholesterol, abrogated the restrictive effect of ATRA. This work demonstrates that targeting the coupled metabolism of Mtb and the macrophage improves control of infection and that it is possible to genetically map the mode of bacterial death using CRISPR interference. IMPORTANCE Tuberculosis, caused by the bacterium Mycobacterium tuberculosis, is a leading cause of death due to infectious disease. Improving the immune response to tuberculosis holds promise for fighting the disease but is limited by our lack of knowledge as to how the immune system kills M. tuberculosis. Our research identifies a potent way to make relevant immune cells more effective at fighting M. tuberculosis and then uses paired human and bacterial genomic methods to determine the mechanism of that improved bacterial clearance.
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10
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Birhanu AG, Gómez-Muñoz M, Kalayou S, Riaz T, Lutter T, Yimer SA, Abebe M, Tønjum T. Proteome Profiling of Mycobacterium tuberculosis Cells Exposed to Nitrosative Stress. ACS OMEGA 2022; 7:3470-3482. [PMID: 35128256 PMCID: PMC8811941 DOI: 10.1021/acsomega.1c05923] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
Reactive nitrogen species (RNS) are secreted by human cells in response to infection by Mycobacterium tuberculosis (Mtb). Although RNS can kill Mtb under some circumstances, Mtb can adapt and survive in the presence of RNS by a process that involves modulation of gene expression. Previous studies focused primarily on stress-related changes in the Mtb transcriptome. This study unveils changes in the Mtb proteome in response to a sub-lethal dose of nitric oxide (NO) over several hours of exposure. Proteins were identified using liquid chromatography coupled with electrospray ionization mass spectrometry (LC-MS/MS). A total of 2911 Mtb proteins were identified, of which 581 were differentially abundant (DA) after exposure to NO in at least one of the four time points (30 min, 2 h, 6 h, and 20 h). The proteomic response to NO was marked by two phases, with few DA proteins in the early phase and a multitude of DA proteins in the later phase. The efflux pump Rv1687 stood out as being the only protein more abundant at all the time points and might play a role in the early protection of Mtb against nitrosative stress. These changes appeared to be compensatory in nature, contributing to iron homeostasis, energy metabolism, and other stress responses. This study thereby provides new insights into the response of Mtb to NO at the level of proteomics.
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Affiliation(s)
- Alemayehu Godana Birhanu
- Department
of Microbiology, University of Oslo, P.O. Box 4950, Nydalen, NO-0424 Oslo, Norway
- Institute
of Biotechnology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia
| | - Marta Gómez-Muñoz
- Department
of Microbiology, University of Oslo, P.O. Box 4950, Nydalen, NO-0424 Oslo, Norway
| | - Shewit Kalayou
- Department
of Microbiology, Oslo University Hospital, P.O. Box 4950, Nydalen, NO-0424 Oslo, Norway
- International
Center of Insect Physiology and Ecology (ICIPE), P.O. Box 30772-00100 Nairobi, Kenya
| | - Tahira Riaz
- Department
of Microbiology, University of Oslo, P.O. Box 4950, Nydalen, NO-0424 Oslo, Norway
| | - Timo Lutter
- Department
of Microbiology, University of Oslo, P.O. Box 4950, Nydalen, NO-0424 Oslo, Norway
| | - Solomon Abebe Yimer
- Department
of Microbiology, University of Oslo, P.O. Box 4950, Nydalen, NO-0424 Oslo, Norway
- Coalition
for Epidemic Preparedness Innovations (CEPI), P.O. Box 123, Torshov, 0412 Oslo, Norway
| | - Markos Abebe
- Armauer
Hansen Research Institute, Jimma Road, P.O. Box 1005 Addis Ababa, Ethiopia
| | - Tone Tønjum
- Department
of Microbiology, University of Oslo, P.O. Box 4950, Nydalen, NO-0424 Oslo, Norway
- Department
of Microbiology, Oslo University Hospital, P.O. Box 4950, Nydalen, NO-0424 Oslo, Norway
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Welte CU, de Graaf R, Dalcin Martins P, Jansen RS, Jetten MSM, Kurth JM. A novel methoxydotrophic metabolism discovered in the hyperthermophilic archaeon Archaeoglobus fulgidus. Environ Microbiol 2021; 23:4017-4033. [PMID: 33913565 PMCID: PMC8359953 DOI: 10.1111/1462-2920.15546] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/26/2021] [Accepted: 04/26/2021] [Indexed: 11/29/2022]
Abstract
Methoxylated aromatic compounds (MACs) are important components of lignin found in significant amounts in the subsurface. Recently, the methanogenic archaeon Methermicoccus shengliensis was shown to be able to use a variety of MACs during methoxydotrophic growth. After a molecular survey, we found that the hyperthermophilic non‐methanogenic archaeon Archaeoglobus fulgidus also encodes genes for a bacterial‐like demethoxylation system. In this study, we performed growth and metabolite analysis, and used transcriptomics to investigate the response of A. fulgidus during growth on MACs in comparison to growth on lactate. We observed that A. fulgidus converts MACs to their hydroxylated derivatives with CO2 as the main product and sulfate as electron acceptor. Furthermore, we could show that MACs improve the growth of A. fulgidus in the presence of organic substrates such as lactate. We also found evidence that other archaea such as Bathyarchaeota, Lokiarchaeota, Verstraetearchaeota, Korarchaeota, Helarchaeota and Nezhaarchaeota encode a demethoxylation system. In summary, we here describe the first non‐methanogenic archaeon with the ability to grow on MACs indicating that methoxydotrophic archaea might play a so far underestimated role in the global carbon cycle.
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Affiliation(s)
- Cornelia U Welte
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands.,Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, Utrecht, 3584 CS, The Netherlands.,Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
| | - Rob de Graaf
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
| | - Paula Dalcin Martins
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
| | - Robert S Jansen
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands.,Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, Utrecht, 3584 CS, The Netherlands.,Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
| | - Julia M Kurth
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands.,Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
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12
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Dong W, Nie X, Zhu H, Liu Q, Shi K, You L, Zhang Y, Fan H, Yan B, Niu C, Lyu LD, Zhao GP, Yang C. Mycobacterial fatty acid catabolism is repressed by FdmR to sustain lipogenesis and virulence. Proc Natl Acad Sci U S A 2021; 118:e2019305118. [PMID: 33853942 PMCID: PMC8072231 DOI: 10.1073/pnas.2019305118] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Host-derived fatty acids are an important carbon source for pathogenic mycobacteria during infection. How mycobacterial cells regulate the catabolism of fatty acids to serve the pathogenicity, however, remains unknown. Here, we identified a TetR-family transcriptional factor, FdmR, as the key regulator of fatty acid catabolism in the pathogen Mycobacterium marinum by combining use of transcriptomics, chromatin immunoprecipitation followed by sequencing, dynamic 13C-based flux analysis, metabolomics, and lipidomics. An M. marinum mutant deficient in FdmR was severely attenuated in zebrafish larvae and adult zebrafish. The mutant showed defective growth but high substrate consumption on fatty acids. FdmR was identified as a long-chain acyl-coenzyme A (acyl-CoA)-responsive repressor of genes involved in fatty acid degradation and modification. We demonstrated that FdmR functions as a valve to direct the flux of exogenously derived fatty acids away from β-oxidation toward lipid biosynthesis, thereby avoiding the overactive catabolism and accumulation of biologically toxic intermediates. Moreover, we found that FdmR suppresses degradation of long-chain acyl-CoAs endogenously synthesized through the type I fatty acid synthase. By modulating the supply of long-chain acyl-CoAs for lipogenesis, FdmR controls the abundance and chain length of virulence-associated lipids and mycolates and plays an important role in the impermeability of the cell envelope. These results reveal that despite the fact that host-derived fatty acids are used as an important carbon source, overactive catabolism of fatty acids is detrimental to mycobacterial cell growth and pathogenicity. This study thus presents FdmR as a potentially attractive target for chemotherapy.
