1
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Holland CK, Jez JM. Fidelity in plant hormone modifications catalyzed by Arabidopsis GH3 acyl acid amido synthetases. J Biol Chem 2024; 300:107421. [PMID: 38815865 PMCID: PMC11253546 DOI: 10.1016/j.jbc.2024.107421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 05/06/2024] [Accepted: 05/22/2024] [Indexed: 06/01/2024] Open
Abstract
GRETCHEN HAGEN 3 (GH3) acyl acid amido synthetases conjugate amino acids to acyl acid hormones to either activate or inactivate the hormone molecule. The largest subgroup of GH3 proteins modify the growth-promoting hormone auxin (indole-3-acetic acid; IAA) with the second largest class activating the defense hormone jasmonic acid (JA). The two-step reaction mechanism of GH3 proteins provides a potential proofreading mechanism to ensure fidelity of hormone modification. Examining pyrophosphate release in the first-half reaction of Arabidopsis GH3 proteins that modify IAA (AtGH3.2/YDK2, AtGH3.5/WES1, AtGH3.17/VAS2), JA (AtGH3.11/JAR1), and other acyl acids (AtGH3.7, AtGH3.12/PBS3) indicates that acyl acid-AMP intermediates are hydrolyzed into acyl acid and AMP in the absence of the amino acid, a typical feature of pre-transfer editing mechanisms. Single-turnover kinetic analysis of AtGH3.2/YDK2 and AtGH3.5/WES1 shows that non-cognate acyl acid-adenylate intermediates are more rapidly hydrolyzed than the cognate IAA-adenylate. In contrast, AtGH3.11/JAR1 only adenylates JA, not IAA. While some of the auxin-conjugating GH3 proteins in Arabidopsis (i.e., AtGH3.5/WES1) accept multiple acyl acid substrates, others, like AtGH3.2/YDK2, are specific for IAA; however, both these proteins share similar active site residues. Biochemical analysis of chimeric variants of AtGH3.2/YDK2 and AtGH3.5/WES1 indicates that the C-terminal domain contributes to selection of cognate acyl acid substrates. These findings suggest that the hydrolysis of non-cognate acyl acid-adenylate intermediates, or proofreading, proceeds via a slowed structural switch that provides a checkpoint for fidelity before the full reaction proceeds.
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Affiliation(s)
- Cynthia K Holland
- Department of Biology, Williams College, Williamstown, Massachusetts; Department of Biology, Washington University in St Louis, St Louis, Missouri
| | - Joseph M Jez
- Department of Biology, Washington University in St Louis, St Louis, Missouri.
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2
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Xu Y, Yang J, Li W, Song S, Shi Y, Wu L, Sun J, Hou M, Wang J, Jia X, Zhang H, Huang M, Lu T, Gan J, Feng Y. Three enigmatic BioH isoenzymes are programmed in the early stage of mycobacterial biotin synthesis, an attractive anti-TB drug target. PLoS Pathog 2022; 18:e1010615. [PMID: 35816546 PMCID: PMC9302846 DOI: 10.1371/journal.ppat.1010615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/21/2022] [Accepted: 05/24/2022] [Indexed: 11/19/2022] Open
Abstract
Tuberculosis (TB) is one of the leading infectious diseases of global concern, and one quarter of the world’s population are TB carriers. Biotin metabolism appears to be an attractive anti-TB drug target. However, the first-stage of mycobacterial biotin synthesis is fragmentarily understood. Here we report that three evolutionarily-distinct BioH isoenzymes (BioH1 to BioH3) are programmed in biotin synthesis of Mycobacterium smegmatis. Expression of an individual bioH isoform is sufficient to allow the growth of an Escherichia coli ΔbioH mutant on the non-permissive condition lacking biotin. The enzymatic activity in vitro combined with biotin bioassay in vivo reveals that BioH2 and BioH3 are capable of removing methyl moiety from pimeloyl-ACP methyl ester to give pimeloyl-ACP, a cognate precursor for biotin synthesis. In particular, we determine the crystal structure of dimeric BioH3 at 2.27Å, featuring a unique lid domain. Apart from its catalytic triad, we also dissect the substrate recognition of BioH3 by pimeloyl-ACP methyl ester. The removal of triple bioH isoforms (ΔbioH1/2/3) renders M. smegmatis biotin auxotrophic. Along with the newly-identified Tam/BioC, the discovery of three unusual BioH isoforms defines an atypical ‘BioC-BioH(3)’ paradigm for the first-stage of mycobacterial biotin synthesis. This study solves a long-standing puzzle in mycobacterial nutritional immunity, providing an alternative anti-TB drug target.
