1
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Gómez-Fernández D, Romero-González A, Suárez-Rivero JM, Cilleros-Holgado P, Álvarez-Córdoba M, Piñero-Pérez R, Romero-Domínguez JM, Reche-López D, López-Cabrera A, Ibáñez-Mico S, Castro de Oliveira M, Rodríguez-Sacristán A, González-Granero S, García-Verdugo JM, Sánchez-Alcázar JA. A Multi-Target Pharmacological Correction of a Lipoyltransferase LIPT1 Gene Mutation in Patient-Derived Cellular Models. Antioxidants (Basel) 2024; 13:1023. [PMID: 39199267 PMCID: PMC11351668 DOI: 10.3390/antiox13081023] [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: 07/19/2024] [Revised: 08/12/2024] [Accepted: 08/20/2024] [Indexed: 09/01/2024] Open
Abstract
Mutations in the lipoyltransferase 1 (LIPT1) gene are rare inborn errors of metabolism leading to a fatal condition characterized by lipoylation defects of the 2-ketoacid dehydrogenase complexes causing early-onset seizures, psychomotor retardation, abnormal muscle tone, severe lactic acidosis, and increased urine lactate, ketoglutarate, and 2-oxoacid levels. In this article, we characterized the disease pathophysiology using fibroblasts and induced neurons derived from a patient bearing a compound heterozygous mutation in LIPT1. A Western blot analysis revealed a reduced expression of LIPT1 and absent expression of lipoylated pyruvate dehydrogenase E2 (PDH E2) and alpha-ketoglutarate dehydrogenase E2 (α-KGDH E2) subunits. Accordingly, activities of PDH and α-KGDH were markedly reduced, associated with cell bioenergetics failure, iron accumulation, and lipid peroxidation. In addition, using a pharmacological screening, we identified a cocktail of antioxidants and mitochondrial boosting agents consisting of pantothenate, nicotinamide, vitamin E, thiamine, biotin, and α-lipoic acid, which is capable of rescuing LIPT1 pathophysiology, increasing the LIPT1 expression and lipoylation of mitochondrial proteins, improving cell bioenergetics, and eliminating iron overload and lipid peroxidation. Furthermore, our data suggest that the beneficial effect of the treatment is mainly mediated by SIRT3 activation. In conclusion, we have identified a promising therapeutic approach for correcting LIPT1 mutations.
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Affiliation(s)
- David Gómez-Fernández
- Centro Andaluz de Biología del Desarrollo (CABD-CSIC-Universidad Pablo de Olavide), 41013 Sevilla, Spain; (D.G.-F.); (A.R.-G.); (J.M.S.-R.); (P.C.-H.); (M.Á.-C.); (R.P.-P.); (J.M.R.-D.); (D.R.-L.); (A.L.-C.)
| | - Ana Romero-González
- Centro Andaluz de Biología del Desarrollo (CABD-CSIC-Universidad Pablo de Olavide), 41013 Sevilla, Spain; (D.G.-F.); (A.R.-G.); (J.M.S.-R.); (P.C.-H.); (M.Á.-C.); (R.P.-P.); (J.M.R.-D.); (D.R.-L.); (A.L.-C.)
| | - Juan M. Suárez-Rivero
- Centro Andaluz de Biología del Desarrollo (CABD-CSIC-Universidad Pablo de Olavide), 41013 Sevilla, Spain; (D.G.-F.); (A.R.-G.); (J.M.S.-R.); (P.C.-H.); (M.Á.-C.); (R.P.-P.); (J.M.R.-D.); (D.R.-L.); (A.L.-C.)
| | - Paula Cilleros-Holgado
- Centro Andaluz de Biología del Desarrollo (CABD-CSIC-Universidad Pablo de Olavide), 41013 Sevilla, Spain; (D.G.-F.); (A.R.-G.); (J.M.S.-R.); (P.C.-H.); (M.Á.-C.); (R.P.-P.); (J.M.R.-D.); (D.R.-L.); (A.L.-C.)
| | - Mónica Álvarez-Córdoba
- Centro Andaluz de Biología del Desarrollo (CABD-CSIC-Universidad Pablo de Olavide), 41013 Sevilla, Spain; (D.G.-F.); (A.R.-G.); (J.M.S.-R.); (P.C.-H.); (M.Á.-C.); (R.P.-P.); (J.M.R.-D.); (D.R.-L.); (A.L.-C.)
| | - Rocío Piñero-Pérez
- Centro Andaluz de Biología del Desarrollo (CABD-CSIC-Universidad Pablo de Olavide), 41013 Sevilla, Spain; (D.G.-F.); (A.R.-G.); (J.M.S.-R.); (P.C.-H.); (M.Á.-C.); (R.P.-P.); (J.M.R.-D.); (D.R.-L.); (A.L.-C.)
| | - José Manuel Romero-Domínguez
- Centro Andaluz de Biología del Desarrollo (CABD-CSIC-Universidad Pablo de Olavide), 41013 Sevilla, Spain; (D.G.-F.); (A.R.-G.); (J.M.S.-R.); (P.C.-H.); (M.Á.-C.); (R.P.-P.); (J.M.R.-D.); (D.R.-L.); (A.L.-C.)
| | - Diana Reche-López
- Centro Andaluz de Biología del Desarrollo (CABD-CSIC-Universidad Pablo de Olavide), 41013 Sevilla, Spain; (D.G.-F.); (A.R.-G.); (J.M.S.-R.); (P.C.-H.); (M.Á.-C.); (R.P.-P.); (J.M.R.-D.); (D.R.-L.); (A.L.-C.)
| | - Alejandra López-Cabrera
- Centro Andaluz de Biología del Desarrollo (CABD-CSIC-Universidad Pablo de Olavide), 41013 Sevilla, Spain; (D.G.-F.); (A.R.-G.); (J.M.S.-R.); (P.C.-H.); (M.Á.-C.); (R.P.-P.); (J.M.R.-D.); (D.R.-L.); (A.L.-C.)
| | - Salvador Ibáñez-Mico
- Hospital Clínico Universitario Virgen de la Arrixaca, Servicio de Neuropediatría, 30120 Murcia, Spain;
| | - Marta Castro de Oliveira
- Neuropediatria, Neurolinkia, C. Jardín de la Isla, 8, Local 4 y 5, 41014 Sevilla, Spain;
- FEA Pediatría, Centro Universitario Hospitalar de Faro, R. Leão Penedo, 8000-386 Faro, Portugal
- Neuropediatria, Servicio de Pediatría, Hospital Universitario Virgen Macarena, 41009 Sevilla, Spain;
| | - Andrés Rodríguez-Sacristán
- Neuropediatria, Servicio de Pediatría, Hospital Universitario Virgen Macarena, 41009 Sevilla, Spain;
- Departamento de Farmacología, Radiología y Pediatría de la Facultad de Medicina de la Universidad de Sevilla, 41009 Sevilla, Spain
| | - Susana González-Granero
- Laboratory of Comparative Neurobiology, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia and CIBERNED-ISCIII, 46980 Valencia, Spain; (S.G.-G.); (J.M.G.-V.)
| | - José Manuel García-Verdugo
- Laboratory of Comparative Neurobiology, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia and CIBERNED-ISCIII, 46980 Valencia, Spain; (S.G.-G.); (J.M.G.-V.)
| | - José A. Sánchez-Alcázar
- Centro Andaluz de Biología del Desarrollo (CABD-CSIC-Universidad Pablo de Olavide), 41013 Sevilla, Spain; (D.G.-F.); (A.R.-G.); (J.M.S.-R.); (P.C.-H.); (M.Á.-C.); (R.P.-P.); (J.M.R.-D.); (D.R.-L.); (A.L.-C.)
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2
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Cronan JE. Lipoic acid attachment to proteins: stimulating new developments. Microbiol Mol Biol Rev 2024; 88:e0000524. [PMID: 38624243 PMCID: PMC11332335 DOI: 10.1128/mmbr.00005-24] [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] [Indexed: 04/17/2024] Open
Abstract
SUMMARYLipoic acid-modified proteins are essential for central metabolism and pathogenesis. In recent years, the Escherichia coli and Bacillus subtilis lipoyl assembly pathways have been modified and extended to archaea and diverse eukaryotes including humans. These extensions include a new pathway to insert the key sulfur atoms of lipoate, several new pathways of lipoate salvage, and a novel use of lipoic acid in sulfur-oxidizing bacteria. Other advances are the modification of E. coli LplA for studies of protein localization and protein-protein interactions in cell biology and in enzymatic removal of lipoate from lipoyl proteins. Finally, scenarios have been put forth for the evolution of lipoate assembly in archaea.
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Affiliation(s)
- John E. Cronan
- Department of Microbiology, University of Illinois, Urbana, Illinois, USA
- Department of Biochemistry, University of Illinois, Urbana, Illinois, USA
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3
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Lennox-Hvenekilde D, Bali AP, Gronenberg LS, Acevedo-Rocha C, Sommer MOA, Genee HJ. Metabolic engineering of Escherichia coli for high-level production of free lipoic acid. Metab Eng 2023; 76:39-49. [PMID: 36639019 DOI: 10.1016/j.ymben.2023.01.004] [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: 09/26/2022] [Revised: 01/04/2023] [Accepted: 01/07/2023] [Indexed: 01/12/2023]
Abstract
L-Lipoic acid (LA) is an important antioxidant with various industrial applications as a nutraceutical and therapeutic. Currently, LA is produced by chemical synthesis. Cell factory development is complex as LA and its direct precursors only occur naturally in protein-bound forms. Here we report a rationally engineered LA cell factory and demonstrate de novo free LA production from glucose for the first time in E. coli. The pathway represents a significant challenge as the three key enzymes, native Octanoyltransferase (LipB) and Lipoyl Synthase (LipA), and heterologous Lipoamidase (LpA), are all toxic to overexpress in E. coli. To overcome the toxicity of LipB, functional metagenomic selection was used to identify a highly active and non-toxic LipB and LipA from S. liquefaciens. Using high throughput screening, we balanced translation initiation rates and dual, orthogonal induction systems for the toxic genes, LipA and LpA. The optimized strain yielded 2.5 mg free LA per gram of glucose in minimal media, expressing carefully balanced LipB and LipA, Enterococcus faecalis LpA, and a truncated, native, Dihydrolipoyllysine-residue acetyltransferase (AceF) lipoylation domain. When the optimized cell factory strain was cultivated in a fed-batch fermentation, a titer of 87 mg/L free LA in the supernatant was reached after 48 h. This titer is ∼3000-fold higher than previously reported free LA titer and ∼8-fold higher than the previous best total, protein-bound LA titer. The strategies presented here could be helpful in designing, constructing and balancing biosynthetic pathways that harbor toxic enzymes with protein-bound intermediates or products.
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Affiliation(s)
- David Lennox-Hvenekilde
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark; Biosyntia ApS, Fruebjergvej 3, 2100, Oesterbro, Denmark
| | - Anne P Bali
- Biosyntia ApS, Fruebjergvej 3, 2100, Oesterbro, Denmark
| | | | | | - Morten O A Sommer
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark
| | - Hans J Genee
- Biosyntia ApS, Fruebjergvej 3, 2100, Oesterbro, Denmark.
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4
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Xiao J, Guo S, Shi X. Metabolic engineering of Escherichia coli for the production of (R)-α-lipoic acid. Biotechnol Lett 2023; 45:273-286. [PMID: 36586051 DOI: 10.1007/s10529-022-03341-z] [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: 09/01/2022] [Revised: 11/08/2022] [Accepted: 12/16/2022] [Indexed: 01/01/2023]
Abstract
OBJECTIVE To increase the production of (R)-α-lipoic acid directly from octanoic acid using engineered Escherichia coli with the regeneration of S-adenosylmethionine. RESULTS The biosynthesis of (R)-α-lipoic acid (LA) in E. coli BL21(DE3) is improved by co-expression of lipoate-protein ligase A (LplA) from E. coli MG1655 and lipoate synthase (LipA) from Vibrio vulnificus. The engineered strain produces 20.99 µg l-1 of LA in shake flask cultures. The titers of LA are increased to 169.28 µg l-1 after the optimization of the medium components and fermentation conditions. We find that the [4Fe-4S] cluster is important for the activity of LipA and co-expression of iscSUA promotes the regeneration of the [4Fe-4S] cluster and leads to the highest LA titer of 589.30 µg l-1. CONCLUSION The method described here can be widely applied for the biosynthesis of (R)-α-lipoic acid and other metabolites.
