title: The TyrA family of aromatic-pathway dehydrogenases in phylogenetic context.
abstract: BACKGROUND
  The TyrA protein family includes members that catalyze two dehydrogenase reactions in distinct pathways leading to L-tyrosine and a third reaction that is not part of tyrosine biosynthesis. Family members share a catalytic core region of about 30 kDa, where inhibitors operate competitively by acting as substrate mimics. This protein family typifies many that are challenging for bioinformatic analysis because of relatively modest sequence conservation and small size.
  
  
  RESULTS
  Phylogenetic relationships of TyrA domains were evaluated in the context of combinatorial patterns of specificity for the two substrates, as well as the presence or absence of a variety of fusions. An interactive tool is provided for prediction of substrate specificity. Interactive alignments for a suite of catalytic-core TyrA domains of differing specificity are also provided to facilitate phylogenetic analysis. tyrA membership in apparent operons (or supraoperons) was examined, and patterns of conserved synteny in relationship to organismal positions on the 16S rRNA tree were ascertained for members of the domain Bacteria. A number of aromatic-pathway genes (hisHb, aroF, aroQ) have fused with tyrA, and it must be more than coincidental that the free-standing counterparts of all of the latter fused genes exhibit a distinct trace of syntenic association.
  
  
  CONCLUSIONS
  We propose that the ancestral TyrA dehydrogenase had broad specificity for both the cyclohexadienyl and pyridine nucleotide substrates. Indeed, TyrA proteins of this type persist today, but it is also common to find instances of narrowed substrate specificities, as well as of acquisition via gene fusion of additional catalytic domains or regulatory domains. In some clades a qualitative change associated with either narrowed substrate specificity or gene fusion has produced an evolutionary "jump" in the vertical genealogy of TyrA homologs. The evolutionary history of gene organizations that include tyrA can be deduced in genome assemblages of sufficiently close relatives, the most fruitful opportunities currently being in the Proteobacteria. The evolution of TyrA proteins within the broader context of how their regulation evolved and to what extent TyrA co-evolved with other genes as common members of aromatic-pathway regulons is now feasible as an emerging topic of ongoing inquiry.
authors.affiliation: Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA. jian@lanl.gov
authors.forename: Jian
authors.initials: J
authors.lastname: Song
authors.forename: Carol A
authors.initials: CA
authors.lastname: Bonner
authors.forename: Murray
authors.initials: M
authors.lastname: Wolinsky
authors.forename: Roy A
authors.initials: RA
authors.lastname: Jensen
mesh_terms: D000595:Amino Acid Sequence; D019843:Archaeal Proteins / Q000235:genetics* / Q000502:physiology; D001426:Bacterial Proteins / Q000145:classification / Q000235:genetics* / Q000502:physiology; D005057:Eukaryotic Cells / Q000201:enzymology*; D008969:Molecular Sequence Data; D009097:Multienzyme Complexes / Q000145:classification / Q000235:genetics* / Q000502:physiology; D005810:Multigene Family / Q000235:genetics*; D010088:Oxidoreductases / Q000145:classification / Q000235:genetics / Q000502:physiology*; D010802:Phylogeny; D011303:Prephenate Dehydrogenase / Q000235:genetics; D020560:Proteobacteria / Q000201:enzymology / Q000235:genetics; D015398:Signal Transduction / Q000235:genetics*
chemical_list: D019843:Archaeal Proteins; D001426:Bacterial Proteins; D009097:Multienzyme Complexes; C076398:TyrA protein, Bacteria; D010088:Oxidoreductases; D011303:Prephenate Dehydrogenase