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Affiliation(s)
- Yongchang Xu
- Departments of Microbiology, and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, The People’s Republic of China
| | - Jie Yang
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Science, Fudan University, Shanghai, The People’s Republic of China
| | - Weihui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, The People’s Republic of China
| | - Shuaijie Song
- Departments of Microbiology, and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, The People’s Republic of China
| | - Yu Shi
- Departments of Microbiology, and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, The People’s Republic of China
| | - Lihan Wu
- Departments of Microbiology, and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, The People’s Republic of China
| | - Jingdu Sun
- Departments of Microbiology, and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, The People’s Republic of China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, The People’s Republic of China
| | - Mengyun Hou
- Departments of Microbiology, and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, The People’s Republic of China
| | - Jinzi Wang
- Guangxi Key Laboratory of Utilization of Microbial and Botanical Resources & Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning, Guangxi, The People’s Republic of China
| | - Xu Jia
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, Sichuan, The People’s Republic of China
| | - Huimin Zhang
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Man Huang
- Departments of Microbiology, and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, The People’s Republic of China
| | - Ting Lu
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Jianhua Gan
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Science, Fudan University, Shanghai, The People’s Republic of China
- * E-mail: (JG); (YF)
| | - Youjun Feng
- Departments of Microbiology, and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, The People’s Republic of China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, The People’s Republic of China
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, Sichuan, The People’s Republic of China
- * E-mail: (JG); (YF)
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3
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Richardson SM, Harrison PJ, Herrera MA, Wang M, Verez R, Ortiz GP, Campopiano DJ. BioWF: A naturally-fused, di-domain biocatalyst from biotin biosynthesis displays an unexpectedly broad substrate scope. Chembiochem 2022; 23:e202200171. [PMID: 35695820 PMCID: PMC9544090 DOI: 10.1002/cbic.202200171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/10/2022] [Indexed: 11/30/2022]
Abstract
The carbon backbone of biotin is constructed from the C7 di‐acid pimelate, which is converted to an acyl‐CoA thioester by an ATP‐dependent, pimeloyl‐CoA synthetase (PCAS, encoded by BioW). The acyl‐thioester is condensed with ʟ‐alanine in a decarboxylative, Claisen‐like reaction to form an aminoketone (8‐amino‐7‐oxononanoic acid, AON). This step is catalysed by the pyridoxal 5’‐phosphate (PLP)‐dependent enzyme (AON synthase, AONS, encoded by BioF). Distinct versions of Bacillus subtilis BioW (BsBioW) and E. coli BioF (EcBioF) display strict substrate specificity. In contrast, a BioW‐BioF fusion from Corynebacterium amycolatum (CaBioWF) accepts a wider range of mono‐ and di‐fatty acids. Analysis of the active site of the BsBioW : pimeloyl‐adenylate complex suggested a key role for a Phe (F192) residue in the CaBioW domain; a F192Y mutant restored the substrate specificity to pimelate. This surprising substrate flexibility also extends to the CaBioF domain, which accepts ʟ‐alanine, ʟ‐serine and glycine. Structural models of the CaBioWF fusion provide insight into how both domains interact with each other and suggest the presence of an intra‐domain tunnel. The CaBioWF fusion catalyses conversion of various fatty acids and amino acids to a range of AON derivatives. Such unexpected, natural broad substrate scope suggests that the CaBioWF fusion is a versatile biocatalyst that can be used to prepare a number of aminoketone analogues.
