This Article Full Text Full Text (PDF) Supplemental material Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Reprints and Permissions Copyright Information Books from ASM Press MicrobeWorld Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Serres, M. H. Articles by Riley, M. Search for Related Content PubMed PubMed Citation Articles by Serres, M. H. Articles by Riley, M.

Genomic Analysis of Carbon Source Metabolism of Shewanella oneidensis MR-1: Predictions versus Experiments

Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts 02543

Received 23 November 2005/ Accepted 14 April 2006

Genomic sequences have been used to find the genetic foundation for carbon source metabolism in Shewanella oneidensis MR-1. Annotated S. oneidensis MR-1 gene products were examined for their sequence similarity to enzymes participating in pathways for utilization of carbon and energy as described in the BioCyc database (http://www.biocyc.org/) or in the primary literature. A picture emerges that relegates five- and six-carbon sugars to minor roles as carbon sources, whereas multiple pathways for utilization of up to three-carbon carbohydrates seem to be present. Capacity to utilize amino acids for carbon and energy is also present. A few contradictions emerged in which enzymes appear to be present by annotations but are not active in the cell according to physiological experiments. Annotations are based on close sequence similarity and will not reveal inactivity due to deleterious mutations or due to lack of coordination of regulation and transport. Genes for a few enzymes known by experiment to be active are not found in the genome. This may be due to extensive divergence after duplication or convergence of function in separate lines in evolution rendering activities undetectable by sequence similarity. To minimize false predictions from protein sequences, we have been conservative in predicting pathways. We did not predict any pathway when, although a partial pathway was seen it was composed largely of enzymes already accounted for in any other complete pathway. This is an example of how a biochemically oriented sequence analysis can generate questions and direct further experimental investigation.

Supplemental material for this article may be found at http://jb.asm.org/.

This article has been cited by other articles:

• Gupta, N., Tanner, S., Jaitly, N., Adkins, J. N., Lipton, M., Edwards, R., Romine, M., Osterman, A., Bafna, V., Smith, R. D., Pevzner, P. A. (2007). Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation. Genome Res. 17: 1362-1377 [Abstract] [Full Text]  
• Meshulam-Simon, G., Behrens, S., Choo, A. D., Spormann, A. M. (2007). Hydrogen Metabolism in Shewanella oneidensis MR-1. Appl. Environ. Microbiol. 73: 1153-1165 [Abstract] [Full Text]  
• Tang, Y. J., Hwang, J. S., Wemmer, D. E., Keasling, J. D. (2007). Shewanella oneidensis MR-1 Fluxome under Various Oxygen Conditions. Appl. Environ. Microbiol. 73: 718-729 [Abstract] [Full Text]  
• Tang, Y. J., Meadows, A. L., Kirby, J., Keasling, J. D. (2007). Anaerobic Central Metabolic Pathways in Shewanella oneidensis MR-1 Reinterpreted in the Light of Isotopic Metabolite Labeling. J. Bacteriol. 189: 894-901 [Abstract] [Full Text]