Molecular Evolution of hisB Genes (original) (raw)
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Journal of Molecular Evolution, 1994
The hisA and hisF genes belong to the histidine operon that has been extensively studied in the enterobacteria Escherichia coli and Salmonella typhimurium where the hisA gene codes for the phosphoribosyl-5-amino-1 -phosphoribosyl-4-imidazolecarboxamide isomerase (EC 5.3.1.16) catalyzing the fourth step of the histidine biosynthetic pathway, and the hisF gene codes for a cyclase catalyzing the sixth reaction.
Molecular evolution of the histidine biosynthetic pathway
Journal of Molecular Evolution, 1995
The available sequences of genes encoding the enzymes associated with histidine biosynthesis suggest that this is an ancient metabolic pathway that was assembled prior to the diversification of the Bacteria, Archaea, and Eucarya. Paralogous duplications, gene elongation, and fusion events involving different his genes have played a major role in shaping this biosynthetic route. Evidence that the hisA and the hisF genes and their homologues are the result of two successive duplication events that apparently took place before the separation of the three cellular lineages is extended. These two successive gene duplication events as well as the homology between the hisH genes and the sequences encoding the TrpG-type amidotransferases support the idea that during the early stages of metabolic evolution at least parts of the histidine biosynthetic pathway were mediated by enzymes of broader substrate specificities. Maximum likelihood trees calculated for the available sequences of genes encoding these enzymes have been obtained. Their topologies support the possibility of an Abbreviations: aa = amino acid; ORF = open reading frame; bp = base pair; kb = 10 3 bp; CarA = carbamoyl phosphate synthetase (EC 6.3.5.5); GAT = glutamine amidotransferase; GuaA = GMP synthetase (EC 6.3.4.1); PabA = 4-amino-4-deoxychorismate synthase (EC 4.1.3-); PyrG = GTP synthetase (EC 6.3.4.2); AICAR = 5-aminoimidazole-4carboxamide-l-[3-D ribofuranosyl 5"-monophosphate; HAL = L-histidinal; HOL = L-histidinol; HP = histidinol phosphate; IAP = imidazole acetol-phosphate; IGP = imidazote glycerol phosphate; PR = phosphoribosyl; PRFAR = N-[(5'-phosphoribulosyl) formimino]-5aminoimidazole-4-carboxamide ribonucleotide; 5'-ProFAR = N1-[(5 'phosphoribosyl) formimino]-5-aminoimidazole-4-carboxamide ribonucleotide; PRPP = phosphoribosyl-pyrophosphate; RFLP = restriction fragment length polymorphism Correspondence to: R. Fani evolutionary proximity of archaebacteria with low GC Gram-positive bacteria. This observation is consistent with those detected by other workers using the sequences of heat-shock proteins (HSP70), glutamine synthetases, glutamate dehydrogenases, and carbamoylphosphate synthetases.
Evolution of the structure and chromosomal distribution of histidine biosynthetic genes
1998
A database of more than 100 histidine biosynthetic genes from different organisms belonging to the three primary domains has been analyzed, including those found in the now completely sequenced genomes of Haemophilus influenzae, Mycoplasma genitalium, Synechocystis sp., Methanococcus jannaschii, and Saccharomyces cerevisiae. The ubiquity of his genes suggests that it is a highly conserved pathway that was probably already present in the last common ancestor of all extant life. The chromosomal distribution of the his genes shows that the enterobacterial histidine operon structure is not the only possible organization, and that there is a diversity of gene arrays for the his pathway. Analysis of the available sequences shows that gene fusions (like those involved in the origin of theEscherichia coli and Salmonella typhimurium hisIE and hisB gene structures) are not universal. In contrast, the elongation event that led to the extant hisA gene from two homologous ancestral modules, as well as the subsequent paralogous duplication that originated hisF, appear to be irreversible and are conserved in all known organisms. The available evidence supports the hypothesis that histidine biosynthesis was assembled by a gene recruitment process.
The Origin and Evolution of Operons: The Piecewise Building of the Proteobacterial Histidine Operon
Journal of Molecular Evolution, 2005
The structure and organization of 470 histidine biosynthetic genes from 47 different proteobacteria were combined with phylogenetic inference to investigate the mechanisms responsible for assembly of the his pathway and the origin of his operons. Data obtained in this work showed that a wide variety of different organization strategies of his gene arrays exist and that some his genes or entire his operons are likely to have been horizontally transferred between bacteria of the same or different proteobacterial branches. We propose a “piecewise” model for the origin and evolution of proteobacterial his operons, according to which the initially scattered his genes of the ancestor of proteobacteria coded for monofunctional enzymes (except possibly for hisD) and underwent a stepwise compacting process that reached its culmination in some γ-proteobacteria. The initial step of operon buildup was the formation of the his “core,” a cluster consisting of four genes (hisBHAF) whose products interconnect histidine biosynthesis to both de novo synthesis of purine metabolism and that occurred in the common ancestor of the α/β/γ branches, possibly after its separation from the ε one. The following step was the formation of three mini-operons (hisGDC, hisBHAF, hisIE) transcribed from independent promoters, that very likely occurred in the ancestor of the β/γ-branch, after its separation from the α one. Then the three mini-operons joined together to give a compact operon. In most γ-proteobacteria the two fusions involving the gene pairs hisN–B and hisI–E occurred. Finally the γ-proteobacterial his operon was horizontally transferred to other proteobacteria, such as Campylobacter jejuni. The biological significance of clustering of his genes is also discussed.
