1
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Schroeter KL, Rolfe N, Forrester TJB, Kimber MS, Seah SYK. Shy is a proteobacterial steroid hydratase which catalyzes steroid side chain degradation without requiring a catalytically inert partner domain. J Biol Chem 2024; 300:107509. [PMID: 38944126 DOI: 10.1016/j.jbc.2024.107509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 06/17/2024] [Accepted: 06/20/2024] [Indexed: 07/01/2024] Open
Abstract
Shy (side chain hydratase) and Sal (side chain aldolase), are involved in successive reactions in the pathway of bile acid side chain catabolism in Proteobacteria. Untagged Shy copurified with His-tagged Sal indicating that the two enzymes form a complex. Shy contains a MaoC and a DUF35 domain. When coexpressed with Sal, the DUF35 domain but not the MaoC domain of Shy was observed to copurify with Sal, indicating Sal interacts with Shy through its DUF35 domain. The MaoC domain of Shy (ShyMaoC) remained catalytically viable and could hydrate cholyl-enoyl-CoA with similar catalytic efficiency as in the Shy-Sal complex. Sal expressed with the DUF35 domain of Shy (Sal-ShyDUF35) was similarly competent for the retro-aldol cleavage of cholyl-3-OH-CoA. ShyMaoC showed a preference for C5 side chain bile acid substrates, exhibiting low activity toward C3 side chain substrates. The ShyMaoC structure was determined by X-ray crystallography, showing a hot dog fold with a short central helix surrounded by a twisted antiparallel β-sheet. Modeling and mutagenesis studies suggest that the bile acid substrate occupies the large open cleft formed by the truncated central helix and repositioning of the active site housing. ShyMaoC therefore contains two substrate binding sites per homodimer, making it distinct from previously characterized MaoC steroid hydratases that are (pseudo) heterodimers with one substrate binding site per dimer. The characterization of Shy provides insight into how MaoC family hydratases have adapted to accommodate large polycyclic substrates that can facilitate future engineering of these enzymes to produce novel steroid pharmaceuticals.
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Affiliation(s)
- Kurt L Schroeter
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Nicolas Rolfe
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Taylor J B Forrester
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Matthew S Kimber
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Stephen Y K Seah
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.
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2
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Narayanan B, Xia C, McAndrew R, Shen AL, Kim JJP. Structural basis for expanded substrate specificities of human long chain acyl-CoA dehydrogenase and related acyl-CoA dehydrogenases. Sci Rep 2024; 14:12976. [PMID: 38839792 PMCID: PMC11153573 DOI: 10.1038/s41598-024-63027-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 05/23/2024] [Indexed: 06/07/2024] Open
Abstract
Crystal structures of human long-chain acyl-CoA dehydrogenase (LCAD) and the catalytically inactive Glu291Gln mutant, have been determined. These structures suggest that LCAD harbors functions beyond its historically defined role in mitochondrial β-oxidation of long and medium-chain fatty acids. LCAD is a homotetramer containing one FAD per 43 kDa subunit with Glu291 as the catalytic base. The substrate binding cavity of LCAD reveals key differences which makes it specific for longer and branched chain substrates. The presence of Pro132 near the start of the E helix leads to helix unwinding that, together with adjacent smaller residues, permits binding of bulky substrates such as 3α, 7α, l2α-trihydroxy-5β-cholestan-26-oyl-CoA. This structural element is also utilized by ACAD11, a eucaryotic ACAD of unknown function, as well as bacterial ACADs known to metabolize sterol substrates. Sequence comparison suggests that ACAD10, another ACAD of unknown function, may also share this substrate specificity. These results suggest that LCAD, ACAD10, ACAD11 constitute a distinct class of eucaryotic acyl CoA dehydrogenases.
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Affiliation(s)
- Beena Narayanan
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | - Chuanwu Xia
- Department of Chemistry and Biochemistry, College of Arts and Sciences, University of North Florida, Jacksonville, FL, 32224, USA
| | - Ryan McAndrew
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94740, USA
| | - Anna L Shen
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jung-Ja P Kim
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.
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3
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Li X, Zhang R, Li J, Liu N, Chen X, Liu Y, Zhao G, Ding K, Yao P, Feng J, Wu Q, Zhu D, Ma Y. Chemo-Enzymatic Strategy for the Efficient Synthesis of Steroidal Drugs with 10α-Methyl Group and a Side Chain at C17-Position from Biorenewable Phytosterols. JACS AU 2024; 4:1356-1364. [PMID: 38665665 PMCID: PMC11040700 DOI: 10.1021/jacsau.3c00688] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/31/2023] [Accepted: 02/28/2024] [Indexed: 04/28/2024]
Abstract
Steroidal pharmaceuticals with a 10α-methyl group or without the methyl group at C10-position are important medicines, but their synthesis is quite challenging, due to that the natural steroidal starting materials usually have a 10β-methyl group which is difficult to be inverted to 10α-methyl group. In this study, 3-((1R,3aS,4S,7aR)-1-((S)-1-hydroxypropan-2-yl)-7a-methyl-5-oxooctahydro-1H-inden-4-yl) propanoic acid (HIP-IPA, 2e) was demonstrated as a valuable intermediate for the synthesis of this kind of active pharmaceutical ingredients (APIs) with a side chain at C17-position. Knockout of a β-hydroxyacyl-CoA dehydrogenase gene and introduction of a sterol aldolase gene into the genetically modified strains of Mycobacterium fortuitum (ATCC 6841) resulted in strains N13Δhsd4AΩthl and N33Δhsd4AΩthl, respectively. Both strains transformed phytosterols into 2e. Compound 2e was produced in 62% isolated yield (25 g) using strain N13Δhsd4AΩthl, and further converted to (3S,3aS,9aS,9bS)-3-acetyl-3a,6-dimethyl-1,2,3,3a,4,5,8,9,9a,9b-decahydro-7H-cyclopenta[a]naphthalen-7-one, which is the key intermediate for the synthesis of dydrogesterone. This study not only overcomes a challenging synthetic problem by enabling an efficient synthesis of dydrogesterone-like steroidal APIs from phytosterols, the well-recognized cheap and readily available biobased raw materials, but also provides insights for redesigning the metabolic pathway of phytosterols to produce other new compounds of relevance to the steroidal pharmaceutical industry.
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Affiliation(s)
- Xuemei Li
- National
Engineering Research Center of Industrial Enzymes and Tianjin Engineering
Research Center of Biocatalytic Technology, Key Laboratory of Engineering Biology for Low-carbon Manufacturing,
National Center of Technology Innovation for Synthetic Biology, and
Tianjin Institute of Industrial Biotechnology, Chinese Academy of
Sciences, Tianjin 300308, China
| | - Rui Zhang
- National
Engineering Research Center of Industrial Enzymes and Tianjin Engineering
Research Center of Biocatalytic Technology, Key Laboratory of Engineering Biology for Low-carbon Manufacturing,
National Center of Technology Innovation for Synthetic Biology, and
Tianjin Institute of Industrial Biotechnology, Chinese Academy of
Sciences, Tianjin 300308, China
| | - Jianjiong Li
- National
Engineering Research Center of Industrial Enzymes and Tianjin Engineering
Research Center of Biocatalytic Technology, Key Laboratory of Engineering Biology for Low-carbon Manufacturing,
National Center of Technology Innovation for Synthetic Biology, and
Tianjin Institute of Industrial Biotechnology, Chinese Academy of
Sciences, Tianjin 300308, China
| | - Na Liu
- National
Engineering Research Center of Industrial Enzymes and Tianjin Engineering
Research Center of Biocatalytic Technology, Key Laboratory of Engineering Biology for Low-carbon Manufacturing,
National Center of Technology Innovation for Synthetic Biology, and
Tianjin Institute of Industrial Biotechnology, Chinese Academy of
Sciences, Tianjin 300308, China
| | - Xi Chen
- National
Engineering Research Center of Industrial Enzymes and Tianjin Engineering
Research Center of Biocatalytic Technology, Key Laboratory of Engineering Biology for Low-carbon Manufacturing,
National Center of Technology Innovation for Synthetic Biology, and
Tianjin Institute of Industrial Biotechnology, Chinese Academy of
Sciences, Tianjin 300308, China
| | - Yiyin Liu
- National
Engineering Research Center of Industrial Enzymes and Tianjin Engineering
Research Center of Biocatalytic Technology, Key Laboratory of Engineering Biology for Low-carbon Manufacturing,
National Center of Technology Innovation for Synthetic Biology, and
Tianjin Institute of Industrial Biotechnology, Chinese Academy of
Sciences, Tianjin 300308, China
| | - Gang Zhao
- CAS
Key Laboratory of Synthetic Chemistry of Natural Substances, Shanghai
Institute of Organic Chemistry, Chinese
Academy of Sciences, Shanghai 200032, China
| | - Kai Ding
- CAS
Key Laboratory of Synthetic Chemistry of Natural Substances, Shanghai
Institute of Organic Chemistry, Chinese
Academy of Sciences, Shanghai 200032, China
| | - Peiyuan Yao
- National
Engineering Research Center of Industrial Enzymes and Tianjin Engineering
Research Center of Biocatalytic Technology, Key Laboratory of Engineering Biology for Low-carbon Manufacturing,
National Center of Technology Innovation for Synthetic Biology, and
Tianjin Institute of Industrial Biotechnology, Chinese Academy of
Sciences, Tianjin 300308, China
| | - Jinhui Feng
- National
Engineering Research Center of Industrial Enzymes and Tianjin Engineering
Research Center of Biocatalytic Technology, Key Laboratory of Engineering Biology for Low-carbon Manufacturing,
National Center of Technology Innovation for Synthetic Biology, and
Tianjin Institute of Industrial Biotechnology, Chinese Academy of
Sciences, Tianjin 300308, China
| | - Qiaqing Wu
- National
Engineering Research Center of Industrial Enzymes and Tianjin Engineering
Research Center of Biocatalytic Technology, Key Laboratory of Engineering Biology for Low-carbon Manufacturing,
National Center of Technology Innovation for Synthetic Biology, and
Tianjin Institute of Industrial Biotechnology, Chinese Academy of
Sciences, Tianjin 300308, China
| | - Dunming Zhu
- National
Engineering Research Center of Industrial Enzymes and Tianjin Engineering
Research Center of Biocatalytic Technology, Key Laboratory of Engineering Biology for Low-carbon Manufacturing,
National Center of Technology Innovation for Synthetic Biology, and
Tianjin Institute of Industrial Biotechnology, Chinese Academy of
Sciences, Tianjin 300308, China
| | - Yanhe Ma
- National
Engineering Research Center of Industrial Enzymes and Tianjin Engineering
Research Center of Biocatalytic Technology, Key Laboratory of Engineering Biology for Low-carbon Manufacturing,
National Center of Technology Innovation for Synthetic Biology, and
Tianjin Institute of Industrial Biotechnology, Chinese Academy of
Sciences, Tianjin 300308, China
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4
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Narayanan B, Xia C, McAndrew R, Shen AL, Kim JJP. Structural Basis for Expanded Substrate Speci ficities of Human Long Chain Acyl-CoA Dehydrogenase and Related Acyl- CoA Dehydrogenases. RESEARCH SQUARE 2024:rs.3.rs-3980524. [PMID: 38464032 PMCID: PMC10925408 DOI: 10.21203/rs.3.rs-3980524/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Crystal structures of human long-chain acyl-CoA dehydrogenase (LCAD) and the E291Q mutant, have been determined. These structures suggest that LCAD harbors functions beyond its historically defined role in mitochondrial β-oxidation of long and medium-chain fatty acids. LCAD is a homotetramer containing one FAD per 43kDa subunit with Glu291 as the catalytic base. The substrate binding cavity of LCAD reveals key differences which makes it specific for longer and branched chain substrates. The presence of Pro132 near the start of the E helix leads to helix unwinding that, together with adjacent smaller residues, permits binding of bulky substrates such as 3α, 7α, l2α-trihydroxy-5β-cholestan-26-oyl-CoA. This structural element is also utilized by ACAD11, a eucaryotic ACAD of unknown function, as well as bacterial ACADs known to metabolize sterol substrates. Sequence comparison suggests that ACAD10, another ACAD of unknown function, may also share this substrate specificity. These results suggest that LCAD, ACAD10, ACAD11 constitute a distinct class of eucaryotic acyl CoA dehydrogenases.
