The role of gene fusions in the evolution of metabolic pathways: the histidine biosynthesis case

Abstract

Background: Histidine biosynthesis is one of the best characterized anabolic pathways. There is a large body of genetic and biochemical information available, including operon structure, gene expression, and increasingly larger sequence databases. For over forty years this pathway has been the subject of extensive studies, mainly in Escherichia coli and Salmonella enterica, in both of which details of histidine biosynthesis appear to be identical. In these two enterobacteria the pathway is unbranched, includes a number of unusual reactions, and consists of nine intermediates; his genes are arranged in a compact operon (hisGDC [NB]HAF [IE]), with three of them (hisNB, hisD and hisIE) coding for bifunctional enzymes. We performed a detailed analysis of his gene fusions in available genomes to understand the role of gene fusions in shaping this pathway.

Results: The analysis of HisA structures revealed that several gene elongation events are at the root of this protein family: internal duplication have been identified by structural superposition of the modules composing the TIM-barrel protein. Several his gene fusions happened in distinct taxonomic lineages; hisNB originated within gamma-proteobacteria and after its appearance it was transferred to Campylobacter species (epsilon-proteobacteria) and to some Bacteria belonging to the CFB group. The transfer involved the entire his operon. The hisIE gene fusion was found in several taxonomic lineages and our results suggest that it probably happened several times in distinct lineages. Gene fusions involving hisIE and hisD genes (HIS4) and hisH and hisF genes (HIS7) took place in the Eukarya domain; the latter has been transferred to some delta-proteobacteria.

Conclusion: Gene duplication is the most widely known mechanism responsible for the origin and evolution of metabolic pathways; however, several other mechanisms might concur in the process of pathway assembly and gene fusion appeared to be one of the most important and common.

Figure 1

Summary of Histidine biosynthesis. Schematic representation of the histidine biosynthetic pathway and the organization of his gene in Escherichia coli. Genes and proteins in color are those involved in fusion events.

Figure 2

HisA "quarters" alignments. Pairwise alignments of Methanocaldococcus jannaschii (mj) HisA subregions corresponding to "quarters" of barrels (named HisA1, HisA2, HisA3, HisA4). Symbols: *,: correspond to identical or similar aminoacids, respectively.

Figure 3

An evolutionary model for hisA and hisF genes. Right-most panel is the evolutionary model that we propose and discuss in the text concerning hisA and hisF origin and evolution. Panels on the left are: the first and the second quarters (top) and two single (β/α) modules of the HisA protein from Thermotoga maritima which illustrates the structural similarities from which we derived our model. The quarters have a structural alignment with only 1.2 Å of RMS on 104 alpha carbons.

Figure 4

HisNB phylogenetic analysis. HisNB Phylogenetic tree. Organisms (groups) in red are bacteria not belonging to γ-proteobacteria and harboring the HisNB fusion.

Figure 5

His7 multialignment. A multialignment of HIS7, HisHF and a set of representative concatenated HisH and HisF sequences from E. coli, S. solfataricus, A. fulgidus and G. sulfurreducens. Yellow shading represent insertions shared only by bifunctional HIS7 and HisHF proteins. Shading of the multialignment has been made with PAM250 matrix.

Figure 6

His7 phylogenetic analysis. Phylogenetic tree of HIS7, HisHF and concatenated HisH and HisF sequences. See Methods for details on phylogenetic tree construction.

Figure 7

HIS4, hisIE and hisD genes. Schematic representation of the archaeal, bacterial and eukaryotic genes coding for phosphoribosyl-ATP pyrophosphohydrolase (hisI), phosphoribosyl-AMP cyclohydrolase (hisE) and histidinol dehydrogenase (hisD). The HisI and HisE proteins are coded by a bifunctional gene or two separate cistrons in both Archaea and Bacteria and by a bifunctional gene in all Eukarya. Homologus regions are represented by the same hatching.

Figure 8

HisD and HisIE phylogenetic analysis. Phylogenetic tree obtained using a multialignment of HisD (a) and HisIE (b) proteins and domains from HIS4 proteins and MrBayes program. Values above nodes are posterior probabilities*100 (for details on phylogenetic tree construction see Methods). See text for details.

Figure 9

A global view of his gene fusions appearance. Schematical representation of his gene fusion appearance and horizontal transfer. Abbreviations used: A, B, E correspond to Archaea, Bacteria and Eukarya, respectively. LUCA stands for the Last Universal Common Ancestor.