These authors contributed equally to this study.
Genome sequence of the model sulfate reducer Desulfovibrio gigas: a comparative analysis within the Desulfovibrio genus†
Article first published online: 23 JUL 2014
© 2014 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.
This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
Volume 3, Issue 4, pages 513–530, August 2014
How to Cite
MicrobiologyOpen 2014; 3(4): 513–530
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.
- Issue published online: 14 AUG 2014
- Article first published online: 23 JUL 2014
- Manuscript Accepted: 15 MAY 2014
- Manuscript Revised: 30 APR 2014
- Manuscript Received: 20 MAR 2014
- Fundação para Ciência e Tecnologia. Grant Numbers: PTDC/BIA-IC/104030/2008, Pest-OE/EQB/LA0004/2011
- Agência de Inovação. Grant Number: ADI/2006/M2.3/003
- STAB Vida
- BIOCANT. Grant Numbers: SFRH/BD/45211/2008, SFRH/BPD/90823/2012, SFRH/BPD/80244/2011
- Coordenação de Aperfeiçoamento de Pessoal de Ensino Superior
- Fundação de Amparo à Pesquisa do Estado de Minas Gerais
- National Counsel of Technological and Scientific Development CNPq
- Rede Integrada de Estudos Genômicos e Proteômicos. Grant Numbers: 476539/2010-2, 301652/2012-0, 560943/2010-5, APQ-02382-10, PRI-00197-12, APQ-01085-12
|mbo3184-sup-0001-Supportinginformation.docx||Word document||94K||Figure S1. Specific genomic organization of Desulfovibrio gigas. (A) Organization of the hcp and hcpR monocistronic operons in D.gigas in comparison with other Desulfovibrio species, where: frdx, ferredoxin; a, Upsa-like protein; b, alcohol dehydrogenase; c, sensory box histidine kinase; d, acpD:acyl carrier protein phosphodiesterase; e, putative lipoprotein; f, polysaccharide export protein; g, cupin 2 conserved barrel domain protein. Gene cluster organization from D. vulgaris Hildenborough, D. alaskensis G20, and D. desulfuricans ATCC27774 were obtained at the DOE Joint Genome Institute (http://www.jgi.doe.gov/). (B) Organization of operons exclusively present in D. gigas genome as compared to other Desulfovibrio spp.: (i) aerobic-type carbon monoxide dehydrogenase complex; (ii) vacuolar-type ATP-synthase complex; and (iii) multisubunit Na+/H+ antiporter complex. Genes were assigned according to the predicted protein function. The unnamed coding regions are either hypothetical proteins or proteins of unknown function.|
|mbo3184-sup-0002-FigS1.tif||image/tif||898K||Figure S2. Interaction network of Desulfovibrio gigas proteins involved in cell size. Purple circles indicate central elements of the network. Yellow circles indicate elements with a fewer number of interactions. Blue lines show protein interactions common to several D. genus as retrieved by the STRING database,whereas red lines correspond to D. gigas specific interactions.|
Table S1. COG functional groups.
Table S2. Codon usage.
Table S3. Transposable elements.
Table S4. Selenocystein-containing proteins.
Table S5. CRISPR proteins.
Table S6. Chemotaxis proteins.
Table S7. Response to oxygen.
Table S8. Nitrogen metabolism.
Table S9. Transcriptional factors sigma 54.
Table S10. Sulfate metabolism.
Table S11. Pentose phosphate pathway.
Table S12. Beta oxidation.
Table S13. Embden-Meyerhof-Parnas pathway.
Table S14: Entner-Doudoroff pathway.
Table S15. TCA cycle.
Table S16. Fumarate metabolism.
Table S17. WoodLjungahl pathway.
Table S18. Alcohol metabolism.
Table S19. Lactate metabolism.
Table S20. Formate metabolism.
Table S21. Oxidation of pyruvate to acetyl-CoA and acetate formation.
Table S22. ATP synthesis.
Table S23. Cytochromes.
Table S24. Hydrogenases.
Table S25. Membranar energy complexes.
Table S26. Nfn complexes.
Table S27. Hdr-like proteins.
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