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Affiliation(s)
- Wenyue Dong
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoqun Nie
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, China
| | - Hong Zhu
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, China
| | - Qingyun Liu
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115
| | - Kunxiong Shi
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/National Health Commission/Chinese Academy of Medical Sciences (MOE/NHC/CAMS), School of Basic Medical Sciences, Department of Microbiology, School of Life Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai 200000, China
| | - Linlin You
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Zhang
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, China
| | - Hongyan Fan
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/National Health Commission/Chinese Academy of Medical Sciences (MOE/NHC/CAMS), School of Basic Medical Sciences, Department of Microbiology, School of Life Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai 200000, China
| | - Bo Yan
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/National Health Commission/Chinese Academy of Medical Sciences (MOE/NHC/CAMS), School of Basic Medical Sciences, Department of Microbiology, School of Life Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai 200000, China
| | - Chen Niu
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/National Health Commission/Chinese Academy of Medical Sciences (MOE/NHC/CAMS), School of Basic Medical Sciences, Department of Microbiology, School of Life Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai 200000, China;
| | - Liang-Dong Lyu
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/National Health Commission/Chinese Academy of Medical Sciences (MOE/NHC/CAMS), School of Basic Medical Sciences, Department of Microbiology, School of Life Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai 200000, China;
| | - Guo-Ping Zhao
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, China
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/National Health Commission/Chinese Academy of Medical Sciences (MOE/NHC/CAMS), School of Basic Medical Sciences, Department of Microbiology, School of Life Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai 200000, China
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200032, China
| | - Chen Yang
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, China;
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13
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Abstract
Enzymes fuel the biochemical activities of all cells. Their substrates and products thus represent a potential window into the physiologic state of a cell. Metabolomics focuses on the global, or systems-level, study of small molecules in a given biological system and has thus provided an experimental tool with which to study cellular physiology, including the biochemistry within pathogenic microorganisms. While metabolomic studies of Mycobacterium tuberculosis are still in their infancy, recent studies have begun to deliver unique insights into the composition, organization, activity, and regulation of the bacterium's physiologic network not accessible by other approaches. Here, we outline practical methods for the culture, collection, and analysis of metabolomic samples from M. tuberculosis that emphasize minimally perturbing sample handling, broad and native metabolite recovery, and sensitive, biologically agnostic metabolite detection.
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Affiliation(s)
- Kyle A Planck
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
| | - Kyu Rhee
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA.
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14
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Choo SW, Rishik S, Wee WY. Comparative genome analyses of Mycobacteroides immunogenum reveals two potential novel subspecies. Microb Genom 2020; 6. [PMID: 33295861 PMCID: PMC8116688 DOI: 10.1099/mgen.0.000495] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mycobacteroides immunogenum is an emerging opportunistic pathogen implicated in nosocomial infections. Comparative genome analyses may provide better insights into its genomic structure, functions and evolution. The present analysis showed that M. immunogenum has an open pan-genome. Approximately 36.8% of putative virulence genes were identified in the accessory regions of M. immunogenum. Phylogenetic analyses revealed two potential novel subspecies of M. immunogenum, supported by evidence from ANIb (average nucleotide identity using blast) and GGDC (Genome to Genome Distance Calculator) analyses. We identified 74 genomic islands (GIs) in Subspecies 1 and 23 GIs in Subspecies 2. All Subspecies 2-harboured GIs were not found in Subspecies 1, indicating that they might have been acquired by Subspecies 2 after their divergence. Subspecies 2 has more defence genes than Subspecies 1, suggesting that it might be more resistant to the insertion of foreign DNA and probably explaining why Subspecies 2 has fewer GIs. Positive selection analysis suggest that M. immunogenum has a lower selection pressure compared to non-pathogenic mycobacteria. Thirteen genes were positively selected and many were involved in virulence.
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Affiliation(s)
- Siew Woh Choo
- College of Science and Technology, Wenzhou-Kean University, 88 Daxue Rd, Ouhai District Wenzhou, Zhejiang CN 325027, PR China
- *Correspondence: Siew Woh Choo,
| | - Shusruto Rishik
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Subang Jaya, Bandar Sunway, Selangor, MY 46150, Malaysia
| | - Wei Yee Wee
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Subang Jaya, Bandar Sunway, Selangor, MY 46150, Malaysia
- *Correspondence: Wei Yee Wee,
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15
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Velázquez-Fernández JB, Ferreira-Souza GHM, Rodríguez-Campos J, Aceves-Sánchez MDJ, Bravo-Madrigal J, Vallejo-Cardona AA, Flores-Valdez MA. Proteomic characterization of a second-generation version of the BCGΔBCG1419c vaccine candidate by means of electrospray-ionization quadrupole time-of-flight mass spectrometry. Pathog Dis 2020; 79:5986614. [PMID: 33201999 DOI: 10.1093/femspd/ftaa070] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 11/13/2020] [Indexed: 01/11/2023] Open
Abstract
Tuberculosis (TB) is the most important infectious disease worldwide, based on the number of new cases and deaths reported by the World Health Organization. Several vaccine candidates against TB have been characterized at preclinical and clinical levels. The BCGΔBCG1419c vaccine candidate, which lacks the BCG1419c gene that encodes for a c-di-GMP phosphodiesterase, provides improved efficacy against chronic TB, reactivation from latent-like infection and against chronic TB in the presence of type 2 diabetes in murine models. We previously reported that compared with wild type BCG, BCGΔBCG1419c changed levels of several proteins. Here, using a label-free proteomic approach, we confirmed that a novel, second-generation version of BCGΔBCG1419c maintains changes in antigenic proteins already reported, and here we further found differences in secreted proteins, as well as that this new BCGΔBCG1419c version modifies its production of proteins involved in redox and nitrogen/protein metabolism compared with wild type BCG. This work contributes to the proteomic characterization of a novel vaccine candidate that is more effective against TB than parental BCG in diverse murine models.
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Affiliation(s)
| | - Gustavo Henrique Martins Ferreira-Souza
- Mass Spectrometry Research & Development Laboratory, SpectraMass Limited, Campinas, São Paulo, Brazil. Rua Monteiro Lobato, 255 - Cidade Universitária, Campinas - SP, 13083-862, Brazil
| | - Jacobo Rodríguez-Campos
- Centro de Investigación y Asistencia en Tecnología y diseño del Estado de Jalisco (CIATEJ), A. C., Unidad de Servicios Analíticos y Metrológicos, Av. Normalistas 800, Col. Colinas de la Normal, 44270 Guadalajara, Jalisco, México
| | - Michel de Jesús Aceves-Sánchez
- Centro de Investigación y Asistencia en Tecnología y diseño del Estado de Jalisco (CIATEJ), A.C., Biotecnología Médica y Farmacéutica, Av. Normalistas 800, Col. Colinas de la Normal, 44270 Guadalajara, Jalisco, México
| | - Jorge Bravo-Madrigal
- Centro de Investigación y Asistencia en Tecnología y diseño del Estado de Jalisco (CIATEJ), A.C., Biotecnología Médica y Farmacéutica, Av. Normalistas 800, Col. Colinas de la Normal, 44270 Guadalajara, Jalisco, México
| | - Alba Adriana Vallejo-Cardona
- CONACYT-CIATEJ, Biotecnología Médica y Farmacéutica, Av. Normalistas 800, Col. Colinas de la Normal, 44270 Guadalajara, Jalisco, México
| | - Mario Alberto Flores-Valdez
- Centro de Investigación y Asistencia en Tecnología y diseño del Estado de Jalisco (CIATEJ), A.C., Biotecnología Médica y Farmacéutica, Av. Normalistas 800, Col. Colinas de la Normal, 44270 Guadalajara, Jalisco, México
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16
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Chen S, Teng T, Wen S, Zhang T, Huang H. The aceE involves in mycolic acid synthesis and biofilm formation in Mycobacterium smegmatis. BMC Microbiol 2020; 20:259. [PMID: 32811434 PMCID: PMC7437000 DOI: 10.1186/s12866-020-01940-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 08/11/2020] [Indexed: 11/26/2022] Open
Abstract
Background The integrity of cell wall structure is highly significant for the in vivo survival of mycobacteria. We hypothesized that changes in morphology may indicate changes in cell wall metabolism and identified an aceE gene mutant (aceE-mut) which presented a deficient colony morphology on 7H10 agar by screening transposon mutagenesis in Mycolicibacterium smegmatis, basonym Mycobacterium smegmatis (M. smegmatis). This study aimed to identify the functional role of aceE gene in cell wall biosynthesis in M. smegmatis. Results We observed that the colony morphology of aceE-mut was quite different, smaller and smoother on the solid culture medium than the wild-type (WT) strain during the transposon library screening of M. smegmatis. Notably, in contrast with the WT, which aggregates and forms biofilm, the aceE-mut lost its ability of growing aggregately and biofilm formation, which are two very important features of mycobacteria. The morphological changes in the aceE-mut strain were further confirmed by electron microscopy which indicated smoother and thinner cell envelope images in contrast with the rough morphology of WT strains. Additionally, the aceE-mut was more fragile to acidic stress and exhibited a pronounced defects in entering the macrophages as compared to the WT. The analysis of mycolic acid (MA) using LC-MS indicated deficiency of alpha-MA and epoxy-MA in aceE-mut strain whereas complementation of the aceE-mut with a wild-type aceE gene restored the composition of MA. Conclusions Over all, this study indicates that aceE gene plays a significant role in the mycolic acid synthesis and affects the colony morphology, biofilm formation of M. smegmatis and bacteria invasion of macrophage.