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Affiliation(s)
- Shona M Richardson
- The University of Edinburgh School of Chemistry, Chemistry, David Brewster Road, EH9 3FJ, Edinburgh, UNITED KINGDOM
| | - Peter J Harrison
- The University of Edinburgh School of Chemistry, Chemistry, UNITED KINGDOM
| | - Michael A Herrera
- The University of Edinburgh School of Chemistry, Chemistry, UNITED KINGDOM
| | - Menglu Wang
- The University of Edinburgh School of Chemistry, Chemistry, UNITED KINGDOM
| | - Rebecca Verez
- The University of Edinburgh School of Chemistry, Chemistry, UNITED KINGDOM
| | | | - Dominic James Campopiano
- The Joseph Black Chemistry Building The King's Buildings, School of Chemistry, EastChem, David Brewster Road, EH9 3FJ, Edinburgh, UNITED KINGDOM
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4
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Biochemical and structural characterization of the BioZ enzyme engaged in bacterial biotin synthesis pathway. Nat Commun 2021; 12:2056. [PMID: 33824341 PMCID: PMC8024396 DOI: 10.1038/s41467-021-22360-4] [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] [Received: 11/22/2019] [Accepted: 03/12/2021] [Indexed: 01/07/2023] Open
Abstract
Biotin is an essential micro-nutrient across the three domains of life. The paradigm earlier step of biotin synthesis denotes "BioC-BioH" pathway in Escherichia coli. Here we report that BioZ bypasses the canonical route to begin biotin synthesis. In addition to its origin of Rhizobiales, protein phylogeny infers that BioZ is domesticated to gain an atypical role of β-ketoacyl-ACP synthase III. Genetic and biochemical characterization demonstrates that BioZ catalyzes the condensation of glutaryl-CoA (or ACP) with malonyl-ACP to give 5'-keto-pimeloyl ACP. This intermediate proceeds via type II fatty acid synthesis (FAS II) pathway, to initiate the formation of pimeloyl-ACP, a precursor of biotin synthesis. To further explore molecular basis of BioZ activity, we determine the crystal structure of Agrobacterium tumefaciens BioZ at 1.99 Å, of which the catalytic triad and the substrate-loading tunnel are functionally defined. In particular, we localize that three residues (S84, R147, and S287) at the distant bottom of the tunnel might neutralize the charge of free C-carboxyl group of the primer glutaryl-CoA. Taken together, this study provides molecular insights into the BioZ biotin synthesis pathway.
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5
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Sirithanakorn C, Cronan JE. Biotin, a universal and essential cofactor: Synthesis, ligation and regulation. FEMS Microbiol Rev 2021; 45:6081095. [PMID: 33428728 DOI: 10.1093/femsre/fuab003] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/08/2021] [Indexed: 12/22/2022] Open
Abstract
Biotin is a covalently attached enzyme cofactor required for intermediary metabolism in all three domains of life. Several important human pathogens (e.g. Mycobacterium tuberculosis) require biotin synthesis for pathogenesis. Humans lack a biotin synthetic pathway hence bacterial biotin synthesis is a prime target for new therapeutic agents. The biotin synthetic pathway is readily divided into early and late segments. Although pimelate, a seven carbon α,ω-dicarboxylic acid that contributes seven of the ten biotin carbons atoms, was long known to be a biotin precursor, its biosynthetic pathway was a mystery until the E. coli pathway was discovered in 2010. Since then, diverse bacteria encode evolutionarily distinct enzymes that replace enzymes in the E. coli pathway. Two new bacterial pimelate synthesis pathways have been elucidated. In contrast to the early pathway the late pathway, assembly of the fused rings of the cofactor, was long thought settled. However, a new enzyme that bypasses a canonical enzyme was recently discovered as well as homologs of another canonical enzyme that functions in synthesis of another protein-bound coenzyme, lipoic acid. Most bacteria tightly regulate transcription of the biotin synthetic genes in a biotin-responsive manner. The bifunctional biotin ligases which catalyze attachment of biotin to its cognate enzymes and repress biotin gene transcription are best understood regulatory system.
