Utility of a Bifunctional Tryptophan Pathway Enzyme for the Classification of the Herbicola-Agglomerans Complex of Bacteria

Ahmad, Suhail; Jensen, Roy A.

doi:10.1099/00207713-39-2-100

Cited by 8 publications

(7 citation statements)

References 18 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Enterocluster 1. Members of enterocluster 1 share a common bifunctional anthranilate synthase:anthranilate 5-phosphoribosylpyrophosphate phosphoribosyltransferase (AS: PRT) gene product of the trpG-trpD fusion (8,37). Two subgroups are proposed: one contains Escherichia, Shigella, Citrobacter and Salmonella; the other contains Klebsiella and Enterobacter.…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Evolution of aromatic amino acid biosynthesis and application to the fine-tuned phylogenetic positioning of enteric bacteria

1990

View full text Add to dashboard Cite

A comprehensive phylogenetic tree for virtually the entire assemblage of enteric bacteria is presented. Character states of aromatic amino acid biosynthesis are used as criteria, and the results are compared with partial trees based upon sequencing of 16S rRNA, 5S rRNA, and tryptophan leader peptide. Three major clusters are apparent. Enterocluster 1 possesses a gene fusion (trpG-trpD) encoding anthranilate synthase: anthranilate 5-phosphoribosylpyrophosphate phosphoribosyltransferase of tryptophan biosynthesis. This cluster includes the genera Escherichia, Shigella, Citrobacter, Salmonella, Klebsiella, and Enterobacter. The remaining two clusters lack the trpG-trpD gene fusion, but differ in the presence (enterocluster 2) or absence (enterocluster 3) of the three-step overflow pathway to L-phenylalanine. Enterocluster 2 consists of the genera Serratia and Erwinia. Enterocluster 3 includes the genera Cedecea, Kluyvera, Edwardsiella, Hafnia, Yersinia, Proteus, Providencia, and Morganella. Within these three major clusters, a tentative hierarchy of subcluster ordering is formulated on the basis of all data available. This hierarchical framework is proposed as a general working basis for continued refinement of the phylogenetic relationships of enteric bacteria.The phylogenetic history of procaryotes, once thought to be inaccessible, is being reconstructed at an impressively rapid pace (33). Nucleotide sequencing techniques have provided the technological thrust, and rRNA has been the molecule of choice because its conservative resistance to evolutionary change allows the entire phylogenetic span of the ancient procaryotes to be analyzed. Initially, phylogenetic trees were based upon 16S rRNA oligonucleotide cataloging (18, 31), but complete sequencing of 16S rRNA is now routine (31). Sequencing of 5S rRNA is also being used (21, 27). In principle, the eventual comparative sequencing of as many cistrons as possible will yield slightly different trees, and the greater the number of trees available, the greater will be the resolution of evolutionary branching.The enteric bacteria are of special microbiological interest because of both pathogenic and nonpathogenic relationships with mammalian systems. (4,8, 22,36,37), and Fig. 1A shows Serratia to be closer to Klebsiella than Klebsiella is to Salmonella, a result that is at variance with those shown in Fig. 1B and C.The comparative enzymology and regulation of aromatic biosynthesis has revealed a rich diversity of biochemical character states (12). These We have carried out an in-depth comparison of aromatic amino acid biosynthesis and regulation in most of the enteric bacteria in line with a general objective to trace the evolutionary history of this biochemical pathway. Since our data, against a background of considerable additional information in the literature, also indicated a basis for fine-tuned relationships of hierarchical branching, we present a dendrogram depiciting three major enteroclusters. Tentative subcluster arrangements are also formulated. MATERI...

show abstract

Section: Resultsmentioning

confidence: 99%

“…(4,8, 22,36,37), and Fig. 1A shows Serratia to be closer to Klebsiella than Klebsiella is to Salmonella, a result that is at variance with those shown in Fig.…”

mentioning

confidence: 80%

Evolution of aromatic amino acid biosynthesis and application to the fine-tuned phylogenetic positioning of enteric bacteria

1990

View full text Add to dashboard Cite

show abstract

“…Jensen and Ahmad (1,41) proposed that a series of nested gene fusions could be exploited as markers of phylogenetic branch points in prokaryotes. Thus, any organism that belongs to the enteric lineage (shaded green in Fig.…”

Section: Nested Gene Fusionsmentioning

confidence: 99%

Ancient Origin of the Tryptophan Operon and the Dynamics of Evolutionary Change

Xie

Keyhani

Bonner

et al. 2003

Microbiol Mol Biol Rev

119

145

View full text Add to dashboard Cite

SUMMARY The seven conserved enzymatic domains required for tryptophan (Trp) biosynthesis are encoded in seven genetic regions that are organized differently (whole-pathway operons, multiple partial-pathway operons, and dispersed genes) in prokaryotes. A comparative bioinformatics evaluation of the conservation and organization of the genes of Trp biosynthesis in prokaryotic operons should serve as an excellent model for assessing the feasibility of predicting the evolutionary histories of genes and operons associated with other biochemical pathways. These comparisons should provide a better understanding of possible explanations for differences in operon organization in different organisms at a genomics level. These analyses may also permit identification of some of the prevailing forces that dictated specific gene rearrangements during the course of evolution. Operons concerned with Trp biosynthesis in prokaryotes have been in a dynamic state of flux. Analysis of closely related organisms among the Bacteria at various phylogenetic nodes reveals many examples of operon scission, gene dispersal, gene fusion, gene scrambling, and gene loss from which the direction of evolutionary events can be deduced. Two milestone evolutionary events have been mapped to the 16S rRNA tree of Bacteria, one splitting the operon in two, and the other rejoining it by gene fusion. The Archaea, though less resolved due to a lesser genome representation, appear to exhibit more gene scrambling than the Bacteria. The trp operon appears to have been an ancient innovation; it was already present in the common ancestor of Bacteria and Archaea. Although the operon has been subjected, even in recent times, to dynamic changes in gene rearrangement, the ancestral gene order can be deduced with confidence. The evolutionary history of the genes of the pathway is discernible in rough outline as a vertical line of descent, with events of lateral gene transfer or paralogy enriching the analysis as interesting features that can be distinguished. As additional genomes are thoroughly analyzed, an increasingly refined resolution of the sequential evolutionary steps is clearly possible. These comparisons suggest that present-day trp operons that possess finely tuned regulatory features are under strong positive selection and are able to resist the disruptive evolutionary events that may be experienced by simpler, poorly regulated operons.