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Affiliation(s)
- Suting Chen
- National Clinical Laboratory on Tuberculosis, Beijing Key laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, 101149, China
| | - Tianlu Teng
- National Clinical Laboratory on Tuberculosis, Beijing Key laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, 101149, China
| | - Shuan Wen
- National Clinical Laboratory on Tuberculosis, Beijing Key laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, 101149, China
| | - Tingting Zhang
- National Clinical Laboratory on Tuberculosis, Beijing Key laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, 101149, China
| | - Hairong Huang
- National Clinical Laboratory on Tuberculosis, Beijing Key laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, 101149, China.
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17
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Domingos RM, Teixeira RD, Zeida A, Agudelo WA, Alegria TGP, da Silva Neto JF, Vieira PS, Murakami MT, Farah CS, Estrin DA, Netto LES. Substrate and Product-Assisted Catalysis: Molecular Aspects behind Structural Switches along Organic Hydroperoxide Resistance Protein Catalytic Cycle. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01257] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Renato M. Domingos
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo, Brazil
| | - Raphael D. Teixeira
- Departamento de Biociências, Instituto de Quı́mica, Universidade de São Paulo, 05508-000 Sao Paulo, Brazil
| | - Ari Zeida
- Departamento de Quı́mica Inorgánica Analı́tica y Quı́mica Fı́sica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
| | - William A. Agudelo
- Departamento de Quı́mica Inorgánica Analı́tica y Quı́mica Fı́sica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
| | - Thiago G. P. Alegria
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo, Brazil
| | - José F. da Silva Neto
- Departamento de Biologia Celular e Molecular e Bioagentes Biociências, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14040-900 São Paulo, Brazil
| | - Plínio S. Vieira
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP 13083-970, Brazil
| | - Mario T. Murakami
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP 13083-970, Brazil
| | - Chuck S. Farah
- Departamento de Biociências, Instituto de Quı́mica, Universidade de São Paulo, 05508-000 Sao Paulo, Brazil
| | - Dario A. Estrin
- Departamento de Quı́mica Inorgánica Analı́tica y Quı́mica Fı́sica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
| | - Luis E. S. Netto
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo, Brazil
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18
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Jenior ML, Moutinho TJ, Dougherty BV, Papin JA. Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments. PLoS Comput Biol 2020; 16:e1007099. [PMID: 32298268 PMCID: PMC7188308 DOI: 10.1371/journal.pcbi.1007099] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 04/28/2020] [Accepted: 02/24/2020] [Indexed: 11/18/2022] Open
Abstract
The metabolic responses of bacteria to dynamic extracellular conditions drives not only the behavior of single species, but also entire communities of microbes. Over the last decade, genome-scale metabolic network reconstructions have assisted in our appreciation of important metabolic determinants of bacterial physiology. These network models have been a powerful force in understanding the metabolic capacity that species may utilize in order to succeed in an environment. Increasingly, an understanding of context-specific metabolism is critical for elucidating metabolic drivers of larger phenotypes and disease. However, previous approaches to use network models in concert with omics data to better characterize experimental systems have met challenges due to assumptions necessary by the various integration platforms or due to large input data requirements. With these challenges in mind, we developed RIPTiDe (Reaction Inclusion by Parsimony and Transcript Distribution) which uses both transcriptomic abundances and parsimony of overall flux to identify the most cost-effective usage of metabolism that also best reflects the cell’s investments into transcription. Additionally, in biological samples where it is difficult to quantify specific growth conditions, it becomes critical to develop methods that require lower amounts of user intervention in order to generate accurate metabolic predictions. Utilizing a metabolic network reconstruction for the model organism Escherichia coli str. K-12 substr. MG1655 (iJO1366), we found that RIPTiDe correctly identifies context-specific metabolic pathway activity without supervision or knowledge of specific media conditions. We also assessed the application of RIPTiDe to in vivo metatranscriptomic data where E. coli was present at high abundances, and found that our approach also effectively predicts metabolic behaviors of host-associated bacteria. In the setting of human health, understanding metabolic changes within bacteria in environments where growth substrate availability is difficult to quantify can have large downstream impacts on our ability to elucidate molecular drivers of disease-associated dysbiosis across the microbiota. Our results indicate that RIPTiDe may have potential to provide understanding of context-specific metabolism of bacteria within complex communities. Transcriptomic analyses of bacteria have become instrumental to our understanding of their responses to changes in their environment. While traditional analyses have been informative, leveraging these datasets within genome-scale metabolic network reconstructions (GENREs) can provide greatly improved context for shifts in pathway utilization and downstream/upstream ramifications for changes in metabolic regulation. Many previous techniques for GENRE transcript integration have focused on creating maximum consensus with input datasets, but these approaches were recently shown to generate less accurate metabolic predictions than a transcript-agnostic method of flux minimization (pFBA), which identifies the most efficient/economic patterns of metabolism given certain growth constraints. Despite this success, growth conditions are not always easily quantifiable and highlights the need for novel platforms that build from these findings. Our new method, RIPTiDe, combines these concepts and utilizes overall minimization of flux weighted by transcriptomic analysis to identify the most energy efficient pathways to achieve growth that include more highly transcribed enzymes, without previous insight into extracellular conditions. Utilizing a well-studied GENRE from Escherichia coli, we demonstrate that this new approach correctly predicts patterns of metabolism utilizing a variety of both in vitro and in vivo transcriptomes. This platform could be important for revealing context-specific bacterial phenotypes in line with governing principles of adaptive evolution, that drive disease manifestation or interactions between microbes.
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Affiliation(s)
- Matthew L. Jenior
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
| | - Thomas J. Moutinho
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
| | - Bonnie V. Dougherty
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
| | - Jason A. Papin
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Medicine, Division of Infectious Diseases & International Health, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, Virginia, United States of America
- * E-mail:
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19
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Hards K, Adolph C, Harold LK, McNeil MB, Cheung CY, Jinich A, Rhee KY, Cook GM. Two for the price of one: Attacking the energetic-metabolic hub of mycobacteria to produce new chemotherapeutic agents. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 152:35-44. [PMID: 31733221 DOI: 10.1016/j.pbiomolbio.2019.11.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 11/12/2019] [Indexed: 12/25/2022]
Abstract
Cellular bioenergetics is an area showing promise for the development of new antimicrobials, antimalarials and cancer therapy. Enzymes involved in central carbon metabolism and energy generation are essential mediators of bacterial physiology, persistence and pathogenicity, lending themselves natural interest for drug discovery. In particular, succinate and malate are two major focal points in both the central carbon metabolism and the respiratory chain of Mycobacterium tuberculosis. Both serve as direct links between the citric acid cycle and the respiratory chain due to the quinone-linked reactions of succinate dehydrogenase, fumarate reductase and malate:quinone oxidoreductase. Inhibitors against these enzymes therefore hold the promise of disrupting two distinct, but essential, cellular processes at the same time. In this review, we discuss the roles and unique adaptations of these enzymes and critically evaluate the role that future inhibitors of these complexes could play in the bioenergetics target space.
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Affiliation(s)
- Kiel Hards
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 9054, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, 1042, Auckland, New Zealand.
| | - Cara Adolph
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 9054, Dunedin, New Zealand
| | - Liam K Harold
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 9054, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, 1042, Auckland, New Zealand
| | - Matthew B McNeil
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 9054, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, 1042, Auckland, New Zealand
| | - Chen-Yi Cheung
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 9054, Dunedin, New Zealand
| | - Adrian Jinich
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Kyu Y Rhee
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Gregory M Cook
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 9054, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, 1042, Auckland, New Zealand.
