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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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2
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Martins MP, Morais MAB, Persinoti GF, Galinari RH, Yu L, Yoshimi Y, Passos Nunes FB, Lima TB, Barbieri SF, Silveira JLM, Lombard V, Terrapon N, Dupree P, Henrissat B, Murakami MT. Glycoside hydrolase subfamily GH5_57 features a highly redesigned catalytic interface to process complex hetero-β-mannans. Acta Cryst Sect D Struct Biol 2022; 78:1358-1372. [DOI: 10.1107/s2059798322009561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/28/2022] [Indexed: 11/05/2022]
Abstract
Glycoside hydrolase family 5 (GH5) harbors diverse substrate specificities and modes of action, exhibiting notable molecular adaptations to cope with the stereochemical complexity imposed by glycosides and carbohydrates such as cellulose, xyloglucan, mixed-linkage β-glucan, laminarin, (hetero)xylan, (hetero)mannan, galactan, chitosan, N-glycan, rutin and hesperidin. GH5 has been divided into subfamilies, many with higher functional specificity, several of which have not been characterized to date and some that have yet to be discovered with the exploration of sequence/taxonomic diversity. In this work, the current GH5 subfamily inventory is expanded with the discovery of the GH5_57 subfamily by describing an endo-β-mannanase (CapGH5_57) from an uncultured Bacteroidales bacterium recovered from the capybara gut microbiota. Biochemical characterization showed that CapGH5_57 is active on glucomannan, releasing oligosaccharides with a degree of polymerization from 2 to 6, indicating it to be an endo-β-mannanase. The crystal structure, which was solved using single-wavelength anomalous diffraction, revealed a massively redesigned catalytic interface compared with GH5 mannanases. The typical aromatic platforms and the characteristic α-helix-containing β6–α6 loop in the positive-subsite region of GH5_7 mannanases are absent in CapGH5_57, generating a large and open catalytic interface that might favor the binding of branched substrates. Supporting this, CapGH5_57 contains a tryptophan residue adjacent and perpendicular to the cleavage site, indicative of an anchoring site for a substrate with a substitution at the −1 glycosyl moiety. Taken together, these results suggest that despite presenting endo activity on glucomannan, CapGH5_57 may have a new type of substituted heteromannan as its natural substrate. This work demonstrates the still great potential for discoveries regarding the mechanistic and functional diversity of this large and polyspecific GH family by unveiling a novel catalytic interface sculpted to recognize complex heteromannans, which led to the establishment of the GH5_57 subfamily.
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3
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Cabral L, Persinoti GF, Paixão DAA, Martins MP, Morais MAB, Chinaglia M, Domingues MN, Sforca ML, Pirolla RAS, Generoso WC, Santos CA, Maciel LF, Terrapon N, Lombard V, Henrissat B, Murakami MT. Gut microbiome of the largest living rodent harbors unprecedented enzymatic systems to degrade plant polysaccharides. Nat Commun 2022; 13:629. [PMID: 35110564 PMCID: PMC8810776 DOI: 10.1038/s41467-022-28310-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 01/14/2022] [Indexed: 12/12/2022] Open
Abstract
The largest living rodent, capybara, can efficiently depolymerize and utilize lignocellulosic biomass through microbial symbiotic mechanisms yet elusive. Herein, we elucidate the microbial community composition, enzymatic systems and metabolic pathways involved in the conversion of dietary fibers into short-chain fatty acids, a main energy source for the host. In this microbiota, the unconventional enzymatic machinery from Fibrobacteres seems to drive cellulose degradation, whereas a diverse set of carbohydrate-active enzymes from Bacteroidetes, organized in polysaccharide utilization loci, are accounted to tackle complex hemicelluloses typically found in gramineous and aquatic plants. Exploring the genetic potential of this community, we discover a glycoside hydrolase family of β-galactosidases (named as GH173), and a carbohydrate-binding module family (named as CBM89) involved in xylan binding that establishes an unprecedented three-dimensional fold among associated modules to carbohydrate-active enzymes. Together, these results demonstrate how the capybara gut microbiota orchestrates the depolymerization and utilization of plant fibers, representing an untapped reservoir of enzymatic mechanisms to overcome the lignocellulose recalcitrance, a central challenge toward a sustainable and bio-based economy. Here, Cabral et al., perform a multi-omics analysis of the gut microbiome of capybara, the largest living rodent, unveiling enzymatic mechanisms for the breakdown of lignocellulosic biomass, and report two undescribed families of carbohydrate-active enzymes.