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Affiliation(s)
- Jianbin Xiao
- College of Biological Science and Engineering, Fuzhou University, No. 2 Xueyuan Road, Fuzhou, 350108, China
| | - Shaobin Guo
- College of Biological Science and Engineering, Fuzhou University, No. 2 Xueyuan Road, Fuzhou, 350108, China.
| | - Xian'ai Shi
- College of Biological Science and Engineering, Fuzhou University, No. 2 Xueyuan Road, Fuzhou, 350108, China.,Fujian Key Lab of Medical Instrument and Biopharmaceutical Technology, Fuzhou University, No. 2 Xueyuan Road, Fuzhou, 350108, China
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5
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Warui D, Sil D, Lee KH, Neti SS, Esakova OA, Knox HL, Krebs C, Booker SJ. In Vitro Demonstration of Human Lipoyl Synthase Catalytic Activity in the Presence of NFU1. ACS BIO & MED CHEM AU 2022; 2:456-468. [PMID: 36281303 PMCID: PMC9585516 DOI: 10.1021/acsbiomedchemau.2c00020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lipoyl synthase (LS) catalyzes the last step in the biosynthesis of the lipoyl cofactor, which is the attachment of sulfur atoms at C6 and C8 of an n-octanoyllysyl side chain of a lipoyl carrier protein (LCP). The protein is a member of the radical S-adenosylmethionine (SAM) superfamily of enzymes, which use SAM as a precursor to a 5'-deoxyadenosyl 5'-radical (5'-dA·). The role of the 5'-dA· in the LS reaction is to abstract hydrogen atoms from C6 and C8 of the octanoyl moiety of the substrate to initiate subsequent sulfur attachment. All radical SAM enzymes have at least one [4Fe-4S] cluster that is used in the reductive cleavage of SAM to generate the 5'-dA·; however, LSs contain an additional auxiliary [4Fe-4S] cluster from which sulfur atoms are extracted during turnover, leading to degradation of the cluster. Therefore, these enzymes catalyze only 1 turnover in the absence of a system that restores the auxiliary cluster. In Escherichia coli, the auxiliary cluster of LS can be regenerated by the iron-sulfur (Fe-S) cluster carrier protein NfuA as fast as catalysis takes place, and less efficiently by IscU. NFU1 is the human ortholog of E. coli NfuA and has been shown to interact directly with human LS (i.e., LIAS) in yeast two-hybrid analyses. Herein, we show that NFU1 and LIAS form a tight complex in vitro and that NFU1 can efficiently restore the auxiliary cluster of LIAS during turnover. We also show that BOLA3, previously identified as being critical in the biosynthesis of the lipoyl cofactor in humans and Saccharomyces cerevisiae, has no direct effect on Fe-S cluster transfer from NFU1 or GLRX5 to LIAS. Further, we show that ISCA1 and ISCA2 can enhance LIAS turnover, but only slightly.
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Affiliation(s)
- Douglas
M. Warui
- Department
of Chemistry and Biochemistry and Molecular Biology and the Howard Hughes
Medical Institute, The Pennsylvania State
University, University
Park, Pennsylvania 16802, United States
| | - Debangsu Sil
- Department
of Chemistry and Biochemistry and Molecular Biology and the Howard Hughes
Medical Institute, The Pennsylvania State
University, University
Park, Pennsylvania 16802, United States
| | - Kyung-Hoon Lee
- Department
of Chemistry and Biochemistry and Molecular Biology and the Howard Hughes
Medical Institute, The Pennsylvania State
University, University
Park, Pennsylvania 16802, United States
| | - Syam Sundar Neti
- Department
of Chemistry and Biochemistry and Molecular Biology and the Howard Hughes
Medical Institute, The Pennsylvania State
University, University
Park, Pennsylvania 16802, United States
| | - Olga A. Esakova
- Department
of Chemistry and Biochemistry and Molecular Biology and the Howard Hughes
Medical Institute, The Pennsylvania State
University, University
Park, Pennsylvania 16802, United States
| | - Hayley L. Knox
- Department
of Chemistry and Biochemistry and Molecular Biology and the Howard Hughes
Medical Institute, The Pennsylvania State
University, University
Park, Pennsylvania 16802, United States
| | - Carsten Krebs
- Department
of Chemistry and Biochemistry and Molecular Biology and the Howard Hughes
Medical Institute, The Pennsylvania State
University, University
Park, Pennsylvania 16802, United States
| | - Squire J. Booker
- Department
of Chemistry and Biochemistry and Molecular Biology and the Howard Hughes
Medical Institute, The Pennsylvania State
University, University
Park, Pennsylvania 16802, United States
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6
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Neti SS, Sil D, Warui DM, Esakova OA, Solinski AE, Serrano DA, Krebs C, Booker SJ. Characterization of LipS1 and LipS2 from Thermococcus kodakarensis: Proteins Annotated as Biotin Synthases, which Together Catalyze Formation of the Lipoyl Cofactor. ACS BIO & MED CHEM AU 2022; 2:509-520. [PMID: 36281299 PMCID: PMC9585515 DOI: 10.1021/acsbiomedchemau.2c00018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 11/28/2022]
Abstract
Lipoic acid is an eight-carbon sulfur-containing biomolecule that functions primarily as a cofactor in several multienzyme complexes. It is biosynthesized as an attachment to a specific lysyl residue on one of the subunits of these multienzyme complexes. In Escherichia coli and many other organisms, this biosynthetic pathway involves two dedicated proteins: octanoyltransferase (LipB) and lipoyl synthase (LipA). LipB transfers an n-octanoyl chain from the octanoyl-acyl carrier protein to the target lysyl residue, and then, LipA attaches two sulfur atoms (one at C6 and one at C8) to give the final lipoyl cofactor. All classical lipoyl synthases (LSs) are radical S-adenosylmethionine (SAM) enzymes, which use an [Fe4S4] cluster to reductively cleave SAM to generate a 5'-deoxyadenosyl 5'-radical. Classical LSs also contain a second [Fe4S4] cluster that serves as the source of both appended sulfur atoms. Recently, a novel pathway for generating the lipoyl cofactor was reported. This pathway replaces the canonical LS with two proteins, LipS1 and LipS2, which act together to catalyze formation of the lipoyl cofactor. In this work, we further characterize LipS1 and LipS2 biochemically and spectroscopically. Although LipS1 and LipS2 were previously annotated as biotin synthases, we show that both proteins, unlike E. coli biotin synthase, contain two [Fe4S4] clusters. We identify the cluster ligands to both iron-sulfur clusters in both proteins and show that LipS2 acts only on an octanoyl-containing substrate, while LipS1 acts only on an 8-mercaptooctanoyl-containing substrate. Therefore, similarly to E. coli biotin synthase and in contrast to E. coli LipA, sulfur attachment takes place initially at the terminal carbon (C8) and then at the C6 methylene carbon.
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Affiliation(s)
- Syam Sundar Neti
- Department
of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Debangsu Sil
- Department
of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Douglas M. Warui
- Department
of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Olga A. Esakova
- Department
of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Amy E. Solinski
- Department
of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Dante A. Serrano
- Department
of Biochemistry and Molecular Biology, The
Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Carsten Krebs
- Department
of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department
of Biochemistry and Molecular Biology, The
Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Squire J. Booker
- Department
of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department
of Biochemistry and Molecular Biology, The
Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Howard
Hughes
Medical Institute, The Pennsylvania State
University, University
Park, Pennsylvania 16802, United States
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7
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WANG M, ZHANG W, WANG N. Covalent flavoproteins: types, occurrence, biogenesis and catalytic mechanisms. Chin J Nat Med 2022; 20:749-760. [DOI: 10.1016/s1875-5364(22)60194-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Indexed: 11/03/2022]
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8
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Clark KA, Bushin LB, Seyedsayamdost MR. RaS-RiPPs in Streptococci and the Human Microbiome. ACS BIO & MED CHEM AU 2022; 2:328-339. [PMID: 35996476 PMCID: PMC9389541 DOI: 10.1021/acsbiomedchemau.2c00004] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Radical S-adenosylmethionine (RaS) enzymes have
quickly advanced to one of the most abundant and versatile enzyme
superfamilies known. Their chemistry is predicated upon reductive
homolytic cleavage of a carbon–sulfur bond in cofactor S-adenosylmethionine forming an oxidizing carbon-based radical,
which can initiate myriad radical transformations. An emerging role
for RaS enzymes is their involvement in the biosynthesis of ribosomally
synthesized and post-translationally modified peptides (RiPPs), a
natural product family that has become known as RaS-RiPPs. These metabolites
are especially prevalent in human and mammalian microbiomes because
the complex chemistry of RaS enzymes gives rise to correspondingly
complex natural products with minimal cellular energy and genomic
fingerprint, a feature that is advantageous in microbes with small,
host-adapted genomes in competitive environments. Herein, we review
the discovery and characterization of RaS-RiPPs from the human microbiome
with a focus on streptococcal bacteria. We discuss the varied chemical
modifications that RaS enzymes introduce onto their peptide substrates
and the diverse natural products that they give rise to. The majority
of RaS-RiPPs remain to be discovered, providing an intriguing avenue
for future investigations at the intersection of metalloenzymology,
chemical ecology, and the human microbiome.
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Affiliation(s)
- Kenzie A Clark
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Leah B Bushin
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States.,Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
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9
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Ye M, Brown AC, Suess DLM. Reversible Alkyl-Group Migration between Iron and Sulfur in [Fe 4S 4] Clusters. J Am Chem Soc 2022; 144:13184-13195. [PMID: 35830717 PMCID: PMC9526375 DOI: 10.1021/jacs.2c03195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Synthetic [Fe4S4] clusters with Fe-R groups (R = alkyl/benzyl) are shown to release organic radicals on an [Fe4S4]3+-R/[Fe4S4]2+ redox couple, the same that has been proposed for a radical-generating intermediate in the superfamily of radical S-adenosyl-l-methionine (SAM) enzymes. In attempts to trap the immediate precursor to radical generation, a species in which the alkyl group has migrated from Fe to S is instead isolated. This S-alkylated cluster is a structurally faithful model of intermediates proposed in a variety of functionally diverse S transferase enzymes and features an "[Fe4S4]+-like" core that exists as a physical mixture of S = 1/2 and 7/2 states. The latter corresponds to an unusual, valence-localized electronic structure as indicated by distortions in its geometric structure and supported by computational analysis. Fe-to-S alkyl group migration is (electro)chemically reversible, and the preference for Fe vs S alkylation is dictated by the redox state of the cluster. These findings link the organoiron and organosulfur chemistry of Fe-S clusters and are discussed in the context of metalloenzymes that are proposed to make and break Fe-S and/or C-S bonds during catalysis.