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5
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Yuan C, Li Y, Han S, He B, Zhai X, Lin W, Shi J, Sun J, Zhang B. Functional analysis of acyl-CoA dehydrogenases and their application to C22 steroid production. Appl Microbiol Biotechnol 2023; 107:3419-3428. [PMID: 37093308 DOI: 10.1007/s00253-023-12541-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/10/2023] [Accepted: 04/14/2023] [Indexed: 04/25/2023]
Abstract
Acyl-CoA dehydrogenase (ChsE) is involved in the steroid side-chain degradation process. However, their function in vivo remains unclear. In this study, three ChsE, ChsE1-ChsE2, ChsE3, and ChsE4-ChsE5, were identified in Mycolicibacterium neoaurum, and their functions in vivo are studied and compared with those from Mycobacterium tuberculosis in vitro. By gene knockout, complementation, and the bioconversion of phytosterols, the function of ChsE was elucidated that ChsE4-ChsE5 could utilize C27, C24, and C22 steroids in vivo. ChsE3 could utilize C27 and C24 steroids in vivo. ChsE1-ChsE2 could utilize C27, C24, and C22 steroids in vivo. What is more, the production strain of a C22 steroid, 3-oxo-4,17-pregadiene-20-carboxylic acid methyl ester (PDCE), is constructed with ChsE overexpression. This study improved the understanding of the steroid bioconversion pathway and proposed a method of the production of a new C22 steroid. KEY POINTS: • Three ChsE paralogs from M. neoaurum are identified and studied. • The function of ChsE is overlapped in vivo. • A C22 steroid (PDCE) producer was constructed with ChsE overexpression.
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Affiliation(s)
- Chenyang Yuan
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yixin Li
- Department of Biology, Colby College, Waterville, ME, 04901, USA
| | - Suwan Han
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Beiru He
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xinghui Zhai
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Weichao Lin
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, China
| | - Jiping Shi
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junsong Sun
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Baoguo Zhang
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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6
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Song S, Su Z. Targeted Mutagenesis of Mycobacterium Strains by Homologous Recombination. Methods Mol Biol 2023; 2704:85-96. [PMID: 37642839 DOI: 10.1007/978-1-0716-3385-4_5] [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: 08/31/2023]
Abstract
Targeted mutagenesis by homologous recombination (TMHR) is an efficient allelic exchange mutagenesis for bacterial genome engineering in synthetic biology. Unlike other allelic exchange methods, TMHR does not require a heterologous recombinase to insert or excise a selectable marker from the genome. In contrast, positive and negative selection is achieved solely by suicide vector-encoded functional and host cell proteins. Here we describe a concise protocol to knock out and knock in a 3-ketosteroid-1,2-dehydrogenase gene (kstd) in Mycobacterium neoaurum HGMS2 using TMHR approach. The homology arms flanking the kstd gene are amplified by PCR in vitro and then subcloned into a common homologous recombination vector. The vector is then electroporated into the HGMS2 competent cells. The replacement of the kstd gene by homologous recombination produces antibiotic-resistant single-crossover recombination via the first allelic exchange. Double-crossover markerless mutants are directly separated using sucrose-mediated counterselection. These two steps can generate seamless mutations down to a single DNA base pair. The whole process takes less than 2 weeks.
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Affiliation(s)
- Shikui Song
- Laboratory of Protein Engineering and Biopharmaceutical Sciences, Key Laboratory of Industrial Fermentation and Cooperative Innovation Center of Industrial Fermentation, Hubei University of Technology, Wuhan, Hubei, China
| | - Zhengding Su
- Laboratory of Protein Engineering and Biopharmaceutical Sciences, Key Laboratory of Industrial Fermentation and Cooperative Innovation Center of Industrial Fermentation, Hubei University of Technology, Wuhan, Hubei, China.
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7
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Bioconversion of Phytosterols to 9-Hydroxy-3-Oxo-4,17-Pregadiene-20-Carboxylic Acid Methyl Ester by Enoyl-CoA Deficiency and Modifying Multiple Genes in Mycolicibacterium neoaurum. Appl Environ Microbiol 2022; 88:e0130322. [PMID: 36286498 PMCID: PMC9680642 DOI: 10.1128/aem.01303-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
C22 steroids are valuable precursors for steroid drug synthesis, but the development of C22 steroids remains unsatisfactory. This study presented a strategy for the one-step bioconversion of phytosterols to a C22 steroid drug precursor, 9-hydroxy-3-oxo-4,17-pregadiene-20-carboxylic acid methyl ester (9-OH-PDCE), by 3-ketosteroid-Δ
1
-dehydrogenase and enoyl-CoA hydratase deficiency with overexpression of 17β-hydroxysteroid dehydrogenase acyl-CoA dehydrogenase in
Mycolicibacterium
.
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8
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The unusual convergence of steroid catabolic pathways in Mycobacterium abscessus. Proc Natl Acad Sci U S A 2022; 119:e2207505119. [PMID: 36161908 DOI: 10.1073/pnas.2207505119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mycobacterium abscessus, an opportunistic pathogen responsible for pulmonary infections, contains genes predicted to encode two steroid catabolic pathways: a cholesterol catabolic pathway similar to that of Mycobacterium tuberculosis and a 4-androstenedione (4-AD) catabolic pathway. Consistent with this prediction, M. abscessus grew on both steroids. In contrast to M. tuberculosis, Rhodococcus jostii RHA1, and other Actinobacteria, the cholesterol and 4-AD catabolic gene clusters of the M. abscessus complex lack genes encoding HsaD, the meta-cleavage product (MCP) hydrolase. However, M. abscessus ATCC 19977 harbors two hsaD homologs elsewhere in its genome. Only one of the encoded enzymes detectably transformed steroid metabolites. Among tested substrates, HsaDMab and HsaDMtb of M. tuberculosis had highest substrate specificities for MCPs with partially degraded side chains thioesterified with coenzyme A (kcat/KM = 1.9 × 104 and 5.7 × 103 mM-1s-1, respectively). Consistent with a dual role in cholesterol and 4-AD catabolism, HsaDMab also transformed nonthioesterified substrates efficiently, and a ΔhsaD mutant of M. abscessus grew on neither steroid. Interestingly, both steroids prevented growth of the mutant on acetate. The ΔhsaD mutant of M. abscessus excreted cholesterol metabolites with a fully degraded side chain, while the corresponding RHA1 mutant excreted metabolites with partially degraded side chains. Finally, the ΔhsaD mutant was not viable in macrophages. Overall, our data establish that the cholesterol and 4-AD catabolic pathways of M. abscessus are unique in that they converge upstream of where this occurs in characterized steroid-catabolizing bacteria. The data further indicate that cholesterol is a substrate for intracellular bacteria and that cholesterol-dependent toxicity is not strictly dependent on coenzyme A sequestration.
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9
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Beites T, Jansen RS, Wang R, Jinich A, Rhee KY, Schnappinger D, Ehrt S. Multiple acyl-CoA dehydrogenase deficiency kills Mycobacterium tuberculosis in vitro and during infection. Nat Commun 2021; 12:6593. [PMID: 34782606 PMCID: PMC8593149 DOI: 10.1038/s41467-021-26941-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 10/26/2021] [Indexed: 11/14/2022] Open
Abstract
The human pathogen Mycobacterium tuberculosis depends on host fatty acids as a carbon source. However, fatty acid β-oxidation is mediated by redundant enzymes, which hampers the development of antitubercular drugs targeting this pathway. Here, we show that rv0338c, which we refer to as etfD, encodes a membrane oxidoreductase essential for β-oxidation in M. tuberculosis. An etfD deletion mutant is incapable of growing on fatty acids or cholesterol, with long-chain fatty acids being bactericidal, and fails to grow and survive in mice. Analysis of the mutant’s metabolome reveals a block in β-oxidation at the step catalyzed by acyl-CoA dehydrogenases (ACADs), which in other organisms are functionally dependent on an electron transfer flavoprotein (ETF) and its cognate oxidoreductase. We use immunoprecipitation to show that M. tuberculosis EtfD interacts with FixA (EtfB), a protein that is homologous to the human ETF subunit β and is encoded in an operon with fixB, encoding a homologue of human ETF subunit α. We thus refer to FixA and FixB as EtfB and EtfA, respectively. Our results indicate that EtfBA and EtfD (which is not homologous to human EtfD) function as the ETF and oxidoreductase for β-oxidation in M. tuberculosis and support this pathway as a potential target for tuberculosis drug development. The pathogen Mycobacterium tuberculosis depends on host fatty acids and cholesterol as carbon sources. Here, Beites et al. identify a protein complex that is essential for fatty acid and cholesterol utilization and thus for survival of M. tuberculosis during infection, supporting this pathway as a potential target for tuberculosis drug development.
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Affiliation(s)
- Tiago Beites
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Robert S Jansen
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York, NY, 10065, USA.,Department of Microbiology, Radboud University, 6525 AJ, Nijmegen, The Netherlands
| | - Ruojun Wang
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, USA.,Department of Molecular Biology, Princeton University, Princeton, NJ, 08540, USA
| | - Adrian Jinich
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Kyu Y Rhee
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, USA.,Division of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, 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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10
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Payros D, Alonso H, Malaga W, Volle A, Mazères S, Déjean S, Valière S, Moreau F, Balor S, Stella A, Combes-Soia L, Burlet-Schiltz O, Bouchez O, Nigou J, Astarie-Dequeker C, Guilhot C. Rv0180c contributes to Mycobacterium tuberculosis cell shape and to infectivity in mice and macrophages. PLoS Pathog 2021; 17:e1010020. [PMID: 34724002 PMCID: PMC8584747 DOI: 10.1371/journal.ppat.1010020] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 11/11/2021] [Accepted: 10/08/2021] [Indexed: 11/19/2022] Open
Abstract
Mycobacterium tuberculosis, the main causative agent of human tuberculosis, is transmitted from person to person via small droplets containing very few bacteria. Optimizing the chance to seed in the lungs is therefore a major adaptation to favor survival and dissemination in the human population. Here we used TnSeq to identify genes important for the early events leading to bacterial seeding in the lungs. Beside several genes encoding known virulence factors, we found three new candidates not previously described: rv0180c, rv1779c and rv1592c. We focused on the gene, rv0180c, of unknown function. First, we found that deletion of rv0180c in M. tuberculosis substantially reduced the initiation of infection in the lungs of mice. Next, we established that Rv0180c enhances entry into macrophages through the use of complement-receptor 3 (CR3), a major phagocytic receptor for M. tuberculosis. Silencing CR3 or blocking the CR3 lectin site abolished the difference in entry between the wild-type parental strain and the Δrv0180c::km mutant. However, we detected no difference in the production of both CR3-known carbohydrate ligands (glucan, arabinomannan, mannan), CR3-modulating lipids (phthiocerol dimycocerosate), or proteins in the capsule of the Δrv0180c::km mutant in comparison to the wild-type or complemented strains. By contrast, we established that Rv0180c contributes to the functionality of the bacterial cell envelope regarding resistance to toxic molecule attack and cell shape. This alteration of bacterial shape could impair the engagement of membrane receptors that M. tuberculosis uses to invade host cells, and open a new perspective on the modulation of bacterial infectivity. The epidemic efficiency of tuberculosis bacilli is determined by their capacity to transmit via aerosol. Currently, the bacterial functions that favor Mycobacterium tuberculosis seeding in the lung of naïve host remain mostly unknown. Here we implemented a genome-wide approach to identify M. tuberculosis mutants deficient for seeding and early replication in the lung of mice. In addition to genes known to encode virulence factors, we identified three genes not previously described. We used complementary approaches to characterize the phenotype of a M. tuberculosis mutant with insertion within the rv0180c gene. We found that this mutant is impaired for seeding in the lung of mice and for invasion and replication in human macrophages. In macrophages, the defect relies on a lack of engagement of CR3 receptor. Although we did not detect any difference between the wild type strain and the rv0180c mutant with regard to potential CR3-ligand, we found that the bacterial cell envelope is altered in the rv0180c mutant. Our study provides new insight into bacterial genes required for early interaction of M. tuberculosis with the host and perspective to understand the bacterial functions enhancing infectivity.