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Affiliation(s)
- Lucelia Cabral
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Gabriela F Persinoti
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil.
| | - Douglas A A Paixão
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Marcele P Martins
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil.,Graduate Program in Functional and Molecular Biology, Institute of Biology, University of Campinas, Campinas, SP, Brazil
| | - Mariana A B Morais
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Mariana Chinaglia
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil.,Graduate Program in Functional and Molecular Biology, Institute of Biology, University of Campinas, Campinas, SP, Brazil
| | - Mariane N Domingues
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Mauricio L Sforca
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Renan A S Pirolla
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Wesley C Generoso
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Clelton A Santos
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Lucas F Maciel
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Nicolas Terrapon
- The Institut National de la Recherche Agronomique, USC 1408 AFMB, 13288, Marseille, France.,Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France
| | - Vincent Lombard
- The Institut National de la Recherche Agronomique, USC 1408 AFMB, 13288, Marseille, France.,Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, 2800 Kgs, Lyngby, Denmark.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mario T Murakami
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil.
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4
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Vieira PS, Bonfim IM, Araujo EA, Melo RR, Lima AR, Fessel MR, Paixão DAA, Persinoti GF, Rocco SA, Lima TB, Pirolla RAS, Morais MAB, Correa JBL, Zanphorlin LM, Diogo JA, Lima EA, Grandis A, Buckeridge MS, Gozzo FC, Benedetti CE, Polikarpov I, Giuseppe PO, Murakami MT. Xyloglucan processing machinery in Xanthomonas pathogens and its role in the transcriptional activation of virulence factors. Nat Commun 2021; 12:4049. [PMID: 34193873 PMCID: PMC8245568 DOI: 10.1038/s41467-021-24277-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 06/07/2021] [Indexed: 02/06/2023] Open
Abstract
Xyloglucans are highly substituted and recalcitrant polysaccharides found in the primary cell walls of vascular plants, acting as a barrier against pathogens. Here, we reveal that the diverse and economically relevant Xanthomonas bacteria are endowed with a xyloglucan depolymerization machinery that is linked to pathogenesis. Using the citrus canker pathogen as a model organism, we show that this system encompasses distinctive glycoside hydrolases, a modular xyloglucan acetylesterase and specific membrane transporters, demonstrating that plant-associated bacteria employ distinct molecular strategies from commensal gut bacteria to cope with xyloglucans. Notably, the sugars released by this system elicit the expression of several key virulence factors, including the type III secretion system, a membrane-embedded apparatus to deliver effector proteins into the host cells. Together, these findings shed light on the molecular mechanisms underpinning the intricate enzymatic machinery of Xanthomonas to depolymerize xyloglucans and uncover a role for this system in signaling pathways driving pathogenesis.
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Affiliation(s)
- Plinio S. Vieira
- grid.452567.70000 0004 0445 0877Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo Brazil
| | - Isabela M. Bonfim
- grid.452567.70000 0004 0445 0877Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo Brazil ,grid.411087.b0000 0001 0723 2494Graduate Program in Functional and Molecular Biology, Institute of Biology, University of Campinas, Campinas, São Paulo Brazil
| | - Evandro A. Araujo
- grid.452567.70000 0004 0445 0877Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo Brazil ,grid.452567.70000 0004 0445 0877Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo Brazil
| | - Ricardo R. Melo
- grid.452567.70000 0004 0445 0877Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo Brazil
| | - Augusto R. Lima
- grid.452567.70000 0004 0445 0877Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo Brazil
| | - Melissa R. Fessel
- grid.418514.d0000 0001 1702 8585Butantan Institute, Butantan Foundation, São Paulo, São Paulo Brazil
| | - Douglas A. A. Paixão
- grid.452567.70000 0004 0445 0877Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo Brazil
| | - Gabriela F. Persinoti
- grid.452567.70000 0004 0445 0877Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo Brazil
| | - Silvana A. Rocco
- grid.452567.70000 0004 0445 0877Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo Brazil
| | - Tatiani B. Lima
- grid.452567.70000 0004 0445 0877Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo Brazil
| | - Renan A. S. Pirolla
- grid.452567.70000 0004 0445 0877Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo Brazil
| | - Mariana A. B. Morais
- grid.452567.70000 0004 0445 0877Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo Brazil
| | - Jessica B. L. Correa
- grid.452567.70000 0004 0445 0877Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo Brazil
| | - Leticia M. Zanphorlin
- grid.452567.70000 0004 0445 0877Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo Brazil
| | - Jose A. Diogo
