| Summary: | <p>Abstract</p> <p>Background</p> <p>Microorganisms and plants are able to produce tryptophan. Enzymes catalysing the last seven steps of tryptophan biosynthesis are encoded in the canonical <it>trp </it>operon. Among the <it>trp </it>genes are most frequently <it>trpA </it>and <it>trpB</it>, which code for the alpha and beta subunit of tryptophan synthase. In several prokaryotic genomes, two variants of <it>trpB </it>(named <it>trpB1 </it>or <it>trpB2</it>) occur in different combinations. The evolutionary history of these <it>trpB </it>genes is under debate.</p> <p>Results</p> <p>In order to study the evolution of <it>trp </it>genes, completely sequenced archaeal and bacterial genomes containing <it>trpB </it>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 <it>trpB1 </it>genes most of which belonged to <it>trp </it>operons. Groups two to four contained <it>trpB2 </it>genes. The largest group (<it>trpB2_o</it>) contained <it>trpB2 </it>genes all located outside of operons. Most of these genes originated from species possessing an operon-based <it>trpB1 </it>in addition. Groups three and four pertain to <it>trpB2 </it>genes of those genomes containing exclusively one or two <it>trpB2 </it>genes, but no <it>trpB1</it>. One group (<it>trpB2_i</it>) consisted of <it>trpB2 </it>genes located inside, the other (<it>trpB2_a</it>) of <it>trpB2 </it>genes located outside the <it>trp </it>operon. TrpA and TrpB form a heterodimer and cooperate biochemically. In order to characterise <it>trpB </it>variants and stages of TrpA/TrpB cooperation <it>in silico</it>, several approaches were combined. Phylogenetic trees were constructed for all <it>trp </it>genes; their structure was assessed <it>via </it>bootstrapping. Alternative models of <it>trpB </it>evolution were evaluated with parsimony arguments. The four groups of <it>trpB </it>variants were correlated with archaeal speciation. Several stages of TrpA/TrpB cooperation were identified and <it>trpB </it>variants were characterised. Most plausibly, <it>trpB2 </it>represents the predecessor of the modern <it>trpB </it>gene, and <it>trpB1 </it>evolved in an ancestral bacterium.</p> <p>Conclusion</p> <p>In archaeal genomes, several stages of <it>trpB </it>evolution, TrpA/TrpB cooperation, and operon formation can be observed. Thus, archaeal <it>trp </it>genes may serve as a model system for studying the evolution of protein-protein interactions and operon formation.</p>
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