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Affiliation(s)
- Mengshan Ye
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Alexandra C. Brown
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Daniel L. M. Suess
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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10
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Rosenberger FA, Tang JX, Sergeant K, Moedas MF, Zierz CM, Moore D, Smith C, Lewis D, Guha N, Hopton S, Falkous G, Lam A, Pyle A, Poulton J, Gorman GS, Taylor RW, Freyer C, Wredenberg A. Pathogenic SLC25A26 variants impair SAH transport activity causing mitochondrial disease. Hum Mol Genet 2022; 31:2049-2062. [PMID: 35024855 PMCID: PMC9239748 DOI: 10.1093/hmg/ddac002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 12/28/2021] [Accepted: 12/31/2021] [Indexed: 01/14/2023] Open
Abstract
The SLC25A26 gene encodes a mitochondrial inner membrane carrier that transports S-adenosylmethionine (SAM) into the mitochondrial matrix in exchange for S-adenosylhomocysteine (SAH). SAM is the predominant methyl-group donor for most cellular methylation processes, of which SAH is produced as a by-product. Pathogenic, biallelic SLC25A26 variants are a recognized cause of mitochondrial disease in children, with a severe neonatal onset caused by decreased SAM transport activity. Here, we describe two, unrelated adult cases, one of whom presented with recurrent episodes of severe abdominal pain and metabolic decompensation with lactic acidosis. Both patients had exercise intolerance and mitochondrial myopathy associated with biallelic variants in SLC25A26, which led to marked respiratory chain deficiencies and mitochondrial histopathological abnormalities in skeletal muscle that are comparable to those previously described in early-onset cases. We demonstrate using both mouse and fruit fly models that impairment of SAH, rather than SAM, transport across the mitochondrial membrane is likely the cause of this milder, late-onset phenotype. Our findings associate a novel pathomechanism with a known disease-causing protein and highlight the quests of precision medicine in optimizing diagnosis, therapeutic intervention and prognosis.
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Affiliation(s)
- Florian A Rosenberger
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 65 Stockholm, Sweden
| | - Jia Xin Tang
- Faculty of Medical Sciences, Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Kate Sergeant
- Oxford Regional Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7LE, UK
| | - Marco F Moedas
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 65 Stockholm, Sweden
| | - Charlotte M Zierz
- Faculty of Medical Sciences, Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - David Moore
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 65 Stockholm, Sweden
| | - Conrad Smith
- Oxford Regional Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7LE, UK
| | - David Lewis
- Department of General Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Nishan Guha
- Department of Clinical Biochemistry, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Sila Hopton
- Faculty of Medical Sciences, Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- NHS Highly Specialised Services for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4HH, UK
| | - Gavin Falkous
- Faculty of Medical Sciences, Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- NHS Highly Specialised Services for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4HH, UK
| | - Amanda Lam
- Neurometabolic Unit, Institute of Neurology, Queen Square House, London WC1N 3BG, UK
| | - Angela Pyle
- Faculty of Medical Sciences, Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Joanna Poulton
- Nuffield Department of Women’s and Reproductive Health, University of Oxford, Oxford OX3 9DU, UK
| | - Gráinne S Gorman
- Faculty of Medical Sciences, Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- NHS Highly Specialised Services for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4HH, UK
| | - Robert W Taylor
- Faculty of Medical Sciences, Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- NHS Highly Specialised Services for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4HH, UK
| | - Christoph Freyer
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 65 Stockholm, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Anna Wredenberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 65 Stockholm, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, 171 76 Stockholm, Sweden
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11
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Biochemical Approaches to Probe the Role of the Auxiliary Iron-Sulfur Cluster of Lipoyl Synthase from Mycobacterium Tuberculosis. Methods Mol Biol 2021. [PMID: 34292556 DOI: 10.1007/978-1-0716-1605-5_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Lipoic acid is an essential sulfur-containing cofactor used by several multienzyme complexes involved in energy metabolism and the breakdown of certain amino acids. It is composed of n-octanoic acid with sulfur atoms appended at C6 and C8. Lipoic acid is biosynthesized de novo in its cofactor form, in which it is covalently bound in an amide linkage to a target lysyl residue on a lipoyl carrier protein (LCP). The n-octanoyl moiety of the cofactor is derived from type 2 fatty acid biosynthesis and is transferred to an LCP to afford an octanoyllysyl amino acid. Next, lipoyl synthase (LipA in bacteria) catalyzes the attachment of the two sulfur atoms to afford the intact cofactor. LipA is a radical S-adenosylmethionine (SAM) enzyme that contains two [4Fe-4S] clusters. One [4Fe-4S] cluster is used to facilitate a reductive cleavage of SAM to render the highly oxidizing 5'-deoxyadenosyl 5'-radical needed to abstract C6 and C8 hydrogen atoms to allow for sulfur attachment. By contrast, the second cluster is the sulfur source, necessitating its destruction during turnover. In Escherichia coli, this auxiliary cluster can be restored after each turnover by NfuA or IscU, which are two iron-sulfur cluster carrier proteins that are implicated in iron-sulfur cluster biogenesis. In this chapter, we describe methods for purifying and characterizing LipA and NfuA from Mycobacterium tuberculosis, a human pathogen for which endogenously synthesized lipoic acid is essential. These studies provide the foundation for assessing lipoic acid biosynthesis as a potential target for the design of novel antituberculosis agents.
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12
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Bouvenot T, Dewitte A, Bennaceur N, Pradel E, Pierre F, Bontemps-Gallo S, Sebbane F. Interplay between Yersinia pestis and its flea vector in lipoate metabolism. THE ISME JOURNAL 2021; 15:1136-1149. [PMID: 33479491 PMCID: PMC8182812 DOI: 10.1038/s41396-020-00839-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 10/22/2020] [Accepted: 11/11/2020] [Indexed: 01/29/2023]
Abstract
To thrive, vector-borne pathogens must survive in the vector's gut. How these pathogens successfully exploit this environment in time and space has not been extensively characterized. Using Yersinia pestis (the plague bacillus) and its flea vector, we developed a bioluminescence-based approach and employed it to investigate the mechanisms of pathogenesis at an unprecedented level of detail. Remarkably, lipoylation of metabolic enzymes, via the biosynthesis and salvage of lipoate, increases the Y. pestis transmission rate by fleas. Interestingly, the salvage pathway's lipoate/octanoate ligase LplA enhances the first step in lipoate biosynthesis during foregut colonization but not during midgut colonization. Lastly, Y. pestis primarily uses lipoate provided by digestive proteolysis (presumably as lipoyl peptides) rather than free lipoate in blood, which is quickly depleted by the vector. Thus, spatial and temporal factors dictate the bacterium's lipoylation strategies during an infection, and replenishment of lipoate by digestive proteolysis in the vector might constitute an Achilles' heel that is exploited by pathogens.
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Affiliation(s)
- Typhanie Bouvenot
- grid.503422.20000 0001 2242 6780Univ. Lille, Inserm, CNRS, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 – CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Amélie Dewitte
- grid.503422.20000 0001 2242 6780Univ. Lille, Inserm, CNRS, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 – CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Nadia Bennaceur
- grid.503422.20000 0001 2242 6780Univ. Lille, Inserm, CNRS, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 – CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Elizabeth Pradel
- grid.503422.20000 0001 2242 6780Univ. Lille, Inserm, CNRS, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 – CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - François Pierre
- grid.503422.20000 0001 2242 6780Univ. Lille, Inserm, CNRS, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 – CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Sébastien Bontemps-Gallo
- grid.503422.20000 0001 2242 6780Univ. Lille, Inserm, CNRS, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 – CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Florent Sebbane
- grid.503422.20000 0001 2242 6780Univ. Lille, Inserm, CNRS, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 – CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
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13
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Ward NP, Kang YP, Falzone A, Boyle TA, DeNicola GM. Nicotinamide nucleotide transhydrogenase regulates mitochondrial metabolism in NSCLC through maintenance of Fe-S protein function. J Exp Med 2021; 217:151572. [PMID: 32196080 PMCID: PMC7971138 DOI: 10.1084/jem.20191689] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 01/06/2020] [Accepted: 02/19/2020] [Indexed: 01/30/2023] Open
Abstract
Human lung tumors exhibit robust and complex mitochondrial metabolism, likely precipitated by the highly oxygenated nature of pulmonary tissue. As ROS generation is a byproduct of this metabolism, reducing power in the form of nicotinamide adenine dinucleotide phosphate (NADPH) is required to mitigate oxidative stress in response to this heightened mitochondrial activity. Nicotinamide nucleotide transhydrogenase (NNT) is known to sustain mitochondrial antioxidant capacity through the generation of NADPH; however, its function in non-small cell lung cancer (NSCLC) has not been established. We found that NNT expression significantly enhances tumor formation and aggressiveness in mouse models of lung tumor initiation and progression. We further show that NNT loss elicits mitochondrial dysfunction independent of substantial increases in oxidative stress, but rather marked by the diminished activities of proteins dependent on resident iron-sulfur clusters. These defects were associated with both NADPH availability and ROS accumulation, suggesting that NNT serves a specific role in mitigating the oxidation of these critical protein cofactors.
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Affiliation(s)
- Nathan P Ward
- Department of Cancer Physiology, Moffitt Cancer Center, Tampa, FL
| | - Yun Pyo Kang
- Department of Cancer Physiology, Moffitt Cancer Center, Tampa, FL
| | - Aimee Falzone
- Department of Cancer Physiology, Moffitt Cancer Center, Tampa, FL
| | - Theresa A Boyle
- Department of Molecular Pathology, Moffitt Cancer Center, Tampa, FL
| | - Gina M DeNicola
- Department of Cancer Physiology, Moffitt Cancer Center, Tampa, FL
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14
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Characterization and Reconstitution of Human Lipoyl Synthase (LIAS) Supports ISCA2 and ISCU as Primary Cluster Donors and an Ordered Mechanism of Cluster Assembly. Int J Mol Sci 2021; 22:ijms22041598. [PMID: 33562493 PMCID: PMC7915201 DOI: 10.3390/ijms22041598] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/18/2021] [Accepted: 01/27/2021] [Indexed: 01/18/2023] Open
Abstract
Lipoyl synthase (LIAS) is an iron-sulfur cluster protein and a member of the radical S-adenosylmethionine (SAM) superfamily that catalyzes the final step of lipoic acid biosynthesis. The enzyme contains two [4Fe-4S] centers (reducing and auxiliary clusters) that promote radical formation and sulfur transfer, respectively. Most information concerning LIAS and its mechanism has been determined from prokaryotic enzymes. Herein, we detail the expression, isolation, and characterization of human LIAS, its reactivity, and evaluation of natural iron-sulfur (Fe-S) cluster reconstitution mechanisms. Cluster donation by a number of possible cluster donor proteins and heterodimeric complexes has been evaluated. [2Fe-2S]-cluster-bound forms of human ISCU and ISCA2 were found capable of reconstituting human LIAS, such that complete product turnover was enabled for LIAS, as monitored via a liquid chromatography-mass spectrometry (LC-MS) assay. Electron paramagnetic resonance (EPR) studies of native LIAS and substituted derivatives that lacked the ability to bind one or the other of LIAS's two [4Fe-4S] clusters revealed a likely order of cluster addition, with the auxiliary cluster preceding the reducing [4Fe-4S] center. These results detail the trafficking of Fe-S clusters in human cells and highlight differences with respect to bacterial LIAS analogs. Likely in vivo Fe-S cluster donors to LIAS are identified, with possible connections to human disease states, and a mechanistic ordering of [4Fe-4S] cluster reconstitution is evident.