- grid.452567.70000 0004 0445 0877Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo Brazil ,grid.411087.b0000 0001 0723 2494Graduate Program in Functional and Molecular Biology, Institute of Biology, University of Campinas, Campinas, São Paulo Brazil
| | - Evandro A. Lima
- grid.452567.70000 0004 0445 0877Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo Brazil
| | - Adriana Grandis
- grid.11899.380000 0004 1937 0722Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Marcos S. Buckeridge
- grid.11899.380000 0004 1937 0722Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Fabio C. Gozzo
- grid.411087.b0000 0001 0723 2494Institute of Chemistry, University of Campinas, Campinas, São Paulo Brazil
| | - Celso E. Benedetti
- grid.452567.70000 0004 0445 0877Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo Brazil
| | - Igor Polikarpov
- grid.11899.380000 0004 1937 0722São Carlos Institute of Physics, University of São Paulo, São Carlos, São Paulo Brazil
| | - Priscila O. Giuseppe
- grid.452567.70000 0004 0445 0877Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo Brazil
| | - Mario T. Murakami
- grid.452567.70000 0004 0445 0877Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo Brazil
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5
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Morais MAB, Coines J, Domingues MN, Pirolla RAS, Tonoli CCC, Santos CR, Correa JBL, Gozzo FC, Rovira C, Murakami MT. Two distinct catalytic pathways for GH43 xylanolytic enzymes unveiled by X-ray and QM/MM simulations. Nat Commun 2021; 12:367. [PMID: 33446650 PMCID: PMC7809346 DOI: 10.1038/s41467-020-20620-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 12/10/2020] [Indexed: 02/07/2023] Open
Abstract
Xylanolytic enzymes from glycoside hydrolase family 43 (GH43) are involved in the breakdown of hemicellulose, the second most abundant carbohydrate in plants. Here, we kinetically and mechanistically describe the non-reducing-end xylose-releasing exo-oligoxylanase activity and report the crystal structure of a native GH43 Michaelis complex with its substrate prior to hydrolysis. Two distinct calcium-stabilized conformations of the active site xylosyl unit are found, suggesting two alternative catalytic routes. These results are confirmed by QM/MM simulations that unveil the complete hydrolysis mechanism and identify two possible reaction pathways, involving different transition state conformations for the cleavage of xylooligosaccharides. Such catalytic conformational promiscuity in glycosidases is related to the open architecture of the active site and thus might be extended to other exo-acting enzymes. These findings expand the current general model of catalytic mechanism of glycosidases, a main reaction in nature, and impact on our understanding about their interaction with substrates and inhibitors.
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Affiliation(s)
- Mariana A B Morais
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
- Departament de Química Inorgànica i Orgànica & Institut de Química Teórica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona, 08028, Spain
| | - Joan Coines
- Departament de Química Inorgànica i Orgànica & Institut de Química Teórica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona, 08028, Spain
| | - Mariane N Domingues
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
| | - Renan A S Pirolla
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
| | - Celisa C C Tonoli
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
| | - Camila R Santos
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
| | - Jessica B L Correa
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
| | - Fabio C Gozzo
- Dalton Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas, Campinas, 13083-970, Brazil
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica & Institut de Química Teórica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona, 08028, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, 08010, Spain.
| | - Mario T Murakami
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil.
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6
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Morais MAB, Giuseppe PO, Souza TACB, Castro H, Honorato RV, Oliveira PSL, Netto LES, Tomas AM, Murakami MT. Calcium and magnesium ions modulate the oligomeric state and function of mitochondrial 2-Cys peroxiredoxins in Leishmania parasites. J Biol Chem 2017; 292:7023-7039. [PMID: 28292930 PMCID: PMC5409470 DOI: 10.1074/jbc.m116.762039] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 03/07/2017] [Indexed: 12/16/2022] Open
Abstract
Leishmania parasites have evolved a number of strategies to cope with the harsh environmental changes during mammalian infection. One of these mechanisms involves the functional gain that allows mitochondrial 2-Cys peroxiredoxins to act as molecular chaperones when forming decamers. This function is critical for parasite infectivity in mammals, and its activation has been considered to be controlled exclusively by the enzyme redox state under physiological conditions. Herein, we have revealed that magnesium and calcium ions play a major role in modulating the ability of these enzymes to act as molecular chaperones, surpassing the redox effect. These ions are directly involved in mitochondrial metabolism and participate in a novel mechanism to stabilize the decameric form of 2-Cys peroxiredoxins in Leishmania mitochondria. Moreover, we have demonstrated that a constitutively dimeric Prx1m mutant impairs the survival of Leishmania under heat stress, supporting the central role of the chaperone function of Prx1m for Leishmania parasites during the transition from insect to mammalian hosts.