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Affiliation(s)
- Delphine Payros
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Henar Alonso
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Wladimir Malaga
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Arnaud Volle
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Serge Mazères
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Sébastien Déjean
- Institut de Mathématiques de Toulouse, UMR5219, Université de Toulouse, CNRS, UPS, Toulouse, France
| | | | - Flavie Moreau
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Stéphanie Balor
- Plateforme de Microscopie Électronique Intégrative (METi), Centre de Biologie Intégrative (CBI), CNRS, Toulouse, France
| | - Alexandre Stella
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Lucie Combes-Soia
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | | | - Jérôme Nigou
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Catherine Astarie-Dequeker
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
- * E-mail: (CAD); (CG)
| | - Christophe Guilhot
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
- * E-mail: (CAD); (CG)
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11
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Mycolicibacterium cell factory for the production of steroid-based drug intermediates. Biotechnol Adv 2021; 53:107860. [PMID: 34710554 DOI: 10.1016/j.biotechadv.2021.107860] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 10/19/2021] [Accepted: 10/19/2021] [Indexed: 12/30/2022]
Abstract
Steroid-based drugs have been developed as the second largest medical category in pharmaceutics. The well-established route of steroid industry includes two steps: the conversion of natural products with a steroid framework to steroid-based drug intermediates and the synthesis of varied steroid-based drugs from steroid-based drug intermediates. The biosynthesis of steroid-based drug intermediates from phytosterols by Mycolicibacterium cell factories bypasses the potential undersupply of diosgenin in the traditional steroid chemical industry. Moreover, the biosynthesis route shows advantages on multiple steroid-based drug intermediate products, more ecofriendly processes, and consecutive reactions carried out in one operation step and in one pot. Androsta-4-ene-3,17-dione (AD), androsta-1,4-diene-3,17-dione (ADD) and 9-hydroxyandrostra-4-ene-3,17-dione (9-OH-AD) are the representative steroid-based drug intermediates synthesized by mycolicibacteria. Other steroid metabolites of mycolicibacteria, like 4-androstene-17β-ol-3-one (TS), 22-hydroxy-23,24-bisnorchol-4-ene-3-one (4-HBC), 22-hydroxy-23,24-bisnorchol-1,4-diene-3-one (1,4-HBC), 9,22-dihydroxy-23,24-bisnorchol-4-ene-3-one (9-OH-HBC), 3aα-H-4α-(3'-propionic acid)-7aβ-methylhexahydro-1,5-indanedione (HIP) and 3aα-H-4α-(3'-propionic acid)-5α-hydroxy-7aβ-methylhexahydro-1-indanone-δ-lactone (HIL), also show values as steroid-based drug intermediates. To improve the bio-production efficiency of the steroid-based drug intermediates, mycolicibacterial strains and biotransformation processes have been continuously studied in the past decades. Many mycolicibacteria that accumulate steroid drug intermediates have been isolated, and subsequently optimized by conventional mutagenesis and genetic engineering. Especially, with the clarification of the mycolicibacterial steroid metabolic pathway and the developments on gene editing technologies, rational design is becoming an important measure for the construction and optimization of engineered mycolicibacteria strains that produce steroid-based drug intermediates. Hence, by reviewing researches in the past two decades, this article updates the overall process of steroid metabolism in mycolicibacteria and provides comprehensive schemes for the rational construction of mycolicibacterial strains that accumulate steroid-based drug intermediates. In addition, the special strategies for the bioconversion of highly hydrophobic steroid in aqueous media are discussed as well.
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Comparative Analysis of Bile-Salt Degradation in Sphingobium sp. Strain Chol11 and Pseudomonas stutzeri Strain Chol1 Reveals Functional Diversity of Proteobacterial Steroid Degradation Enzymes and Suggests a Novel Pathway for Side Chain Degradation. Appl Environ Microbiol 2021; 87:e0145321. [PMID: 34469190 DOI: 10.1128/aem.01453-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The reaction sequence for aerobic degradation of bile salts by environmental bacteria resembles degradation of other steroid compounds. Recent findings show that bacteria belonging to the Sphingomonadaceae use a pathway variant for bile-salt degradation. This study addresses this so-called Δ4,6-variant by comparative analysis of unknown degradation steps in Sphingobium sp. strain Chol11 with known reactions found in Pseudomonas stutzeri Chol1. Investigations of strain Chol11 revealed an essential function of the acyl-CoA dehydrogenase (ACAD) Scd4AB for growth with bile salts. Growth of the scd4AB deletion mutant was restored with a metabolite containing a double bond within the side chain which was produced by the Δ22-ACAD Scd1AB from P. stutzeri Chol1. Expression of scd1AB in the scd4AB deletion mutant fully restored growth with bile salts, while expression of scd4AB only enabled constricted growth in P. stutzeri Chol1 scd1A or scd1B deletion mutants. Strain Chol11 Δscd4A accumulated hydroxylated steroid metabolites which were degraded and activated with coenzyme A by the wild type. Activities of five Rieske type monooxygenases of strain Chol11 were screened by heterologous expression and compared to the B-ring cleaving KshABChol1 from P. stutzeri Chol1. Three of the Chol11 enzymes catalyzed B-ring cleavage of only Δ4,6-steroids, while KshABChol1 was more versatile. Expression of a fourth KshA homolog, Nov2c228, led to production of metabolites with hydroxylations at an unknown position. These results indicate functional diversity of proteobacterial enzymes for bile-salt degradation and suggest a novel side chain degradation pathway involving an essential ACAD reaction and a steroid hydroxylation step. IMPORTANCE This study highlights the biochemical diversity of bacterial degradation of steroid compounds in different aspects. First, it further elucidates an unexplored variant in the degradation of bile-salt side chains by sphingomonads, a group of environmental bacteria that is well-known for their broad metabolic capabilities. Moreover, it adds a so far unknown hydroxylation of steroids to the reactions Rieske monooxygenases can catalyze with steroids. Additionally, it analyzes a proteobacterial ketosteroid-9α-hydroxylase and shows that this enzyme is able to catalyze side reactions with nonnative substrates.
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13
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Feller FM, Holert J, Yücel O, Philipp B. Degradation of Bile Acids by Soil and Water Bacteria. Microorganisms 2021; 9:1759. [PMID: 34442838 PMCID: PMC8399759 DOI: 10.3390/microorganisms9081759] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/22/2021] [Accepted: 08/12/2021] [Indexed: 02/07/2023] Open
Abstract
Bile acids are surface-active steroid compounds with a C5 carboxylic side chain at the steroid nucleus. They are produced by vertebrates, mainly functioning as emulsifiers for lipophilic nutrients, as signaling compounds, and as an antimicrobial barrier in the duodenum. Upon excretion into soil and water, bile acids serve as carbon- and energy-rich growth substrates for diverse heterotrophic bacteria. Metabolic pathways for the degradation of bile acids are predominantly studied in individual strains of the genera Pseudomonas, Comamonas, Sphingobium, Azoarcus, and Rhodococcus. Bile acid degradation is initiated by oxidative reactions of the steroid skeleton at ring A and degradation of the carboxylic side chain before the steroid nucleus is broken down into central metabolic intermediates for biomass and energy production. This review summarizes the current biochemical and genetic knowledge on aerobic and anaerobic degradation of bile acids by soil and water bacteria. In addition, ecological and applied aspects are addressed, including resistance mechanisms against the toxic effects of bile acids.
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Affiliation(s)
- Franziska Maria Feller
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Corrensstr. 3, 48149 Münster, Germany; (F.M.F.); (J.H.); (O.Y.)
| | - Johannes Holert
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Corrensstr. 3, 48149 Münster, Germany; (F.M.F.); (J.H.); (O.Y.)
| | - Onur Yücel
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Corrensstr. 3, 48149 Münster, Germany; (F.M.F.); (J.H.); (O.Y.)
| | - Bodo Philipp
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Corrensstr. 3, 48149 Münster, Germany; (F.M.F.); (J.H.); (O.Y.)
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Auf dem Aberg 1, 57392 Schmallenberg, Germany
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14
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Proteome, bioinformatic and functional analyses reveal a distinct and conserved metabolic pathway for bile salt degradation in the Sphingomonadaceae. Appl Environ Microbiol 2021; 87:e0098721. [PMID: 34260303 DOI: 10.1128/aem.00987-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bile salts are amphiphilic steroids chain with digestive functions in vertebrates. Upon excretion, bile salts are degraded by environmental bacteria. Degradation of the bile-salt steroid skeleton resembles the well-studied pathway for other steroids like testosterone, while specific differences occur during side-chain degradation and the initiating transformations of the steroid skeleton. Of the latter, two variants via either Δ1,4- or Δ4,6-3-ketostructures of the steroid skeleton exist for 7-hydroxy bile salts. While the Δ1,4- variant is well-known from many model organisms, the Δ4,6-variant involving a 7-hydroxysteroid dehydratase as key enzyme has not been systematically studied. Here, combined proteomic, bioinformatic and functional analyses of the Δ4,6-variant in Sphingobium sp. strain Chol11 were performed. They revealed a degradation of the steroid rings similar to the Δ1,4-variant except for the elimination of the 7-OH as a key difference. In contrast, differential production of the respective proteins revealed a putative gene cluster degradation of the C5 carboxylic side chain encoding a CoA-ligase, an acyl-CoA dehydrogenase, a Rieske monooxygenase, and an amidase, but lacking most canonical genes known from other steroid-degrading bacteria. Bioinformatic analyses predicted the Δ4,6-variant to be widespread among the Sphingomonadaceae, which was verified for three type strains which also have the predicted side-chain degradation cluster. A second amidase in the side-chain degradation gene cluster of strain Chol11 was shown to cleave conjugated bile salts while having low similarity to known bile-salt hydrolases. This study signifies members of the Sphingomonadaceae remarkably well-adapted to the utilization of bile salts via a partially distinct metabolic pathway. Importance This study highlights the biochemical diversity of bacterial degradation of steroid compounds, in particular bile salts. Furthermore, it substantiates and advances knowledge of a variant pathway for degradation of steroids by sphingomonads, a group of environmental bacteria that are well-known for their broad metabolic capabilities. Biodegradation of bile salts is a critical process due to the high input of these compounds from manure into agricultural soils and wastewater treatment plants. In addition, these results may also be relevant for the biotechnological production of bile salts or other steroid compounds with pharmaceutical functions.
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15
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Yuan T, Werman JM, Yin X, Yang M, Garcia-Diaz M, Sampson NS. Enzymatic β-Oxidation of the Cholesterol Side Chain in Mycobacterium tuberculosis Bifurcates Stereospecifically at Hydration of 3-Oxo-cholest-4,22-dien-24-oyl-CoA. ACS Infect Dis 2021; 7:1739-1751. [PMID: 33826843 PMCID: PMC8204306 DOI: 10.1021/acsinfecdis.1c00069] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
![]()
The unique ability
of Mycobacterium tuberculosis (Mtb) to utilize host
lipids such as cholesterol for survival, persistence,
and virulence has made the metabolic pathway of cholesterol an area
of great interest for therapeutics development. Herein, we identify
and characterize two genes from the Cho-region (genomic locus responsible
for cholesterol catabolism) of the Mtb genome, chsH3 (Rv3538) and chsB1 (Rv3502c). Their protein products
catalyze two sequential stereospecific hydration and dehydrogenation
steps in the β-oxidation of the cholesterol side chain. ChsH3
favors the 22S hydration of 3-oxo-cholest-4,22-dien-24-oyl-CoA
in contrast to the previously reported EchA19 (Rv3516), which catalyzes
formation of the (22R)-hydroxy-3-oxo-cholest-4-en-24-oyl-CoA
from the same enoyl-CoA substrate. ChsB1 is stereospecific and catalyzes
dehydrogenation of the ChsH3 product but not the EchA19 product. The
X-ray crystallographic structure of the ChsB1 apo-protein was determined
at a resolution of 2.03 Å, and the holo-enzyme with bound NAD+ cofactor was determined at a resolution of 2.21 Å. The
homodimeric structure is representative of a classical NAD+-utilizing short-chain type alcohol dehydrogenase/reductase, including
a Rossmann-fold motif, but exhibits a unique substrate binding site
architecture that is of greater length and width than its homologous
counterparts, likely to accommodate the bulky steroid substrate. Intriguingly,
Mtb utilizes hydratases from the MaoC-like family in sterol side-chain
catabolism in contrast to fatty acid β-oxidation in other species
that utilize the evolutionarily distinct crotonase family of hydratases.