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15
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Jin J, Chen H, Wang N, Zhu K, Liu H, Shi D, Xin J, Liu H. A Novel Lipoate-Protein Ligase, Mhp-LplJ, Is Required for Lipoic Acid Metabolism in Mycoplasma hyopneumoniae. Front Microbiol 2021; 11:631433. [PMID: 33584596 PMCID: PMC7873978 DOI: 10.3389/fmicb.2020.631433] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 12/30/2020] [Indexed: 11/21/2022] Open
Abstract
Lipoic acid is a conserved cofactor necessary for the activation of several critical enzyme complexes in the aerobic metabolism of 2-oxoacids and one-carbon metabolism. Lipoate metabolism enzymes are key for lipoic acid biosynthesis and salvage. In this study, we found that Mycoplasma hyopneumoniae (M. hyopneumoniae) Mhp-Lpl, which had been previously shown to have lipoate-protein ligase activity against glycine cleavage system H protein (GcvH) in vitro, did not lipoylate the lipoate-dependent subunit of dihydrolipoamide dehydrogenase (PdhD). Further studies indicated that a new putative lipoate-protein ligase in M. hyopneumoniae, MHP_RS00640 (Mhp-LplJ), catalyzes free lipoic acid attachment to PdhD in vitro. In a model organism, Mhp-LplJ exhibited lipoate and octanoate ligase activities against PdhD. When the enzyme activity of Mhp-LplJ was disrupted by lipoic acid analogs, 8-bromooctanoic acid (8-BrO) and 6,8-dichlorooctanoate (6,8-diClO), M. hyopneumoniae growth was arrested in vitro. Taken together, these results indicate that Mhp-LplJ plays a vital role in lipoic acid metabolism of M. hyopneumoniae, which is of great significance to further understand the metabolism of M. hyopneumoniae and develop new antimicrobials against it.
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Affiliation(s)
- Jin Jin
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.,Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Huan Chen
- Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment and SUSTech-HKU Joint Laboratories for Matrix Biology and Diseases, Southern University of Science and Technology, Shenzhen, China
| | - Ning Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Kemeng Zhu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Huanhuan Liu
- College of Life Science, Yangtze University, Kingchow, China
| | - Dongfang Shi
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Jiuqing Xin
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Henggui Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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16
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Zhu W, Klinman JP. Biogenesis of the peptide-derived redox cofactor pyrroloquinoline quinone. Curr Opin Chem Biol 2020; 59:93-103. [PMID: 32731194 PMCID: PMC7736144 DOI: 10.1016/j.cbpa.2020.05.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/04/2020] [Accepted: 05/06/2020] [Indexed: 12/15/2022]
Abstract
Pyrroloquinoline quinone (PQQ) is a peptide-derived redox cofactor produced by prokaryotes that also plays beneficial roles in organisms from other kingdoms. We review recent developments on the pathway of PQQ biogenesis, focusing on the mechanisms of PqqE, PqqF/G, and PqqB. These advances may shed light on other, uncharacterized biosynthetic pathways.
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Affiliation(s)
- Wen Zhu
- California Institute for Quantitative Biosciences and Department of Chemistry, University of California, Berkeley, CA, 94720-3220, USA
| | - Judith P Klinman
- California Institute for Quantitative Biosciences and Department of Chemistry, University of California, Berkeley, CA, 94720-3220, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720-3220, USA.
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17
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Bím D, Alonso-Gil S, Srnec M. From Synthetic to Biological Fe 4 S 4 Complexes: Redox Properties Correlated to Function of Radical S-Adenosylmethionine Enzymes. Chempluschem 2020; 85:2534-2541. [PMID: 33245201 DOI: 10.1002/cplu.202000663] [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] [Received: 10/16/2020] [Revised: 11/02/2020] [Indexed: 11/10/2022]
Abstract
By employing the computational protocol for calculation of reduction potentials of the Fe4 S4 -containing species validated using a representative series of well-defined synthetic complexes, we focused on redox properties of two prototypical radical SAM enzymes to reveal how they transform SAM into the reactive 5'-deoxyadenosyl radical, and how they tune this radical for its proper biological function. We found the reduction potential of SAM is indeed elevated by 0.3-0.4 V upon coordination to Fe4 S4 , which was previously speculated in the literature. This makes a generation of 5'-deoxyadenosyl radical from SAM less endergonic (by ca. 7-9 kcal mol-1 ) and hence more feasible in both enzymes as compared to the identical process in water. Furthermore, our calculations indicate that the enzyme-bound 5'-deoxyadenosyl radical has a significantly lower reduction potential than in referential aqueous solution, which may help the enzymes to suppress potential side redox reactions and simultaneously elevate its proton-philic character, which may, in turn, promote the radical hydrogen-atom abstraction ability.
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Affiliation(s)
- Daniel Bím
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, Prague, 8 182 23, Czech Republic
| | - Santiago Alonso-Gil
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, Prague, 8 182 23, Czech Republic
| | - Martin Srnec
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, Prague, 8 182 23, Czech Republic
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18
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Cronan JE. Progress in the Enzymology of the Mitochondrial Diseases of Lipoic Acid Requiring Enzymes. Front Genet 2020; 11:510. [PMID: 32508887 PMCID: PMC7253636 DOI: 10.3389/fgene.2020.00510] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 04/27/2020] [Indexed: 12/12/2022] Open
Abstract
Three human mitochondrial diseases that directly affect lipoic acid metabolism result from heterozygous missense and nonsense mutations in the LIAS, LIPT1, and LIPT2 genes. However, the functions of the proteins encoded by these genes in lipoic acid metabolism remained uncertain due to a lack of biochemical analysis at the enzyme level. An exception was the LIPT1 protein for which a perplexing property had been reported, a ligase lacking the ability to activate its substrate. This led to several models, some contradictory, to accommodate the role of LIPT1 protein activity in explaining the phenotypes of the afflicted neonatal patients. Recent evidence indicates that this LIPT1 protein activity is a misleading evolutionary artifact and that the physiological role of LIPT1 is in transfer of lipoic acid moieties from one protein to another. This and other new biochemical data now define a straightforward pathway that fully explains each of the human disorders specific to the assembly of lipoic acid on its cognate enzyme proteins.
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Affiliation(s)
- John E Cronan
- B103 Chemical and Life Sciences Laboratory, Departments of Microbiology and Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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19
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Zhu K, Chen H, Jin J, Wang N, Ma G, Huang J, Feng Y, Xin J, Zhang H, Liu H. Functional Identification and Structural Analysis of a New Lipoate Protein Ligase in Mycoplasma hyopneumoniae. Front Cell Infect Microbiol 2020; 10:156. [PMID: 32373550 PMCID: PMC7186572 DOI: 10.3389/fcimb.2020.00156] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 03/24/2020] [Indexed: 11/13/2022] Open
Abstract
Mycoplasma hyopneumoniae (M. hyopneumoniae) is the causative agent of pandemic pneumonia among pigs, namely, swine enzootic pneumonia. Although M. hyopneumoniae was first identified in 1965, little is known regarding its metabolic pathways, which might play a pivotal role during disease pathogenesis. Lipoate is an essential cofactor for enzymes important for central metabolism. However, the lipoate metabolism pathway in M. hyopneumoniae is definitely unclear. Here, we identified a novel gene, lpl, encoding a lipoate protein ligase in the genome of M. hyopneumoniae (Mhp-Lpl). This gene contains 1,032 base pairs and encodes a protein of 343 amino acids, which is between 7.5 and 36.09% identical to lipoate protein ligases (Lpls) of other species. Similar to its homologs in other species, Mhp-Lpl catalyzes the ATP-dependent activation of lipoate to lipoyl-AMP and the transfer of the activated lipoyl onto the lipoyl domains of M. hyopneumoniae GcvH (Mhp H) in vitro. Enzymatic and mutagenesis analysis indicate that residue K56 within the SKT sequence of Mhp H protein is the lipoyl moiety acceptor site. The three-dimensional structure showed typical lipoate protein ligase folding, with a large N-terminal domain and a small C-terminal domain. The large N-terminal domain is responsible for the full enzymatic activity of Mhp-Lpl. The identification and characterization of Mhp-Lpl will be beneficial to our understanding of M. hyopneumoniae metabolism. Summary Lipoic acid is an essential cofactor for the activation of some enzyme complexes involved in key metabolic processes. Lipoate protein ligases (Lpls) are responsible for the metabolism of lipoic acid. To date, little is known regarding the Lpls in M. hyopneumoniae. In this study, we identified a lipoate protein ligase of M. hyopneumoniae. We further analyzed the function, overall structure and ligand-binding site of this protein. The lipoate acceptor site on M. hyopneumoniae GcvH was also identified. Together, these findings reveal that Lpl exists in M. hyopneumoniae and will provide a basis for further exploration of the pathway of lipoic acid metabolism in M. hyopneumoniae.
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Affiliation(s)
- Kemeng Zhu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin, China
| | - Huan Chen
- Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment and SUSTech-HKU Joint Laboratories for Matrix Biology and Diseases, Southern University of Science and Technology, Shenzhen, China.,School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Jin Jin
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin, China
| | - Ning Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin, China
| | - Guixing Ma
- Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment and SUSTech-HKU Joint Laboratories for Matrix Biology and Diseases, Southern University of Science and Technology, Shenzhen, China
| | - Jiandong Huang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Youjun Feng
- Department of Pathogen Biology and Microbiology, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiuqing Xin
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin, China
| | - Hongmin Zhang
- Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment and SUSTech-HKU Joint Laboratories for Matrix Biology and Diseases, Southern University of Science and Technology, Shenzhen, China
| | - Henggui Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin, China
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21
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Zhang B, Arcinas AJ, Radle MI, Silakov A, Booker SJ, Krebs C. First Step in Catalysis of the Radical S-Adenosylmethionine Methylthiotransferase MiaB Yields an Intermediate with a [3Fe-4S] 0-Like Auxiliary Cluster. J Am Chem Soc 2020; 142:1911-1924. [PMID: 31899624 PMCID: PMC7008301 DOI: 10.1021/jacs.9b11093] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The enzyme MiaB catalyzes the attachment of a methylthio (-SCH3) group at the C2 position of N6-(isopentenyl)adenosine (i6A) in the final step of the biosynthesis of the hypermodified tRNA nucleotide 2-methythio-N6-(isopentenyl)adenosine (ms2i6A). MiaB belongs to the expanding subgroup of enzymes of the radical S-adenosylmethionine (SAM) superfamily that harbor one or more auxiliary [4Fe-4S] clusters in addition to the [4Fe-4S] cluster that all family members require for the reductive cleavage of SAM to afford the common 5'-deoxyadenosyl 5'-radical (5'-dA•) intermediate. While the role of the radical SAM cluster in generating the 5'-dA• is well understood, the detailed role of the auxiliary cluster, which is essential for MiaB catalysis, remains unclear. It has been proposed that the auxiliary cluster may serve as a coordination site for exogenously derived sulfur destined for attachment to the substrate or that the cluster itself provides the sulfur atom and is sacrificed during turnover. In this work, we report spectroscopic and biochemical evidence that the auxiliary [4Fe-4S]2+ cluster in Bacteroides thetaiotaomicron (Bt) MiaB is converted to a [3Fe-4S]0-like cluster during the methylation step of catalysis. Mössbauer characterization of the MiaB [3Fe-4S]0-like cluster revealed unusual spectroscopic properties compared to those of other well-characterized cuboidal [3Fe-4S]0 clusters. Specifically, the Fe sites of the mixed-valent moiety do not have identical Mössbauer parameters. Our results support a mechanism where the auxiliary [4Fe-4S] cluster is the direct sulfur source during catalysis.
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22
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Daher R, Mansouri A, Martelli A, Bayart S, Manceau H, Callebaut I, Moulouel B, Gouya L, Puy H, Kannengiesser C, Karim Z. GLRX5 mutations impair heme biosynthetic enzymes ALA synthase 2 and ferrochelatase in Human congenital sideroblastic anemia. Mol Genet Metab 2019; 128:342-351. [PMID: 30660387 DOI: 10.1016/j.ymgme.2018.12.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 12/26/2018] [Accepted: 12/27/2018] [Indexed: 01/20/2023]
Abstract
Non-syndromic microcytic congenital sideroblastic anemia (cSA) is predominantly caused by defective genes encoding for either ALAS2, the first enzyme of heme biosynthesis pathway or SLC25A38, the mitochondrial importer of glycine, an ALAS2 substrate. Herein we explored a new case of cSA with two mutations in GLRX5, a gene for which only two patients have been reported so far. The patient was a young female with biallelic compound heterozygous mutations in GLRX5 (p.Cys67Tyr and p.Met128Lys). Three-D structure analysis confirmed the involvement of Cys67 in the coordination of the [2Fe2S] cluster and suggested a potential role of Met128 in partner interactions. The protein-level of ferrochelatase, the terminal-enzyme of heme process, was increased both in patient-derived lymphoblastoid and CD34+ cells, however, its activity was drastically decreased. The activity of ALAS2 was found altered and possibly related to a defect in the biogenesis of its co-substrate, the succinyl-CoA. Thus, the patient exhibits both a very low ferrochelatase activity without any accumulation of porphyrins precursors in contrast to what is reported in erythropoietic protoporphyria with solely impaired ferrochelatase activity. A significant oxidative stress was evidenced by decreased reduced glutathione and aconitase activity, and increased MnSOD protein expression. This oxidative stress depleted and damaged mtDNA, decreased complex I and IV activities and depleted ATP content. Collectively, our study demonstrates the key role of GLRX5 in modulating ALAS2 and ferrochelatase activities and in maintaining mitochondrial function.