A study in evolution: The histidine utilization genes of enteric bacteria
Journal of Molecular Biology, 1979
The histidine utilization (hut) system, MIGCPUH, comprises two operons, whose promoters are M and P. The DNA segments of phage h vectors coding for the hut genes of Salmonella typhimurium and Klebsiella aerogenes were compared by using electron microscopy to study the nature of the hut DNA homology. The hut S. typhimuriumlhut K. aerogenes DNA heteroduplexes were spread and mounted for electron microscopy under more and more denaturing conditions. The homology between hut S. typhimurium and hut K. aerogenes is extensive but, as denaturing conditions make base-pairing more difficult, the regions of lower homology are melt,ed, while the regions of higher homology remain base-paired. The denat,uration map could be correlated with the genetic map by the use of Ahut S. typhimurium phages carrying different portions of the hut genome. The sequences with the highest homology are in the structural genes for the four enzymes, while the regulatory regions, the promoters and t,lre hut repressor gene, are much less homologous.
Proteobacterial Histidine-Biosynthetic Pathways Are Paraphyletic
Journal of Molecular Evolution, 2000
In Lactococcus lactis there is a protein, HisZ, in the histidine-biosynthetic operon that exhibits significant sequence identity with histidyl-tRNA synthetase (HisRS) but does not aminoacylate tRNA. HisRS homologs that, like HisZ, cannot aminoacylate tRNA are represented in a highly divergent set of bacteria (including an aquificale, cyanobacteria, firmicutes, and proteobacteria), yet are missing from other bacteria, including mycrobacteria and certain proteobacteria. Phylogenetic analysis of the HisRS and HisRS-like family suggests that the HisZ proteins form a monophyletic group that attaches outside the predominant bacterial HisRS clade. These observations are consistent with a model in which the absences of HisZ from bacteria are due to its loss during evolution. It has recently been shown that HisZ from L. lactis binds to the ATP-PRPP transferase (HisG) and that both HisZ and HisG are required for catalyzing the first reaction in histidine biosynthesis. Phylogenetic analysis of HisG sequences shows conclusively that proteobacterial HisG and histidinol dehydrogenase (HisD) sequences are paraphyletic and that the partition of the Proteobacteria associated with the presence/absence of HisZ corresponds to that based on HisG and HisD paraphyly. Our results suggest that horizontal gene transfer played an important role in the evolution of the regulation of histidine biosynthesis.
The role of gene fusions in the evolution of metabolic pathways: the histidine biosynthesis case
BMC Evolutionary Biology, 2007
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 γ -proteobacteria and after its appearance it was transferred to Campylobacter species (ε -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 δ -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.
The origin and evolution of eucaryal HIS7 genes: from metabolon to bifunctional proteins
Gene, 2004
The fifth step of histidine biosynthesis is catalysed by an imidazole glycerol-phosphate (IGP) synthase. In Archaea and Bacteria, the active form of IGP synthase is a stable 1:1 dimeric complex constituted by a glutamine amidotransferase (GAT) and a cyclase, the products of hisH and hisF. In Eucarya, the two activities are associated with a single bifunctional polypeptide encoded by HIS7. In this work, we report a comparative analysis of the amino acid sequence of all the available HisH, HisF and HIS7 proteins, which allowed depicting a likely evolutionary pathway leading to the present-day bifunctional HIS7 genes. According to the model that we propose, the bifunctional HIS7 gene is the outcome of a gene fusion event between two independent ancestral cistrons encoding an amidotransferase and a cyclase, respectively. The phylogenetic distribution of the eucaryal HIS7 genes and the analysis of all the available prokaryotic counterparts (hisH and hisF) revealed the absence of such fusions in prokaryotes, suggesting that the fusion event very likely occurred in an early stage of eucaryal evolution and was fixed in the nucleated cells. The biological significance of this gene fusion is also discussed. D
Journal of Molecular Evolution, 2009
The available sequences of genes encoding the enzymes associated with histidine biosynthesis suggest that this is an ancient metabolic pathway that was assembled prior to the diversification of Bacteria, Archaea, and Eucarya. Paralogous duplication, gene elongation, and fusion events of several different his genes have played a major role in shaping this biosynthetic route. We have analyzed the structure and organization of histidine biosynthetic genes from 55 complete archaeal genomes and combined it with phylogenetic inference in order to investigate the mechanisms responsible for the assembly of the his pathway and the origin of his operons. We show that a wide variety of different organizations of his genes exists in Archaea and that some his genes or entire his (sub-)operons have been likely transferred horizontally between Archaea and Bacteria. However, we show that, in most Archaea, his genes are monofunctional (except for hisD) and scattered throughout