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Affiliation(s)
- Tianao Yuan
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Joshua M. Werman
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Xingyu Yin
- Biochemistry and Structural Biology Graduate Program, Stony Brook University, Stony Brook, New York 11794-5215, United States
| | - Meng Yang
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Miguel Garcia-Diaz
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794-8651, United States
| | - Nicole S. Sampson
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
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16
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Rohman A, Dijkstra BW. Application of microbial 3-ketosteroid Δ 1-dehydrogenases in biotechnology. Biotechnol Adv 2021; 49:107751. [PMID: 33823268 DOI: 10.1016/j.biotechadv.2021.107751] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 03/27/2021] [Accepted: 04/02/2021] [Indexed: 11/19/2022]
Abstract
3-Ketosteroid Δ1-dehydrogenase catalyzes the 1(2)-dehydrogenation of 3-ketosteroid substrates using flavin adenine dinucleotide as a cofactor. The enzyme plays a crucial role in microbial steroid degradation, both under aerobic and anaerobic conditions, by initiating the opening of the steroid nucleus. Indeed, many microorganisms are known to possess one or more 3-ketosteroid Δ1-dehydrogenases. In the pharmaceutical industry, 3-ketosteroid Δ1-dehydrogenase activity is exploited to produce Δ1-3-ketosteroids, a class of steroids that display various biological activities. Many of them are used as active pharmaceutical ingredients in drug products, or as key precursors to produce pharmaceutically important steroids. Since 3-ketosteroid Δ1-dehydrogenase activity requires electron acceptors, among other considerations, Δ1-3-ketosteroid production has been industrially implemented using whole-cell fermentation with growing or metabolically active resting cells, in which the electron acceptors are available, rather than using the isolated enzyme. In this review we discuss biotechnological applications of microbial 3-ketosteroid Δ1-dehydrogenases, covering commonly used steroid-1(2)-dehydrogenating microorganisms, the bioprocess for preparing Δ1-3-ketosteroids, genetic engineering of 3-ketosteroid Δ1-dehydrogenases and related genes for constructing new, productive industrial strains, and microbial fermentation strategies for enhancing the product yield. Furthermore, we also highlight the recent development in the use of isolated 3-ketosteroid Δ1-dehydrogenases combined with a FAD cofactor regeneration system. Finally, in a somewhat different context, we summarize the role of 3-ketosteroid Δ1-dehydrogenase in cholesterol degradation by Mycobacterium tuberculosis and other mycobacteria. Because the enzyme is essential for the pathogenicity of these organisms, it may be a potential target for drug development to combat mycobacterial infections.
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Affiliation(s)
- Ali Rohman
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Surabaya 60115, Indonesia; Laboratory of Proteomics, Research Center for Bio-Molecule Engineering (BIOME), Universitas Airlangga, Surabaya 60115, Indonesia; Laboratory of Biophysical Chemistry, University of Groningen, 9747 AG Groningen, the Netherlands.
| | - Bauke W Dijkstra
- Laboratory of Biophysical Chemistry, University of Groningen, 9747 AG Groningen, the Netherlands.
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17
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Shtratnikova VY, Sсhelkunov MI, Fokina VV, Bragin EY, Shutov AA, Donova MV. Different genome-wide transcriptome responses of Nocardioides simplex VKM Ac-2033D to phytosterol and cortisone 21-acetate. BMC Biotechnol 2021; 21:7. [PMID: 33441120 PMCID: PMC7807495 DOI: 10.1186/s12896-021-00668-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/14/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bacterial degradation/transformation of steroids is widely investigated to create biotechnologically relevant strains for industrial application. The strain of Nocardioides simplex VKM Ac-2033D is well known mainly for its superior 3-ketosteroid Δ1-dehydrogenase activity towards various 3-oxosteroids and other important reactions of sterol degradation. However, its biocatalytic capacities and the molecular fundamentals of its activity towards natural sterols and synthetic steroids were not fully understood. In this study, a comparative investigation of the genome-wide transcriptome profiling of the N. simplex VKM Ac-2033D grown on phytosterol, or in the presence of cortisone 21-acetate was performed with RNA-seq. RESULTS Although the gene patterns induced by phytosterol generally resemble the gene sets involved in phytosterol degradation pathways in mycolic acid rich actinobacteria such as Mycolicibacterium, Mycobacterium and Rhodococcus species, the differences in gene organization and previously unreported genes with high expression level were revealed. Transcription of the genes related to KstR- and KstR2-regulons was mainly enhanced in response to phytosterol, and the role in steroid catabolism is predicted for some dozens of the genes in N. simplex. New transcription factors binding motifs and new candidate transcription regulators of steroid catabolism were predicted in N. simplex. Unlike phytosterol, cortisone 21-acetate does not provide induction of the genes with predicted KstR and KstR2 sites. Superior 3-ketosteroid-Δ1-dehydrogenase activity of N. simplex VKM Ac-2033D is due to the kstDs redundancy in the genome, with the highest expression level of the gene KR76_27125 orthologous to kstD2, in response to cortisone 21-acetate. The substrate spectrum of N. simplex 3-ketosteroid-Δ1-dehydrogenase was expanded in this study with progesterone and its 17α-hydroxylated and 11α,17α-dihydroxylated derivatives, that effectively were 1(2)-dehydrogenated in vivo by the whole cells of the N. simplex VKM Ac-2033D. CONCLUSION The results contribute to the knowledge of biocatalytic features and diversity of steroid modification capabilities of actinobacteria, defining targets for further bioengineering manipulations with the purpose of expansion of their biotechnological applications.
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Affiliation(s)
- Victoria Yu Shtratnikova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie gory, h. 1, b. 40, Moscow, Russian Federation 119991
| | - Mikhail I. Sсhelkunov
- Skolkovo Institute of Science and Technology, Nobelya str., 3, Moscow, Russian Federation 121205
- Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoy Karetny per., h. 19, b. 1, Moscow, Russian Federation 127994
| | - Victoria V. Fokina
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Center for Biological Research of the Russian Academy of Sciences”, pr. Nauki, 5, Pushchino, Moscow Region, Russian Federation 142290
- Pharmins, Ltd., R&D, Institutskaya str, 4, Pushchino, Moscow Region, Russian Federation 142290
| | - Eugeny Y. Bragin
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Center for Biological Research of the Russian Academy of Sciences”, pr. Nauki, 5, Pushchino, Moscow Region, Russian Federation 142290
| | - Andrey A. Shutov
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Center for Biological Research of the Russian Academy of Sciences”, pr. Nauki, 5, Pushchino, Moscow Region, Russian Federation 142290
- Pharmins, Ltd., R&D, Institutskaya str, 4, Pushchino, Moscow Region, Russian Federation 142290
| | - Marina V. Donova
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Center for Biological Research of the Russian Academy of Sciences”, pr. Nauki, 5, Pushchino, Moscow Region, Russian Federation 142290
- Pharmins, Ltd., R&D, Institutskaya str, 4, Pushchino, Moscow Region, Russian Federation 142290
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18
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Stirling AJ, Gilbert SE, Conner M, Mallette E, Kimber MS, Seah SYK. A Key Glycine in Bacterial Steroid-Degrading Acyl-CoA Dehydrogenases Allows Flavin-Ring Repositioning and Modulates Substrate Side Chain Specificity. Biochemistry 2020; 59:4081-4092. [PMID: 33040522 DOI: 10.1021/acs.biochem.0c00568] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A wide variety of steroid metabolites synthesized by eukaryotes are all ultimately catabolized by bacteria; while generally saprophytic, pathogenic Mycobacteria have repurposed these pathways to utilize host intracellular cholesterol pools. Steroid degradation is complex, but a recurring theme is that cycles of β-oxidation are used to iteratively remove acetyl- or propanoyl-CoA groups. These β-oxidation cycles are initiated by the FAD-dependent oxidation of acyl groups, catalyzed by acyl-CoA dehydrogenases (ACADs). We show here that the tcur3481 and tcur3483 genes of Thermomonospora curvata encode subunits of a single ACAD that degrades steroid side chains with a preference for three-carbon over five-carbon substituents. The structure confirms that this enzyme is heterotetrameric, with active sites only in the Tcur3483 subunits. In comparison with the steroid ACAD FadE26-FadE27 from Mycobacterium tuberculosis, the active site is narrower and closed at the steroid-binding end, suggesting that Tcur3481-Tcur3483 is in a catalytically productive state, while FadE26-FadE27 is opened up to allow substrate entry. The flavin rings in Tcur3481-Tcur3483 sit in an unusual pocket created by Gly363, a residue conserved as Ala in steroid ACADs narrowly specific for five-carbon side chains, including FadE34. A Gly363Ala variant of Tcur3481-Tcur3483 prefers five-carbon side chains, while an inverse Ala691Gly FadE34 variant enables three-carbon side chain steroid oxidation. We determined the structure of the Tcur3483 Gly363Ala variant, showing that the flavin rings shift into the more conventional position. Modeling suggests that the shifted flavin position made possible by Gly363 is required to allow the bulky, inflexible three-carbon steroid to bind productively in the active site.
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Affiliation(s)
- Alexander J Stirling
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 5E9
| | - Stephanie E Gilbert
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 5E9
| | - Megan Conner
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 5E9
| | - Evan Mallette
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 5E9
| | - Matthew S Kimber
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 5E9
| | - Stephen Y K Seah
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 5E9
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19
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Structural basis for the broad substrate specificity of two acyl-CoA dehydrogenases FadE5 from mycobacteria. Proc Natl Acad Sci U S A 2020; 117:16324-16332. [PMID: 32601219 PMCID: PMC7368279 DOI: 10.1073/pnas.2002835117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
FadE, an acyl-CoA dehydrogenase, introduces unsaturation to carbon chains in lipid metabolism pathways. Here, we report that FadE5 from Mycobacterium tuberculosis (MtbFadE5) and Mycobacterium smegmatis (MsFadE5) play roles in drug resistance and exhibit broad specificity for linear acyl-CoA substrates but have a preference for those with long carbon chains. Here, the structures of MsFadE5 and MtbFadE5, in the presence and absence of substrates, have been determined. These reveal the molecular basis for the broad substrate specificity of these enzymes. FadE5 interacts with the CoA region of the substrate through a large number of hydrogen bonds and an unusual π-π stacking interaction, allowing these enzymes to accept both short- and long-chain substrates. Residues in the substrate binding cavity reorient their side chains to accommodate substrates of various lengths. Longer carbon-chain substrates make more numerous hydrophobic interactions with the enzyme compared with the shorter-chain substrates, resulting in a preference for this type of substrate.
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20
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Gadbery JE, Round JW, Yuan T, Wipperman MF, Story KT, Crowe AM, Casabon I, Liu J, Yang X, Eltis LD, Sampson NS. IpdE1-IpdE2 Is a Heterotetrameric Acyl Coenzyme A Dehydrogenase That Is Widely Distributed in Steroid-Degrading Bacteria. Biochemistry 2020; 59:1113-1123. [PMID: 32101684 PMCID: PMC7081610 DOI: 10.1021/acs.biochem.0c00005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Steroid-degrading bacteria, including Mycobacterium tuberculosis (Mtb), utilize an architecturally distinct subfamily of acyl coenzyme A dehydrogenases (ACADs) for steroid catabolism. These ACADs are α2β2 heterotetramers that are usually encoded by adjacent fadE-like genes. In mycobacteria, ipdE1 and ipdE2 (formerly fadE30 and fadE33) occur in divergently transcribed operons associated with the catabolism of 3aα-H-4α(3'-propanoate)-7aβ-methylhexahydro-1,5-indanedione (HIP), a steroid metabolite. In Mycobacterium smegmatis, ΔipdE1 and ΔipdE2 mutants had similar phenotypes, showing impaired growth on cholesterol and accumulating 5-OH HIP in the culture supernatant. Bioinformatic analyses revealed that IpdE1 and IpdE2 share many of the features of the α- and β-subunits, respectively, of heterotetrameric ACADs that are encoded by adjacent genes in many steroid-degrading proteobacteria. When coproduced in a rhodococcal strain, IpdE1 and IpdE2 of Mtb formed a complex that catalyzed the dehydrogenation of 5OH-HIP coenzyme A (5OH-HIP-CoA) to 5OH-3aα-H-4α(3'-prop-1-enoate)-7aβ-methylhexa-hydro-1,5-indanedione coenzyme A ((E)-5OH-HIPE-CoA). This corresponds to the initial step in the pathway that leads to degradation of steroid C and D rings via β-oxidation. Small-angle X-ray scattering revealed that the IpdE1-IpdE2 complex was an α2β2 heterotetramer typical of other ACADs involved in steroid catabolism. These results provide insight into an important class of steroid catabolic enzymes and a potential virulence determinant in Mtb.