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Affiliation(s)
- Chaiyos Sirithanakorn
- Faculty of Medicine, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand.,Department of Microbiology, University of Illinois, Urbana, IL 61801, USA
| | - John E Cronan
- Department of Microbiology, University of Illinois, Urbana, IL 61801, USA.,Department of Biochemistry, University of Illinois, Urbana, IL 61801, USA
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6
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Holland CK, Westfall CS, Schaffer JE, De Santiago A, Zubieta C, Alvarez S, Jez JM. Brassicaceae-specific Gretchen Hagen 3 acyl acid amido synthetases conjugate amino acids to chorismate, a precursor of aromatic amino acids and salicylic acid. J Biol Chem 2019; 294:16855-16864. [PMID: 31575658 DOI: 10.1074/jbc.ra119.009949] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/29/2019] [Indexed: 11/06/2022] Open
Abstract
To modulate responses to developmental or environmental cues, plants use Gretchen Hagen 3 (GH3) acyl acid amido synthetases to conjugate an amino acid to a plant hormone, a reaction that regulates free hormone concentration and downstream responses. The model plant Arabidopsis thaliana has 19 GH3 proteins, of which 8 have confirmed biochemical functions. One Brassicaceae-specific clade of GH3 proteins was predicted to use benzoate as a substrate and includes AtGH3.7 and AtGH3.12/PBS3. Previously identified as a 4-hydroxybenzoic acid-glutamate synthetase, AtGH3.12/PBS3 influences pathogen defense responses through salicylic acid. Recent work has shown that AtGH3.12/PBS3 uses isochorismate as a substrate, forming an isochorismate-glutamate conjugate that converts into salicylic acid. Here, we show that AtGH3.7 and AtGH3.12/PBS3 can also conjugate chorismate to cysteine and glutamate, which act as precursors to aromatic amino acids and salicylic acid, respectively. The X-ray crystal structure of AtGH3.12/PBS3 in complex with AMP and chorismate at 1.94 Å resolution, along with site-directed mutagenesis, revealed how the active site potentially accommodates this substrate. Examination of Arabidopsis knockout lines indicated that the gh3.7 mutants do not alter growth and showed no increased susceptibility to the pathogen Pseudomonas syringae, unlike gh3.12 mutants, which were more susceptible than WT plants, as was the gh3.7/gh3.12 double mutant. The findings of our study suggest that GH3 proteins can use metabolic precursors of aromatic amino acids as substrates.
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Affiliation(s)
- Cynthia K Holland
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Corey S Westfall
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Jason E Schaffer
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | | | - Chloe Zubieta
- Laboratoire de Physiologie Cellulaire & Végétale, University Grenoble Alpes, CNRS, CEA, INRA, IRIG, Grenoble, France
| | - Sophie Alvarez
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska 68583
| | - Joseph M Jez
- Department of Biology, Washington University, St. Louis, Missouri 63130
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7
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Peracchi A. The Limits of Enzyme Specificity and the Evolution of Metabolism. Trends Biochem Sci 2018; 43:984-996. [DOI: 10.1016/j.tibs.2018.09.015] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 09/16/2018] [Accepted: 09/19/2018] [Indexed: 12/23/2022]
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8
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Cronan JE. Advances in synthesis of biotin and assembly of lipoic acid. Curr Opin Chem Biol 2018; 47:60-66. [PMID: 30236800 PMCID: PMC6289770 DOI: 10.1016/j.cbpa.2018.08.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 08/07/2018] [Indexed: 11/27/2022]
Abstract
Although biotin and lipoic acid are two universally conserved cofactors essential for intermediary metabolism, their synthetic pathways have become known only in recent years. Both pathways have unusual features. Biotin synthesis in Escherichia coli requires a methylation that is later removed whereas lipoic acid is assembled on the enzymes where it is required for activity by two different pathways.
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Affiliation(s)
- John E Cronan
- Department of Microbiology, University of Illinois, Urbana, IL 61801, USA; Department of Biochemistry, University of Illinois, Urbana, IL 61801, USA.
