Amino Acid Biosynthesis

Amino Acid Biosynthesis
By Laura Voss
Biosynthesis vs. Metabolism
• Not the same as amino acid metabolism
– Synthesis of most amino acids is only one or
two steps removed from another pathway or
– Missing genes = metabolites not produced.
Many metabolites are not essential to the cell.
Biosynthesis Pathways
• Valine, leucine, and isoleucine
– Essential pathways complete
• Lysine biosynthesis
– Essential genes missing
• Phenylalanine, tyrosine, and tryptophan
– Essential genes missing
Valine, Leucine, and Isoleucine
• One missing gene:, (R)-citramalate synthase
• (R)-citramalate synthase found by name in
JGI and Manatee, not RAST
– Run BLAST for amino acid sequences from
JGI and Manatee on RAST
• Recognizes amino acid sequences but ID’s them
as isopropylmalate synthase – same COG as
citramalate synthase.
Lysine – missing genes
• One “cluster” of genes missing
• Either or must be present
• Neither appear in any of the databases
– Searching for parts of their names brings up
nonspecific similar compounds, which H.
utahensis might use to work around the
missing genes.
– Many genes don’t appear in H. marismortui
Phenylalanine, Tyrosine, and Tryptophan
Missing Genes:
• (3-dehydroquinate synthase)
– Found, via name search, in all 3 databases
• (Chorismate mutase)
– Found, with E.C. Number intact, in JGI and
Manatee; E.C. number not in RAST.
• (3-deoxy-7-phosphoheptulonate
synthase or DHAP synthase)
– Not found in any database or in BLASTer
•EXPASY tags as DHAP
•Searching for DHAP
synthase in Pfam and
other protein databases
gives no result.
•Redirects to DHAP
synthetase, class I –
also not found.
•Also missing in H.
marismortui KEGG.
Conclusions and Remaining
• Valine, leucine, and isoleucine complete as they
appear on KEGG
• Lysine does not, but alternative proteins may be
present, allowing a way around missing genes.
• Phenylalanine, tyrosine, and tryptophan are
incomplete; no obvious substitute proteins, plus’s absense from Pfam.
– Possibility: Use HMM Logo for DHAP synthetase?
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