Amino Acid Biosynthesis

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Amino Acid Biosynthesis

• By Laura Voss

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Biosynthesis vs. Metabolism

• Not the same as amino acid metabolism pathways.
• Synthesis of most amino acids is only one or two
  steps removed from another pathway or cycle.
• Missing genes metabolites not produced. Many
  metabolites are not essential to the cell.

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Biosynthesis Pathways

• Valine, leucine, and isoleucine biosynthesis
• Essential pathways complete
• Lysine biosynthesis
• Essential genes missing
• Phenylalanine, tyrosine, and tryptophan
  biosynthesis
• Essential genes missing

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Valine, Leucine, and Isoleucine

• One missing gene 2.3.1.182, (R)-citramalate
  synthase

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Found

• (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 IDs them as
  isopropylmalate synthase same COG as
  citramalate synthase.

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Lysine
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Lysine missing genes

• One cluster of genes missing
• Either 1.4.1.6 or 5.1.1.7 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 dont appear in H. marismortui either.

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Phenylalanine, Tyrosine, and Tryptophan
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Missing Genes

• 4.2.3.4 (3-dehydroquinate synthase)
• Found, via name search, in all 3 databases
• 5.4.99.5 (Chorismate mutase)
• Found, with E.C. Number intact, in JGI and
  Manatee E.C. number not in RAST.
• 2.5.1.54 (3-deoxy-7-phosphoheptulonate synthase
  or DHAP synthase)
• Not found in any database or in BLASTer search!)

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• EXPASY tags as DHAP synthase.
• 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.

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Conclusions and Remaining Questions

• 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
  2.5.1.54s absense from Pfam.
• Possibility Use HMM Logo for DHAP synthetase?