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9
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Manandhar M, Cronan JE. A Canonical Biotin Synthesis Enzyme, 8-Amino-7-Oxononanoate Synthase (BioF), Utilizes Different Acyl Chain Donors in Bacillus subtilis and Escherichia coli. Appl Environ Microbiol 2018; 84:e02084-17. [PMID: 29054876 PMCID: PMC5734022 DOI: 10.1128/aem.02084-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 10/15/2017] [Indexed: 12/24/2022] Open
Abstract
BioF (8-amino-7-oxononanoate synthase) is a strictly conserved enzyme that catalyzes the first step in assembly of the fused heterocyclic rings of biotin. The BioF acyl chain donor has long been thought to be pimeloyl-CoA. Indeed, in vitro the Escherichia coli and Bacillus sphaericus enzymes have been shown to condense pimeloyl-CoA with l-alanine in a pyridoxal 5'-phosphate-dependent reaction with concomitant CoA release and decarboxylation of l-alanine. However, recent in vivo studies of E. coli and Bacillus subtilis suggested that the BioF proteins of the two bacteria could have different specificities for pimelate thioesters in that E. coli BioF may utilize either pimeloyl coenzyme A (CoA) or the pimelate thioester of the acyl carrier protein (ACP) of fatty acid synthesis. In contrast, B. subtilis BioF seemed likely to be specific for pimeloyl-CoA and unable to utilize pimeloyl-ACP. We now report genetic and in vitro data demonstrating that B. subtilis BioF specifically utilizes pimeloyl-CoA.IMPORTANCE Biotin is an essential vitamin required by mammals and birds because, unlike bacteria, plants, and some fungi, these organisms cannot make biotin. Currently, the biotin included in vitamin tablets and animal feeds is made by chemical synthesis. This is partly because the biosynthetic pathways in bacteria are incompletely understood. This paper defines an enzyme of the Bacillus subtilis pathway and shows that it differs from that of Escherichia coli in the ability to utilize specific precursors. These bacteria have been used in biotin production and these data may aid in making biotin produced by biotechnology commercially competitive with that produced by chemical synthesis.
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Affiliation(s)
- Miglena Manandhar
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - John E Cronan
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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10
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Manandhar M, Cronan JE. Pimelic acid, the first precursor of the Bacillus subtilis biotin synthesis pathway, exists as the free acid and is assembled by fatty acid synthesis. Mol Microbiol 2017; 104:595-607. [PMID: 28196402 PMCID: PMC5426962 DOI: 10.1111/mmi.13648] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biotin synthetic pathways are readily separated into two stages, synthesis of the seven carbon α, ω-dicarboxylic acid pimelate moiety and assembly of the fused heterocyclic rings. The biotin pathway genes responsible for pimelate moiety synthesis vary widely among bacteria whereas the ring synthesis genes are highly conserved. Bacillus subtilis seems to have redundant genes, bioI and bioW, for generation of the pimelate intermediate. Largely consistent with previous genetic studies it was found that deletion of bioW caused a biotin auxotrophic phenotype whereas deletion of bioI did not. BioW is a pimeloyl-CoA synthetase that converts pimelic acid to pimeloyl-CoA. The essentiality of BioW for biotin synthesis indicates that the free form of pimelic acid is an intermediate in biotin synthesis although this is not the case in E. coli. Since the origin of pimelic acid in Bacillus subtilis is unknown, 13 C-NMR studies were carried out to decipher the pathway for its generation. The data provided evidence for the role of free pimelate in biotin synthesis and the involvement of fatty acid synthesis in pimelate production. Cerulenin, an inhibitor of the key fatty acid elongation enzyme, FabF, markedly decreased biotin production by B. subtilis resting cells whereas a strain having a cerulenin-resistant FabF mutant produced more biotin. In addition, supplementation with pimelic acid fully restored biotin production in cerulenin-treated cells. These results indicate that pimelic acid originating from fatty acid synthesis pathway is a bona fide precursor of biotin in B. subtilis.
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Affiliation(s)
- Miglena Manandhar
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - John E Cronan
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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11
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Using the pimeloyl-CoA synthetase adenylation fold to synthesize fatty acid thioesters. Nat Chem Biol 2017; 13:660-667. [PMID: 28414710 DOI: 10.1038/nchembio.2361] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 01/12/2017] [Indexed: 02/05/2023]
Abstract
Biotin is an essential vitamin in plants and mammals, functioning as the carbon dioxide carrier within central lipid metabolism. Bacterial pimeloyl-CoA synthetase (BioW) acts as a highly specific substrate-selection gate, ensuring the integrity of the carbon chain in biotin synthesis. BioW catalyzes the condensation of pimelic acid (C7 dicarboxylic acid) with CoASH in an ATP-dependent manner to form pimeloyl-CoA, the first dedicated biotin building block. Multiple structures of Bacillus subtilis BioW together capture all three substrates, as well as the intermediate pimeloyl-adenylate and product pyrophosphate (PPi), indicating that the enzyme uses an internal ruler to select the correct dicarboxylic acid substrate. Both the catalytic mechanism and the surprising stability of the adenylate intermediate were rationalized through site-directed mutagenesis. Building on this understanding, BioW was engineered to synthesize high-value heptanoyl (C7) and octanoyl (C8) monocarboxylic acid-CoA and C8 dicarboxylic-CoA products, highlighting the enzyme's synthetic potential.