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Affiliation(s)
- John E Gadbery
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - James W Round
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Tianao Yuan
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Matthew F Wipperman
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States.,Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States.,Clinical & Translational Science Center, Weill Cornell Medicine, New York, New York 10065, United States
| | - Keith T Story
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Adam M Crowe
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Israel Casabon
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Jie Liu
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Xinxin Yang
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Lindsay D Eltis
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.,Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Nicole S Sampson
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
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21
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Yuan T, Yang M, Gehring K, Sampson NS. Mycobacterium tuberculosis Exploits a Heterohexameric Enoyl-CoA Hydratase Retro-Aldolase Complex for Cholesterol Catabolism. Biochemistry 2019; 58:4224-4235. [PMID: 31568719 DOI: 10.1021/acs.biochem.9b00673] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cholesterol catabolism plays an important role in Mycobacterium tuberculosis's (Mtb's) survival and persistence in the host. Mtb exploits three β-oxidation cycles to fully degrade the side chain of cholesterol. Five cistronic genes in a single operon encode three enzymes, 3-oxo-4-pregnene-20-carboxyl-CoA dehydrogenase (ChsE1-ChsE2), 3-oxo-4,17-pregnadiene-20-carboxyl-CoA hydratase (ChsH1-ChsH2), and 17-hydroxy-3-oxo-4-pregnene-20-carboxyl-CoA retro-aldolase (Ltp2), to perform the last β-oxidation cycle in this pathway. Among these three enzymes, ChsH1-ChsH2 and Ltp2 form a protein complex that is required for the catalysis of carbon-carbon bond cleavage. In this work, we report the structure of the full length ChsH1-ChsH2-Ltp2 complex based on small-angle X-ray scattering and single-particle electron microscopy data. Mutagenesis experiments confirm the requirement for Ltp2 to catalyze the retro-aldol reaction. The structure illustrates how acyl transfer between enzymes may occur. Each protomer of the ChsH1-ChsH2-Ltp2 complex contains three protein components: a chain of ChsH1, a chain of ChsH2, and a chain of Ltp2. Two protomers dimerize at the interface of Ltp2 to form a heterohexameric structure. This unique heterohexameric structure of the ChsH1-ChsH2-Ltp2 complex provides entry to further understand the mechanism of cholesterol catabolism in Mtb.
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Affiliation(s)
- Tianao Yuan
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794-3400 , United States
| | - Meng Yang
- Department of Biochemistry , McGill University , Montreal , Quebec H3A 0G4 , Canada
| | - Kalle Gehring
- Department of Biochemistry , McGill University , Montreal , Quebec H3A 0G4 , Canada
| | - Nicole S Sampson
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794-3400 , United States
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22
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Olivera ER, Luengo JM. Steroids as Environmental Compounds Recalcitrant to Degradation: Genetic Mechanisms of Bacterial Biodegradation Pathways. Genes (Basel) 2019; 10:E512. [PMID: 31284586 PMCID: PMC6678751 DOI: 10.3390/genes10070512] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 07/02/2019] [Accepted: 07/03/2019] [Indexed: 12/29/2022] Open
Abstract
Steroids are perhydro-1,2-cyclopentanophenanthrene derivatives that are almost exclusively synthesised by eukaryotic organisms. Since the start of the Anthropocene, the presence of these molecules, as well as related synthetic compounds (ethinylestradiol, dexamethasone, and others), has increased in different habitats due to farm and municipal effluents and discharge from the pharmaceutical industry. In addition, the highly hydrophobic nature of these molecules, as well as the absence of functional groups, makes them highly resistant to biodegradation. However, some environmental bacteria are able to modify or mineralise these compounds. Although steroid-metabolising bacteria have been isolated since the beginning of the 20th century, the genetics and catabolic pathways used have only been characterised in model organisms in the last few decades. Here, the metabolic alternatives used by different bacteria to metabolise steroids (e.g., cholesterol, bile acids, testosterone, and other steroid hormones), as well as the organisation and conservation of the genes involved, are reviewed.
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Affiliation(s)
- Elías R Olivera
- Departamento Biología Molecular (Área Bioquímica y Biología Molecular), Universidad de León, 24007 León, Spain.
| | - José M Luengo
- Departamento Biología Molecular (Área Bioquímica y Biología Molecular), Universidad de León, 24007 León, Spain
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23
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Rohman A, Dijkstra BW. The role and mechanism of microbial 3-ketosteroid Δ 1-dehydrogenases in steroid breakdown. J Steroid Biochem Mol Biol 2019; 191:105366. [PMID: 30991094 DOI: 10.1016/j.jsbmb.2019.04.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/26/2019] [Accepted: 04/12/2019] [Indexed: 02/08/2023]
Abstract
3-Ketosteroid Δ1-dehydrogenases are FAD-dependent enzymes that catalyze the introduction of a double bond between the C1 and C2 atoms of the A-ring of 3-ketosteroid substrates. These enzymes are found in a large variety of microorganisms, especially in bacteria belonging to the phylum Actinobacteria. They play a critical role in the early steps of the degradation of the steroid core. 3-Ketosteroid Δ1-dehydrogenases are of particular interest for the etiology of some infectious diseases, for the production of starting materials for the pharmaceutical industry, and for environmental bioremediation applications. Here we summarize and discuss the biochemical and enzymological properties of these enzymes, their microbial sources, and their natural diversity. The three-dimensional structure of a 3-ketosteroid Δ1-dehydrogenase in connection with the enzyme mechanism is highlighted.
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Affiliation(s)
- Ali Rohman
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Surabaya 60115, Indonesia; The Laboratory of Proteomics, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60115, Indonesia; The Laboratory of Biophysical Chemistry, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Bauke W Dijkstra
- The Laboratory of Biophysical Chemistry, University of Groningen, 9747 AG Groningen, the Netherlands.
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24
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Bragin EY, Shtratnikova VY, Schelkunov MI, Dovbnya DV, Donova MV. Genome-wide response on phytosterol in 9-hydroxyandrostenedione-producing strain of Mycobacterium sp. VKM Ac-1817D. BMC Biotechnol 2019; 19:39. [PMID: 31238923 PMCID: PMC6593523 DOI: 10.1186/s12896-019-0533-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 06/10/2019] [Indexed: 01/07/2023] Open
Abstract
Background Aerobic side chain degradation of phytosterols by actinobacteria is the basis for the industrial production of androstane steroids which are the starting materials for the synthesis of steroid hormones. A native strain of Mycobacterium sp. VKM Ac-1817D effectively produces 9α-hydroxyandrost-4-ene-3,17-dione (9-OH-AD) from phytosterol, but also is capable of slow steroid core degradation. However, the set of the genes with products that are involved in phytosterol oxidation, their organisation and regulation remain poorly understood. Results High-throughput sequencing of the global transcriptomes of the Mycobacterium sp. VKM Ac-1817D cultures grown with or without phytosterol was carried out. In the presence of phytosterol, the expression of 260 genes including those related to steroid catabolism pathways significantly increased. Two of the five genes encoding the oxygenase unit of 3-ketosteroid-9α-hydroxylase (kshA) were highly up-regulated in response to phytosterol (55- and 25-fold, respectively) as well as one of the two genes encoding its reductase subunit (kshB) (40-fold). Only one of the five putative genes encoding 3-ketosteroid-∆1-dehydrogenase (KstD_1) was up-regulated in the presence of phytosterol (61-fold), but several substitutions in the conservative positions of its product were revealed. Among the genes over-expressed in the presence of phytosterol, several dozen genes did not possess binding sites for the known regulatory factors of steroid catabolism. In the promoter regions of these genes, a regularly occurring palindromic motif was revealed. The orthologue of TetR-family transcription regulator gene Rv0767c of M. tuberculosis was identified in Mycobacterium sp. VKM Ac-1817D as G155_05115. Conclusions High expression levels of the genes related to the sterol side chain degradation and steroid 9α-hydroxylation in combination with possible defects in KstD_1 may contribute to effective 9α-hydroxyandrost-4-ene-3,17-dione accumulation from phytosterol provided by this biotechnologically relevant strain. The TetR-family transcription regulator gene G155_05115 presumably associated with the regulation of steroid catabolism. The results are of significance for the improvement of biocatalytic features of the microbial strains for the steroid industry. Electronic supplementary material The online version of this article (10.1186/s12896-019-0533-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eugeny Y Bragin
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Center for Biological Research of the Russian Academy of Sciences", Nauki, 5, Pushchino, Russian Federation, 142290. .,Pharmins Ltd., Institutskaya, 4, Pushchino, Russian Federation, 142290.
| | - Victoria Y Shtratnikova
- A.N. Belozersky Research Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskye gory, 1, building 40, Moscow, Russian Federation, 119992
| | - Mikhail I Schelkunov
- Skolkovo Institute of Science and Technology, Nobelya, 3, Moscow, Russian Federation, 121205.,Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoy Karetny, 19, build. 1, Moscow, Russian Federation, 127051
| | - Dmitry V Dovbnya
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Center for Biological Research of the Russian Academy of Sciences", Nauki, 5, Pushchino, Russian Federation, 142290.,Pharmins Ltd., Institutskaya, 4, Pushchino, Russian Federation, 142290
| | - Marina V Donova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Center for Biological Research of the Russian Academy of Sciences", Nauki, 5, Pushchino, Russian Federation, 142290.,Pharmins Ltd., Institutskaya, 4, Pushchino, Russian Federation, 142290
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25
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Rani N, Hazra S, Singh A, Surolia A. Functional annotation of putative fadE9 of Mycobacterium tuberculosis as isobutyryl-CoA dehydrogenase involved in valine catabolism. Int J Biol Macromol 2019; 122:45-57. [DOI: 10.1016/j.ijbiomac.2018.10.040] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 10/10/2018] [Accepted: 10/10/2018] [Indexed: 12/21/2022]
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26
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Wilburn KM, Fieweger RA, VanderVen BC. Cholesterol and fatty acids grease the wheels of Mycobacterium tuberculosis pathogenesis. Pathog Dis 2018; 76:4931720. [PMID: 29718271 PMCID: PMC6251666 DOI: 10.1093/femspd/fty021] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 03/06/2018] [Indexed: 01/23/2023] Open
Abstract
Tuberculosis is a distinctive disease in which the causative agent, Mycobacterium tuberculosis, can persist in humans for decades by avoiding clearance from host immunity. During infection, M. tuberculosis maintains viability by extracting and utilizing essential nutrients from the host, and this is a prerequisite for all of the pathogenic activities that are deployed by the bacterium. In particular, M. tuberculosis preferentially acquires and metabolizes host-derived lipids (fatty acids and cholesterol), and the bacterium utilizes these substrates to cause and maintain disease. In this review, we discuss our current understanding of lipid utilization by M. tuberculosis, and we describe how these pathways promote pathogenesis to fuel metabolic processes in the bacillus. Finally, we highlight weaknesses in these pathways that potentially can be targeted for drug discovery.
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Affiliation(s)
- Kaley M Wilburn
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York 14850, USA
| | - Rachael A Fieweger
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York 14850, USA
| | - Brian C VanderVen
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York 14850, USA
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27
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Han van der Kolk JH, Gross JJ, Gerber V, Bruckmaier RM. Disturbed bovine mitochondrial lipid metabolism: a review. Vet Q 2017; 37:262-273. [PMID: 28712316 DOI: 10.1080/01652176.2017.1354561] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In mammals, excess energy is stored primarily as triglycerides, which are mobilized when energy demands arise and cannot be covered by feed intake. This review mainly focuses on the role of long chain fatty acids in disturbed energy metabolism of the bovine species. Long chain fatty acids regulate energy metabolism as ligands of peroxisome proliferator-activated receptors. Carnitine acts as a carrier of fatty acyl groups as long-chain acyl-CoA derivatives do not penetrate the mitochondrial inner membrane. There are two different types of disorders in lipid metabolism which can occur in cattle, namely the hypoglycaemic-hypoinsulinaemic and the hyperglycaemic-hyperinsulinaemic type with the latter not always associated with ketosis. There is general agreement that fatty acid β-oxidation capability is limited in the liver of (ketotic) cows. In accord, supplemental L-carnitine decreased liver lipid accumulation in periparturient Holstein cows. Of note, around parturition concurrent oxidation of fatty acids in skeletal muscle is highly activated. Also peroxisomal β-oxidation in liver of dairy cows may be part of the hepatic adaptations to a negative energy balance (NEB) to break down fatty acids. An elevated blood concentration of nonesterified fatty acids is one of the indicators of NEB in cattle among others like increased β-hydroxy butyrate concentration, and decreased concentrations of glucose, insulin, and insulin-like growth factor-I. Assuming that liver carnitine concentrations might limit hepatic fatty acid oxidation capacity in dairy cows, further study of the role of acyl-CoA dehydrogenases and/or riboflavin in bovine ketosis is warranted.
