ArticleProceedings of the National Academy of Sciences of the United States of America2000
Functional analysis of gapped microbial genomes: amino acid metabolism of Thiobacillus ferrooxidans.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2000. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 67 citations in OpenAlex.
- Advances in bioleaching of waste lithium batteries under metal ion stress.Bioresources and bioprocessing · 2023Review
- Sulfur enhancement effects for uranium bioleaching in column reactors from a refractory uranium ore.Frontiers in microbiology · 2023Article
- Overlying water fluoride concentrations influence dissolved organic matter composition and migration from pore water in sediment via bacterial mechanisms.Environmental science and ecotechnology · 2022Article
- Navigating Microbiological Food Safety in the Era of Whole-Genome Sequencing.Clinical microbiology reviews · 2016Review
- Omics on bioleaching: current and future impacts.Applied microbiology and biotechnology · 2015Review
- Sequence Analysis of Inducible Prophage phIS3501 Integrated into the Haemolysin II Gene of Bacillus thuringiensis var israelensis ATCC35646.Genetics research international · 2012Article
- Draft genome sequence of the extremely acidophilic bacterium Acidithiobacillus caldus ATCC 51756 reveals metabolic versatility in the genus Acidithiobacillus.Journal of bacteriology · 2009Article
- Diversity and strain specificity of plant cell wall degrading enzymes revealed by the draft genome of Ruminococcus flavefaciens FD-1.PloS one · 2009Article
- Computational biology methods and their application to the comparative genomics of endocellular symbiotic bacteria of insects.Biological procedures online · 2009Article
- Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications.BMC genomics · 2008Article
- Sorting out the mix in microbial genomics.Environmental microbiology · 2008Article
- Analysis of Aspergillus nidulans metabolism at the genome-scale.BMC genomics · 2008Article
- Genomic insights into the iron uptake mechanisms of the biomining microorganism Acidithiobacillus ferrooxidans.Journal of industrial microbiology & biotechnology · 2005Review
- Metabolic reconstruction of sulfur assimilation in the extremophile Acidithiobacillus ferrooxidans based on genome analysis.BMC genomics · 2003Article
- Genome analysis of F. nucleatum sub spp vincentii and its comparison with the genome of F. nucleatum ATCC 25586.Genome research · 2003Article
- Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network.Genome research · 2003Article
- The ERGO genome analysis and discovery system.Nucleic acids research · 2003Article
- The value of complete microbial genome sequencing (you get what you pay for).Journal of bacteriology · 2002Review
- Draft sequencing and comparative genomics of Xylella fastidiosa strains reveal novel biological insights.Genome research · 2002Article
- Whole-genome comparative analysis of three phytopathogenic Xylella fastidiosa strains.Proceedings of the National Academy of Sciences of the United States of America · 2002Article
Corrections and comments
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Authors and funding
9 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A gapped genome sequence of the biomining bacterium Thiobacillus ferrooxidans strain ATCC23270 was assembled from sheared DNA fragments (3.2-times coverage) into 1,912 contigs. A total of 2,712 potential genes (ORFs) were identified in 2.6 Mbp (megabase pairs) of Thiobacillus genomic sequence. Of these genes, 2,159 could be assigned functions by using the WIT-Pro/EMP genome analysis system, most with a high degree of certainty. Nine hundred of the genes have been assigned roles in metabolic pathways, producing an overview of cellular biosynthesis, bioenergetics, and catabolism. Sequence similarities, relative gene positions on the chromosome, and metabolic reconstruction (placement of gene products in metabolic pathways) were all used to aid gene assignments and for development of a functional overview. Amino acid biosynthesis was chosen to demonstrate the analytical capabilities of this approach. Only 10 expected enzymatic activities, of the nearly 150 involved in the biosynthesis of all 20 amino acids, are currently unassigned in the Thiobacillus genome. This result compares favorably with 10 missing genes for amino acid biosynthesis in the complete Escherichia coli genome. Gapped genome analysis can therefore give a decent picture of the central metabolism of a microorganism, equivalent to that of a complete sequence, at significantly lower cost.
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