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Affiliation(s)
- Raêd Daher
- INSERM U1149, Centre de Recherche sur l'inflammation (CRI), Paris, France; Université Paris Diderot, site Bichat, Sorbonne Paris cité, DHU UNITY, Paris, France; Laboratory of excellence GR-Ex, Paris, France; AP-HP, Centre Français des Porphyries (CFP), Hôpital Louis Mourier, Colombes, France; AP-HP, Département de Génétique, Hôpital Bichât, Paris, France
| | - Abdellah Mansouri
- INSERM U1149, Centre de Recherche sur l'inflammation (CRI), Paris, France; Université Paris Diderot, site Bichat, Sorbonne Paris cité, DHU UNITY, Paris, France
| | - Alain Martelli
- Department of Translational Medicine and Neurogenetics, Illkirch, France
| | - Sophie Bayart
- Department of Pediatric Hematology, Hôpital Sud, CHU, Rennes, France
| | - Hana Manceau
- INSERM U1149, Centre de Recherche sur l'inflammation (CRI), Paris, France; Université Paris Diderot, site Bichat, Sorbonne Paris cité, DHU UNITY, Paris, France; Laboratory of excellence GR-Ex, Paris, France
| | - Isabelle Callebaut
- CNRS UMR7590, Sorbonne Universités, Université Pierre et Marie Curie-Paris6-MNHN-IRD-IUC, Paris, France
| | - Boualem Moulouel
- AP-HP, Centre Français des Porphyries (CFP), Hôpital Louis Mourier, Colombes, France
| | - Laurent Gouya
- INSERM U1149, Centre de Recherche sur l'inflammation (CRI), Paris, France; Université Paris Diderot, site Bichat, Sorbonne Paris cité, DHU UNITY, Paris, France; Laboratory of excellence GR-Ex, Paris, France; AP-HP, Centre Français des Porphyries (CFP), Hôpital Louis Mourier, Colombes, France
| | - Hervé Puy
- INSERM U1149, Centre de Recherche sur l'inflammation (CRI), Paris, France; Université Paris Diderot, site Bichat, Sorbonne Paris cité, DHU UNITY, Paris, France; Laboratory of excellence GR-Ex, Paris, France; AP-HP, Centre Français des Porphyries (CFP), Hôpital Louis Mourier, Colombes, France.
| | - Caroline Kannengiesser
- INSERM U1149, Centre de Recherche sur l'inflammation (CRI), Paris, France; Université Paris Diderot, site Bichat, Sorbonne Paris cité, DHU UNITY, Paris, France; Laboratory of excellence GR-Ex, Paris, France; AP-HP, Département de Génétique, Hôpital Bichât, Paris, France
| | - Zoubida Karim
- INSERM U1149, Centre de Recherche sur l'inflammation (CRI), Paris, France; Université Paris Diderot, site Bichat, Sorbonne Paris cité, DHU UNITY, Paris, France; Laboratory of excellence GR-Ex, Paris, France.
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23
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Lipoic acid. CHEMTEXTS 2019. [DOI: 10.1007/s40828-019-0091-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Camponeschi F, Muzzioli R, Ciofi-Baffoni S, Piccioli M, Banci L. Paramagnetic 1H NMR Spectroscopy to Investigate the Catalytic Mechanism of Radical S-Adenosylmethionine Enzymes. J Mol Biol 2019; 431:4514-4522. [PMID: 31493409 DOI: 10.1016/j.jmb.2019.08.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/30/2019] [Accepted: 08/30/2019] [Indexed: 10/26/2022]
Abstract
Iron-sulfur clusters in radical S-adenosylmethionine (SAM) enzymes catalyze an astonishing array of complex and chemically challenging reactions across all domains of life. Here we showed that 1H NMR spectroscopy experiments tailored to reveal hyperfine-shifted signals of metal-ligands is a powerful tool to monitor the binding of SAM and of the octanoyl-peptide substrate to the two [4Fe-4S] clusters of human lipoyl synthase. The paramagnetically shifted signals of the iron-ligands were specifically assigned to each of the two bound [4Fe-4S] clusters, and then used to examine the interaction of SAM and substrate molecules with each of the two [4Fe-4S] clusters of human lipoyl synthase. 1H NMR spectroscopy can therefore contribute to the description of the catalityc mechanism of radical SAM enzymes.
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Affiliation(s)
- Francesca Camponeschi
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Riccardo Muzzioli
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Simone Ciofi-Baffoni
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Mario Piccioli
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Lucia Banci
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy.
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25
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Liu H, Marsafari M, Wang F, Deng L, Xu P. Engineering acetyl-CoA metabolic shortcut for eco-friendly production of polyketides triacetic acid lactone in Yarrowia lipolytica. Metab Eng 2019; 56:60-68. [PMID: 31470116 DOI: 10.1016/j.ymben.2019.08.017] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 08/08/2019] [Accepted: 08/22/2019] [Indexed: 12/25/2022]
Abstract
Acetyl-CoA is the central metabolic node connecting glycolysis, Krebs cycle and fatty acids synthase. Plant-derived polyketides, are assembled from acetyl-CoA and malonyl-CoA, represent a large family of biological compounds with diversified bioactivity. Harnessing microbial bioconversion is considered as a feasible approach to large-scale production of polyketides from renewable feedstocks. Most of the current polyketide production platform relied on the lengthy glycolytic steps to provide acetyl-CoA, which inherently suffers from complex regulation with metabolically-costly cofactor/ATP requirements. Using the simplest polyketide triacetic acid lactone (TAL) as a testbed molecule, we demonstrate that acetate uptake pathway in oleaginous yeast (Yarrowia lipolytica) could function as an acetyl-CoA shortcut to achieve metabolic optimality in producing polyketides. We identified the metabolic bottlenecks to rewire acetate utilization for efficient TAL production in Y. lipolytica, including generation of the driving force for acetyl-CoA, malonyl-CoA and NADPH. The engineered strain, with the overexpression of endogenous acetyl-CoA carboxylase (ACC1), malic enzyme (MAE1) and a bacteria-derived cytosolic pyruvate dehydrogenase (PDH), affords robust TAL production with titer up to 4.76 g/L from industrial glacier acetic acid in shake flasks, representing 8.5-times improvement over the parental strain. The acetate-to-TAL conversion ratio (0.149 g/g) reaches 31.9% of the theoretical maximum yield. The carbon flux through this acetyl-CoA metabolic shortcut exceeds the carbon flux afforded by the native glycolytic pathways. Potentially, acetic acid could be manufactured in large-quantity at low-cost from Syngas fermentation or heterogenous catalysis (methanol carbonylation). This alternative carbon sources present a metabolic advantage over glucose to unleash intrinsic pathway limitations and achieve high carbon conversion efficiency and cost-efficiency. This work also highlights that low-cost acetic acid could be sustainably upgraded to high-value polyketides by oleaginous yeast species in an eco-friendly and cost-efficient manner.
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Affiliation(s)
- Huan Liu
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland, Baltimore County, Baltimore, MD, 21250, USA; College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Monireh Marsafari
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland, Baltimore County, Baltimore, MD, 21250, USA; Department of Agronomy and Plant Breeding, University of Guilan, Rasht, Islamic Republic of Iran
| | - Fang Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Li Deng
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.
| | - Peng Xu
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland, Baltimore County, Baltimore, MD, 21250, USA.
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26
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Ruszczycky MW, Zhong A, Liu HW. Following the electrons: peculiarities in the catalytic cycles of radical SAM enzymes. Nat Prod Rep 2019; 35:615-621. [PMID: 29485151 DOI: 10.1039/c7np00058h] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Radical SAM enzymes use S-adenosyl-l-methionine as an oxidant to initiate radical-mediated transformations that would otherwise not be possible with Lewis acid/base chemistry alone. These reactions are either redox neutral or oxidative leading to certain expectations regarding the role of SAM as either a reusable cofactor or the ultimate electron acceptor during each turnover. However, these expectations are frequently not realized resulting in fundamental questions regarding the redox handling and movement of electrons associated with these biological catalysts. Herein we provide a focused perspective on several of these questions and associated hypotheses with an emphasis on recently discovered radical SAM enzymes.
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Affiliation(s)
- Mark W Ruszczycky
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, USA.
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27
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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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28
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Holliday GL, Akiva E, Meng EC, Brown SD, Calhoun S, Pieper U, Sali A, Booker SJ, Babbitt PC. Atlas of the Radical SAM Superfamily: Divergent Evolution of Function Using a "Plug and Play" Domain. Methods Enzymol 2018; 606:1-71. [PMID: 30097089 DOI: 10.1016/bs.mie.2018.06.004] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The radical SAM superfamily contains over 100,000 homologous enzymes that catalyze a remarkably broad range of reactions required for life, including metabolism, nucleic acid modification, and biogenesis of cofactors. While the highly conserved SAM-binding motif responsible for formation of the key 5'-deoxyadenosyl radical intermediate is a key structural feature that simplifies identification of superfamily members, our understanding of their structure-function relationships is complicated by the modular nature of their structures, which exhibit varied and complex domain architectures. To gain new insight about these relationships, we classified the entire set of sequences into similarity-based subgroups that could be visualized using sequence similarity networks. This superfamily-wide analysis reveals important features that had not previously been appreciated from studies focused on one or a few members. Functional information mapped to the networks indicates which members have been experimentally or structurally characterized, their known reaction types, and their phylogenetic distribution. Despite the biological importance of radical SAM chemistry, the vast majority of superfamily members have never been experimentally characterized in any way, suggesting that many new reactions remain to be discovered. In addition to 20 subgroups with at least one known function, we identified additional subgroups made up entirely of sequences of unknown function. Importantly, our results indicate that even general reaction types fail to track well with our sequence similarity-based subgroupings, raising major challenges for function prediction for currently identified and new members that continue to be discovered. Interactive similarity networks and other data from this analysis are available from the Structure-Function Linkage Database.
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Affiliation(s)
- Gemma L Holliday
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States.
| | - Eyal Akiva
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States
| | - Elaine C Meng
- Resource for Biocomputing, Visualization, and Informatics, Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, United States
| | - Shoshana D Brown
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States
| | - Sara Calhoun
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States; Graduate Program in Biophysics, University of California, San Francisco, CA, United States
| | - Ursula Pieper
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States; Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, United States; Quantitative Biosciences Institute, University of California, San Francisco, CA, United States
| | - Squire J Booker
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States; Department of Chemistry, The Pennsylvania State University, University Park, PA, United States; The Howard Hughes Medical Institute, The Pennsylvania State University, University Park, PA, United States
| | - Patricia C Babbitt
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States; Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, United States; Quantitative Biosciences Institute, University of California, San Francisco, CA, United States.