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20
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Rizvi A, Shankar A, Chatterjee A, More TH, Bose T, Dutta A, Balakrishnan K, Madugulla L, Rapole S, Mande SS, Banerjee S, Mande SC. Rewiring of Metabolic Network in Mycobacterium tuberculosis During Adaptation to Different Stresses. Front Microbiol 2019; 10:2417. [PMID: 31736886 PMCID: PMC6828651 DOI: 10.3389/fmicb.2019.02417] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 10/07/2019] [Indexed: 12/15/2022] Open
Abstract
Metabolic adaptation of Mycobacterium tuberculosis (M. tuberculosis) to microbicidal intracellular environment of host macrophages is fundamental to its pathogenicity. However, an in-depth understanding of metabolic adjustments through key reaction pathways and networks is limited. To understand how such changes occur, we measured the cellular metabolome of M. tuberculosis subjected to four microbicidal stresses using liquid chromatography-mass spectrometric multiple reactions monitoring (LC-MRM/MS). Overall, 87 metabolites were identified. The metabolites best describing the separation between stresses were identified through multivariate analysis. The coupling of the metabolite measurements with existing genome-scale metabolic model, and using constraint-based simulation led to several new concepts and unreported observations in M. tuberculosis; such as (i) the high levels of released ammonia as an adaptive response to acidic stress was due to increased flux through L-asparaginase rather than urease activity; (ii) nutrient starvation-induced anaplerotic pathway for generation of TCA intermediates from phosphoenolpyruvate using phosphoenolpyruvate kinase; (iii) quenching of protons through GABA shunt pathway or sugar alcohols as possible mechanisms of early adaptation to acidic and oxidative stresses; and (iv) usage of alternate cofactors by the same enzyme as a possible mechanism of rewiring metabolic pathways to overcome stresses. Besides providing new leads and important nodes that can be used for designing intervention strategies, the study advocates the strength of applying flux balance analyses coupled with metabolomics to get a global picture of complex metabolic adjustments.
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Affiliation(s)
- Arshad Rizvi
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Arvind Shankar
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., Pune, India
| | | | | | - Tungadri Bose
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., Pune, India
| | - Anirban Dutta
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., Pune, India
| | - Kannan Balakrishnan
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Lavanya Madugulla
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | | | - Sharmila S Mande
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., Pune, India
| | - Sharmistha Banerjee
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
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21
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Wagner T, Boyko A, Alzari PM, Bunik VI, Bellinzoni M. Conformational transitions in the active site of mycobacterial 2-oxoglutarate dehydrogenase upon binding phosphonate analogues of 2-oxoglutarate: From a Michaelis-like complex to ThDP adducts. J Struct Biol 2019; 208:182-190. [PMID: 31476368 DOI: 10.1016/j.jsb.2019.08.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 08/22/2019] [Accepted: 08/29/2019] [Indexed: 11/17/2022]
Abstract
Mycobacterial KGD, the thiamine diphosphate (ThDP)-dependent E1o component of the 2-oxoglutarate dehydrogenase complex (OGDHC), is known to undergo significant conformational changes during catalysis with two distinct conformational states, previously named as the early and late state. In this work, we employ two phosphonate analogues of 2-oxoglutarate (OG), i.e. succinyl phosphonate (SP) and phosphono ethyl succinyl phosphonate (PESP), as tools to isolate the first catalytic steps and understand the significance of conformational transitions for the enzyme regulation. The kinetics showed a more efficient inhibition of mycobacterial E1o by SP (Ki 0.043 ± 0.013 mM) than PESP (Ki 0.88 ± 0.28 mM), consistent with the different circular dichroism spectra of the corresponding complexes. PESP allowed us to get crystallographic snapshots of the Michaelis-like complex, the first one for 2-oxo acid dehydrogenases, followed by the covalent adduction of the inhibitor to ThDP, mimicking the pre-decarboxylation complex. In addition, covalent ThDP-phosphonate complexes obtained with both compounds by co-crystallization were in the late conformational state, probably corresponding to slowly dissociating enzyme-inhibitor complexes. We discuss the relevance of these findings in terms of regulatory features of the mycobacterial E1o enzymes, and in the perspective of developing tools for species-specific metabolic regulation.
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Affiliation(s)
- Tristan Wagner
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS, Université de Paris, F-75724 Paris, France
| | - Alexandra Boyko
- A.N. Belozersky Institute of Physicochemical Biology and Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russia
| | - Pedro M Alzari
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS, Université de Paris, F-75724 Paris, France
| | - Victoria I Bunik
- A.N. Belozersky Institute of Physicochemical Biology and Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russia
| | - Marco Bellinzoni
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS, Université de Paris, F-75724 Paris, France.
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22
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Metabolic principles of persistence and pathogenicity in Mycobacterium tuberculosis. Nat Rev Microbiol 2019; 16:496-507. [PMID: 29691481 DOI: 10.1038/s41579-018-0013-4] [Citation(s) in RCA: 137] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Metabolism was once relegated to the supply of energy and biosynthetic precursors, but it has now become clear that it is a specific mediator of nearly all physiological processes. In the context of microbial pathogenesis, metabolism has expanded outside its canonical role in bacterial replication. Among human pathogens, this expansion has emerged perhaps nowhere more visibly than for Mycobacterium tuberculosis, the causative agent of tuberculosis. Unlike most pathogens, M. tuberculosis has evolved within humans, which are both host and reservoir. This makes unrestrained replication and perpetual quiescence equally incompatible strategies for survival as a species. In this Review, we summarize recent work that illustrates the diversity of metabolic functions that not only enable M. tuberculosis to establish and maintain a state of chronic infection within the host but also facilitate its survival in the face of drug pressure and, ultimately, completion of its life cycle.
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23
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Baker JJ, Dechow SJ, Abramovitch RB. Acid Fasting: Modulation of Mycobacterium tuberculosis Metabolism at Acidic pH. Trends Microbiol 2019; 27:942-953. [PMID: 31324436 DOI: 10.1016/j.tim.2019.06.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/29/2019] [Accepted: 06/14/2019] [Indexed: 01/22/2023]
Abstract
Mycobacterium tuberculosis (Mtb) senses and adapts to acidic host environments during the course of pathogenesis. Mutants defective in acidic pH-dependent adaptations are often attenuated during macrophage or animal infections, supporting that these pathways are essential for pathogenesis and represent important new targets for drug discovery. This review examines a confluence of findings supporting that Mtb has restricted metabolism at acidic pH that results in the slowing of bacterial growth and changes in redox homeostasis. It is proposed that induction of the PhoPR regulon and anaplerotic metabolism, in concert with the restricted use of specific carbon sources, functions to counter reductive stress associated with acidic pH.
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Affiliation(s)
- Jacob J Baker
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Shelby J Dechow
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Robert B Abramovitch
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA.
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24
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Bunik VI. Redox-Driven Signaling: 2-Oxo Acid Dehydrogenase Complexes as Sensors and Transmitters of Metabolic Imbalance. Antioxid Redox Signal 2019; 30:1911-1947. [PMID: 30187773 DOI: 10.1089/ars.2017.7311] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
SIGNIFICANCE This article develops a holistic view on production of reactive oxygen species (ROS) by 2-oxo acid dehydrogenase complexes. Recent Advances: Catalytic and structural properties of the complexes and their components evolved to minimize damaging effects of side reactions, including ROS generation, simultaneously exploiting the reactions for homeostatic signaling. CRITICAL ISSUES Side reactions of the complexes, characterized in vitro, are analyzed in view of protein interactions and conditions in vivo. Quantitative data support prevalence of the forward 2-oxo acid oxidation over the backward NADH oxidation in feeding physiologically significant ROS production by the complexes. Special focus on interactions between the active sites within 2-oxo acid dehydrogenase complexes highlights the central relevance of the complex-bound thiyl radicals in regulation of and signaling by complex-generated ROS. The thiyl radicals arise when dihydrolipoyl residues of the complexes regenerate FADH2 from the flavin semiquinone coproduced with superoxide anion radical in 1e- oxidation of FADH2 by molecular oxygen. FUTURE DIRECTIONS Interaction of 2-oxo acid dehydrogenase complexes with thioredoxins (TRXs), peroxiredoxins, and glutaredoxins mediates scavenging of the thiyl radicals and ROS generated by the complexes, underlying signaling of disproportional availability of 2-oxo acids, CoA, and NAD+ in key metabolic branch points through thiol/disulfide exchange and medically important hypoxia-inducible factor, mammalian target of rapamycin (mTOR), poly (ADP-ribose) polymerase, and sirtuins. High reactivity of the coproduced ROS and thiyl radicals to iron/sulfur clusters and nitric oxide, peroxynitrite reductase activity of peroxiredoxins and transnitrosylating function of thioredoxin, implicate the side reactions of 2-oxo acid dehydrogenase complexes in nitric oxide-dependent signaling and damage.
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Affiliation(s)
- Victoria I Bunik
- 1 Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation.,2 Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russian Federation
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25
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Piacenza L, Trujillo M, Radi R. Reactive species and pathogen antioxidant networks during phagocytosis. J Exp Med 2019; 216:501-516. [PMID: 30792185 PMCID: PMC6400530 DOI: 10.1084/jem.20181886] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 01/04/2019] [Accepted: 02/04/2019] [Indexed: 11/23/2022] Open
Abstract
The generation of phagosomal cytotoxic reactive species (i.e., free radicals and oxidants) by activated macrophages and neutrophils is a crucial process for the control of intracellular pathogens. The chemical nature of these species, the reactions they are involved in, and the subsequent effects are multifaceted and depend on several host- and pathogen-derived factors that influence their production rates and catabolism inside the phagosome. Pathogens rely on an intricate and synergistic antioxidant armamentarium that ensures their own survival by detoxifying reactive species. In this review, we discuss the generation, kinetics, and toxicity of reactive species generated in phagocytes, with a focus on the response of macrophages to internalized pathogens and concentrating on Mycobacterium tuberculosis and Trypanosoma cruzi as examples of bacterial and parasitic infection, respectively. The ability of pathogens to deal with host-derived reactive species largely depends on the competence of their antioxidant networks at the onset of invasion, which in turn can tilt the balance toward pathogen survival, proliferation, and virulence over redox-dependent control of infection.
