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Energy metabolism in Desulfovibrio vulgaris Hildenborough: insights from transcriptome analysis

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Abstract

Sulphate-reducing bacteria are important players in the global sulphur and carbon cycles, with considerable economical and ecological impact. However, the process of sulphate respiration is still incompletely understood. Several mechanisms of energy conservation have been proposed, but it is unclear how the different strategies contribute to the overall process. In order to obtain a deeper insight into the energy metabolism of sulphate-reducers whole-genome microarrays were used to compare the transcriptional response of Desulfovibrio vulgaris Hildenborough grown with hydrogen/sulphate, pyruvate/sulphate, pyruvate with limiting sulphate, and lactate/thiosulphate, relative to growth in lactate/sulphate. Growth with hydrogen/sulphate showed the largest number of differentially expressed genes and the largest changes in transcript levels. In this condition the most up-regulated energy metabolism genes were those coding for the periplasmic [NiFeSe] hydrogenase, followed by the Ech hydrogenase. The results also provide evidence for the involvement of formate cycling and the recently proposed ethanol pathway during growth in hydrogen. The pathway involving CO cycling is relevant during growth on lactate and pyruvate, but not during growth in hydrogen as the most down-regulated genes were those coding for the CO-induced hydrogenase. Growth on lactate/thiosulphate reveals a down-regulation of several energy metabolism genes similar to what was observed in the presence of nitrite. This study identifies the role of several proteins involved in the energy metabolism of D. vulgaris and highlights several novel genes related to this process, revealing a more complex bioenergetic metabolism than previously considered.

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Abbreviations

HS:

Hydrogen/sulphate medium

LS:

Lactate/sulphate medium

LT:

Lactate/thiosulphate medium

PS:

Pyruvate/sulphate medium

P:

Pyruvate medium

SRB:

Sulphate-reducing bacteria

TpIc3 :

Type I cytochrome c3

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Acknowledgements

This work was supported by Fundação para a Ciência e Tecnologia grants PPCDT/2004/QUI/55690 to ROL and PTDC/QUI/68368/2006 to IACP, co-funded by FEDER program, and by the United States Department of Energy under Genomics:GTL program through the Virtual Institute of Microbial Stress and Survival (VIMSS; http://www.vimss.lbl.gov), Office of Biological and Environmental Research, Office of Science to JZ. PMP was a recipient of the FCT PhD grant SFRH/BD/5231/2001. The authors are grateful to Prof. Gerrit Voordouw for helpful discussions and sharing data prior to publication.

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Authors and Affiliations

  1. Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República (EAN), 2781-901, Oeiras, Portugal

    Patrícia M. Pereira, Filipa M. A. Valente, António V. Xavier, Inês A. C. Pereira & Ricardo O. Louro

  2. Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA

    Qiang He & Jizhong Zhou

  3. Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, TN, 37996, USA

    Qiang He

  4. The Center for Environmental Biotechnology, The University of Tennessee, Knoxville, TN, 37996, USA

    Qiang He

  5. Virtual Institute for Microbial Stress and Survival, Berkeley, CA, 94720, USA

    Jizhong Zhou

  6. Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, OK, 73019, USA

    Jizhong Zhou

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  1. Patrícia M. Pereira
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  2. Qiang He
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  3. Filipa M. A. Valente
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  4. António V. Xavier
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  6. Inês A. C. Pereira
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  7. Ricardo O. Louro
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Correspondence to Ricardo O. Louro.

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Pereira, P.M., He, Q., Valente, F.M.A. et al. Energy metabolism in Desulfovibrio vulgaris Hildenborough: insights from transcriptome analysis. Antonie van Leeuwenhoek 93, 347–362 (2008). https://doi.org/10.1007/s10482-007-9212-0

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