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12
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Estrada P, Manandhar M, Dong SH, Deveryshetty J, Agarwal V, Cronan JE, Nair SK. The pimeloyl-CoA synthetase BioW defines a new fold for adenylate-forming enzymes. Nat Chem Biol 2017; 13:668-674. [PMID: 28414711 DOI: 10.1038/nchembio.2359] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 03/02/2017] [Indexed: 01/11/2023]
Abstract
Reactions that activate carboxylates through acyl-adenylate intermediates are found throughout biology and include acyl- and aryl-CoA synthetases and tRNA synthetases. Here we describe the characterization of Aquifex aeolicus BioW, which represents a new protein fold within the superfamily of adenylating enzymes. Substrate-bound structures identified the enzyme active site and elucidated the mechanistic strategy for conjugating CoA to the seven-carbon α,ω-dicarboxylate pimelate, a biotin precursor. Proper position of reactive groups for the two half-reactions is achieved solely through movements of active site residues, as confirmed by site-directed mutational analysis. The ability of BioW to hydrolyze adenylates of noncognate substrates is reminiscent of pre-transfer proofreading observed in some tRNA synthetases, and we show that this activity can be abolished by mutation of a single residue. These studies illustrate how BioW can carry out three different biologically prevalent chemical reactions (adenylation, thioesterification, and proofreading) in the context of a new protein fold.
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Affiliation(s)
- Paola Estrada
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Miglena Manandhar
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Shi-Hui Dong
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Institute for Genomic Biology University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jaigeeth Deveryshetty
- Institute for Genomic Biology University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Vinayak Agarwal
- Institute for Genomic Biology University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - John E Cronan
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Institute for Genomic Biology University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Satish K Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Institute for Genomic Biology University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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13
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Arabidopsis thaliana GH3.5 acyl acid amido synthetase mediates metabolic crosstalk in auxin and salicylic acid homeostasis. Proc Natl Acad Sci U S A 2016; 113:13917-13922. [PMID: 27849615 DOI: 10.1073/pnas.1612635113] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
In Arabidopsis thaliana, the acyl acid amido synthetase Gretchen Hagen 3.5 (AtGH3.5) conjugates both indole-3-acetic acid (IAA) and salicylic acid (SA) to modulate auxin and pathogen response pathways. To understand the molecular basis for the activity of AtGH3.5, we determined the X-ray crystal structure of the enzyme in complex with IAA and AMP. Biochemical analysis demonstrates that the substrate preference of AtGH3.5 is wider than originally described and includes the natural auxin phenylacetic acid (PAA) and the potential SA precursor benzoic acid (BA). Residues that determine IAA versus BA substrate preference were identified. The dual functionality of AtGH3.5 is unique to this enzyme although multiple IAA-conjugating GH3 proteins share nearly identical acyl acid binding sites. In planta analysis of IAA, PAA, SA, and BA and their respective aspartyl conjugates were determined in wild-type and overexpressing lines of A thaliana This study suggests that AtGH3.5 conjugates auxins (i.e., IAA and PAA) and benzoates (i.e., SA and BA) to mediate crosstalk between different metabolic pathways, broadening the potential roles for GH3 acyl acid amido synthetases in plants.