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Affiliation(s)
- Lucía Piacenza
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
- Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Madia Trujillo
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
- Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Rafael Radi
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
- Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
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26
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Chawla M, Mishra S, Anand K, Parikh P, Mehta M, Vij M, Verma T, Singh P, Jakkala K, Verma HN, AjitKumar P, Ganguli M, Narain Seshasayee AS, Singh A. Redox-dependent condensation of the mycobacterial nucleoid by WhiB4. Redox Biol 2018; 19:116-133. [PMID: 30149290 PMCID: PMC6111044 DOI: 10.1016/j.redox.2018.08.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/02/2018] [Accepted: 08/11/2018] [Indexed: 12/22/2022] Open
Abstract
Oxidative stress response in bacteria is mediated through coordination between the regulators of oxidant-remediation systems (e.g. OxyR, SoxR) and nucleoid condensation (e.g. Dps, Fis). However, these genetic factors are either absent or rendered non-functional in the human pathogen Mycobacterium tuberculosis (Mtb). Therefore, how Mtb organizes genome architecture and regulates gene expression to counterbalance oxidative imbalance is unknown. Here, we report that an intracellular redox-sensor, WhiB4, dynamically links genome condensation and oxidative stress response in Mtb. Disruption of WhiB4 affects the expression of genes involved in maintaining redox homeostasis, central metabolism, and respiration under oxidative stress. Notably, disulfide-linked oligomerization of WhiB4 in response to oxidative stress activates the protein’s ability to condense DNA. Further, overexpression of WhiB4 led to hypercondensation of nucleoids, redox imbalance and increased susceptibility to oxidative stress, whereas WhiB4 disruption reversed this effect. In accordance with the findings in vitro, ChIP-Seq data demonstrated non-specific binding of WhiB4 to GC-rich regions of the Mtb genome. Lastly, data indicate that WhiB4 deletion affected the expression of ~ 30% of genes preferentially bound by the protein, suggesting both direct and indirect effects on gene expression. We propose that WhiB4 structurally couples Mtb’s response to oxidative stress with genome organization and transcription. Genome condensation is involved in the management of oxidative stress in bacteria. A relation between the genome condensation and oxidative stress is unclear in Mtb. A redox sensor WhiB4 calibrates genome-condensation and antioxidants in Mtb. Over-expression of WhiB4 hyper-condensed genome and induced killing by oxidants. WhiB4 deficiency delayed genome condensation and promoted oxidative stress survival.
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Affiliation(s)
- Manbeena Chawla
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Saurabh Mishra
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Kushi Anand
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Pankti Parikh
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Mansi Mehta
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Manika Vij
- Department of Structural Biology, CSIR-Institute of Genomics and Integrative Biology, South Campus, Mathura Road, New Delhi 110020, India; Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India
| | - Taru Verma
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India; Centre for BioSystems Science and Engineering (BSSE), Indian Institute of Science, Bangalore 560012, India
| | - Parul Singh
- National Centre for Biological Science, Bangalore 560065, India; SASTRA University, Thanjavur 613401, Tamil Nadu, India
| | - Kishor Jakkala
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - H N Verma
- Jaipur National University, Jagatpura, Jaipur 302017, India
| | - Parthasarathi AjitKumar
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Munia Ganguli
- Department of Structural Biology, CSIR-Institute of Genomics and Integrative Biology, South Campus, Mathura Road, New Delhi 110020, India; Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India
| | | | - Amit Singh
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India.
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27
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Lee JJ, Lim J, Gao S, Lawson CP, Odell M, Raheem S, Woo J, Kang SH, Kang SS, Jeon BY, Eoh H. Glutamate mediated metabolic neutralization mitigates propionate toxicity in intracellular Mycobacterium tuberculosis. Sci Rep 2018; 8:8506. [PMID: 29855554 PMCID: PMC5981324 DOI: 10.1038/s41598-018-26950-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 05/23/2018] [Indexed: 11/09/2022] Open
Abstract
Metabolic networks in biological systems are interconnected, such that malfunctioning parts can be corrected by other parts within the network, a process termed adaptive metabolism. Unlike Bacillus Calmette-Guérin (BCG), Mycobacterium tuberculosis (Mtb) better manages its intracellular lifestyle by executing adaptive metabolism. Here, we used metabolomics and identified glutamate synthase (GltB/D) that converts glutamine to glutamate (Q → E) as a metabolic effort used to neutralize cytoplasmic pH that is acidified while consuming host propionate carbon through the methylcitrate cycle (MCC). Methylisocitrate lyase, the last step of the MCC, is intrinsically downregulated in BCG, leading to obstruction of carbon flux toward central carbon metabolism, accumulation of MCC intermediates, and interference with GltB/D mediated neutralizing activity against propionate toxicity. Indeed, vitamin B12 mediated bypass MCC and additional supplement of glutamate led to selectively correct the phenotypic attenuation in BCG and restore the adaptive capacity of BCG to the similar level of Mtb phenotype. Collectively, a defective crosstalk between MCC and Q → E contributes to attenuation of intracellular BCG. Furthermore, GltB/D inhibition enhances the level of propionate toxicity in Mtb. Thus, these findings revealed a new adaptive metabolism and propose GltB/D as a synergistic target to improve the antimicrobial outcomes of MCC inhibition in Mtb.
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Affiliation(s)
- Jae Jin Lee
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Juhyeon Lim
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Shengjia Gao
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Christopher P Lawson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, G4 0RE, United Kingdom
| | - Mark Odell
- School of Life Sciences, University of Lincoln, Brayford Pool, Lincoln, LN6 7TS, United Kingdom.,Department of Life Sciences, Faculty of Science and Technology, University of Westminster, W1W 6UV, London, United Kingdom
| | - Saki Raheem
- Department of Life Sciences, Faculty of Science and Technology, University of Westminster, W1W 6UV, London, United Kingdom
| | - JeongIm Woo
- Department of Biomedical Laboratory Science, College of Health Science, Yonsei University, Wonju, 26493, Korea
| | - Sung-Ho Kang
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Shin-Seok Kang
- Chungbuk Veterinary Service Laboratory, 380-230, Chungju, Republic of Korea
| | - Bo-Young Jeon
- Department of Biomedical Laboratory Science, College of Health Science, Yonsei University, Wonju, 26493, Korea
| | - Hyungjin Eoh
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.
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28
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Nieto R LM, Mehaffy C, Islam MN, Fitzgerald B, Belisle J, Prenni J, Dobos K. Biochemical Characterization of Isoniazid-resistant Mycobacterium tuberculosis: Can the Analysis of Clonal Strains Reveal Novel Targetable Pathways? Mol Cell Proteomics 2018; 17:1685-1701. [PMID: 29844232 DOI: 10.1074/mcp.ra118.000821] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Indexed: 01/01/2023] Open
Abstract
Tuberculosis (TB) continues to be an important public health threat worldwide, due in part to drug resistant Mycobacterium tuberculosis (Mtb) strains. The United States recently reported a shortage of isoniazid (INH), which could drive higher INH resistance rates. Changes in the Mtb proteome before and after acquisition of INH resistance in a clean genetic background remain understudied and may elucidate alternate drug targets. Here, we focused on Mtb clonal strains to characterize the consequences of INH resistance on mycobacterial metabolism. Proteomic analysis was conducted by liquid-chromatography tandem mass spectrometry (LC-MS/MS) of cellular and secreted fractions, followed by a normalized spectral counting (NSAF) analysis (data are available via ProteomeXchange with identifier PXD009549). Two different Mtb clonal pairs representing a specific genetic lineage (one clinical and one generated in the laboratory) but sharing a katG mutation associated with INH resistance, were used in our analysis. Overall, we found 26 Mtb proteins with altered abundances after acquisition of INH resistance across both Mtb genetic lineages studied. These proteins were involved in ATP synthesis, lipid metabolism, regulatory events, and virulence, detoxification, and adaptation processes. Proteomic findings were validated by Western blotting analyses whenever possible. Mycolic acid (MA) analysis through LC/MS in the clonal Mtb pairs did not reveal a common trend in the alteration of these fatty acids across both INHr strains but revealed a significant reduction in levels of the two more abundant α-MA features in the clinical INHr strain. Interestingly, the clinical clonal pair demonstrated more variation in the abundance of the proteins involved in the FAS II pathway. Together, the proteomic and lipidomic data highlight the identification of potential drug targets such as alternative lipid biosynthetic pathways that may be exploited to combat clinically relevant Mtb INHr strains.
