ArticleJournal of bacteriology2006
Genomic analysis of carbon source metabolism of Shewanella oneidensis MR-1: Predictions versus experiments.
Article in Journal of bacteriology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- A common inducer molecule enhances sugar utilization by Shewanella oneidensis MR-1.Journal of industrial microbiology & biotechnology · 2023Article
- Flux-Balance Analysis and Mobile CRISPRi-Guided Deletion of a Conditionally Essential Gene inACS synthetic biology · 2022Article
- Application of comparative genomics ofFrontiers in microbiology · 2022Article
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- Genomic insights into diverse bacterial taxa that degrade extracellular DNA in marine sediments.Nature microbiology · 2021Article
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- Roles of d-Lactate Dehydrogenases in the Anaerobic Growth ofApplied and environmental microbiology · 2019Article
- Dissociation between Iron and Heme Biosyntheses Is Largely Accountable for Respiration Defects ofApplied and environmental microbiology · 2018Article
- Pan-genome analyses of 24Biotechnology for biofuels · 2018Article
- Growth Trade-Offs Accompany the Emergence of Glycolytic Metabolism in Shewanella oneidensis MR-1.Journal of bacteriology · 2017Article
- Loss of OxyR reduces efficacy of oxygen respiration in Shewanella oneidensis.Scientific reports · 2017Article
- EngineeringBiotechnology for biofuels · 2017Article
- CRP Regulates D-Lactate Oxidation inFrontiers in microbiology · 2017Article
- Reduced expression of cytochrome oxidases largely explains cAMP inhibition of aerobic growth in Shewanella oneidensis.Scientific reports · 2016Article
- Catabolic and regulatory systems in Shewanella oneidensis MR-1 involved in electricity generation in microbial fuel cells.Frontiers in microbiology · 2015Review
- Theoretical exploration of optimal metabolic flux distributions for extracellular electron transfer by Shewanella oneidensis MR-1.Biotechnology for biofuels · 2014Article
- Indirect and suboptimal control of gene expression is widespread in bacteria.Molecular systems biology · 2013Article
- Mislocalization of Rieske protein PetA predominantly accounts for the aerobic growth defect of Tat mutants in Shewanella oneidensis.PloS one · 2013Article
- Large-scale comparative phenotypic and genomic analyses reveal ecological preferences of shewanella species and identify metabolic pathways conserved at the genus level.Applied and environmental microbiology · 2011Article
Corrections and comments
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Authors and funding
2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
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.
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