Evidence for horizontal gene transfer in Escherichia coli speciation

Médigue, Claudine; Rouxel, Thierry; Vigier, Philippe; Hénaut, Alain; Danchin, Antoine

doi:10.1016/0022-2836(91)90575-q

Cited by 349 publications

(265 citation statements)

References 13 publications

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“…Genes from E. coli and B. subtilis (Fig. 1A,B) are clustered into three distinct groups or classes (Medigue et al 1991; The functional classification available in the COG database (Tatusov et al 2000) was used. The table shows the number and the group percentage of the genes proposed as being acquired by HGT.…”

Section: Discussionmentioning

confidence: 99%

Horizontal Gene Transfer in Bacterial and Archaeal Complete Genomes

Garcı́a-Vallvé

Romeu²,

Palau³

2000

Genome Research

322

228

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Section: Discussionmentioning

confidence: 99%

Horizontal Gene Transfer in Bacterial and Archaeal Complete Genomes

Garcı́a-Vallvé

Romeu²,

Palau³

2000

Genome Research

322

228

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“…Genes with high CAI values in fast-growing organisms are commonly interpreted as those which are involved in maintaining this growth rate or in enzymatic activities with a rapid response (Gouy and Gautier 1982;Sharp and Li 1987;Sharp et al 1988;Me´digue et al 1991;Shields and Sharp 1987;Carbone et al 2004). Genes with such properties are coding for ribosomal proteins, heat shock proteins, antioxidant proteins, proteins involved in the respiratory chain, structural genes (for eukaryotes), and enzymes involved in the metabolic pathways of amino acids biosynthesis.…”

Section: Metabolic Activities Derived From Cai Valuesmentioning

confidence: 99%

Insights on the Evolution of Metabolic Networks of Unicellular Translationally Biased Organisms from Transcriptomic Data and Sequence Analysis

Carbone

Madden

2005

J Mol Evol

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Abstract. Codon bias is related to metabolic functions in translationally biased organisms, and two facts are argued about. First, genes with high codon bias describe in meaningful ways the metabolic characteristics of the organism; important metabolic pathways corresponding to crucial characteristics of the lifestyle of an organism, such as photosynthesis, nitrification, anaerobic versus aerobic respiration, sulfate reduction, methanogenesis, and others, happen to involve especially biased genes. Second, gene transcriptional levels of sets of experiments representing a significant variation of biological conditions strikingly confirm, in the case of Saccharomyces cerevisiae, that metabolic preferences are detectable by purely statistical analysis: the high metabolic activity of yeast during fermentation is encoded in the high bias of enzymes involved in the associated pathways, suggesting that this genome was affected by a strong evolutionary pressure that favored a predominantly fermentative metabolism of yeast in the wild. The ensemble of metabolic pathways involving enzymes with high codon bias is rather well defined and remains consistent across many species, even those that have not been considered as translationally biased, such as Helicobacter pylori, for instance, reveal some weak form of translational bias for this genome. We provide numerical evidence, supported by experimental data, of these facts and conclude that the metabolic networks of translationally biased genomes, observable today as projections of eons of evolutionary pressure, can be analyzed numerically and predictions of the role of specific pathways during evolution can be derived. The new concepts of Comparative Pathway Index, used to compare organisms with respect to their metabolic networks, and Evolutionary Pathway Index, used to detect evolutionarily meaningful bias in the genetic code from transcriptional data, are introduced.

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“…6 (a), the distribution of GC3 content of orthologous genes in Ph was regarded as a Gaussian distribution having an average and standard deviation of 0.365 and 0.0709, respectively. It was reported that 780 genes in the DNA sequence of Escherichia coli, which was corresponded to approximately thirty percent of the whole genome sequence, were analyzed by Fractional Correspondence Analysis and the dynamic clustering method and the genes were classified into three classes [33] [34]. The 111 genes constituting the horizontally inherited transfer genes comprised the class with the smallest codon bias among the three classes [34].…”

Section: Distribution Of the G+c Content At The Third Position Of Synmentioning

confidence: 99%

“…It was reported that 780 genes in the DNA sequence of Escherichia coli, which was corresponded to approximately thirty percent of the whole genome sequence, were analyzed by Fractional Correspondence Analysis and the dynamic clustering method and the genes were classified into three classes [33] [34]. The 111 genes constituting the horizontally inherited transfer genes comprised the class with the smallest codon bias among the three classes [34]. Therefore, the score of 0.142 with respect to the total genes analyzed, suggests these genes to be transferred in this DNA sequence.…”

Section: Distribution Of the G+c Content At The Third Position Of Synmentioning

confidence: 99%

Identification of lateral gene in the genomic DNA sequence, by using the G+C content at the third position of synonymous codons of orthologous genes as an index

Ohfuku

Tanaka

Uebayasi

2002

CBIJ

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All open reading frames (ORFs) of 6 Archaebacterial and 17 Eubacterial species showed a strong positive correlation between the G+C content (GC content) of the genomic DNA sequences and the G+C content of the third position of the codons (GC3 content). Among them, 1217 pairs of genes that are orthologous between Pyrococcus horikoshii OT3 (Ph) and Pyrococcus abyssi (Pa) were identified. The codons of each pair of orthologous genes were classified into three categories, identical codons coding for the same amino acid (IC), different codon coding for the different amino acids (DC) and synonymous codons coding for the same amino acids (IA). In a comparison of the GC3 content of these three types in all orthologous genes between Ph and Pa, the GC3 content of IA (GC3 content of synonymous codons) deviated the most from the expected value for the GC content of the genome sequences used in this analysis. Therefore the GC3 content of synonymous codon was suggested to be an index that would be able to distinguish a lateral gene from the orthologous genes of the genomic DNA sequence.By analysis of the GC3 content of synonymous codons, two remarkable regions were found in the genome sequence of Ph. In one region between 300 Kbp and 420 Kbp, the genes have a higher GC3 content in the synonymous codon, and in the other between 1,320 Kbp and 1,400 Kbp, the genes have a lower GC3 content in the synonymous codons. In the former region, twelve of sixteen orthologous genes were homologous to genes of Eubacteria or Archaebacteria. Especially, four orthologous genes showed homology to genes related to synthesis of the cell wall or lipopolysaccharides from Streptococcus. These four genes would be suggested to be lateral genes and to represent a lateral region from Eubacterial species. In the latter region, eight out of thirteen orthologous genes were homologous to genes of Archaebacteria or Eukarya. Six of these eight orthologous genes show homology to the genes related to the function of translation. These genes would be indicated as the stable genes in the progress of evolution, after the divergence between Pyrococcus horikoshii OT3 and Pyrococcus abyssi.

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Evidence for horizontal gene transfer in Escherichia coli speciation

Cited by 349 publications

References 13 publications

Horizontal Gene Transfer in Bacterial and Archaeal Complete Genomes

Horizontal Gene Transfer in Bacterial and Archaeal Complete Genomes

Insights on the Evolution of Metabolic Networks of Unicellular Translationally Biased Organisms from Transcriptomic Data and Sequence Analysis

Identification of lateral gene in the genomic DNA sequence, by using the G+C content at the third position of synonymous codons of orthologous genes as an index

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