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Affiliation(s)
- J H Han van der Kolk
- a Division of Clinical Veterinary Medicine, Swiss Institute for Equine Medicine (ISME), Department of Clinical Veterinary Medicine, Vetsuisse Faculty , University of Bern and Agroscope , Bern , Switzerland
| | - J J Gross
- b Veterinary Physiology, Vetsuisse Faculty , University of Bern , Bern , Switzerland
| | - V Gerber
- a Division of Clinical Veterinary Medicine, Swiss Institute for Equine Medicine (ISME), Department of Clinical Veterinary Medicine, Vetsuisse Faculty , University of Bern and Agroscope , Bern , Switzerland
| | - R M Bruckmaier
- b Veterinary Physiology, Vetsuisse Faculty , University of Bern , Bern , Switzerland
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28
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Weyrauch P, Zaytsev AV, Stephan S, Kocks L, Schmitz OJ, Golding BT, Meckenstock RU. Conversion of cis-2-carboxycyclohexylacetyl-CoA in the downstream pathway of anaerobic naphthalene degradation. Environ Microbiol 2017; 19:2819-2830. [PMID: 28574200 DOI: 10.1111/1462-2920.13806] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 05/23/2017] [Accepted: 05/27/2017] [Indexed: 11/29/2022]
Abstract
The cyclohexane derivative cis-2-(carboxymethyl)cyclohexane-1-carboxylic acid [(1R,2R)-/(1S,2S)-2-(carboxymethyl)cyclohexane-1-carboxylic acid] has previously been identified as metabolite in the pathway of anaerobic degradation of naphthalene by sulfate-reducing bacteria. We tested the corresponding CoA esters of isomers and analogues of this compound for conversion in cell free extracts of the anaerobic naphthalene degraders Desulfobacterium strain N47 and Deltaproteobacterium strain NaphS2. Conversion was only observed for the cis-isomer, verifying that this is a true intermediate and not a dead-end product. Mass-spectrometric analyses confirmed that conversion is performed by an acyl-CoA dehydrogenase and a subsequent hydratase yielding an intermediate with a tertiary hydroxyl-group. We propose that a novel kind of ring-opening lyase is involved in the further catabolic pathway proceeding via pimeloyl-CoA. In contrast to degradation pathways of monocyclic aromatic compounds where ring-cleavage is achieved via hydratases, this lyase might represent a new ring-opening strategy for the degradation of polycyclic compounds. Conversion of the potential downstream metabolites pimeloyl-CoA and glutaryl-CoA was proved in cell free extracts, yielding 2,3-dehydropimeloyl-CoA, 3-hydroxypimeloyl-CoA, 3-oxopimeloyl-CoA, glutaconyl-CoA, crotonyl-CoA, 3-hydroxybutyryl-CoA and acetyl-CoA as observable intermediates. This indicates a link to central metabolism via β-oxidation, a non-decarboxylating glutaryl-CoA dehydrogenase and a subsequent glutaconyl-CoA decarboxylase.
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Affiliation(s)
- Philip Weyrauch
- Biofilm Centre, University of Duisburg-Essen, Essen, Germany.,Institute of Groundwater Ecology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Andrey V Zaytsev
- School of Chemistry, Newcastle University, Newcastle, UK.,Health and Life Sciences, Northumberland University, Newcastle, UK
| | - Susanne Stephan
- Applied Analytical Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Lena Kocks
- Biofilm Centre, University of Duisburg-Essen, Essen, Germany
| | - Oliver J Schmitz
- Applied Analytical Chemistry, University of Duisburg-Essen, Essen, Germany
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29
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Effect of methyl-β-cyclodextrin on gene expression in microbial conversion of phytosterol. Appl Microbiol Biotechnol 2017; 101:4659-4667. [DOI: 10.1007/s00253-017-8288-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 03/20/2017] [Accepted: 03/27/2017] [Indexed: 11/26/2022]
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30
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Abuhammad A. Cholesterol metabolism: a potential therapeutic target in Mycobacteria. Br J Pharmacol 2017; 174:2194-2208. [PMID: 28002883 DOI: 10.1111/bph.13694] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 11/06/2016] [Accepted: 12/16/2016] [Indexed: 12/14/2022] Open
Abstract
Tuberculosis (TB), although a curable disease, is still one of the most difficult infections to treat. Mycobacterium tuberculosis infects 10 million people worldwide and kills 1.5 million people each year. Reactivation of a latent infection is the major cause of TB. Cholesterol is a critical carbon source during latent infection. Catabolism of cholesterol contributes to the pool of propionyl-CoA, a precursor that is incorporated into lipid virulence factors. The M. tuberculosis genome contains a large regulon of cholesterol catabolic genes suggesting that the microorganism can utilize host sterol for infection and persistence. The protein products of these genes present ideal targets for rational drug discovery programmes. This review summarizes the development of enzyme inhibitors targeting the cholesterol pathway in M. tuberculosis. This knowledge is essential for the discovery of novel agents to treat M. tuberculosis infection. LINKED ARTICLES This article is part of a themed section on Drug Metabolism and Antibiotic Resistance in Micro-organisms. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v174.14/issuetoc.
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31
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Wrońska N, Brzostek A, Szewczyk R, Soboń A, Dziadek J, Lisowska K. The Role of fadD19 and echA19 in Sterol Side Chain Degradation by Mycobacterium smegmatis. Molecules 2016; 21:molecules21050598. [PMID: 27164074 PMCID: PMC6273163 DOI: 10.3390/molecules21050598] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 04/20/2016] [Accepted: 05/02/2016] [Indexed: 11/23/2022] Open
Abstract
Mycobacteria are able to degrade natural sterols and use them as a source of carbon and energy. Several genes which play an important role in cholesterol ring degradation have been described in Mycobacterium smegmatis. However, there are limited data describing the molecular mechanism of the aliphatic side chain degradation by Mycobacterium spp. In this paper, we analyzed the role of the echA19 and fadD19 genes in the degradation process of the side chain of cholesterol and β-sitosterol. We demonstrated that the M. smegmatis fadD19 and echA19 genes are not essential for viability. FadD19 is required in the initial step of the biodegradation of C-24 branched sterol side chains in Mycobacterium smegmatis mc2155, but not those carrying a straight chain like cholesterol. Additionally, we have shown that echA19 is not essential in the degradation of either substrate. This is the first report, to our knowledge, on the molecular characterization of the genes playing an essential role in C-24 branched side chain sterol degradation in M. smegmatis mc2155.
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Affiliation(s)
- Natalia Wrońska
- Department of Industrial Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha Street, 90-237 Lodz, Poland.
| | - Anna Brzostek
- Institute of Medical Biology, Polish Academy of Sciences, 106 Lodowa Street, 93-232 Lodz, Poland.
| | - Rafał Szewczyk
- Department of Industrial Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha Street, 90-237 Lodz, Poland.
| | - Adrian Soboń
- Department of Industrial Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha Street, 90-237 Lodz, Poland.
| | - Jarosław Dziadek
- Institute of Medical Biology, Polish Academy of Sciences, 106 Lodowa Street, 93-232 Lodz, Poland.
| | - Katarzyna Lisowska
- Department of Industrial Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha Street, 90-237 Lodz, Poland.
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32
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Unraveling and engineering the production of 23,24-bisnorcholenic steroids in sterol metabolism. Sci Rep 2016; 6:21928. [PMID: 26898409 PMCID: PMC4761994 DOI: 10.1038/srep21928] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 02/02/2016] [Indexed: 11/12/2022] Open
Abstract
The catabolism of sterols in mycobacteria is highly important due to its close relevance in the pathogenesis of pathogenic strains and the biotechnological applications of nonpathogenic strains for steroid synthesis. However, some key metabolic steps remain unknown. In this study, the hsd4A gene from Mycobacterium neoaurum ATCC 25795 was investigated. The encoded protein, Hsd4A, was characterized as a dual-function enzyme, with both 17β-hydroxysteroid dehydrogenase and β-hydroxyacyl-CoA dehydrogenase activities in vitro. Using a kshAs-null strain of M. neoaurum ATCC 25795 (NwIB-XII) as a model, Hsd4A was further confirmed to exert dual-function in sterol catabolism in vivo. The deletion of hsd4A in NwIB-XII resulted in the production of 23,24-bisnorcholenic steroids (HBCs), indicating that hsd4A plays a key role in sterol side-chain degradation. Therefore, two competing pathways, the AD and HBC pathways, were proposed for the side-chain degradation. The proposed HBC pathway has great value in illustrating the production mechanism of HBCs in sterol catabolism and in developing HBCs producing strains for industrial application via metabolic engineering. Through the combined modification of hsd4A and other genes, three HBCs producing strains were constructed that resulted in promising productivities of 0.127, 0.109 and 0.074 g/l/h, respectively.
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33
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Holert J, Yücel O, Jagmann N, Prestel A, Möller HM, Philipp B. Identification of bypass reactions leading to the formation of one central steroid degradation intermediate in metabolism of different bile salts inPseudomonassp. strain Chol1. Environ Microbiol 2016; 18:3373-3389. [DOI: 10.1111/1462-2920.13192] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 12/17/2015] [Indexed: 12/13/2022]
Affiliation(s)
- Johannes Holert
- Institut für Molekulare Mikrobiologie und Biotechnologie; Westfälische Wilhelms-Universität Münster; Corrensstr. 3 Münster 48149 Germany
| | - Onur Yücel
- Institut für Molekulare Mikrobiologie und Biotechnologie; Westfälische Wilhelms-Universität Münster; Corrensstr. 3 Münster 48149 Germany
| | - Nina Jagmann
- Institut für Molekulare Mikrobiologie und Biotechnologie; Westfälische Wilhelms-Universität Münster; Corrensstr. 3 Münster 48149 Germany
| | | | | | - Bodo Philipp
- Institut für Molekulare Mikrobiologie und Biotechnologie; Westfälische Wilhelms-Universität Münster; Corrensstr. 3 Münster 48149 Germany
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34
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Shtratnikova VY, Schelkunov MI, Fokina VV, Pekov YA, Ivashina T, Donova MV. Genome-wide bioinformatics analysis of steroid metabolism-associated genes in Nocardioides simplex VKM Ac-2033D. Curr Genet 2016; 62:643-56. [PMID: 26832142 DOI: 10.1007/s00294-016-0568-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 01/04/2016] [Accepted: 01/16/2016] [Indexed: 11/27/2022]
Abstract
Actinobacteria comprise diverse groups of bacteria capable of full degradation, or modification of different steroid compounds. Steroid catabolism has been characterized best for the representatives of suborder Corynebacterineae, such as Mycobacteria, Rhodococcus and Gordonia, with high content of mycolic acids in the cell envelope, while it is poorly understood for other steroid-transforming actinobacteria, such as representatives of Nocardioides genus belonging to suborder Propionibacterineae. Nocardioides simplex VKM Ac-2033D is an important biotechnological strain which is known for its ability to introduce ∆(1)-double bond in various 1(2)-saturated 3-ketosteroids, and perform convertion of 3β-hydroxy-5-ene steroids to 3-oxo-4-ene steroids, hydrolysis of acetylated steroids, reduction of carbonyl groups at C-17 and C-20 of androstanes and pregnanes, respectively. The strain is also capable of utilizing cholesterol and phytosterol as carbon and energy sources. In this study, a comprehensive bioinformatics genome-wide screening was carried out to predict genes related to steroid metabolism in this organism, their clustering and possible regulation. The predicted operon structure and number of candidate gene copies paralogs have been estimated. Binding sites of steroid catabolism regulators KstR and KstR2 specified for N. simplex VKM Ac-2033D have been calculated de novo. Most of the candidate genes grouped within three main clusters, one of the predicted clusters having no analogs in other actinobacteria studied so far. The results offer a base for further functional studies, expand the understanding of steroid catabolism by actinobacteria, and will contribute to modifying of metabolic pathways in order to generate effective biocatalysts capable of producing valuable bioactive steroids.