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Affiliation(s)
- Mariana A B Morais
- From the Biosciences National Laboratory, National Center for Research in Energy and Materials, Rua Giuseppe Maximo Scolfaro 10000, 13083-100 Campinas/SP, Brazil
| | - Priscila O Giuseppe
- From the Biosciences National Laboratory, National Center for Research in Energy and Materials, Rua Giuseppe Maximo Scolfaro 10000, 13083-100 Campinas/SP, Brazil
| | - Tatiana A C B Souza
- the Proteomics and Protein Engineering Laboratory, Carlos Chagas Institute, Fiocruz, Rua Professor Algacyr Munhoz Mader 2135, 81310-020 Curitiba/PR, Brazil
| | - Helena Castro
- the i3S-Institute for Investigation and Innovation in Health, University of Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- the Institute of Molecular and Cell Biology (IBMC), University of Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Rodrigo V Honorato
- From the Biosciences National Laboratory, National Center for Research in Energy and Materials, Rua Giuseppe Maximo Scolfaro 10000, 13083-100 Campinas/SP, Brazil
| | - Paulo S L Oliveira
- From the Biosciences National Laboratory, National Center for Research in Energy and Materials, Rua Giuseppe Maximo Scolfaro 10000, 13083-100 Campinas/SP, Brazil
| | - Luis E S Netto
- the Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of the State of São Paulo, Rua do Matão 14, 05508-090 São Paulo/SP, Brazil, and
| | - Ana M Tomas
- the i3S-Institute for Investigation and Innovation in Health, University of Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- the Institute of Molecular and Cell Biology (IBMC), University of Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- the Abel Salazar Biomedical Sciences Institute, University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Mario T Murakami
- From the Biosciences National Laboratory, National Center for Research in Energy and Materials, Rua Giuseppe Maximo Scolfaro 10000, 13083-100 Campinas/SP, Brazil,
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7
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Morais MAB, Giuseppe PO, Souza TACB, Alegria TGP, Oliveira MA, Netto LES, Murakami MT. How pH modulates the dimer-decamer interconversion of 2-Cys peroxiredoxins from the Prx1 subfamily. J Biol Chem 2015; 290:8582-90. [PMID: 25666622 DOI: 10.1074/jbc.m114.619205] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
2-Cys peroxiredoxins belonging to the Prx1 subfamily are Cys-based peroxidases that control the intracellular levels of H2O2 and seem to assume a chaperone function under oxidative stress conditions. The regulation of their peroxidase activity as well as the observed functional switch from peroxidase to chaperone involves changes in their quaternary structure. Multiple factors can modulate the oligomeric transitions of 2-Cys peroxiredoxins such as redox state, post-translational modifications, and pH. However, the molecular basis for the pH influence on the oligomeric state of these enzymes is still elusive. Herein, we solved the crystal structure of a typical 2-Cys peroxiredoxin from Leishmania in the dimeric (pH 8.5) and decameric (pH 4.4) forms, showing that conformational changes in the catalytic loop are associated with the pH-induced decamerization. Mutagenesis and biophysical studies revealed that a highly conserved histidine (His(113)) functions as a pH sensor that, at acidic conditions, becomes protonated and forms an electrostatic pair with Asp(76) from the catalytic loop, triggering the decamerization. In these 2-Cys peroxiredoxins, decamer formation is important for the catalytic efficiency and has been associated with an enhanced sensitivity to oxidative inactivation by overoxidation of the peroxidatic cysteine. In eukaryotic cells, exposure to high levels of H2O2 can trigger intracellular pH variations, suggesting that pH changes might act cooperatively with H2O2 and other oligomerization-modulator factors to regulate the structure and function of typical 2-Cys peroxiredoxins in response to oxidative stress.
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Affiliation(s)
- Mariana A B Morais
- From the Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas/SP, 13083-970
| | - Priscila O Giuseppe
- From the Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas/SP, 13083-970
| | - Tatiana A C B Souza
- the Laboratório de Proteômica e Engenharia de Proteínas, Instituto Carlos Chagas, Fiocruz, Curitiba/PR, 81350-010
| | - Thiago G P Alegria
- the Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo/SP, 05508-900, and
| | - Marcos A Oliveira
- the Departamento de Biologia, Universidade Estadual Paulista Júlio de Mesquita Filho, Campus do Litoral Paulista, São Vicente/SP 11330-900, Brazil
| | - Luis E S Netto
- the Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo/SP, 05508-900, and
| | - Mario T Murakami
- From the Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas/SP, 13083-970,
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