ArticleBMC evolutionary biology2007
Modelling the evolution of the archeal tryptophan synthase.
Article in BMC evolutionary biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed, 33 citations in OpenAlex.
- A naturally occurring standalone TrpB enzyme provides insights into allosteric communication within tryptophan synthase.Protein science : a publication of the Protein Society · 2025Article
- Genomic insights into local-scale evolution of ocularMicrobial genomics · 2024Article
- Article
- Analysis of allosteric communication in a multienzyme complex by ancestral sequence reconstruction.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Conserved genomic neighborhood is a strong but no perfect indicator for a direct interaction of microbial gene products.BMC bioinformatics · 2020Article
- Generation of a Stand-Alone Tryptophan Synthase α-Subunit by Mimicking an Evolutionary Blueprint.Chembiochem : a European journal of chemical biology · 2019Article
- Article
- A Panel of TrpB Biocatalysts Derived from Tryptophan Synthase through the Transfer of Mutations that Mimic Allosteric Activation.Angewandte Chemie (International ed. in English) · 2016Article
- The genome sequence of Geobacter metallireducens: features of metabolism, physiology and regulation common and dissimilar to Geobacter sulfurreducens.BMC microbiology · 2009Article
- GO4genome: a prokaryotic phylogeny based on genome organization.Journal of molecular evolution · 2009Article
- Evolution of bacterial trp operons and their regulation.Current opinion in microbiology · 2008Review
- TrpY regulation of trpB2 transcription in Methanothermobacter thermautotrophicus.Journal of bacteriology · 2008Article
- H2r: identification of evolutionary important residues by means of an entropy based analysis of multiple sequence alignments.BMC bioinformatics · 2008Article
- The tryptophan pathway genes of the Sargasso Sea metagenome: new operon structures and the prevalence of non-operon organization.Genome biology · 2008Article
- TRAP-5' stem loop interaction increases the efficiency of transcription termination in the Bacillus subtilis trpEDCFBA operon leader region.RNA (New York, N.Y.) · 2007Article
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1 author at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundMicroorganisms and plants are able to produce tryptophan. Enzymes catalysing the last seven steps of tryptophan biosynthesis are encoded in the canonical trp operon. Among the trp genes are most frequently trpA and trpB, which code for the alpha and beta subunit of tryptophan synthase. In several prokaryotic genomes, two variants of trpB (named trpB1 or trpB2) occur in different combinations. The evolutionary history of these trpB genes is under debate.
resultsIn order to study the evolution of trp genes, completely sequenced archeal and bacterial genomes containing trpB were analysed. Phylogenetic trees indicated that TrpB sequences constitute four distinct groups; their composition is in agreement with the location of respective genes. The first group consisted exclusively of trpB1 genes most of which belonged to trp operons. Groups two to four contained trpB2 genes. The largest group (trpB2_o) contained trpB2 genes all located outside of operons. Most of these genes originated from species possessing an operon-based trpB1 in addition. Groups three and four pertain to trpB2 genes of those genomes containing exclusively one or two trpB2 genes, but no trpB1. One group (trpB2_i) consisted of trpB2 genes located inside, the other (trpB2_a) of trpB2 genes located outside the trp operon. TrpA and TrpB form a heterodimer and cooperate biochemically. In order to characterise trpB variants and stages of TrpA/TrpB cooperation in silico, several approaches were combined. Phylogenetic trees were constructed for all trp genes; their structure was assessed via bootstrapping. Alternative models of trpB evolution were evaluated with parsimony arguments. The four groups of trpB variants were correlated with archeal speciation. Several stages of TrpA/TrpB cooperation were identified and trpB variants were characterised. Most plausibly, trpB2 represents the predecessor of the modern trpB gene, and trpB1 evolved in an ancestral bacterium.
conclusionIn archeal genomes, several stages of trpB evolution, TrpA/TrpB cooperation, and operon formation can be observed. Thus, archeal trp genes may serve as a model system for studying the evolution of protein-protein interactions and operon formation.
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