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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 freestanding counterparts of all of the latter fused genes exhibit a distinct trace of syntenic association. Conclusion:more » 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.« less

Authors:
 [1];  [2];  [1];  [3]
  1. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  2. Univ. of Florida, Gainesville, FL (United States). Emerson Hall
  3. Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Univ. of Florida, Gainesville, FL (United States). Emerson Hall
Publication Date:
Research Org.:
Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division; National Institutes of Health (NIH)
OSTI Identifier:
1626596
Grant/Contract Number:  
AC52-06NA25396; G13 LM008297
Resource Type:
Accepted Manuscript
Journal Name:
BMC Biology
Additional Journal Information:
Journal Volume: 3; Journal Issue: 1; Journal ID: ISSN 1741-7007
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Life Sciences & Biomedicine - Other Topics

Citation Formats

Song, Jian, Bonner, Carol A., Wolinsky, Murray, and Jensen, Roy A. The TyrA family of aromatic-pathway dehydrogenases in phylogenetic context. United States: N. p., 2005. Web. doi:10.1186/1741-7007-3-13.
Song, Jian, Bonner, Carol A., Wolinsky, Murray, & Jensen, Roy A. The TyrA family of aromatic-pathway dehydrogenases in phylogenetic context. United States. https://doi.org/10.1186/1741-7007-3-13
Song, Jian, Bonner, Carol A., Wolinsky, Murray, and Jensen, Roy A. Thu . "The TyrA family of aromatic-pathway dehydrogenases in phylogenetic context". United States. https://doi.org/10.1186/1741-7007-3-13. https://www.osti.gov/servlets/purl/1626596.
@article{osti_1626596,
title = {The TyrA family of aromatic-pathway dehydrogenases in phylogenetic context},
author = {Song, Jian and Bonner, Carol A. and Wolinsky, Murray and Jensen, Roy A.},
abstractNote = {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 freestanding counterparts of all of the latter fused genes exhibit a distinct trace of syntenic association. Conclusion: 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.},
doi = {10.1186/1741-7007-3-13},
journal = {BMC Biology},
number = 1,
volume = 3,
place = {United States},
year = {2005},
month = {5}
}

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Works referencing / citing this record:

Pathway optimization by re-design of untranslated regions for L-tyrosine production in Escherichia coli
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