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29
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McCarthy EL, Booker SJ. Biochemical Approaches for Understanding Iron-Sulfur Cluster Regeneration in Escherichia coli Lipoyl Synthase During Catalysis. Methods Enzymol 2018; 606:217-239. [PMID: 30097094 DOI: 10.1016/bs.mie.2018.06.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Lipoyl synthase (LipA in bacteria) is a radical S-adenosylmethionine (SAM) enzyme that catalyzes the second step of the de novo biosynthesis of the lipoyl cofactor: the insertion of sulfur at C6 and C8 of a pendant octanoyl chain. In addition to the [4Fe4S] cluster that is characteristic of the radical SAM (RS) enzymes, LipA contains a second [4Fe4S] cluster that, though controversial, has been proposed to be degraded during turnover to supply the inserted sulfur atoms. A consequence of this proposed role is that the destruction of its iron-sulfur cluster renders the enzyme in an inactive state. Recently, it was shown that Escherichia coli proteins NfuA or IscU can confer catalytic properties to E. coli LipA in vitro. In this chapter, we present methods for characterizing LipA and analyzing its activity in vitro, and provide strategies to monitor the pathway for the regeneration of LipA's auxiliary cluster by E. coli iron-sulfur carrier protein NfuA.
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Affiliation(s)
- Erin L McCarthy
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Squire J Booker
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States; Department of Chemistry, The Pennsylvania State University, University Park, PA, United States; The Howard Hughes Medical Institute, The Pennsylvania State University, University Park, PA, United States.
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30
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Yokoyama K, Lilla EA. C-C bond forming radical SAM enzymes involved in the construction of carbon skeletons of cofactors and natural products. Nat Prod Rep 2018; 35:660-694. [PMID: 29633774 PMCID: PMC6051890 DOI: 10.1039/c8np00006a] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: up to the end of 2017 C-C bond formations are frequently the key steps in cofactor and natural product biosynthesis. Historically, C-C bond formations were thought to proceed by two electron mechanisms, represented by Claisen condensation in fatty acids and polyketide biosynthesis. These types of mechanisms require activated substrates to create a nucleophile and an electrophile. More recently, increasing number of C-C bond formations catalyzed by radical SAM enzymes are being identified. These free radical mediated reactions can proceed between almost any sp3 and sp2 carbon centers, allowing introduction of C-C bonds at unconventional positions in metabolites. Therefore, free radical mediated C-C bond formations are frequently found in the construction of structurally unique and complex metabolites. This review discusses our current understanding of the functions and mechanisms of C-C bond forming radical SAM enzymes and highlights their important roles in the biosynthesis of structurally complex, naturally occurring organic molecules. Mechanistic consideration of C-C bond formation by radical SAM enzymes identifies the significance of three key mechanistic factors: radical initiation, acceptor substrate activation and radical quenching. Understanding the functions and mechanisms of these characteristic enzymes will be important not only in promoting our understanding of radical SAM enzymes, but also for understanding natural product and cofactor biosynthesis.
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Affiliation(s)
- Kenichi Yokoyama
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.
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31
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Arends J, Griego M, Thomanek N, Lindemann C, Kutscher B, Meyer HE, Narberhaus F. An Integrated Proteomic Approach Uncovers Novel Substrates and Functions of the Lon Protease in Escherichia coli. Proteomics 2018; 18:e1800080. [PMID: 29710379 DOI: 10.1002/pmic.201800080] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/20/2018] [Indexed: 01/29/2023]
Abstract
Controlling the cellular abundance and proper function of proteins by proteolysis is a universal process in all living organisms. In Escherichia coli, the ATP-dependent Lon protease is crucial for protein quality control and regulatory processes. To understand how diverse substrates are selected and degraded, unbiased global approaches are needed. We employed a quantitative Super-SILAC (stable isotope labeling with amino acids in cell culture) mass spectrometry approach and compared the proteomes of a lon mutant and a strain producing the protease to discover Lon-dependent physiological functions. To identify Lon substrates, we took advantage of a Lon trapping variant, which is able to translocate substrates but unable to degrade them. Lon-associated proteins were identified by label-free LC-MS/MS. The combination of both approaches revealed a total of 14 novel Lon substrates. Besides the identification of known pathways affected by Lon, for example, the superoxide stress response, our cumulative data suggests previously unrecognized fundamental functions of Lon in sulfur assimilation, nucleotide biosynthesis, amino acid and central energy metabolism.
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Affiliation(s)
- Jan Arends
- Department of Microbial Biology, Ruhr University Bochum, Universitätsstraße 150, D-44801, Bochum, Germany
| | - Marcena Griego
- Department of Microbial Biology, Ruhr University Bochum, Universitätsstraße 150, D-44801, Bochum, Germany
| | - Nikolas Thomanek
- Medical Proteome Center, Ruhr University Bochum, Universitätsstraße 150, D-44801, Bochum, Germany
| | - Claudia Lindemann
- Medical Proteome Center, Ruhr University Bochum, Universitätsstraße 150, D-44801, Bochum, Germany
| | - Blanka Kutscher
- Department of Microbial Biology, Ruhr University Bochum, Universitätsstraße 150, D-44801, Bochum, Germany
| | - Helmut E Meyer
- Medical Proteome Center, Ruhr University Bochum, Universitätsstraße 150, D-44801, Bochum, Germany.,Department of Biomedical Research, Leibniz-Institut für Analytische Wissenschaften - ISAS - e. V., Bunsen-Kirchhoff-Straße 11, D-44139, Dortmund, Germany
| | - Franz Narberhaus
- Department of Microbial Biology, Ruhr University Bochum, Universitätsstraße 150, D-44801, Bochum, Germany
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32
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Dong M, Zhang Y, Lin H. Noncanonical Radical SAM Enzyme Chemistry Learned from Diphthamide Biosynthesis. Biochemistry 2018; 57:3454-3459. [PMID: 29708734 DOI: 10.1021/acs.biochem.8b00287] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Radical S-adenosylmethionine (SAM) enzymes are a superfamily of enzymes that use SAM and reduced [4Fe-4S] cluster to generate a 5'-deoxyadenosyl radical to catalyze numerous challenging reactions. We have reported a type of noncanonical radical SAM enzymes in the diphthamide biosynthesis pathway. These enzymes also use SAM and reduced [4Fe-4S] clusters, but generate a 3-amino-3-carboxypropyl (ACP) radical to modify the substrate protein, translation elongation factor 2. The regioselective cleavage of a different C-S bond of the sulfonium center of SAM in these enzymes comparing to canonical radical SAM enzymes is intriguing. Here, we highlight some recent findings in the mechanism of these types of enzymes, showing that the diphthamide biosynthetic radial SAM enzymes bound SAM with a distinct geometry. In this way, the unique iron of the [4Fe-4S] cluster in the enzyme can only attack the carbon on the ACP group to form an organometallic intermediate. The homolysis of the organometallic intermediate releases the ACP radical and generates the EF2 radial.
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Affiliation(s)
- Min Dong
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
| | - Yugang Zhang
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
| | - Hening Lin
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States.,Howard Hughes Medical Institute; Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
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33
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Laczkovich I, Teoh WP, Flury S, Grayczyk JP, Zorzoli A, Alonzo F. Increased flexibility in the use of exogenous lipoic acid by Staphylococcus aureus. Mol Microbiol 2018; 109:150-168. [PMID: 29660187 DOI: 10.1111/mmi.13970] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2018] [Indexed: 02/06/2023]
Abstract
Lipoic acid is a cofactor required for intermediary metabolism that is either synthesized de novo or acquired from environmental sources. The bacterial pathogen Staphylococcus aureus encodes enzymes required for de novo biosynthesis, but also encodes two ligases, LplA1 and LplA2, that are sufficient for lipoic acid salvage during infection. S. aureus also encodes two H proteins, GcvH of the glycine cleavage system and the homologous GcvH-L encoded in an operon with LplA2. GcvH is a recognized conduit for lipoyl transfer to α-ketoacid dehydrogenase E2 subunits, while the function of GcvH-L remains unclear. The potential to produce two ligases and two H proteins is an unusual characteristic of S. aureus that is unlike most other Gram positive Firmicutes and might allude to an expanded pathway of lipoic acid acquisition in this microorganism. Here, we demonstrate that LplA1 and LplA2 facilitate lipoic acid salvage by differentially targeting lipoyl domain-containing proteins; LplA1 targets H proteins and LplA2 targets α-ketoacid dehydrogenase E2 subunits. Furthermore, GcvH and GcvH-L both facilitate lipoyl relay to E2 subunits. Altogether, these studies identify an expanded mode of lipoic acid salvage used by S. aureus and more broadly underscore the importance of bacterial adaptations when faced with nutritional limitation.
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Affiliation(s)
- Irina Laczkovich
- Department of Microbiology and Immunology, Loyola University Chicago - Stritch School of Medicine, 2160 S. First Avenue, Maywood, IL, 60153, USA
| | - Wei Ping Teoh
- Department of Microbiology and Immunology, Loyola University Chicago - Stritch School of Medicine, 2160 S. First Avenue, Maywood, IL, 60153, USA
| | - Sarah Flury
- Department of Microbiology and Immunology, Loyola University Chicago - Stritch School of Medicine, 2160 S. First Avenue, Maywood, IL, 60153, USA
| | - James P Grayczyk
- Department of Microbiology and Immunology, Loyola University Chicago - Stritch School of Medicine, 2160 S. First Avenue, Maywood, IL, 60153, USA
| | - Azul Zorzoli
- Department of Microbiology and Immunology, Loyola University Chicago - Stritch School of Medicine, 2160 S. First Avenue, Maywood, IL, 60153, USA
| | - Francis Alonzo
- Department of Microbiology and Immunology, Loyola University Chicago - Stritch School of Medicine, 2160 S. First Avenue, Maywood, IL, 60153, USA
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34
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Dong G, Cao L, Ryde U. Insight into the reaction mechanism of lipoyl synthase: a QM/MM study. J Biol Inorg Chem 2018; 23:221-229. [PMID: 29204715 PMCID: PMC5816104 DOI: 10.1007/s00775-017-1522-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 11/28/2017] [Indexed: 11/26/2022]
Abstract
Lipoyl synthase (LipA) catalyses the final step of the biosynthesis of the lipoyl cofactor by insertion of two sulfur atoms at the C6 and C8 atoms of the protein-bound octanoyl substrate. In this reaction, two [4Fe4S] clusters and two molecules of S-adenosyl-L-methionine are used. One of the two FeS clusters is responsible for the generation of a powerful oxidant, the 5'-deoxyadenosyl radical (5'-dA•). The other (the auxiliary cluster) is the source of both sulfur atoms that are inserted into the substrate. In this paper, the spin state of the FeS clusters and the reaction mechanism is investigated by the combined quantum mechanical and molecular mechanics approach. The calculations show that the ground state of the two FeS clusters, both in the [4Fe4S]2+ oxidation state, is a singlet state with antiferromagnetically coupled high-spin Fe ions and that there is quite a large variation of the energies of the various broken-symmetry states, up to 40 kJ/mol. For the two S-insertion reactions, the highest energy barrier is found for the hydrogen-atom abstraction from the octanoyl substrate by 5'-dA•. The formation of 5'-dA• is very facile for LipA, with an energy barrier of 6 kJ/mol for the first S-insertion reaction and without any barrier for the second S-insertion reaction. In addition, the first S ion attack on the C6 radical of octanoyl was found to take place directly by the transfer of the H6 from the substrate to 5'-dA•, whereas for the second S-insertion reaction, a C8 radical intermediate was formed with a rate-limiting barrier of 71 kJ/mol.
