Reductive divergence of enterobacterial repetitive intergenic consensus sequences among Gammaproteobacteria genomes. 2011

Young-Gun Zo
Department of Biology, Kyungsung University, Busan, 608-736, Republic of Korea. zoyful@gmail.com

Enterobacterial repetitive intergenic consensus (ERIC) sequence is a transcription-modulating, nonautonomous, miniature inverted-repeat transposable element. Its origin and the mechanism of highly varying incidences, limited to Enterobacteriaceae and Vibrionaceae, have not been identified. In this study, distribution and divergence of ERICs along bacterial taxonomie units were analyzed. ERICs were found among five families of gammaproteobacteria, with the copy numbers varying with exponential increments. The variability was explained by genus (45%) and species (36%) affiliations, indicating that copy numbers are specific to sub-family taxa. ERICs were interspersed in genomes with considerable divergences. Locations of ERICs in a genome appeared to be strongly conserved in a strain, moderately in a species or a genus, and weakly in a family. ERICs in different species of a genus were from the identical population of sequences while ERICs in different genera of a family were nearly identical. However, ERICs in different families formed distinct monophylectic groups, implying vertical transmission of diverging population of sequences. In spite of large difference in copy numbers, overall intra-genome evolutionary distances among ERICs were similar among different species, except for a few genomes. The exceptions substantiated hypotheses of genetic drifts and horizontal gene transfers of mobility capacity. Therefore, the confined, variable distribution of ERIC could be explained as a two-step evolution: introduction and proliferation of ERIC in one of the progenitors of gammaproteobacteria, followed by vertical transmission under negative selection. Deterioration of sequences and reduction in copy number were concluded to be the predominant patterns in the evolution of ERIC loci.

UI MeSH Term Description Entries
D011110 Polymorphism, Genetic The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level. Gene Polymorphism,Genetic Polymorphism,Polymorphism (Genetics),Genetic Polymorphisms,Gene Polymorphisms,Polymorphism, Gene,Polymorphisms (Genetics),Polymorphisms, Gene,Polymorphisms, Genetic
D012091 Repetitive Sequences, Nucleic Acid Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES). DNA Repetitious Region,Direct Repeat,Genes, Selfish,Nucleic Acid Repetitive Sequences,Repetitive Region,Selfish DNA,Selfish Genes,DNA, Selfish,Repetitious Region, DNA,Repetitive Sequence,DNA Repetitious Regions,DNAs, Selfish,Direct Repeats,Gene, Selfish,Repeat, Direct,Repeats, Direct,Repetitious Regions, DNA,Repetitive Regions,Repetitive Sequences,Selfish DNAs,Selfish Gene
D004251 DNA Transposable Elements Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom. DNA Insertion Elements,DNA Transposons,IS Elements,Insertion Sequence Elements,Tn Elements,Transposable Elements,Elements, Insertion Sequence,Sequence Elements, Insertion,DNA Insertion Element,DNA Transposable Element,DNA Transposon,Element, DNA Insertion,Element, DNA Transposable,Element, IS,Element, Insertion Sequence,Element, Tn,Element, Transposable,Elements, DNA Insertion,Elements, DNA Transposable,Elements, IS,Elements, Tn,Elements, Transposable,IS Element,Insertion Element, DNA,Insertion Elements, DNA,Insertion Sequence Element,Sequence Element, Insertion,Tn Element,Transposable Element,Transposable Element, DNA,Transposable Elements, DNA,Transposon, DNA,Transposons, DNA
D004269 DNA, Bacterial Deoxyribonucleic acid that makes up the genetic material of bacteria. Bacterial DNA
D016680 Genome, Bacterial The genetic complement of a BACTERIA as represented in its DNA. Bacterial Genome,Bacterial Genomes,Genomes, Bacterial
D018628 Gene Dosage The number of copies of a given gene present in the cell of an organism. An increase in gene dosage (by GENE DUPLICATION for example) can result in higher levels of gene product formation. GENE DOSAGE COMPENSATION mechanisms result in adjustments to the level GENE EXPRESSION when there are changes or differences in gene dosage. Gene Copy Number,Copy Number, Gene,Copy Numbers, Gene,Dosage, Gene,Dosages, Gene,Gene Copy Numbers,Gene Dosages,Number, Gene Copy,Numbers, Gene Copy
D019143 Evolution, Molecular The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations. Molecular Evolution,Genetic Evolution,Evolution, Genetic
D020563 Gammaproteobacteria A group of the proteobacteria comprised of facultatively anaerobic and fermentative gram-negative bacteria. gamma Proteobacteria,Proteobacteria gamma
D022761 Gene Transfer, Horizontal The naturally occurring transmission of genetic information between organisms, related or unrelated, circumventing parent-to-offspring transmission. Horizontal gene transfer may occur via a variety of naturally occurring processes such as GENETIC CONJUGATION; GENETIC TRANSDUCTION; and TRANSFECTION. It may result in a change of the recipient organism's genetic composition (TRANSFORMATION, GENETIC). Gene Transfer, Lateral,Horizontal Gene Transfer,Lateral Gene Transfer,Recombination, Interspecies,Recombination, Interspecific,Gene Transfers, Lateral,Interspecies Recombination,Interspecific Recombination,Lateral Gene Transfers

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