Modelling the evolution of the archeal tryptophan synthase

Rainer Merkl

doi:10.1186/1471-2148-7-59

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.

Highlights

Microorganisms and plants are able to produce tryptophan
Assessing the composition of trp gene clusters In order to describe the composition of trp regulons in a quantitative manner and to compare their content in archaeal and bacterial genomes, AMIGOS [27] was used
A reason for the lower score of tryptophan synthase β subunit (trpB) in archaeal trp operons was the occurrence of two trpB variants in these species

Summary

Introduction

Enzymes catalysing the last seven steps of tryptophan biosynthesis are encoded in the canonical trp operon. The synthesis of tryptophan is a common metabolic capability of microorganisms and higher plants, which is not provided by mammals. The prokaryotic trp operon encodes the enzymes catalysing the final and pathwayspecific steps from chorismate to L-tryptophan. For more than 40 years, the enterobacterial operon has been the classical model system for studying the evolutionary relation of genes and enzymes (see [1,2] and references therein) as well as gene regulation. BMC Evolutionary Biology 2007, 7:59 http://www.biomedcentral.com/1471-2148/7/59 ulation, several, conceptually quite different mechanisms have been described for the trp operon. The trp operon is besides the ribosomal protein operons one of the best-characterised gene clusters occurring in microorganisms. Its investigation has provided fundamental insights into many aspects of bacterial genetics and enzymology; see [2]

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