| Retention and loss of amino acid biosynthetic pathways based on analysis of whole-genome sequences. | |
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MedLine Citation:
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PMID: 16467468 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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Plants and fungi can synthesize each of the 20 amino acids by using biosynthetic pathways inherited from their bacterial ancestors. However, the ability to synthesize nine amino acids (Phe, Trp, Ile, Leu, Val, Lys, His, Thr, and Met) was lost in a wide variety of eukaryotes that evolved the ability to feed on other organisms. Since the biosynthetic pathways and their respective enzymes are well characterized, orthologs can be recognized in whole genomes to understand when in evolution pathways were lost. The pattern of pathway loss and retention was analyzed in the complete genomes of three early-diverging protist parasites, the amoeba Dictyostelium, and six animals. The nine pathways were lost independently in animals, Dictyostelium, Leishmania, Plasmodium, and Cryptosporidium. Seven additional pathways appear to have been lost in one or another parasite, demonstrating that they are dispensable in a nutrition-rich environment. Our predictions of pathways retained and pathways lost based on computational analyses of whole genomes are validated by minimal-medium studies with mammals, fish, worms, and Dictyostelium. The apparent selective advantages of retaining biosynthetic capabilities for amino acids available in the diet are considered. |
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Authors:
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Samuel H Payne; William F Loomis |
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Publication Detail:
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Type: Journal Article; Research Support, N.I.H., Extramural; Research Support, U.S. Gov't, Non-P.H.S. |
Journal Detail:
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Title: Eukaryotic cell Volume: 5 ISSN: 1535-9778 ISO Abbreviation: Eukaryotic Cell Publication Date: 2006 Feb |
Date Detail:
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Created Date: 2006-02-09 Completed Date: 2006-05-08 Revised Date: 2010-09-16 |
Medline Journal Info:
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Nlm Unique ID: 101130731 Medline TA: Eukaryot Cell Country: United States |
Other Details:
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Languages: eng Pagination: 272-6 Citation Subset: IM |
Affiliation:
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Bioinformatics Program, Division of Biological Sciences, University of California San Diego, MC 0368, 9500 Gilman Dr., La Jolla, CA 92093, USA. spayne@ucsd.edu |
Export Citation:
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APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
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Amino Acids
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administration & dosage,
biosynthesis*,
metabolism Animals Base Sequence Dictyostelium / genetics Diet Genome* Parasites / genetics Phylogeny |
| Grant Support | |
ID/Acronym/Agency:
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GM08806/GM/NIGMS NIH HHS; GM62350/GM/NIGMS NIH HHS |
| Chemical | |
Reg. No./Substance:
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0/Amino Acids |
| Comments/Corrections | |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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