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Affiliation(s)
- Geng Dong
- Department of Theoretical Chemistry, Chemical Centre, Lund University, P.O. Box 124, 221 00, Lund, Sweden.
| | - Lili Cao
- Department of Theoretical Chemistry, Chemical Centre, Lund University, P.O. Box 124, 221 00, Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Chemical Centre, Lund University, P.O. Box 124, 221 00, Lund, Sweden
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35
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McCarthy EL, Booker SJ. Destruction and reformation of an iron-sulfur cluster during catalysis by lipoyl synthase. Science 2018; 358:373-377. [PMID: 29051382 DOI: 10.1126/science.aan4574] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 09/06/2017] [Indexed: 01/15/2023]
Abstract
Lipoyl synthase (LipA) catalyzes the last step in the biosynthesis of the lipoyl cofactor, which is the attachment of two sulfhydryl groups to C6 and C8 of a pendant octanoyl chain. The appended sulfur atoms derive from an auxiliary [4Fe-4S] cluster on the protein that is degraded during turnover, limiting LipA to one turnover in vitro. We found that the Escherichia coli iron-sulfur (Fe-S) cluster carrier protein NfuA efficiently reconstitutes the auxiliary cluster during LipA catalysis in a step that is not rate-limiting. We also found evidence for a second pathway for cluster regeneration involving the E. coli protein IscU. These results show that enzymes that degrade their Fe-S clusters as a sulfur source can nonetheless act catalytically. Our results also explain why patients with NFU1 gene deletions exhibit phenotypes that are indicative of lipoyl cofactor deficiencies.
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Affiliation(s)
- Erin L McCarthy
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Squire J Booker
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA. .,Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.,Howard Hughes Medical Institute, Pennsylvania State University, University Park, PA 16802, USA
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36
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Solmonson A, DeBerardinis RJ. Lipoic acid metabolism and mitochondrial redox regulation. J Biol Chem 2017; 293:7522-7530. [PMID: 29191830 DOI: 10.1074/jbc.tm117.000259] [Citation(s) in RCA: 228] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Lipoic acid is an essential cofactor for mitochondrial metabolism and is synthesized de novo using intermediates from mitochondrial fatty-acid synthesis type II, S-adenosylmethionine and iron-sulfur clusters. This cofactor is required for catalysis by multiple mitochondrial 2-ketoacid dehydrogenase complexes, including pyruvate dehydrogenase, α-ketoglutarate dehydrogenase, and branched-chain ketoacid dehydrogenase. Lipoic acid also plays a critical role in stabilizing and regulating these multienzyme complexes. Many of these dehydrogenases are regulated by reactive oxygen species, mediated through the disulfide bond of the prosthetic lipoyl moiety. Collectively, its functions explain why lipoic acid is required for cell growth, mitochondrial activity, and coordination of fuel metabolism.
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Affiliation(s)
- Ashley Solmonson
- From the Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Ralph J DeBerardinis
- From the Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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37
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Davis KM, Boal AK. Mechanism-Based Strategies for Structural Characterization of Radical SAM Reaction Intermediates. Methods Enzymol 2017; 595:331-359. [PMID: 28882206 DOI: 10.1016/bs.mie.2017.07.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
X-ray crystallographic characterization of enzymes at different stages in their reaction cycles can provide unique insight into the reaction pathway, the number and type of intermediates formed, and their structural context. The known mechanistic diversity in the radical S-adenosylmethionine (SAM) superfamily of enzymes makes it an appealing target for such studies as more than 100,000 sequences have been identified to date with wide-ranging reactivities that share a pattern of complex radical-mediated chemistry. Here, we review selected examples of radical SAM enzyme crystal structures representative of reactant, product, and intermediate state complexes with a particular emphasis on the strategies employed to capture these states. Broader application of structural characterization techniques to analyze mechanism and substrate specificity is certain to play an important role as more members of this family become tractable for biochemical study.
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Affiliation(s)
- Katherine M Davis
- Princeton University, Princeton, NJ, United States; The Pennsylvania State University, University Park, PA, United States
| | - Amie K Boal
- The Pennsylvania State University, University Park, PA, United States.
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38
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Mulliez E, Duarte V, Arragain S, Fontecave M, Atta M. On the Role of Additional [4Fe-4S] Clusters with a Free Coordination Site in Radical-SAM Enzymes. Front Chem 2017; 5:17. [PMID: 28361051 PMCID: PMC5352715 DOI: 10.3389/fchem.2017.00017] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 03/03/2017] [Indexed: 11/13/2022] Open
Abstract
The canonical CysXXXCysXXCys motif is the hallmark of the Radical-SAM superfamily. This motif is responsible for the ligation of a [4Fe-4S] cluster containing a free coordination site available for SAM binding. The five enzymes MoaA, TYW1, MiaB, RimO and LipA contain in addition a second [4Fe-4S] cluster itself bound to three other cysteines and thus also displaying a potentially free coordination site. This review article summarizes recent important achievements obtained on these five enzymes with the main focus to delineate the role of this additional [4Fe-4S] cluster in catalysis.
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Affiliation(s)
- Etienne Mulliez
- Biosciences and Biotechnology Institute of Grenoble, Laboratoire de Chimie et Biologie des Métaux, UMR 5249 CEA-Centre National de la Recherche Scientifique-UGA Grenoble, France
| | - Victor Duarte
- Biosciences and Biotechnology Institute of Grenoble, Laboratoire de Chimie et Biologie des Métaux, UMR 5249 CEA-Centre National de la Recherche Scientifique-UGA Grenoble, France
| | - Simon Arragain
- Laboratoire de Chimie des Processus Biologiques, UMR 8229, Collége de France-Centre National de la Recherche Scientifique-Université P. et M. Curie Paris, France
| | - Marc Fontecave
- Biosciences and Biotechnology Institute of Grenoble, Laboratoire de Chimie et Biologie des Métaux, UMR 5249 CEA-Centre National de la Recherche Scientifique-UGAGrenoble, France; Laboratoire de Chimie des Processus Biologiques, UMR 8229, Collége de France-Centre National de la Recherche Scientifique-Université P. et M. CurieParis, France
| | - Mohamed Atta
- Biosciences and Biotechnology Institute of Grenoble, Laboratoire de Chimie et Biologie des Métaux, UMR 5249 CEA-Centre National de la Recherche Scientifique-UGA Grenoble, France
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39
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Jhuang HY, Lee HY, Leu JY. Mitochondrial-nuclear co-evolution leads to hybrid incompatibility through pentatricopeptide repeat proteins. EMBO Rep 2016; 18:87-101. [PMID: 27920033 DOI: 10.15252/embr.201643311] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 10/09/2016] [Accepted: 10/21/2016] [Indexed: 01/09/2023] Open
Abstract
Mitochondrial-nuclear incompatibility has a major role in reproductive isolation between species. However, the underlying mechanism and driving force of mitochondrial-nuclear incompatibility remain elusive. Here, we report a pentatricopeptide repeat-containing (PPR) protein, Ccm1, and its interacting partner, 15S rRNA, to be involved in hybrid incompatibility between two yeast species, Saccharomyces cerevisiae and Saccharomyces bayanus S. bayanus-Ccm1 has reduced binding affinity for S. cerevisiae-15S rRNA, leading to respiratory defects in hybrid cells. This incompatibility can be rescued by single mutations on several individual PPR motifs, demonstrating the highly evolvable nature of PPR proteins. When we examined other PPR proteins in the closely related Saccharomyces sensu stricto yeasts, about two-thirds of them showed detectable incompatibility. Our results suggest that fast co-evolution between flexible PPR proteins and their mitochondrial RNA substrates may be a common driving force in the development of mitochondrial-nuclear hybrid incompatibility.
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Affiliation(s)
- Han-Ying Jhuang
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan.,Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Hsin-Yi Lee
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan.,Molecular and Cell Biology, Taiwan International Graduate Program, Graduate Institute of Life Sciences, National Defense Medical Center and Academia Sinica, Taipei, Taiwan
| | - Jun-Yi Leu
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan .,Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
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40
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Engineering Escherichia coli to produce branched-chain fatty acids in high percentages. Metab Eng 2016; 38:148-158. [DOI: 10.1016/j.ymben.2016.07.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 06/04/2016] [Accepted: 07/12/2016] [Indexed: 12/18/2022]
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41
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Zorzoli A, Grayczyk JP, Alonzo F. Staphylococcus aureus Tissue Infection During Sepsis Is Supported by Differential Use of Bacterial or Host-Derived Lipoic Acid. PLoS Pathog 2016; 12:e1005933. [PMID: 27701474 PMCID: PMC5049849 DOI: 10.1371/journal.ppat.1005933] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 09/13/2016] [Indexed: 01/31/2023] Open
Abstract
To thrive in diverse environments, bacteria must shift their metabolic output in response to nutrient bioavailability. In many bacterial species, such changes in metabolic flux depend upon lipoic acid, a cofactor required for the activity of enzyme complexes involved in glycolysis, the citric acid cycle, glycine catabolism, and branched chain fatty acid biosynthesis. The requirement of lipoic acid for metabolic enzyme activity necessitates that bacteria synthesize the cofactor and/or scavenge it from environmental sources. Although use of lipoic acid is a conserved phenomenon, the mechanisms behind its biosynthesis and salvage can differ considerably between bacterial species. Furthermore, low levels of circulating free lipoic acid in mammals underscore the importance of lipoic acid acquisition for pathogenic microbes during infection. In this study, we used a genetic approach to characterize the mechanisms of lipoic acid biosynthesis and salvage in the bacterial pathogen Staphylococcus aureus and evaluated the requirements for both pathways during murine sepsis. We determined that S. aureus lipoic acid biosynthesis and salvage genes exist in an arrangement that directly links redox stress response and acetate biosynthesis genes. In addition, we found that lipoic acid salvage is dictated by two ligases that facilitate growth and lipoylation in distinct environmental conditions in vitro, but that are fully compensatory for survival in vivo. Upon infection of mice, we found that de novo biosynthesis or salvage promotes S. aureus survival in a manner that depends upon the infectious site. In addition, when both lipoic acid biosynthesis and salvage are blocked S. aureus is rendered avirulent, implying an inability to induce lipoic acid-independent metabolic programs to promote survival. Together, our results define the major pathways of lipoic acid biosynthesis and salvage in S. aureus and support the notion that bacterial nutrient acquisition schemes are instrumental in dictating pathogen proclivity for an infectious niche. Staphylococcus aureus is a predominant cause of infectious diseases ranging from superficial skin and soft tissue infections to necrotizing pneumonia and sepsis. A remarkable aspect of S. aureus pathobiology lies in the ability of the microorganism to infect a wide variety of host tissues. This infectious promiscuity implies S. aureus exhibits significant adaptability when faced with disparate environments and nutritional deficiencies. In this work, we examine the mechanisms by which S. aureus acquires lipoic acid, a key cofactor involved in maintaining metabolic flux. Our studies determine that S. aureus engages in both de novo biosynthesis and salvage of lipoic acid in a manner that is reminiscent of pathways used by both B. subtilis and L. monocytogenes combined. Further, our work suggests that the complex mechanisms of lipoic acid acquisition dictate the range of tissues S. aureus infects and identifies a lipoic acid salvage enzyme that is dispensable for growth in vitro, but required for S. aureus pathogenesis in vivo. In sum, our results highlight the adaptability of S. aureus in the face of nutrient paucity; the importance of complex nutrient acquisition/biosynthesis pathways in promoting infection; and identify potential novel therapeutic targets that may be effective against S. aureus.
