Molecular and evolutionary relationships among enteric bacteria

Lawrence, Jeffrey G.; Ochman, Howard; Hartl, Daniel L.

doi:10.1099/00221287-137-8-1911

Cited by 120 publications

(78 citation statements)

References 37 publications

(24 reference statements)

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“…Because of sequence divergence between the gene copies, direct sequencing of PCR products is seldom suitable for achieving a representative sequence (Cilia et al, 1996;Hill & Harnish, 1981). Other genes, such as gap and ompA (Lawrence et al, 1991), rpoB (Mollet et al, 1997) and infB (Hedegaard et al, 1999), have been used to resolve the phylogeny of enterobacteria. However, none of these studies covered an extensive number of species.…”

Section: Introductionmentioning

confidence: 99%

Phylogeny of the Enterobacteriaceae based on genes encoding elongation factor Tu and F-ATPase β-subunit

Paradis

Boissinot

Paquette³

et al. 2005

International Journal of Systematic and Evolutionary Microbiology

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The phylogeny of enterobacterial species commonly found in clinical samples was analysed by comparing partial sequences of their elongation factor Tu gene (tuf ) and of their F-ATPase b-subunit gene (atpD). An 884 bp fragment for tuf and an 884 or 871 bp fragment for atpD were sequenced for 96 strains representing 78 species from 31 enterobacterial genera. The atpD sequence analysis exhibited an indel specific to Pantoea and Tatumella species, showing, for the first time, a tight phylogenetic affiliation between these two genera. Comprehensive tuf and atpD phylogenetic trees were constructed and are in agreement with each other. Monophyletic genera are Cedecea, Edwardsiella, Proteus, Providencia, Salmonella, Serratia, Raoultella and Yersinia. Analogous trees based on 16S rRNA gene sequences available from databases were also reconstructed. The tuf and atpD phylogenies are in agreement with the 16S rRNA gene sequence analysis, and distance comparisons revealed that the tuf and atpD genes provide better discrimination for pairs of species belonging to the family Enterobacteriaceae. In conclusion, phylogeny based on tuf and atpD conserved genes allows discrimination between species of the Enterobacteriaceae. INTRODUCTIONMembers of the family Enterobacteriaceae are facultatively anaerobic, Gram-negative rods that are catalase-positive and oxidase-negative (Brenner, 1984). They are found in soil, water and plants, and also in animals ranging from insects to humans. Many enterobacteria are opportunistic pathogens. In fact, members of this family are responsible for about 50 % of nosocomial infections in the US (Brenner, 1984). Therefore, this family is of considerable clinical importance.The major classification studies on the family Enterobacteriaceae were based on phenotypic traits (Brenner et al., , 1999Dickey & Zumoff, 1988;Farmer et al., 1980Farmer et al., , 1985a such as biochemical reactions and physiological characteristics. However, phenotypically distinct strains may be closely related by genotypic criteria and may belong to the same genospecies (Bercovier et al., 1980;Hartl & Dykhuizen, 1984). Also, phenotypically close strains (biogroups) may belong to different genospecies, like Klebsiella pneumoniae and Enterobacter aerogenes (Brenner, 1984), for example. Consequently, identification and classification of certain species may be ambiguous with techniques based on phenotypic tests (Janda et al., 1999;Kitch et al., 1994;Sharma et al., 1990).More advances in the classification of members of the family Enterobacteriaceae have come from DNA-DNA hybridization studies (Brenner et al., , 1986(Brenner et al., , 1993Farmer et al., 1980Farmer et al., , 1985aIzard et al., 1981;Steigerwalt et al., 1976). The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA, tuf and atpD gene sequences obtained in this study are listed in Furthermore, the phylogenetic significance of bacterial classification based on 16S rRNA gene sequences has been recognized by many workers Wayne et al., 1987). However, members of the family En...

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Section: Introductionmentioning

confidence: 99%

Phylogeny of the Enterobacteriaceae based on genes encoding elongation factor Tu and F-ATPase β-subunit

Paradis

Boissinot

Paquette³

et al. 2005

International Journal of Systematic and Evolutionary Microbiology

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“…(Graur and Li, 1990 Kier et al (1979). Relationships amonE species are based on the sequences of tryptophan biosynthetic enz (Nichols et al, 1980;Yanofsky, 1984), glyceraldehyde-3-phospha dehydrogenase (Lawrence et al, 1991) and rRNAs (Stackerbrand Woese, 1981;MacDonell et al, 1986;Stackerbrandt and Woese, 1981) and follow those presented in Ahmad et al (1990 (Kier et al, 1979), which encodes a major transcriptional regulator of Salmonella virulence (Groisman and Saier, 1990) homologous to the family of environmentally responsive two-component systems . Unlike phoN, the presence of phoP is not limited to the salmonellae and homologs have been found in 12 Gram-negative bacteria (Fields et al, 1989 (Groisman and Casadaban, 1987;Groisman, 1991).…”

Section: Phylogenetic Origins Of Phonmentioning

confidence: 99%

“…For example, the major expressed form of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) in enteric bacteria is more similar to eukaryotic GAPDH sequences than to GAPDHs from other bacteria (Doolittle et al, 1990;Lawrence et al, 1991). Based on the high degree of sequence similarity, other candidates for lateral gene transfer include the glutamine synthetase gene of Bradyrhizobium (Carlson and Chelm, 1986), certain sugar transport proteins in bacteria and mammals (Maiden et al, 1987), the penicillin binding protein gene in Streptococcus 1312 (Dowson et al, 1990), the celC genes of E. coli and Staphylococcus aureus (Parker and Hall, 1990) and hemoglobin in vitreoscilla (Wakabayashi et al, 1986).…”

