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Rade LL, Generoso WC, Das S, Souza AS, Silveira RL, Avila MC, Vieira PS, Miyamoto RY, Lima ABB, Aricetti JA, de Melo RR, Milan N, Persinoti GF, Bonomi AMFLJ, Murakami MT, Makris TM, Zanphorlin LM. Dimer-assisted mechanism of (un)saturated fatty acid decarboxylation for alkene production. Proc Natl Acad Sci U S A 2023; 120:e2221483120. [PMID: 37216508 PMCID: PMC10235961 DOI: 10.1073/pnas.2221483120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 04/24/2023] [Indexed: 05/24/2023] Open
Abstract
The enzymatic decarboxylation of fatty acids (FAs) represents an advance toward the development of biological routes to produce drop-in hydrocarbons. The current mechanism for the P450-catalyzed decarboxylation has been largely established from the bacterial cytochrome P450 OleTJE. Herein, we describe OleTPRN, a poly-unsaturated alkene-producing decarboxylase that outrivals the functional properties of the model enzyme and exploits a distinct molecular mechanism for substrate binding and chemoselectivity. In addition to the high conversion rates into alkenes from a broad range of saturated FAs without dependence on high salt concentrations, OleTPRN can also efficiently produce alkenes from unsaturated (oleic and linoleic) acids, the most abundant FAs found in nature. OleTPRN performs carbon-carbon cleavage by a catalytic itinerary that involves hydrogen-atom transfer by the heme-ferryl intermediate Compound I and features a hydrophobic cradle at the distal region of the substrate-binding pocket, not found in OleTJE, which is proposed to play a role in the productive binding of long-chain FAs and favors the rapid release of products from the metabolism of short-chain FAs. Moreover, it is shown that the dimeric configuration of OleTPRN is involved in the stabilization of the A-A' helical motif, a second-coordination sphere of the substrate, which contributes to the proper accommodation of the aliphatic tail in the distal and medial active-site pocket. These findings provide an alternative molecular mechanism for alkene production by P450 peroxygenases, creating new opportunities for biological production of renewable hydrocarbons.
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Affiliation(s)
- Leticia L. Rade
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas13083-100, Brazil
| | - Wesley C. Generoso
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas13083-100, Brazil
| | - Suman Das
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC27695-7622
| | - Amanda S. Souza
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas13083-100, Brazil
| | - Rodrigo L. Silveira
- Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro21941-594, Brazil
| | - Mayara C. Avila
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas13083-100, Brazil
| | - Plinio S. Vieira
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas13083-100, Brazil
| | - Renan Y. Miyamoto
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas13083-100, Brazil
| | - Ana B. B. Lima
- Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro21941-594, Brazil
| | - Juliana A. Aricetti
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas13083-100, Brazil
| | - Ricardo R. de Melo
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas13083-100, Brazil
| | - Natalia Milan
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas13083-100, Brazil
| | - Gabriela F. Persinoti
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas13083-100, Brazil
| | - Antonio M. F. L. J. Bonomi
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas13083-100, Brazil
| | - Mario T. Murakami
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas13083-100, Brazil
| | - Thomas M. Makris
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC27695-7622
| | - Leticia M. Zanphorlin
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas13083-100, Brazil
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Cordeiro RL, Santos CR, Domingues MN, Lima TB, Pirolla RAS, Morais MAB, Colombari FM, Miyamoto RY, Persinoti GF, Borges AC, de Farias MA, Stoffel F, Li C, Gozzo FC, van Heel M, Guerin ME, Sundberg EJ, Wang LX, Portugal RV, Giuseppe PO, Murakami MT. Mechanism of high-mannose N-glycan breakdown and metabolism by Bifidobacterium longum. Nat Chem Biol 2023; 19:218-229. [PMID: 36443572 PMCID: PMC10367113 DOI: 10.1038/s41589-022-01202-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 10/06/2022] [Indexed: 11/30/2022]
Abstract
Bifidobacteria are early colonizers of the human gut and play central roles in human health and metabolism. To thrive in this competitive niche, these bacteria evolved the capacity to use complex carbohydrates, including mammalian N-glycans. Herein, we elucidated pivotal biochemical steps involved in high-mannose N-glycan utilization by Bifidobacterium longum. After N-glycan release by an endo-β-N-acetylglucosaminidase, the mannosyl arms are trimmed by the cooperative action of three functionally distinct glycoside hydrolase 38 (GH38) α-mannosidases and a specific GH125 α-1,6-mannosidase. High-resolution cryo-electron microscopy structures revealed that bifidobacterial GH38 α-mannosidases form homotetramers, with the N-terminal jelly roll domain contributing to substrate selectivity. Additionally, an α-glucosidase enables the processing of monoglucosylated N-glycans. Notably, the main degradation product, mannose, is isomerized into fructose before phosphorylation, an unconventional metabolic route connecting it to the bifid shunt pathway. These findings shed light on key molecular mechanisms used by bifidobacteria to use high-mannose N-glycans, a perennial carbon and energy source in the intestinal lumen.
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Affiliation(s)
- Rosa L Cordeiro
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Graduate Program in Functional and Molecular Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Camila R Santos
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Mariane N Domingues
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Tatiani B Lima
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Renan A S Pirolla
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Mariana A B Morais
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Felippe M Colombari
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Renan Y Miyamoto
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Gabriela F Persinoti
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Antonio C Borges
- Brazilian Nanotechnology National Laboratory (LNNano), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Marcelo A de Farias
- Brazilian Nanotechnology National Laboratory (LNNano), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Fabiane Stoffel
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Department of Chemistry, Federal University of Santa Catarina, Santa Catarina, Brazil
| | - Chao Li
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
| | - Fabio C Gozzo
- Institute of Chemistry, University of Campinas, Campinas, Brazil
| | - Marin van Heel
- Brazilian Nanotechnology National Laboratory (LNNano), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Marcelo E Guerin
- Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Spain
- Structural Glycobiology Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Eric J Sundberg
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Lai-Xi Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
| | - Rodrigo V Portugal
- Brazilian Nanotechnology National Laboratory (LNNano), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil.
| | - Priscila O Giuseppe
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil.
| | - Mario T Murakami
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil.
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Miyamoto RY, José AHM, Lopes MM, Rodrigues RC. Effectiveness of Baffled Flasks on the Growth of Scheffersomyces stipitis CBS 6054 Inoculum for Ethanol Production in Corncob Hemicellulosic Hydrolysate. Ind Biotechnol (New Rochelle N Y) 2020. [DOI: 10.1089/ind.2020.0023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Renan Y. Miyamoto
- Department of Biotechnology, Engineering School of Lorena, University of São Paulo, Lorena, São Paulo, Brazil
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
- Institute of Biology, State University of Campinas, Campinas, São Paulo, Brazil
| | - Alvaro H. M. José
- Department of Biotechnology, Engineering School of Lorena, University of São Paulo, Lorena, São Paulo, Brazil
| | - Milena M. Lopes
- Department of Biotechnology, Engineering School of Lorena, University of São Paulo, Lorena, São Paulo, Brazil
| | - Rita C.L.B. Rodrigues
- Department of Biotechnology, Engineering School of Lorena, University of São Paulo, Lorena, São Paulo, Brazil
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