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Affiliation(s)
| | | | - M Nurul Islam
- From the ‡Department of Microbiology, Immunology and Pathology
| | | | - John Belisle
- From the ‡Department of Microbiology, Immunology and Pathology
| | - Jessica Prenni
- §Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, CO
| | - Karen Dobos
- From the ‡Department of Microbiology, Immunology and Pathology,
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29
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Negri A, Javidnia P, Mu R, Zhang X, Vendome J, Gold B, Roberts J, Barman D, Ioerger T, Sacchettini JC, Jiang X, Burns-Huang K, Warrier T, Ling Y, Warren JD, Oren DA, Beuming T, Wang H, Wu J, Li H, Rhee KY, Nathan CF, Liu G, Somersan-Karakaya S. Identification of a Mycothiol-Dependent Nitroreductase from Mycobacterium tuberculosis. ACS Infect Dis 2018; 4:771-787. [PMID: 29465985 PMCID: PMC5952258 DOI: 10.1021/acsinfecdis.7b00111] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
![]()
The success of Mycobacterium tuberculosis (Mtb) as a pathogen depends on
the redundant and complex mechanisms it has evolved for resisting
nitrosative and oxidative stresses inflicted by host immunity. Improving
our understanding of these defense pathways can reveal vulnerable
points in Mtb pathogenesis. In this study, we combined genetic, structural,
computational, biochemical, and biophysical approaches to identify
a novel enzyme class represented by Rv2466c. We show that Rv2466c
is a mycothiol-dependent nitroreductase of Mtb and can reduce the
nitro group of a novel mycobactericidal compound using mycothiol as
a cofactor. In addition to its function as a nitroreductase, Rv2466c
confers partial protection to menadione stress.
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Affiliation(s)
- Ana Negri
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Prisca Javidnia
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065, United States
| | | | | | - Jeremie Vendome
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | | | | | | | | | | | | | | | | | | | | | - Deena A. Oren
- Structural Biology Resource Center, Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Thijs Beuming
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | | | | | | | - Kyu Y. Rhee
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065, United States
| | | | | | - Selin Somersan-Karakaya
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065, United States
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30
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Baker JJ, Abramovitch RB. Genetic and metabolic regulation of Mycobacterium tuberculosis acid growth arrest. Sci Rep 2018; 8:4168. [PMID: 29520087 PMCID: PMC5843633 DOI: 10.1038/s41598-018-22343-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 02/21/2018] [Indexed: 01/02/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) senses and adapts to acidic environments during the course of infection. Acidic pH-dependent adaptations include the induction of metabolic genes associated with anaplerosis and growth arrest on specific carbon sources. Here we report that deletion of isocitrate lyase or phosphoenolpyruvate carboxykinase results in reduced growth at acidic pH and altered metabolite profiles, supporting that remodeling of anaplerotic metabolism is required for pH-dependent adaptation. Mtb cultured at pH 5.7 in minimal medium containing glycerol as a single carbon source exhibits an acid growth arrest phenotype, where the bacterium is non-replicating but viable and metabolically active. The bacterium assimilates and metabolizes glycerol and maintains ATP pools during acid growth arrest and becomes tolerant to detergent stress and the antibiotics isoniazid and rifampin. A forward genetic screen identified mutants that do not arrest their growth at acidic pH, including four enhanced acid growth (eag) mutants with three distinct mutations in the proline-proline-glutamate (PPE) gene MT3221 (also named ppe51). Overexpression of the MT3221(S211R) variant protein in wild type Mtb results in enhanced acid growth and reduced drug tolerance. These findings support that acid growth arrest is a genetically controlled, adaptive process and not simply a physiological limitation associated with acidic pH.
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Affiliation(s)
- Jacob J Baker
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, 48824, United States
| | - Robert B Abramovitch
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, 48824, United States.
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31
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Allosteric pyruvate kinase-based "logic gate" synergistically senses energy and sugar levels in Mycobacterium tuberculosis. Nat Commun 2017; 8:1986. [PMID: 29215013 PMCID: PMC5719368 DOI: 10.1038/s41467-017-02086-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 11/06/2017] [Indexed: 01/16/2023] Open
Abstract
Pyruvate kinase (PYK) is an essential glycolytic enzyme that controls glycolytic flux and is critical for ATP production in all organisms, with tight regulation by multiple metabolites. Yet the allosteric mechanisms governing PYK activity in bacterial pathogens are poorly understood. Here we report biochemical, structural and metabolomic evidence that Mycobacterium tuberculosis (Mtb) PYK uses AMP and glucose-6-phosphate (G6P) as synergistic allosteric activators that function as a molecular "OR logic gate" to tightly regulate energy and glucose metabolism. G6P was found to bind to a previously unknown site adjacent to the canonical site for AMP. Kinetic data and structural network analysis further show that AMP and G6P work synergistically as allosteric activators. Importantly, metabolome profiling in the Mtb surrogate, Mycobacterium bovis BCG, reveals significant changes in AMP and G6P levels during nutrient deprivation, which provides insights into how a PYK OR gate would function during the stress of Mtb infection.
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Nathan C. Kunkel Lecture: Fundamental immunodeficiency and its correction. J Exp Med 2017; 214:2175-2191. [PMID: 28701368 PMCID: PMC5551579 DOI: 10.1084/jem.20170637] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 06/27/2017] [Accepted: 06/27/2017] [Indexed: 02/05/2023] Open
Abstract
"Fundamental immunodeficiency" is the inability of the encoded immune system to protect an otherwise healthy host from every infection that could threaten its life. In contrast to primary immunodeficiencies, fundamental immunodeficiency is not rare but nearly universal. It results not from variation in a given host gene but from the rate and extent of variation in the genes of other organisms. The remedy for fundamental immunodeficiency is "adopted immunity," not to be confused with adaptive or adoptive immunity. Adopted immunity arises from four critical societal contributions to the survival of the human species: sanitation, nutrition, vaccines, and antimicrobial agents. Immunologists have a great deal to contribute to the development of vaccines and antimicrobial agents, but they have focused chiefly on vaccines, and vaccinology is thriving. In contrast, the effect of antimicrobial agents in adopted immunity, although fundamental, is fragile and failing. Immunologists can aid the development of sorely needed antimicrobial agents, and the study of antimicrobial agents can help immunologists discover targets and mechanisms of host immunity.
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Affiliation(s)
- Carl Nathan
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY
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Mishra S, Shukla P, Bhaskar A, Anand K, Baloni P, Jha RK, Mohan A, Rajmani RS, Nagaraja V, Chandra N, Singh A. Efficacy of β-lactam/β-lactamase inhibitor combination is linked to WhiB4-mediated changes in redox physiology of Mycobacterium tuberculosis. eLife 2017; 6:e25624. [PMID: 28548640 PMCID: PMC5473688 DOI: 10.7554/elife.25624] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 05/24/2017] [Indexed: 12/15/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) expresses a broad-spectrum β-lactamase (BlaC) that mediates resistance to one of the highly effective antibacterials, β-lactams. Nonetheless, β-lactams showed mycobactericidal activity in combination with β-lactamase inhibitor, clavulanate (Clav). However, the mechanistic aspects of how Mtb responds to β-lactams such as Amoxicillin in combination with Clav (referred as Augmentin [AG]) are not clear. Here, we identified cytoplasmic redox potential and intracellular redox sensor, WhiB4, as key determinants of mycobacterial resistance against AG. Using computer-based, biochemical, redox-biosensor, and genetic strategies, we uncovered a functional linkage between specific determinants of β-lactam resistance (e.g. β-lactamase) and redox potential in Mtb. We also describe the role of WhiB4 in coordinating the activity of β-lactamase in a redox-dependent manner to tolerate AG. Disruption of WhiB4 enhances AG tolerance, whereas overexpression potentiates AG activity against drug-resistant Mtb. Our findings suggest that AG can be exploited to diminish drug-resistance in Mtb through redox-based interventions.
