Genome sequence of the model sulfate reducer Desulfovibrio gigas: a comparative analysis within the Desulfovibrio genus

Authors

  • Fabio O. Morais-Silva,

    1. Instituto de Tecnologia Quómica e Biológica – Antonio Xavier, Universidade Nova de Lisboa (ITQB-UNL), Oeiras, Portugal
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    • These authors contributed equally to this study.
  • Antonio Mauro Rezende,

    1. Grupo Informática de Biossistemas, Centro de Pesquisa René Rachou – FIOCRUZ, Belo Horizonte, Minas Gerais, Brazil
    Current affiliation:
    1. Departamento de Microbiologia, Centro de Pesquisas Aggeu Magalhães – FIOCRUZ PE, Recife/PE, Brazil
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    • These authors contributed equally to this study.
  • Catarina Pimentel,

    1. Instituto de Tecnologia Quómica e Biológica – Antonio Xavier, Universidade Nova de Lisboa (ITQB-UNL), Oeiras, Portugal
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  • Catia I. Santos,

    1. Instituto de Tecnologia Quómica e Biológica – Antonio Xavier, Universidade Nova de Lisboa (ITQB-UNL), Oeiras, Portugal
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  • Carla Clemente,

    1. STAB VIDA - Madan Parque Rua dos Inventores s/sala 2.18, Caparica, Portugal
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  • Ana Varela–Raposo,

    1. Instituto de Tecnologia Quómica e Biológica – Antonio Xavier, Universidade Nova de Lisboa (ITQB-UNL), Oeiras, Portugal
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  • Daniela M. Resende,

    1. Grupo Informática de Biossistemas, Centro de Pesquisa René Rachou – FIOCRUZ, Belo Horizonte, Minas Gerais, Brazil
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  • Sofia M. da Silva,

    1. Instituto de Tecnologia Quómica e Biológica – Antonio Xavier, Universidade Nova de Lisboa (ITQB-UNL), Oeiras, Portugal
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  • Luciana Márcia de Oliveira,

    1. Grupo Informática de Biossistemas, Centro de Pesquisa René Rachou – FIOCRUZ, Belo Horizonte, Minas Gerais, Brazil
    2. Departamento de Microbiologia, Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais, Brazil
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  • Marcia Matos,

    1. STAB VIDA - Madan Parque Rua dos Inventores s/sala 2.18, Caparica, Portugal
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  • Daniela A. Costa,

    1. Grupo Informática de Biossistemas, Centro de Pesquisa René Rachou – FIOCRUZ, Belo Horizonte, Minas Gerais, Brazil
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  • Orfeu Flores,

    Corresponding author
    1. STAB VIDA - Madan Parque Rua dos Inventores s/sala 2.18, Caparica, Portugal
    • Correspondence

      Claudina Rodrigues-Pousada, Instituto de Tecnologia Química e Biológica António Xavier, Av da República (EAN), 2780-157 Oeiras, Portugal. Tel: +351214469624; Fax: +351214469625; E-mail: claudina@itqb.unl.pt

      Jerónimo C. Cruz, Grupo Informática de Biossistemas, Centro de Pesquisa René Rachou – FIOCRUZ, Belo Horizonte, 3019002 Minas Gerais, Brasil. Tel: +55 31 3349 7700; Fax: +351 21 043 860; E-mail: jeronimo@cpqrr.fiocruz.br

      Orfeu Flores, STAB VIDA - Madan Parque Rua dos Inventores s/sala 2.18, 2825-182 Caparica, Portugal. Tel: +351960022300; Fax: +553132953115; E-mail: orfeu@stabvida.com

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  • Jerónimo C. Ruiz,

    Corresponding author
    1. Grupo Informática de Biossistemas, Centro de Pesquisa René Rachou – FIOCRUZ, Belo Horizonte, Minas Gerais, Brazil
    • Correspondence

      Claudina Rodrigues-Pousada, Instituto de Tecnologia Química e Biológica António Xavier, Av da República (EAN), 2780-157 Oeiras, Portugal. Tel: +351214469624; Fax: +351214469625; E-mail: claudina@itqb.unl.pt

      Jerónimo C. Cruz, Grupo Informática de Biossistemas, Centro de Pesquisa René Rachou – FIOCRUZ, Belo Horizonte, 3019002 Minas Gerais, Brasil. Tel: +55 31 3349 7700; Fax: +351 21 043 860; E-mail: jeronimo@cpqrr.fiocruz.br

      Orfeu Flores, STAB VIDA - Madan Parque Rua dos Inventores s/sala 2.18, 2825-182 Caparica, Portugal. Tel: +351960022300; Fax: +553132953115; E-mail: orfeu@stabvida.com

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  • Claudina Rodrigues-Pousada

    Corresponding author
    1. Instituto de Tecnologia Quómica e Biológica – Antonio Xavier, Universidade Nova de Lisboa (ITQB-UNL), Oeiras, Portugal
    • Correspondence

      Claudina Rodrigues-Pousada, Instituto de Tecnologia Química e Biológica António Xavier, Av da República (EAN), 2780-157 Oeiras, Portugal. Tel: +351214469624; Fax: +351214469625; E-mail: claudina@itqb.unl.pt

      Jerónimo C. Cruz, Grupo Informática de Biossistemas, Centro de Pesquisa René Rachou – FIOCRUZ, Belo Horizonte, 3019002 Minas Gerais, Brasil. Tel: +55 31 3349 7700; Fax: +351 21 043 860; E-mail: jeronimo@cpqrr.fiocruz.br

      Orfeu Flores, STAB VIDA - Madan Parque Rua dos Inventores s/sala 2.18, 2825-182 Caparica, Portugal. Tel: +351960022300; Fax: +553132953115; E-mail: orfeu@stabvida.com

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  • This paper is dedicated to the memory of Professors Jean LeGall and António V. Xavier who have introduced us to the study of Desulfovibrio gigas and have greatly stimulated its research.

Abstract

Desulfovibrio gigas is a model organism of sulfate-reducing bacteria of which energy metabolism and stress response have been extensively studied. The complete genomic context of this organism was however, not yet available. The sequencing of the D. gigas genome provides insights into the integrated network of energy conserving complexes and structures present in this bacterium. Comparison with genomes of other Desulfovibrio spp. reveals the presence of two different CRISPR/Cas systems in D. gigas. Phylogenetic analysis using conserved protein sequences (encoded by rpoB and gyrB) indicates two main groups of Desulfovibrio spp, being D. gigas more closely related to D. vulgaris and D. desulfuricans strains. Gene duplications were found such as those encoding fumarate reductase, formate dehydrogenase, and superoxide dismutase. Complexes not yet described within Desulfovibrio genus were identified: Mnh complex, a v-type ATP-synthase as well as genes encoding the MinCDE system that could be responsible for the larger size of D. gigas when compared to other members of the genus. A low number of hydrogenases and the absence of the codh/acs and pfl genes, both present in D. vulgaris strains, indicate that intermediate cycling mechanisms may contribute substantially less to the energy gain in D. gigas compared to other Desulfovibrio spp. This might be compensated by the presence of other unique genomic arrangements of complexes such as the Rnf and the Hdr/Flox, or by the presence of NAD(P)H related complexes, like the Nuo, NfnAB or Mnh.

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