Abstract
BackgroundThe lysine, threonine, and methionine biosynthetic pathways share the three initial enzymatic steps, which are referred to as the Common Pathway (CP). In Escherichia coli three different aspartokinases (AKI, AKII, AKIII, the products of thrA, metL and lysC, respectively) can perform the first step of the CP. Moreover, two of them (AKI and AKII) are bifunctional, carrying also homoserine dehydrogenasic activity (hom product). The second step of the CP is catalyzed by a single aspartate semialdehyde dehydrogenase (ASDH, the product of asd). Thus, in the CP of E. coli while a single copy of ASDH performs the same reaction for three different metabolic routes, three different AKs perfom a unique step. Why and how such a situation did emerge and maintain? How is it correlated to the different regulatory mechanisms acting on these genes? The aim of this work was to trace the evolutionary pathway leading to the extant scenario in proteobacteria.ResultsThe analysis of the structure, organization, phylogeny, and distribution of ask and hom genes revealed that the presence of multiple copies of these genes and their fusion events are restricted to the γ-subdivision of proteobacteria. This allowed us to depict a model to explain the evolution of ask and hom according to which the fused genes are the outcome of a cascade of gene duplication and fusion events that can be traced in the ancestor of γ-proteobacteria. Moreover, the appearance of fused genes paralleled the assembly of operons of different sizes, suggesting a strong correlation between the structure and organization of these genes. A statistic analysis of microarray data retrieved from experiments carried out on E. coli and Pseudomonas aeruginosa was also performed.ConclusionThe integration of data concerning gene structure, organization, phylogeny, distribution, and microarray experiments allowed us to depict a model for the evolution of ask and hom genes in proteobacteria and to suggest a biological significance for the extant scenario.
Highlights
The lysine, threonine, and methionine biosynthetic pathways share the three initial enzymatic steps, which are referred to as the Common Pathway (CP)
In some bacteria each CP step is catalyzed by enzymes coded for by single monofunctional genes, whereas in the enterobacterium Escherichia coli it has been shown [2] (Figure 1) that: i) the first step of the CP can be performed by three different aspartokinases (AKI, AKII and AKIII); ii) the second step is catalyzed by a monofunctional ASDH encoded by lysC; and, lastly, iii) the third step is carried out by two different homoserine dehydrogenases, referred to as HDI and HDII, which are fused to two of the three AKs: AKI and AKII, respectively
Structure and phylogenetic distribution of the genes coding for AK, ASDH and HD in Proteobacteria The aminoacid sequences of the E. coli AK, ASDH, and HD sequences were used as a query to probe the protein database of completely sequenced proteobacterial genomes with the BLASTP option of BLAST program [13], in order to retrieve the most similar sequences
Summary
The lysine, threonine, and methionine biosynthetic pathways share the three initial enzymatic steps, which are referred to as the Common Pathway (CP). In some bacteria each CP step is catalyzed by enzymes coded for by single monofunctional genes, whereas in the enterobacterium Escherichia coli it has been shown [2] (Figure 1) that: i) the first step of the CP can be performed by three different aspartokinases (AKI, AKII and AKIII); ii) the second step is catalyzed by a monofunctional ASDH encoded by lysC; and, lastly, iii) the third step is carried out by two different homoserine dehydrogenases, referred to as HDI and HDII, which are fused to two of the three AKs: AKI and AKII, respectively. These two bifunctional proteins are coded for by two genes, thrA and metL, respectively
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