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Affiliation(s)
- Saurabh Mishra
- Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India
| | - Prashant Shukla
- Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | | | - Kushi Anand
- Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India
| | - Priyanka Baloni
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Rajiv Kumar Jha
- Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India
| | - Abhilash Mohan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Raju S Rajmani
- Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India
| | - Valakunja Nagaraja
- Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Amit Singh
- Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India
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PknG senses amino acid availability to control metabolism and virulence of Mycobacterium tuberculosis. PLoS Pathog 2017; 13:e1006399. [PMID: 28545104 PMCID: PMC5448819 DOI: 10.1371/journal.ppat.1006399] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 05/30/2017] [Accepted: 05/04/2017] [Indexed: 11/19/2022] Open
Abstract
Sensing and response to changes in nutrient availability are essential for the lifestyle of environmental and pathogenic bacteria. Serine/threonine protein kinase G (PknG) is required for virulence of the human pathogen Mycobacterium tuberculosis, and its putative substrate GarA regulates the tricarboxylic acid cycle in M. tuberculosis and other Actinobacteria by protein-protein binding. We sought to understand the stimuli that lead to phosphorylation of GarA, and the roles of this regulatory system in pathogenic and non-pathogenic bacteria. We discovered that M. tuberculosis lacking garA was severely attenuated in mice and macrophages and furthermore that GarA lacking phosphorylation sites failed to restore the growth of garA deficient M. tuberculosis in macrophages. Additionally we examined the impact of genetic disruption of pknG or garA upon protein phosphorylation, nutrient utilization and the intracellular metabolome. We found that phosphorylation of GarA requires PknG and depends on nutrient availability, with glutamate and aspartate being the main stimuli. Disruption of pknG or garA caused opposing effects on metabolism: a defect in glutamate catabolism or depletion of intracellular glutamate, respectively. Strikingly, disruption of the phosphorylation sites of GarA was sufficient to recapitulate defects caused by pknG deletion. The results suggest that GarA is a cellular target of PknG and the metabolomics data demonstrate that the function of this signaling system is in metabolic regulation. This function in amino acid homeostasis is conserved amongst the Actinobacteria and provides an example of the close relationship between metabolism and virulence.
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Ziveri J, Barel M, Charbit A. Importance of Metabolic Adaptations in Francisella Pathogenesis. Front Cell Infect Microbiol 2017; 7:96. [PMID: 28401066 PMCID: PMC5368251 DOI: 10.3389/fcimb.2017.00096] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 03/13/2017] [Indexed: 01/25/2023] Open
Abstract
Francisella tularensis is a highly infectious Gram-negative bacterium and the causative agent of the zoonotic disease tularemia. This bacterial pathogen can infect a broad variety of animal species and can be transmitted to humans in numerous ways with various clinical outcomes. Although, Francisella possesses the capacity to infect numerous mammalian cell types, the macrophage constitutes the main intracellular niche, used for in vivo bacterial dissemination. To survive and multiply within infected macrophages, Francisella must imperatively escape from the phagosomal compartment. In the cytosol, the bacterium needs to control the host innate immune response and adapt its metabolism to this nutrient-restricted niche. Our laboratory has shown that intracellular Francisella mainly relied on host amino acid as major gluconeogenic substrates and provided evidence that the host metabolism was also modified upon Francisella infection. We will review here our current understanding of how Francisella copes with the available nutrient sources provided by the host cell during the course of infection.
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Affiliation(s)
- Jason Ziveri
- Sorbonne Paris Cité, Université Paris DescartesParis, France; Institut National de la Santé et de la Recherche Médicale U1151 - Centre National de la Recherche Scientifique UMR 8253, Institut Necker-Enfants Malades, Team 11: Pathogenesis of Systemic InfectionsParis, France
| | - Monique Barel
- Sorbonne Paris Cité, Université Paris DescartesParis, France; Institut National de la Santé et de la Recherche Médicale U1151 - Centre National de la Recherche Scientifique UMR 8253, Institut Necker-Enfants Malades, Team 11: Pathogenesis of Systemic InfectionsParis, France
| | - Alain Charbit
- Sorbonne Paris Cité, Université Paris DescartesParis, France; Institut National de la Santé et de la Recherche Médicale U1151 - Centre National de la Recherche Scientifique UMR 8253, Institut Necker-Enfants Malades, Team 11: Pathogenesis of Systemic InfectionsParis, France
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36
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Ruecker N, Jansen R, Trujillo C, Puckett S, Jayachandran P, Piroli GG, Frizzell N, Molina H, Rhee KY, Ehrt S. Fumarase Deficiency Causes Protein and Metabolite Succination and Intoxicates Mycobacterium tuberculosis. Cell Chem Biol 2017; 24:306-315. [PMID: 28219662 DOI: 10.1016/j.chembiol.2017.01.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Revised: 12/07/2016] [Accepted: 01/19/2017] [Indexed: 12/22/2022]
Abstract
Enzymes of central carbon metabolism are essential mediators of Mycobacterium tuberculosis (Mtb) physiology and pathogenicity, but are often perceived to lack sufficient species selectivity to be pursued as potential drug targets. Fumarase (Fum) is an enzyme of the canonical tricarboxylic acid cycle and is dispensable in many organisms. Transposon mutagenesis studies in Mtb, however, indicate that Fum is required for optimal growth. Here, we report the generation and characterization of a genetically engineered Mtb strain in which Fum expression is conditionally regulated. This revealed that Fum deficiency is bactericidal in vitro and during both the acute and chronic phases of mouse infection. This essentiality is linked to marked accumulations of fumarate resulting in protein and metabolite succination, a covalent modification of cysteine thiol residues. These results identify Mtb Fum as a potentially species-specific drug target whose inactivation may kill Mtb through a covalently irreversible form of metabolic toxicity.
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Affiliation(s)
- Nadine Ruecker
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Robert Jansen
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Carolina Trujillo
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Susan Puckett
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Pradeepa Jayachandran
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Gerardo G Piroli
- Department of Pharmacology, Physiology & Neuroscience, School of Medicine, University of South Carolina, Columbia, SC 29209, USA
| | - Norma Frizzell
- Department of Pharmacology, Physiology & Neuroscience, School of Medicine, University of South Carolina, Columbia, SC 29209, USA
| | - Henrik Molina
- Proteomics Resource Center, Rockefeller University, New York, NY 10065, USA
| | - Kyu Y Rhee
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10065, USA.
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37
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Emerging Approaches to Tuberculosis Drug Development: At Home in the Metabolome. Trends Pharmacol Sci 2017; 38:393-405. [PMID: 28169001 DOI: 10.1016/j.tips.2017.01.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 01/06/2017] [Accepted: 01/09/2017] [Indexed: 01/24/2023]
Abstract
Once considered a crowning achievement of modern drug development, tuberculosis (TB) chemotherapy has proven increasingly unable to keep pace with the spread of the pandemic and rise of drug resistance. Efforts to revive the TB drug development pipeline have, in the meantime, faltered. Closer analysis reveals key experimental deficiencies that have hindered our ability to 'reverse engineer' knowledge of antibiotic mechanisms into rational drug development. Here, we discuss the emerging potential of metabolomics; the systems level study of small molecule metabolites, to help overcome these gaps and serve as a unique biochemical bridge between the phenotypic properties of chemical compounds and biological targets.
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38
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Hartman TE, Wang Z, Jansen RS, Gardete S, Rhee KY. Metabolic Perspectives on Persistence. Microbiol Spectr 2017; 5:10.1128/microbiolspec.TBTB2-0026-2016. [PMID: 28155811 PMCID: PMC5302851 DOI: 10.1128/microbiolspec.tbtb2-0026-2016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Indexed: 02/07/2023] Open
Abstract
Accumulating evidence has left little doubt about the importance of persistence or metabolism in the biology and chemotherapy of tuberculosis. However, knowledge of the intersection between these two factors has only recently begun to emerge. Here, we provide a focused review of metabolic characteristics associated with Mycobacterium tuberculosis persistence. We focus on metabolism because it is the biochemical foundation of all physiologic processes and a distinguishing hallmark of M. tuberculosis physiology and pathogenicity. In addition, it serves as the chemical interface between host and pathogen. Existing knowledge, however, derives largely from physiologic contexts in which replication is the primary biochemical objective. The goal of this review is to reframe current knowledge of M. tuberculosis metabolism in the context of persistence, where quiescence is often a key distinguishing characteristic. Such a perspective may help ongoing efforts to develop more efficient cures and inform on novel strategies to break the cycle of transmission sustaining the pandemic.