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Affiliation(s)
- Victoria Y Shtratnikova
- Department of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Leninskie Gory, h. 1, b. 73, Moscow, 119991, Russian Federation.
| | - Mikhail I Schelkunov
- Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoy Karetny per. 19, b. 1, Moscow, 127051, Russian Federation
- A.N. Belozersky Research Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskye Gory, h. 1, b. 41, Moscow, 119991, Russian Federation
| | - Victoria V Fokina
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Prospekt Nauki, 5, Puschino, Moscow, 142290, Russian Federation
| | - Yury A Pekov
- Department of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Leninskie Gory, h. 1, b. 73, Moscow, 119991, Russian Federation
| | - Tanya Ivashina
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Prospekt Nauki, 5, Puschino, Moscow, 142290, Russian Federation
| | - Marina V Donova
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Prospekt Nauki, 5, Puschino, Moscow, 142290, Russian Federation
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Unsaturated Lipid Assimilation by Mycobacteria Requires Auxiliary cis-trans Enoyl CoA Isomerase. ACTA ACUST UNITED AC 2015; 22:1577-87. [DOI: 10.1016/j.chembiol.2015.10.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 10/13/2015] [Accepted: 10/15/2015] [Indexed: 11/30/2022]
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Lu R, Schmitz W, Sampson NS. α-Methyl Acyl CoA Racemase Provides Mycobacterium tuberculosis Catabolic Access to Cholesterol Esters. Biochemistry 2015; 54:5669-72. [PMID: 26348625 DOI: 10.1021/acs.biochem.5b00911] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Metabolism of cholesterol by Mycobacterium tuberculosis (Mtb) contributes to its pathogenesis. We show that ChsE4-ChsE5 (Rv3504/Rv3505) specifically catalyzes dehydrogenation of the (25S)-3-oxo-cholest-4-en-26-oyl-CoA diastereomer in cholesterol side chain β-oxidation. Thus, a dichotomy between the supply of both 25R and 25S metabolic precursors by upstream cytochrome P450s and the substrate stereospecificity of ChsE4-ChsE5 exists. We reconcile the dilemma of 25R metabolite production by demonstrating that mycobacterial MCR (Rv1143) can efficiently epimerize C25 diastereomers of 3-oxo-cholest-4-en-26-oyl-CoA. Our data suggest that cholesterol and cholesterol ester precursors can converge into a single catabolic pathway, thus widening the metabolic niche in which Mtb survives.
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Affiliation(s)
- Rui Lu
- Department of Chemistry, Stony Brook University , Stony Brook, New York 11794-3400, United States
| | - Werner Schmitz
- Lehrstuhl für Biochemie und Molekularbiologie, Biozentrum-Am Hubland , 7074 Würzburg, Germany
| | - Nicole S Sampson
- Department of Chemistry, Stony Brook University , Stony Brook, New York 11794-3400, United States
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Li W, Ge F, Zhang Q, Ren Y, Yuan J, He J, Li W, Chen G, Zhang G, Zhuang Y, Xu L. Identification of gene expression profiles in the actinomycete Gordonia neofelifaecis grown with different steroids. Genome 2015; 57:345-53. [PMID: 25264805 DOI: 10.1139/gen-2014-0030] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Gordonia neofelifaecis NRRL B-59395 was initially isolated from the fresh feces of a clouded leopard based on its ability to degrade cholesterol. The transcriptome profiles of G. neofelifaecis NRRL B-59395 grown with cholesterol, androstenedione (AD), and pyruvic acid were compared by RNA-Seq. The sterol catabolic genes are highly conserved in G. neofelifaecis, Rhodococcus jostii RHA1, and Mycobacterium tuberculosis. The RNA-Seq results indicated that the genes involved in the sterol side chain cleavage were exclusively induced by cholesterol, while the genes involved in the degradation of rings A/B and C/D were up-regulated by both cholesterol and AD. It appears that the induction mechanisms for the genes responsible for side chain cleavage and those for degradation of rings are different. There are approximately 21 genes encoding transporter proteins that are differentially expressed in cholesterol or AD compared with pyruvic acid. The genes camABCD and camM encode two systems that take up cholate, and they have been shown to be cholesterol- and AD-inducible. The potential biological functions of other differentially expressed genes are also discussed. These results will promote the functional characterization of the sterol catabolic genes and also provide important clues in understanding the mechanisms of their gene expression, and they may help us understand the mechanism underlying microbial cholesterol catabolism.
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Affiliation(s)
- Wenjing Li
- College of life Sciences, Sichuan Normal University, Chengdu 610101, P.R. China
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38
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Yang M, Lu R, Guja KE, Wipperman M, St. Clair JR, Bonds AC, Garcia-Diaz M, Sampson NS. Unraveling Cholesterol Catabolism in Mycobacterium tuberculosis: ChsE4-ChsE5 α 2β 2 Acyl-CoA Dehydrogenase Initiates β-Oxidation of 3-Oxo-cholest-4-en-26-oyl CoA. ACS Infect Dis 2015; 1:110-125. [PMID: 26161441 PMCID: PMC4489319 DOI: 10.1021/id500033m] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Indexed: 01/15/2023]
Abstract
The metabolism of host cholesterol by Mycobacterium tuberculosis (Mtb) is an important factor for both its virulence and pathogenesis, although how and why cholesterol metabolism is required is not fully understood. Mtb uses a unique set of catabolic enzymes that are homologous to those required for classical β-oxidation of fatty acids but are specific for steroid-derived substrates. Here, we identify and assign the substrate specificities of two of these enzymes, ChsE4-ChsE5 (Rv3504-Rv3505) and ChsE3 (Rv3573c), that carry out cholesterol side chain oxidation in Mtb. Steady-state assays demonstrate that ChsE4-ChsE5 preferentially catalyzes the oxidation of 3-oxo-cholest-4-en-26-oyl CoA in the first cycle of cholesterol side chain β-oxidation that ultimately yields propionyl-CoA, whereas ChsE3 specifically catalyzes the oxidation of 3-oxo-chol-4-en-24-oyl CoA in the second cycle of β-oxidation that generates acetyl-CoA. However, ChsE4-ChsE5 can catalyze the oxidation of 3-oxo-chol-4-en-24-oyl CoA as well as 3-oxo-4-pregnene-20-carboxyl-CoA. The functional redundancy of ChsE4-ChsE5 explains the in vivo phenotype of the igr knockout strain of Mycobacterium tuberculosis; the loss of ChsE1-ChsE2 can be compensated for by ChsE4-ChsE5 during the chronic phase of infection. The X-ray crystallographic structure of ChsE4-ChsE5 was determined to a resolution of 2.0 Å and represents the first high-resolution structure of a heterotetrameric acyl-CoA dehydrogenase (ACAD). Unlike typical homotetrameric ACADs that bind four flavin adenine dinucleotide (FAD) cofactors, ChsE4-ChsE5 binds one FAD at each dimer interface, resulting in only two substrate-binding sites rather than the classical four active sites. A comparison of the ChsE4-ChsE5 substrate-binding site to those of known mammalian ACADs reveals an enlarged binding cavity that accommodates steroid substrates and highlights novel prospects for designing inhibitors against the committed β-oxidation step in the first cycle of cholesterol side chain degradation by Mtb.
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Affiliation(s)
- Meng Yang
- Department of Chemistry, Department of Pharmacological
Sciences, and Biochemistry and
Structural Biology Graduate Program, Stony
Brook University, Stony Brook, New York 11794, United States
| | - Rui Lu
- Department of Chemistry, Department of Pharmacological
Sciences, and Biochemistry and
Structural Biology Graduate Program, Stony
Brook University, Stony Brook, New York 11794, United States
| | - Kip E. Guja
- Department of Chemistry, Department of Pharmacological
Sciences, and Biochemistry and
Structural Biology Graduate Program, Stony
Brook University, Stony Brook, New York 11794, United States
| | - Matthew
F. Wipperman
- Department of Chemistry, Department of Pharmacological
Sciences, and Biochemistry and
Structural Biology Graduate Program, Stony
Brook University, Stony Brook, New York 11794, United States
| | - Johnna R. St. Clair
- Department of Chemistry, Department of Pharmacological
Sciences, and Biochemistry and
Structural Biology Graduate Program, Stony
Brook University, Stony Brook, New York 11794, United States
| | - Amber C. Bonds
- Department of Chemistry, Department of Pharmacological
Sciences, and Biochemistry and
Structural Biology Graduate Program, Stony
Brook University, Stony Brook, New York 11794, United States
| | - Miguel Garcia-Diaz
- Department of Chemistry, Department of Pharmacological
Sciences, and Biochemistry and
Structural Biology Graduate Program, Stony
Brook University, Stony Brook, New York 11794, United States
| | - Nicole S. Sampson
- Department of Chemistry, Department of Pharmacological
Sciences, and Biochemistry and
Structural Biology Graduate Program, Stony
Brook University, Stony Brook, New York 11794, United States
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Rienksma RA, Suarez-Diez M, Mollenkopf HJ, Dolganov GM, Dorhoi A, Schoolnik GK, Martins Dos Santos VA, Kaufmann SH, Schaap PJ, Gengenbacher M. Comprehensive insights into transcriptional adaptation of intracellular mycobacteria by microbe-enriched dual RNA sequencing. BMC Genomics 2015; 16:34. [PMID: 25649146 PMCID: PMC4334782 DOI: 10.1186/s12864-014-1197-2] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 12/22/2014] [Indexed: 02/06/2023] Open
Abstract
Background The human pathogen Mycobacterium tuberculosis has the capacity to escape eradication by professional phagocytes. During infection, M. tuberculosis resists the harsh environment of phagosomes and actively manipulates macrophages and dendritic cells to ensure prolonged intracellular survival. In contrast to other intracellular pathogens, it has remained difficult to capture the transcriptome of mycobacteria during infection due to an unfavorable host-to-pathogen ratio. Results We infected the human macrophage-like cell line THP-1 with the attenuated M. tuberculosis surrogate M. bovis Bacillus Calmette–Guérin (M. bovis BCG). Mycobacterial RNA was up to 1000-fold underrepresented in total RNA preparations of infected host cells. We employed microbial enrichment combined with specific ribosomal RNA depletion to simultaneously analyze the transcriptional responses of host and pathogen during infection by dual RNA sequencing. Our results confirm that mycobacterial pathways for cholesterol degradation and iron acquisition are upregulated during infection. In addition, genes involved in the methylcitrate cycle, aspartate metabolism and recycling of mycolic acids were induced. In response to M. bovis BCG infection, host cells upregulated de novo cholesterol biosynthesis presumably to compensate for the loss of this metabolite by bacterial catabolism. Conclusions Dual RNA sequencing allows simultaneous capture of the global transcriptome of host and pathogen, during infection. However, mycobacteria remained problematic due to their relatively low number per host cell resulting in an unfavorable bacterium-to-host RNA ratio. Here, we use a strategy that combines enrichment for bacterial transcripts and dual RNA sequencing to provide the most comprehensive transcriptome of intracellular mycobacteria to date. The knowledge acquired into the pathogen and host pathways regulated during infection may contribute to a solid basis for the deployment of novel intervention strategies to tackle infection. Electronic supplementary material The online version of this article (doi:10.1186/s12864-014-1197-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rienk A Rienksma
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research Centre, Dreijenplein 10, 6703, HB, Wageningen, the Netherlands.
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research Centre, Dreijenplein 10, 6703, HB, Wageningen, the Netherlands.
| | - Hans-Joachim Mollenkopf
- Core Facility Microarray/Genomics, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117, Berlin, Germany.
| | - Gregory M Dolganov
- Department of Microbiology and Immunology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305-5124, USA.
| | - Anca Dorhoi
- Department of Immunology, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117, Berlin, Germany.
| | - Gary K Schoolnik
- Department of Microbiology and Immunology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305-5124, USA.
| | - Vitor Ap Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research Centre, Dreijenplein 10, 6703, HB, Wageningen, the Netherlands. .,LifeGlimmer GmbH, Markelstrasse 38, 12163, Berlin, Germany.
| | - Stefan He Kaufmann
- Department of Immunology, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117, Berlin, Germany.
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research Centre, Dreijenplein 10, 6703, HB, Wageningen, the Netherlands.
| | - Martin Gengenbacher
- Department of Immunology, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117, Berlin, Germany. .,Present address: Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore, 117545, Singapore.
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40
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Characterization of novel acyl coenzyme A dehydrogenases involved in bacterial steroid degradation. J Bacteriol 2015; 197:1360-7. [PMID: 25645564 DOI: 10.1128/jb.02420-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
UNLABELLED The acyl coenzyme A (acyl-CoA) dehydrogenases (ACADs) FadE34 and CasC, encoded by the cholesterol and cholate gene clusters of Mycobacterium tuberculosis and Rhodococcus jostii RHA1, respectively, were successfully purified. Both enzymes differ from previously characterized ACADs in that they contain two fused acyl-CoA dehydrogenase domains in a single polypeptide. Site-specific mutagenesis showed that only the C-terminal ACAD domain contains the catalytic glutamate base required for enzyme activity, while the N-terminal ACAD domain contains an arginine required for ionic interactions with the pyrophosphate of the flavin adenine dinucleotide (FAD) cofactor. Therefore, the two ACAD domains must associate to form a single active site. FadE34 and CasC were not active toward the 3-carbon side chain steroid metabolite 3-oxo-23,24-bisnorchol-4-en-22-oyl-CoA (4BNC-CoA) but were active toward steroid CoA esters containing 5-carbon side chains. CasC has similar specificity constants for cholyl-CoA, deoxycholyl-CoA, and 3β-hydroxy-5-cholen-24-oyl-CoA, while FadE34 has a preference for the last compound, which has a ring structure similar to that of cholesterol metabolites. Knockout of the casC gene in R. jostii RHA1 resulted in a reduced growth on cholate as a sole carbon source and accumulation of a 5-carbon side chain cholate metabolite. FadE34 and CasC represent unique members of ACADs with primary structures and substrate specificities that are distinct from those of previously characterized ACADs. IMPORTANCE We report here the identification and characterization of acyl-CoA dehydrogenases (ACADs) involved in the metabolism of 5-carbon side chains of cholesterol and cholate. The two homologous enzymes FadE34 and CasC, from M. tuberculosis and Rhodococcus jostii RHA1, respectively, contain two ACAD domains per polypeptide, and we show that these two domains interact to form a single active site. FadE34 and CasC are therefore representatives of a new class of ACADs with unique primary and quaternary structures. The bacterial steroid degradation pathway is important for the removal of steroid waste in the environment and for survival of the pathogen M. tuberculosis within host macrophages. FadE34 is a potential target for development of new antibiotics against tuberculosis.