Section: Phylogenetic Origins Of Phonmentioning

confidence: 99%

“…To amplify successfully the regions from M.mnorganii and P.stuartii homologous tophoN we used the primers 5'-GGCTCU7ACCCTT-CCGGGCATAC-3' and 5'-ACATCGCTFIGCCAGTGAGCACCGCA-3'. Nucleotide sequences of PCR products were determined as described by Lawrence et al (1991) with Sequenase v2.0 (United States Biochemical) using 32P-labeled dATP.…”

Section: Dna Sequencing Of Pcr Amplified Productsmentioning

confidence: 99%

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Horizontal transfer of a phosphatase gene as evidence for mosaic structure of the Salmonella genome.

1992

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The genomes of Escherichia coli and Salmonella typhimurium are similar with respect to base composition, chromosome size, and the order, orientation and spacing of genes, but differ with respect to some 29 ‘loops’, regions unique to one species. To evaluate the genetic basis for the structure and organization of the enteric bacterial genomes, we examined the gene encoding a non‐specific acid phosphatase (phoN) which maps to a loop at 96 min on the S.typhimurium chromosome. We detected atypical base composition, codon usage pattern and trinucleotide frequencies. The 1.4 kb region containing phoN had an overall base composition of 43% G+C, while the G+C content at the third positions of codons in the phoN reading frame is only 39%, much lower than the Salmonella chromosome which averages 52%. Non‐specific acid phosphatase activity, assayed in 14 Gram‐negative species, was detected only in Morganella morganii and Providencia stuartii, organisms with low genomic G+C contents. Upstream of the phoN gene in Salmonella is a sequence with high similarity to the oriT region of incFII plasmids, suggesting that the phoN gene, and perhaps the entire loop structure, was acquired by lateral transmission in a plasmid‐mediated event.

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“…The genus Escherichia contains five species: Escherichia blattae, E. coli, E. fergusonii, E. hermannii, and E. vulneris whose relationships to one another, and to other enteric species, have been resolved by the phylogenetic analysis of gapA and ompA sequences (Lawrence et al 1991 (Whittam 1997). It is probably safe to say that more is known about the degree, appointment and maintenance of genetic variation in E. coli than in any other bacterial species.…”

Section: Enterobacteriaceae: What's In a Name?mentioning

confidence: 99%

Phylogenetic Relationships of Bacteria with Special Reference to Endosymbionts and Enteric Species

Francino¹,

Santos²,

Ochman³

SpringerReference

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INTRODUCTIONThe latter half of the 20 th century saw two developments that revolutionized the study of bacterial systematics and our conceptions about microbial diversity. The first was the use of molecular genetic information, as gained through the analysis of protein and nucleic acid sequences, for the identification, typing and classification of microorganisms. The second was the application of PCR for the recovery of DNA sequences from non-cultivable organisms.By decoupling cultivation and classification, and by providing a common yardstick by which all organisms could be compared (i.e., small subunit ribosomal DNA sequences; hereafter referred to as SSU rRNA), these procedures added a new dimension to our knowledge of the microbial world. It is no longer necessary to test organisms against a panel of known phenotypic or biochemical properties, which, in themselves, are often variable in occurrence and can lead to cases of misclassification, or carry a preconceived notion about the characters that define a particular taxonomic group.Despite the considerable advances made from applying these innovations, such an approach is not without its limitations. Characterization of a single conserved sequence, while often adequate for taxonomic purposes, does not reveal very much about the evolutionary history or biology of the organism per se. Whereas the placement of an organism (i.e., sequence) into an evolutionary framework may prompt numerous predictions about its morphology, ecology, physiology and biochemistry, virtually nothing can be said about its unique biology without cultivation or additional sequence information.Other problems can arise when attempting to classify bacteria and to determine their relationships. These derive from two sources: the specific characters used to represent an organism (the choice of data), and the algorithms used to infer relationships (the methods used to construct the phylogeny or tree). With this in mind, genotypic data hold several advantages over phenotypic characters for phylogenetic reconstruction in that: (i) variation in molecular sequences is discrete and well-defined; (ii) molecular sequences comprise hundreds, if not thousands, of characters bearing potentially useful information; (iii) molecular sequences accumulate informative changes, even when the resulting phenotypes are conserved; (iv) informational macromolecules (DNA and proteins) change according to well-defined models of sequence evolution; and (v) identical phenotypes can arise by very different genetic mechanisms or pathways, such that changes other than those attributable to common ancestry can lead to the same phenotype.Questions of character convergence are not limited to phenotypic traits: portions of molecular sequences may be identical due to chance, natural selection, or lateral gene transfer.Furthermore, because the analysis of relatively small regions of DNA can furnish so much information, phylogenetic relationships are often based on data collected from a very limited portion of the genome, w...

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Molecular and evolutionary relationships among enteric bacteria

Cited by 120 publications

References 37 publications

Phylogeny of the Enterobacteriaceae based on genes encoding elongation factor Tu and F-ATPase β-subunit

Phylogeny of the Enterobacteriaceae based on genes encoding elongation factor Tu and F-ATPase β-subunit

Horizontal transfer of a phosphatase gene as evidence for mosaic structure of the Salmonella genome.

Phylogenetic Relationships of Bacteria with Special Reference to Endosymbionts and Enteric Species

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