Retention and loss of amino acid biosynthetic pathways based on analysis of whole-genome sequences.

TitleRetention and loss of amino acid biosynthetic pathways based on analysis of whole-genome sequences.
Publication TypeJournal Article
Year of Publication2006
AuthorsPayne SH, Loomis WF
JournalEukaryot Cell
Volume5
Issue2
Pagination272-6
Date Published2006 Feb
ISSN1535-9778
KeywordsAmino Acids, Animals, Base Sequence, Dictyostelium, Diet, Genome, Parasites, Phylogeny
Abstract

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.

DOI10.1128/EC.5.2.272-276.2006
PubMed URLhttp://www.ncbi.nlm.nih.gov/pubmed/16467468?dopt=Abstract
PMCPMC1405893
Alternate JournalEukaryotic Cell
PubMed ID16467468