show abstract

“…The trees show the branching order rather than the actual distances. terial groups that diverged at almost the same time; amino acid sequence homologies, for other proteins that are not so highly conserved, and gene-fusion events may be more appropriate methods (Ahmad & Jensen, 1989;Jensen & Ahmad, 1990). Furthermore, a study based on a very small number of genes could give misleading results if one of the genes had been horizontally transferred across bacterial groups at an earlier stage of divergence.…”

Section: Introductionmentioning

confidence: 99%

“…However, it has been shown that the resolution power of rRNA sequences Is limited when closely related organisms that diverged at almost the same time are being Falah & Gupta, 1994; Gupta, 1995;Gupta & Golding, 1993;Gupta et a/., 1989). These analyses have revealed a number of important differences relative to rRNA-based phylogenies (Boorstein et al, 1994;Brown et al, 1994;Gupta & Golding, 1993 terial groups that diverged at almost the same time; amino acid sequence homologies, for other proteins that are not so highly conserved, and gene-fusion events may be more appropriate methods (Ahmad & Jensen, 1989; Jensen & Ahmad, 1990). Furthermore, a study based on a very small number of genes could give misleading results if one of the genes had been horizontally transferred across bacterial groups at an earlier stage of divergence.…”

mentioning

confidence: 99%

A protein-based phylogenetic tree for Gram-positive bacteria derived from hrcA, a unique heat-shock regulatory gene

Ahmad

Selvapandiyan

Bhatnagar

1999

International Journal of Systematic and Evolutionary Microbiology

View full text Add to dashboard Cite

The dnaK operon from Bacillus subtilis and other Gram-positive bacteria with low G+C DNA content contains additional heat-shock genes, including hrcA. The hrcA gene encodes a transcription factor that negatively regulates heatshock genes and is uniformly present in all Gram-positive bacteria studied to date. An hrcA homologue is also present in Synechocystis species, Leptospira in terrogans, Chlamydia trachoma tis, Cauloba cter crescen tus and Methanococcus jannaschii, organisms that diverged early on f rom the common ancestor of all Gram-positive bacteria and Profeobacteria, according to 165 rRNA phylogeny. A partial, protein-based phylogenetic tree, derived using amino acid sequence homology of hrcA proteins from Gram-positive bacteria, is presented here, and the results are compared with the phylogenetic trees generated from 16s rRNA, dnaK and dnal sequences. The location of the hrcA gene and the genome organization of the dnaK operon support the division of all Gram-positive bacteria into three major groups: one group contains high-G+C Gram-positive bacteria, and two others contain low-G+C Gram-positive bacteria. Among the Gram-positive bacteria with low G+C DNA content, the results indicate that there is a close phylogenetic relationship between Bacillus species and Clostridium species on the one hand and between Lactococcus lactis and Streptococcus mutans on the other. Streptomyces and Mycobacterium species also exhibited a close relationship. A hierarchical arrangement of Gram-positive bacteria based on HrcA sequences is proposed as an additional refinement of the phylogenetic relationships within this important bacterial group.Keywords : hrcA, dnaK operon, Gram-positive bacteria, phylogeny INTRODUCTIONThe evolutionary relationships among microorganisms are being determined by partial or complete sequencing of 5s and 16s rRNA genes (Olsen & Woese, 1993 ;Stackebrandt & Goebel, 1994 ;Stackebrandt et al., 1997;Woese, 1994) mainly because their resistance to evolutionary change allows the entire phylogenetic span of ancient and modern prokaryotes to be analysed simultaneously. However, it has been shown that the resolution power of rRNA sequences Is limited when closely related organisms that diverged at almost the same time are being Falah & Gupta, 1994; Gupta, 1995;Gupta & Golding, 1993;Gupta et a/., 1989). These analyses have revealed a number of important differences relative to rRNA-based phylogenies (Boorstein et al., 1994;Brown et al., 1994;Gupta & Golding, 1993 terial groups that diverged at almost the same time; amino acid sequence homologies, for other proteins that are not so highly conserved, and gene-fusion events may be more appropriate methods (Ahmad & Jensen, 1989; Jensen & Ahmad, 1990). Furthermore, a study based on a very small number of genes could give misleading results if one of the genes had been horizontally transferred across bacterial groups at an earlier stage of divergence. Thus, greater resolution of evolutionary branching can be achieved only by using a greater number of evol...

show abstract

Utility of a Bifunctional Tryptophan Pathway Enzyme for the Classification of the Herbicola-Agglomerans Complex of Bacteria

Cited by 8 publications

References 18 publications

Evolution of aromatic amino acid biosynthesis and application to the fine-tuned phylogenetic positioning of enteric bacteria

Evolution of aromatic amino acid biosynthesis and application to the fine-tuned phylogenetic positioning of enteric bacteria

Ancient Origin of the Tryptophan Operon and the Dynamics of Evolutionary Change

A protein-based phylogenetic tree for Gram-positive bacteria derived from hrcA, a unique heat-shock regulatory gene

Contact Info

Product

Resources

About