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41
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Yang M, Guja KE, Thomas ST, Garcia-Diaz M, Sampson NS. A distinct MaoC-like enoyl-CoA hydratase architecture mediates cholesterol catabolism in Mycobacterium tuberculosis. ACS Chem Biol 2014; 9:2632-45. [PMID: 25203216 PMCID: PMC4245171 DOI: 10.1021/cb500232h] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
![]()
The Mycobacterium tuberculosis (Mtb) igr operon plays an essential
role in Mtb cholesterol metabolism, which is critical
for pathogenesis
during the latent stage of Mtb infection. Here we
report the first structure of a heterotetrameric MaoC-like enoyl-CoA
hydratase, ChsH1-ChsH2, which is encoded by two adjacent genes from
the igr operon. We demonstrate that ChsH1-ChsH2 catalyzes
the hydration of a steroid enoyl-CoA, 3-oxo-4,17-pregnadiene-20-carboxyl-CoA,
in the modified β-oxidation pathway for cholesterol side chain
degradation. The ligand-bound and apoenzyme structures of ChsH1-ChsH2N reveal an unusual, modified hot-dog fold with a severely
truncated central α-helix that creates an expanded binding site
to accommodate the bulkier steroid ring system. The structures show
quaternary structure shifts that accommodate the four rings of the
steroid substrate and offer an explanation for why the unusual heterotetrameric
assembly is utilized for hydration of this steroid. The unique αβ
heterodimer architecture utilized by ChsH1-ChsH2 to bind its distinctive
substrate highlights an opportunity for the development of new antimycobacterial
drugs that target a pathway specific to Mtb.
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Affiliation(s)
- Meng Yang
- Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Kip E. Guja
- Department
of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794-8651, United States
| | - Suzanne T. Thomas
- Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Miguel Garcia-Diaz
- Department
of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794-8651, United States
| | - Nicole S. Sampson
- Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
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Wipperman MF, Sampson NS, Thomas ST. Pathogen roid rage: cholesterol utilization by Mycobacterium tuberculosis. Crit Rev Biochem Mol Biol 2014; 49:269-93. [PMID: 24611808 PMCID: PMC4255906 DOI: 10.3109/10409238.2014.895700] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The ability of science and medicine to control the pathogen Mycobacterium tuberculosis (Mtb) requires an understanding of the complex host environment within which it resides. Pathological and biological evidence overwhelmingly demonstrate how the mammalian steroid cholesterol is present throughout the course of infection. Better understanding Mtb requires a more complete understanding of how it utilizes molecules like cholesterol in this environment to sustain the infection of the host. Cholesterol uptake, catabolism and broader utilization are important for maintenance of the pathogen in the host and it has been experimentally validated to contribute to virulence and pathogenesis. Cholesterol is catabolized by at least three distinct sub-pathways, two for the ring system and one for the side chain, yielding dozens of steroid intermediates with varying biochemical properties. Our ability to control this worldwide infectious agent requires a greater knowledge of how Mtb uses cholesterol to its advantage throughout the course of infection. Herein, the current state of knowledge of cholesterol metabolism by Mtb is reviewed from a biochemical perspective with a focus on the metabolic genes and pathways responsible for cholesterol steroid catabolism.
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Affiliation(s)
| | - Nicole S. Sampson
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400
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Identification of 3-sulfinopropionyl coenzyme A (CoA) desulfinases within the Acyl-CoA dehydrogenase superfamily. J Bacteriol 2013; 196:882-93. [PMID: 24317404 DOI: 10.1128/jb.01265-13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
In a previous study, the essential role of 3-sulfinopropionyl coenzyme A (3SP-CoA) desulfinase acyl-CoA dehydrogenase (Acd) in Advenella mimigardefordensis strain DPN7(T) (AcdDPN7) during degradation of 3,3'-dithiodipropionic acid (DTDP) was elucidated. DTDP is a sulfur-containing precursor substrate for biosynthesis of polythioesters (PTEs). AcdDPN7 showed high amino acid sequence similarity to acyl-CoA dehydrogenases but was unable to catalyze a dehydrogenation reaction. Hence, it was investigated in the present study whether 3SP-CoA desulfinase activity is an uncommon or a widespread property within the acyl-CoA dehydrogenase superfamily. Therefore, proteins of the acyl-CoA dehydrogenase superfamily from Advenella kashmirensis WT001, Bacillus cereus DSM31, Cupriavidus necator N-1, Escherichia coli BL21, Pseudomonas putida KT2440, Burkholderia xenovorans LB400, Ralstonia eutropha H16, Variovorax paradoxus B4, Variovorax paradoxus S110, and Variovorax paradoxus TBEA6 were expressed in E. coli strains. All purified acyl-CoA dehydrogenases appeared as homotetramers, as revealed by size exclusion chromatography. AcdS110, AcdB4, AcdH16, and AcdKT2440 were able to dehydrogenate isobutyryl-CoA. AcdKT2440 additionally dehydrogenated butyryl-CoA and valeryl-CoA, whereas AcdDSM31 dehydrogenated only butyryl-CoA and valeryl-CoA. No dehydrogenation reactions were observed with propionyl-CoA, isovaleryl-CoA, succinyl-CoA, and glutaryl-CoA for any of the investigated acyl-CoA dehydrogenases. Only AcdTBEA6, AcdN-1, and AcdLB400 desulfinated 3SP-CoA and were thus identified as 3SP-CoA desulfinases within the acyl-CoA dehydrogenase family, although none of these three Acds dehydrogenated any of the tested acyl-CoA thioesters. No appropriate substrates were identified for AcdBL21 and AcdWT001. Spectrophotometric assays provided apparent Km and Vmax values for active substrates and indicated the applicability of phylogenetic analyses to predict the substrate range of uncharacterized acyl-CoA dehydrogenases. Furthermore, C. necator N-1 was found to utilize 3SP as the sole source of carbon and energy.
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Actinobacterial acyl coenzyme A synthetases involved in steroid side-chain catabolism. J Bacteriol 2013; 196:579-87. [PMID: 24244004 DOI: 10.1128/jb.01012-13] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Bacterial steroid catabolism is an important component of the global carbon cycle and has applications in drug synthesis. Pathways for this catabolism involve multiple acyl coenzyme A (CoA) synthetases, which activate alkanoate substituents for β-oxidation. The functions of these synthetases are poorly understood. We enzymatically characterized four distinct acyl-CoA synthetases from the cholate catabolic pathway of Rhodococcus jostii RHA1 and the cholesterol catabolic pathway of Mycobacterium tuberculosis. Phylogenetic analysis of 70 acyl-CoA synthetases predicted to be involved in steroid metabolism revealed that the characterized synthetases each represent an orthologous class with a distinct function in steroid side-chain degradation. The synthetases were specific for the length of alkanoate substituent. FadD19 from M. tuberculosis H37Rv (FadD19Mtb) transformed 3-oxo-4-cholesten-26-oate (kcat/Km = 0.33 × 10(5) ± 0.03 × 10(5) M(-1) s(-1)) and represents orthologs that activate the C8 side chain of cholesterol. Both CasGRHA1 and FadD17Mtb are steroid-24-oyl-CoA synthetases. CasG and its orthologs activate the C5 side chain of cholate, while FadD17 and its orthologs appear to activate the C5 side chain of one or more cholesterol metabolites. CasIRHA1 is a steroid-22-oyl-CoA synthetase, representing orthologs that activate metabolites with a C3 side chain, which accumulate during cholate catabolism. CasI had similar apparent specificities for substrates with intact or extensively degraded steroid nuclei, exemplified by 3-oxo-23,24-bisnorchol-4-en-22-oate and 1β(2'-propanoate)-3aα-H-4α(3″-propanoate)-7aβ-methylhexahydro-5-indanone (kcat/Km = 2.4 × 10(5) ± 0.1 × 10(5) M(-1) s(-1) and 3.2 × 10(5) ± 0.3 × 10(5) M(-1) s(-1), respectively). Acyl-CoA synthetase classes involved in cholate catabolism were found in both Actinobacteria and Proteobacteria. Overall, this study provides insight into the physiological roles of acyl-CoA synthetases in steroid catabolism and a phylogenetic classification enabling prediction of specific functions of related enzymes.
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Casabon I, Zhu SH, Otani H, Liu J, Mohn WW, Eltis LD. Regulation of the KstR2 regulon of Mycobacterium tuberculosis by a cholesterol catabolite. Mol Microbiol 2013; 89:1201-12. [PMID: 23879670 DOI: 10.1111/mmi.12340] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2013] [Indexed: 11/28/2022]
Abstract
Cholesterol catabolism is widespread in actinobacteria and is critical for Mycobacterium tuberculosis (Mtb) virulence. Catabolism of steroid nucleus rings C and D is poorly understood: it is initiated by the CoA thioesterification of 3aα-H-4α(3'-propanoate)-7aβ-methylhexahydro-1,5-indanedione (HIP) by FadD3, whose gene is part of the KstR2 regulon. In Mtb, genes of this regulon were upregulated up to 30- and 22-fold during growth on cholesterol and HIP, respectively, versus another minimal medium. In contrast, genes involved in degrading the cholesterol side-chain and nucleus rings A and B were only upregulated during growth on cholesterol. Similar results were obtained in Rhodococcus jostii RHA1. Moreover, the regulon was not upregulated in a ΔfadD3 mutant unable to produce HIP-CoA. In electrophoretic mobility shift assays, HIP-CoA relieved the binding of KstR2(Mtb) to each of three KstR2 boxes: CoASH, HIP and a related CoA thioester did not. Inspection of the structure of KstR2(RHA1) revealed no obvious HIP-CoA binding pocket. The results establish that Mtb can catabolize the entire cholesterol molecule and that HIP-CoA is an effector of KstR2. They further indicate that KstR2 specifically represses the expression of the HIP degradation genes in actinobacteria, which encode a lower pathway involved in the catabolism of multiple steroids.
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Affiliation(s)
- Israël Casabon
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
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46
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Mycobacterium tuberculosis cholesterol catabolism requires a new class of acyl coenzyme A dehydrogenase. J Bacteriol 2013; 195:4319-21. [PMID: 23893117 DOI: 10.1128/jb.00867-13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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47
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Shrinking the FadE proteome of Mycobacterium tuberculosis: insights into cholesterol metabolism through identification of an α2β2 heterotetrameric acyl coenzyme A dehydrogenase family. J Bacteriol 2013; 195:4331-41. [PMID: 23836861 DOI: 10.1128/jb.00502-13] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The ability of the pathogen Mycobacterium tuberculosis to metabolize steroids like cholesterol and the roles that these compounds play in the virulence and pathogenesis of this organism are increasingly evident. Here, we demonstrate through experiments and bioinformatic analysis the existence of an architecturally distinct subfamily of acyl coenzyme A (acyl-CoA) dehydrogenase (ACAD) enzymes that are α2β2 heterotetramers with two active sites. These enzymes are encoded by two adjacent ACAD (fadE) genes that are regulated by cholesterol. FadE26-FadE27 catalyzes the dehydrogenation of 3β-hydroxy-chol-5-en-24-oyl-CoA, an analog of the 5-carbon side chain cholesterol degradation intermediate. Genes encoding the α2β2 heterotetrameric ACAD structures are present in multiple regions of the M. tuberculosis genome, and subsets of these genes are regulated by four different transcriptional repressors or activators: KstR1 (also known as KstR), KstR2, Mce3R, and SigE. Homologous ACAD gene pairs are found in other Actinobacteria, as well as Proteobacteria. Their structures and genomic locations suggest that the α2β2 heterotetrameric structural motif has evolved to enable catalysis of dehydrogenation of steroid- or polycyclic-CoA substrates and that they function in four subpathways of cholesterol metabolism.
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