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Affiliation(s)
- Azul Zorzoli
- Department of Microbiology and Immunology, Loyola University Chicago—Stritch School of Medicine, Maywood, Illinois, United States of America
| | - James P. Grayczyk
- Department of Microbiology and Immunology, Loyola University Chicago—Stritch School of Medicine, Maywood, Illinois, United States of America
| | - Francis Alonzo
- Department of Microbiology and Immunology, Loyola University Chicago—Stritch School of Medicine, Maywood, Illinois, United States of America
- * E-mail:
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42
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Abstract
Lipoyl synthase (LipA) catalyzes the insertion of two sulfur atoms at the unactivated C6 and C8 positions of a protein-bound octanoyl chain to produce the lipoyl cofactor. To activate its substrate for sulfur insertion, LipA uses a [4Fe-4S] cluster and S-adenosylmethionine (AdoMet) radical chemistry; the remainder of the reaction mechanism, especially the source of the sulfur, has been less clear. One controversial proposal involves the removal of sulfur from a second (auxiliary) [4Fe-4S] cluster on the enzyme, resulting in destruction of the cluster during each round of catalysis. Here, we present two high-resolution crystal structures of LipA from Mycobacterium tuberculosis: one in its resting state and one at an intermediate state during turnover. In the resting state, an auxiliary [4Fe-4S] cluster has an unusual serine ligation to one of the irons. After reaction with an octanoyllysine-containing 8-mer peptide substrate and 1 eq AdoMet, conditions that allow for the first sulfur insertion but not the second insertion, the serine ligand dissociates from the cluster, the iron ion is lost, and a sulfur atom that is still part of the cluster becomes covalently attached to C6 of the octanoyl substrate. This intermediate structure provides a clear picture of iron-sulfur cluster destruction in action, supporting the role of the auxiliary cluster as the sulfur source in the LipA reaction and describing a radical strategy for sulfur incorporation into completely unactivated substrates.
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43
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Assembly of Lipoic Acid on Its Cognate Enzymes: an Extraordinary and Essential Biosynthetic Pathway. Microbiol Mol Biol Rev 2016; 80:429-50. [PMID: 27074917 DOI: 10.1128/mmbr.00073-15] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Although the structure of lipoic acid and its role in bacterial metabolism were clear over 50 years ago, it is only in the past decade that the pathways of biosynthesis of this universally conserved cofactor have become understood. Unlike most cofactors, lipoic acid must be covalently bound to its cognate enzyme proteins (the 2-oxoacid dehydrogenases and the glycine cleavage system) in order to function in central metabolism. Indeed, the cofactor is assembled on its cognate proteins rather than being assembled and subsequently attached as in the typical pathway, like that of biotin attachment. The first lipoate biosynthetic pathway determined was that of Escherichia coli, which utilizes two enzymes to form the active lipoylated protein from a fatty acid biosynthetic intermediate. Recently, a more complex pathway requiring four proteins was discovered in Bacillus subtilis, which is probably an evolutionary relic. This pathway requires the H protein of the glycine cleavage system of single-carbon metabolism to form active (lipoyl) 2-oxoacid dehydrogenases. The bacterial pathways inform the lipoate pathways of eukaryotic organisms. Plants use the E. coli pathway, whereas mammals and fungi probably use the B. subtilis pathway. The lipoate metabolism enzymes (except those of sulfur insertion) are members of PFAM family PF03099 (the cofactor transferase family). Although these enzymes share some sequence similarity, they catalyze three markedly distinct enzyme reactions, making the usual assignment of function based on alignments prone to frequent mistaken annotations. This state of affairs has possibly clouded the interpretation of one of the disorders of human lipoate metabolism.
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44
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Lanz ND, Lee KH, Horstmann AK, Pandelia ME, Cicchillo RM, Krebs C, Booker SJ. Characterization of Lipoyl Synthase from Mycobacterium tuberculosis. Biochemistry 2016; 55:1372-83. [PMID: 26841001 DOI: 10.1021/acs.biochem.5b01216] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The prevalence of multiple and extensively drug-resistant strains of Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, is on the rise, necessitating the identification of new targets to combat an organism that has infected one-third of the world's population, according to the World Health Organization. The biosynthesis of the lipoyl cofactor is one possible target, given its critical importance in cellular metabolism and the apparent lack of functional salvage pathways in Mtb that are found in humans and many other organisms. The lipoyl cofactor is synthesized de novo in two committed steps, involving the LipB-catalyzed transfer of an octanoyl chain derived from fatty acid biosynthesis to a lipoyl carrier protein and the LipA-catalyzed insertion of sulfur atoms at C6 and C8 of the octanoyl chain. A number of in vitro studies of lipoyl synthases from Escherichia coli, Sulfolobus solfataricus, and Thermosynechococcus elongatus have been conducted, but the enzyme from Mtb has not been characterized. Herein, we show that LipA from Mtb contains two [4Fe-4S] clusters and converts an octanoyl peptide substrate to the corresponding lipoyl peptide product via the same C6-monothiolated intermediate as that observed in the E. coli LipA reaction. In addition, we show that LipA from Mtb forms a complex with the H protein of the glycine cleavage system and that the strength of association is dependent on the presence of S-adenosyl-l-methionine. We also show that LipA from Mtb can complement a lipA mutant of E. coli, demonstrating the commonalities of the two enzymes. Lastly, we show that the substrate for LipA, which normally acts on a post-translationally modified protein, can be reduced to carboxybenzyl-octanoyllysine.
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Affiliation(s)
- Nicholas D Lanz
- Department of Biochemistry and Molecular Biology, ‡Department of Chemistry, and §The Howard Hughes Medical Institute, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Kyung-Hoon Lee
- Department of Biochemistry and Molecular Biology, ‡Department of Chemistry, and §The Howard Hughes Medical Institute, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Abigail K Horstmann
- Department of Biochemistry and Molecular Biology, ‡Department of Chemistry, and §The Howard Hughes Medical Institute, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Maria-Eirini Pandelia
- Department of Biochemistry and Molecular Biology, ‡Department of Chemistry, and §The Howard Hughes Medical Institute, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Robert M Cicchillo
- Department of Biochemistry and Molecular Biology, ‡Department of Chemistry, and §The Howard Hughes Medical Institute, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Carsten Krebs
- Department of Biochemistry and Molecular Biology, ‡Department of Chemistry, and §The Howard Hughes Medical Institute, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Squire J Booker
- Department of Biochemistry and Molecular Biology, ‡Department of Chemistry, and §The Howard Hughes Medical Institute, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
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45
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Kim MC, Zhu Y, Chen C. How are they different? A quantitative domain comparison of information visualization and data visualization (2000–2014). Scientometrics 2016. [DOI: 10.1007/s11192-015-1830-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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46
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Abstract
Two vitamins, biotin and lipoic acid, are essential in all three domains of life. Both coenzymes function only when covalently attached to key metabolic enzymes. There they act as "swinging arms" that shuttle intermediates between two active sites (= covalent substrate channeling) of key metabolic enzymes. Although biotin was discovered over 100 years ago and lipoic acid 60 years ago, it was not known how either coenzyme is made until recently. In Escherichia coli the synthetic pathways for both coenzymes have now been worked out for the first time. The late steps of biotin synthesis, those involved in assembling the fused rings, were well described biochemically years ago, although recent progress has been made on the BioB reaction, the last step of the pathway in which the biotin sulfur moiety is inserted. In contrast, the early steps of biotin synthesis, assembly of the fatty acid-like "arm" of biotin were unknown. It has now been demonstrated that the arm is made by using disguised substrates to gain entry into the fatty acid synthesis pathway followed by removal of the disguise when the proper chain length is attained. The BioC methyltransferase is responsible for introducing the disguise, and the BioH esterase is responsible for its removal. In contrast to biotin, which is attached to its cognate proteins as a finished molecule, lipoic acid is assembled on its cognate proteins. An octanoyl moiety is transferred from the octanoyl acyl carrier protein of fatty acid synthesis to a specific lysine residue of a cognate protein by the LipB octanoyltransferase followed by sulfur insertion at carbons C-6 and C-8 by the LipA lipoyl synthetase. Assembly on the cognate proteins regulates the amount of lipoic acid synthesized, and, thus, there is no transcriptional control of the synthetic genes. In contrast, transcriptional control of the biotin synthetic genes is wielded by a remarkably sophisticated, yet simple, system, exerted through BirA, a dual-function protein that both represses biotin operon transcription and ligates biotin to its cognate proteins.
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47
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Abstract
Two vitamins, biotin and lipoic acid, are essential in all three domains of life. Both coenzymes function only when covalently attached to key metabolic enzymes. There they act as "swinging arms" that shuttle intermediates between two active sites (= covalent substrate channeling) of key metabolic enzymes. Although biotin was discovered over 100 years ago and lipoic acid was discovered 60 years ago, it was not known how either coenzyme is made until recently. In Escherichia coli the synthetic pathways for both coenzymes have now been worked out for the first time. The late steps of biotin synthesis, those involved in assembling the fused rings, were well described biochemically years ago, although recent progress has been made on the BioB reaction, the last step of the pathway, in which the biotin sulfur moiety is inserted. In contrast, the early steps of biotin synthesis, assembly of the fatty acid-like "arm" of biotin, were unknown. It has now been demonstrated that the arm is made by using disguised substrates to gain entry into the fatty acid synthesis pathway followed by removal of the disguise when the proper chain length is attained. The BioC methyltransferase is responsible for introducing the disguise and the BioH esterase for its removal. In contrast to biotin, which is attached to its cognate proteins as a finished molecule, lipoic acid is assembled on its cognate proteins. An octanoyl moiety is transferred from the octanoyl-ACP of fatty acid synthesis to a specific lysine residue of a cognate protein by the LipB octanoyl transferase, followed by sulfur insertion at carbons C6 and C8 by the LipA lipoyl synthetase. Assembly on the cognate proteins regulates the amount of lipoic acid synthesized, and thus there is no transcriptional control of the synthetic genes. In contrast, transcriptional control of the biotin synthetic genes is wielded by a remarkably sophisticated, yet simple, system exerted through BirA, a dual-function protein that both represses biotin operon transcription and ligates biotin to its cognate protein.
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48
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Affiliation(s)
- Perry Allen Frey
- From the Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
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49
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McLaughlin M, Lanz N, Goldman P, Lee KH, Booker S, Drennan C. Caught in the Act: Snapshots of Sulfur Insertion by Lipoyl Synthase. FASEB J 2015. [DOI: 10.1096/fasebj.29.1_supplement.895.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Martin McLaughlin
- Dept. of Chemistry MITCambridgeMAUnited States
- Dept. of Chemistry Penn State UniversityState CollegePAUnited States
| | - Nicholas Lanz
- Dept. of Biochemistry & Molecular Biology Penn State University State CollegePAUnited States
| | | | - Kyung Hoon Lee
- Dept. of Chemistry Penn State UniversityState CollegePAUnited States
| | - Squire Booker
- Dept. of Chemistry Penn State UniversityState CollegePAUnited States
- Dept. of Biochemistry & Molecular Biology Penn State University State CollegePAUnited States
| | - Catherine Drennan
- Dept. of Chemistry MITCambridgeMAUnited States
- Dept. of BiologyMITCambridgeMAUnited States
- Howard Hughes Medical Institute MITCambridgeMAUnited States
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50
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Grell TAJ, Goldman PJ, Drennan CL. SPASM and twitch domains in S-adenosylmethionine (SAM) radical enzymes. J Biol Chem 2015; 290:3964-71. [PMID: 25477505 PMCID: PMC4326806 DOI: 10.1074/jbc.r114.581249] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
S-Adenosylmethionine (SAM, also known as AdoMet) radical enzymes use SAM and a [4Fe-4S] cluster to catalyze a diverse array of reactions. They adopt a partial triose-phosphate isomerase (TIM) barrel fold with N- and C-terminal extensions that tailor the structure of the enzyme to its specific function. One extension, termed a SPASM domain, binds two auxiliary [4Fe-4S] clusters and is present within peptide-modifying enzymes. The first structure of a SPASM-containing enzyme, anaerobic sulfatase-maturating enzyme (anSME), revealed unexpected similarities to two non-SPASM proteins, butirosin biosynthetic enzyme 2-deoxy-scyllo-inosamine dehydrogenase (BtrN) and molybdenum cofactor biosynthetic enzyme (MoaA). The latter two enzymes bind one auxiliary cluster and exhibit a partial SPASM motif, coined a Twitch domain. Here we review the structure and function of auxiliary cluster domains within the SAM radical enzyme superfamily.
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Affiliation(s)
| | | | - Catherine L Drennan
- From the Departments of Chemistry and Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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