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Liu Z, Beaufils D, Rossi JC, Pascal R. Evolutionary importance of the intramolecular pathways of hydrolysis of phosphate ester mixed anhydrides with amino acids and peptides. Sci Rep 2014; 4:7440. [PMID: 25501391 PMCID: PMC4262824 DOI: 10.1038/srep07440] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 11/21/2014] [Indexed: 01/31/2023] Open
Abstract
Aminoacyl adenylates (aa-AMPs) constitute essential intermediates of protein biosynthesis. Their polymerization in aqueous solution has often been claimed as a potential route to abiotic peptides in spite of a highly efficient CO2-promoted pathway of hydrolysis. Here we investigate the efficiency and relevance of this frequently overlooked pathway from model amino acid phosphate mixed anhydrides including aa-AMPs. Its predominance was demonstrated at CO2 concentrations matching that of physiological fluids or that of the present-day ocean, making a direct polymerization pathway unlikely. By contrast, the occurrence of the CO2-promoted pathway was observed to increase the efficiency of peptide bond formation owing to the high reactivity of the N-carboxyanhydride (NCA) intermediate. Even considering CO2 concentrations in early Earth liquid environments equivalent to present levels, mixed anhydrides would have polymerized predominantly through NCAs. The issue of a potential involvement of NCAs as biochemical metabolites could even be raised. The formation of peptide–phosphate mixed anhydrides from 5(4H)-oxazolones (transiently formed through prebiotically relevant peptide activation pathways) was also observed as well as the occurrence of the reverse cyclization process in the reactions of these mixed anhydrides. These processes constitute the core of a reaction network that could potentially have evolved towards the emergence of translation.
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Affiliation(s)
- Ziwei Liu
- Institut des Biomolécules Max Mousseron, UMR5247 CNRS - University of Montpellier
| | - Damien Beaufils
- Institut des Biomolécules Max Mousseron, UMR5247 CNRS - University of Montpellier
| | | | - Robert Pascal
- Institut des Biomolécules Max Mousseron, UMR5247 CNRS - University of Montpellier
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Tang Q, Li X, Zou T, Zhang H, Wang Y, Gao R, Li Z, He J, Feng Y. Mycobacterium smegmatis BioQ defines a new regulatory network for biotin metabolism. Mol Microbiol 2014; 94:1006-1023. [PMID: 25287944 DOI: 10.1111/mmi.12817] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2014] [Indexed: 02/06/2023]
Abstract
Biotin (vitamin H), the sulfur-containing enzyme cofactor, is an essential micronutrient for three domains of life. Given the fact that biotin is an energetically expensive molecule whose de novo biosynthesis demands 20 ATP equivalents each, it is reasonable that bacteria have evolved diversified mechanisms in various microorganisms to tightly control biotin metabolism. Unlike the Escherichia coli BirA, the prototypical bi-functional version of biotin protein ligase (BPL) in that it acts as a repressor for biotin biosynthesis pathway, the BirA protein of Mycobacterium smegmatis (M. smegmatis), a closely relative of the tuberculosis-causing pathogen, Mycobacterium tuberculosis, lacked the DNA-binding activity. It raised a possibility that an alternative new regulator might be present to compensate the loss of regulatory function. Here we report that this is the case. Genomic context analyses of M. smegmatis detected a newly identified BioQ homolog classified into the TetR family of transcription factor and its recognizable palindromes. The M. smegmatis BioQ protein was overexpressed and purified to homogeneity. Size-exclusion chromatography combined with chemical cross-linking studies demonstrated that the BioQ protein had a propensity to dimerize. The promoters of bioFD and bioQ/B were mapped using 5'-RACE. Electrophoretic mobility shift assays revealed that BioQ binds specifically to the promoter regions of bioFD and bioQ/B. Further DNase I foot-printing elucidated the BioQ-binding palindromes. Site-directed mutagenesis suggested the important residues critical for BioQ/DNA binding. The isogenic mutant of bioQ (ΔbioQ) was generated using the approach of homologous recombination. The in vivo data from the real-time qPCR combined with the lacZ transcriptional fusion experiments proved that removal of bioQ gave significant increment with expression of bio operons. Also, expression of bio operons were repressed by exogenous addition of biotin, and this repression seemed to depend on the presence of BioQ protein. Thereby, we believed that M. smegmatis BioQ is not only a negative auto-regulator but also a repressor for bioFD and bioB operons involved in the biotin biosynthesis pathway. Collectively, this finding defined the two-protein paradigm of BirA and BioQ, representing a new mechanism for bacterial biotin metabolism.
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Affiliation(s)
- Qing Tang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
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Cronan JE. A new pathway of exogenous fatty acid incorporation proceeds by a classical phosphoryl transfer reaction. Mol Microbiol 2014; 92:217-21. [DOI: 10.1111/mmi.12558] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2014] [Indexed: 02/01/2023]
Affiliation(s)
- John E. Cronan
- Departments of Microbiology and Biochemistry; University of Illinois; Urbana IL 61801 USA
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