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Affiliation(s)
- Travis E. Hartman
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medical College, New York, NY 10065
| | - Zhe Wang
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medical College, New York, NY 10065
| | - Robert S. Jansen
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medical College, New York, NY 10065
| | - Susana Gardete
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medical College, New York, NY 10065
| | - Kyu Y. Rhee
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medical College, New York, NY 10065
- Department of Microbiology & Immunology, Division of Infectious Diseases, Weill Cornell Medical College, New York, NY 10065
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39
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Nieto R LM, Mehaffy C, Creissen E, Troudt J, Troy A, Bielefeldt-Ohmann H, Burgos M, Izzo A, Dobos KM. Virulence of Mycobacterium tuberculosis after Acquisition of Isoniazid Resistance: Individual Nature of katG Mutants and the Possible Role of AhpC. PLoS One 2016; 11:e0166807. [PMID: 27893795 PMCID: PMC5125630 DOI: 10.1371/journal.pone.0166807] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 11/03/2016] [Indexed: 11/28/2022] Open
Abstract
In the last decade, there were 10 million new tuberculosis cases per year globally. Around 9.5% of these cases were caused by isoniazid resistant (INHr) Mycobacterium tuberculosis (Mtb) strains. Although isoniazid resistance in Mtb is multigenic, mutations in the catalase-peroxidase (katG) gene predominate among the INHr strains. The effect of these drug-resistance-conferring mutations on Mtb fitness and virulence is variable. Here, we assessed differences in bacterial growth, immune response and pathology induced by Mtb strains harboring mutations at the N-terminus of the katG gene. We studied one laboratory and one clinically isolated Mtb clonal pair from different genetic lineages. The INHr strain in each pair had one and two katG mutations with significantly reduced levels of the enzyme and peroxidase activity. Both strains share the V1A mutation, while the double mutant clinical INHr had also the novel E3V katG mutation. Four groups of C57BL/6 mice were infected with one of the Mtb strains previously described. We observed a strong reduction in virulence (reduced bacterial growth), lower induction of proinflammatory cytokines and significantly reduced pathology scores in mice infected with the clinical INHr strain compared to the infection caused by its INHs progenitor strain. On the other hand, there was a subtle reduction of bacteria growth without differences in the pathology scores in mice infected with the laboratory INHr strain. Our results also showed distinct alkyl-hydroperoxidase C (AhpC) levels in the katG mutant strains, which could explain the difference in the virulence profile observed. The difference in the AhpC levels between clonal strains was not related to a genetic defect in the gene or its promoter. Cumulatively, our results indicate that the virulence, pathology and fitness of INHr strains could be negatively affected by multiple mutations in katG, lack of the peroxidase activity and reduced AhpC levels.
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Affiliation(s)
- Luisa Maria Nieto R
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Carolina Mehaffy
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Elizabeth Creissen
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - JoLynn Troudt
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Amber Troy
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Helle Bielefeldt-Ohmann
- School of Veterinary Science, University of Queensland, Gatton, Queensland, Australia; Australian Infectious Diseases Research Centre, University of Queensland, St Lucia, Queensland, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
| | - Marcos Burgos
- Division of Infectious Diseases, Department of Medicine, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Angelo Izzo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Karen M. Dobos
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
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40
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Noy T, Vergnolle O, Hartman TE, Rhee KY, Jacobs WR, Berney M, Blanchard JS. Central Role of Pyruvate Kinase in Carbon Co-catabolism of Mycobacterium tuberculosis. J Biol Chem 2016; 291:7060-9. [PMID: 26858255 DOI: 10.1074/jbc.m115.707430] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Indexed: 11/06/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) displays a high degree of metabolic plasticity to adapt to challenging host environments. Genetic evidence suggests thatMtbrelies mainly on fatty acid catabolism in the host. However,Mtbalso maintains a functional glycolytic pathway and its role in the cellular metabolism ofMtbhas yet to be understood. Pyruvate kinase catalyzes the last and rate-limiting step in glycolysis and theMtbgenome harbors one putative pyruvate kinase (pykA, Rv1617). Here we show thatpykAencodes an active pyruvate kinase that is allosterically activated by glucose 6-phosphate (Glc-6-P) and adenosine monophosphate (AMP). Deletion ofpykApreventsMtbgrowth in the presence of fermentable carbon sources and has a cidal effect in the presence of glucose that correlates with elevated levels of the toxic catabolite methylglyoxal. Growth attenuation was also observed in media containing a combination of short chain fatty acids and glucose and surprisingly, in media containing odd and even chain fatty acids alone. Untargeted high sensitivity metabolomics revealed that inactivation of pyruvate kinase leads to accumulation of phosphoenolpyruvate (P-enolpyruvate), citrate, and aconitate, which was consistent with allosteric inhibition of isocitrate dehydrogenase by P-enolpyruvate. This metabolic block could be relieved by addition of the α-ketoglutarate precursor glutamate. Taken together, our study identifies an essential role of pyruvate kinase in preventing metabolic block during carbon co-catabolism inMtb.
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Affiliation(s)
- Tahel Noy
- From the Departments of Biochemistry and
| | | | - Travis E Hartman
- the Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10021
| | - Kyu Y Rhee
- the Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10021
| | - William R Jacobs
- the Department of Microbiology and Immunology, Howard Hughes Medical Institute at Albert Einstein College of Medicine, New York, New York 10461, and Microbiology and Immunology, Albert Einstein College of Medicine, New York, New York 10461
| | - Michael Berney
- Microbiology and Immunology, Albert Einstein College of Medicine, New York, New York 10461,
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41
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Glutamate Dehydrogenase Is Required by Mycobacterium bovis BCG for Resistance to Cellular Stress. PLoS One 2016; 11:e0147706. [PMID: 26824899 PMCID: PMC4732601 DOI: 10.1371/journal.pone.0147706] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 01/07/2016] [Indexed: 11/19/2022] Open
Abstract
We recently reported on our success to generate deletion mutants of the genes encoding glutamate dehydrogenase (GDH) and glutamine oxoglutarate aminotransferase (GOGAT) in M. bovis BCG, despite their in vitro essentiality in M. tuberculosis. We could use these mutants to delineate the roles of GDH and GOGAT in mycobacterial nitrogen metabolism by using M. bovis BCG as a model for M. tuberculosis specifically. Here, we extended our investigation towards the involvement of GDH and GOGAT in other aspects of M. bovis BCG physiology, including the use of glutamate as a carbon source and resistance to known phagosomal stresses, as well as in survival inside macrophages. We find that gdh is indispensable for the utilization of glutamate as a major carbon source, in low pH environments and when challenged with nitric oxide. On the other hand, the gltBD mutant had increased viability under low pH conditions and was unaffected by a challenge with nitric oxide. Strikingly, GDH was required to sustain M. bovis BCG during infection of both murine RAW 264.7 and bone-marrow derived and macrophages, while GOGAT was not. We conclude that the catabolism of glutamate in slow growing mycobacteria may be a crucial function during infection of macrophage cells and demonstrate a novel requirement for M. bovis BCG GDH in the protection against acidic and nitrosative stress. These results provide strong clues on the role of GDH in intracellular survival of M. tuberculosis, in which the essentiality of the gdh gene complicates knock out studies making the study of the role of this enzyme in pathogenesis difficult.
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42
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Metabolic plasticity of central carbon metabolism protects mycobacteria. Proc Natl Acad Sci U S A 2015; 112:13135-6. [PMID: 26483480 DOI: 10.1073/pnas.1518171112] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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43
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Maksymiuk C, Ioerger T, Balakrishnan A, Bryk R, Rhee K, Sacchettini J, Nathan C. Comparison of transposon and deletion mutants in Mycobacterium tuberculosis: The case of rv1248c, encoding 2-hydroxy-3-oxoadipate synthase. Tuberculosis (Edinb) 2015; 95:689-694. [PMID: 26547230 DOI: 10.1016/j.tube.2015.08.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 08/27/2015] [Accepted: 08/31/2015] [Indexed: 11/30/2022]
Abstract
We compared phenotypes of five strains of Mycobacterium tuberculosis (Mtb) differing in their expression of rv1248c and its product, 2-hydroxy-3-oxoadipate synthase (HOAS), with a focus on carbon source-dependent growth rates and attenuation in mice. Surprisingly, an rv1248c transposon mutant on a CDC1551 background grew differently than an rv1248c deletion mutant on the same background. Moreover, the same rv1248c deletion in two different yet genetically similar strain backgrounds (CDC1551 and H37Rv) gave different phenotypes, though each could be complemented. Whole genome re-sequencing did not provide an obvious explanation for these discrepancies. These observations offer a cautionary lesson about the strength of inference from complementation and sequence analysis, and commend consideration of more complex phenomena than usually contemplated in Mtb, such as epigenetic control.
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Affiliation(s)
- Christina Maksymiuk
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Thomas Ioerger
- Department of Computer Science and Engineering, Texas A&M University, USA
| | - Anand Balakrishnan
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Ruslana Bryk
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Kyu Rhee
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - James Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, USA
| | - Carl Nathan
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10065, USA.
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