Document Detail


Retention and loss of amino acid biosynthetic pathways based on analysis of whole-genome sequences.
MedLine Citation:
PMID:  16467468     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
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.
Authors:
Samuel H Payne; William F Loomis
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural; Research Support, U.S. Gov't, Non-P.H.S.    
Journal Detail:
Title:  Eukaryotic cell     Volume:  5     ISSN:  1535-9778     ISO Abbreviation:  Eukaryotic Cell     Publication Date:  2006 Feb 
Date Detail:
Created Date:  2006-02-09     Completed Date:  2006-05-08     Revised Date:  2010-09-16    
Medline Journal Info:
Nlm Unique ID:  101130731     Medline TA:  Eukaryot Cell     Country:  United States    
Other Details:
Languages:  eng     Pagination:  272-6     Citation Subset:  IM    
Affiliation:
Bioinformatics Program, Division of Biological Sciences, University of California San Diego, MC 0368, 9500 Gilman Dr., La Jolla, CA 92093, USA. spayne@ucsd.edu
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MeSH Terms
Descriptor/Qualifier:
Amino Acids / administration & dosage,  biosynthesis*,  metabolism
Animals
Base Sequence
Dictyostelium / genetics
Diet
Genome*
Parasites / genetics
Phylogeny
Grant Support
ID/Acronym/Agency:
GM08806/GM/NIGMS NIH HHS; GM62350/GM/NIGMS NIH HHS
Chemical
Reg. No./Substance:
0/Amino Acids
Comments/Corrections

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