Selection effects on the positioning of genes and gene structures from the interplay of replication and transcription in bacterial genomes

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6 Citations (Scopus)

Abstract

Bacterial chromosomes are partly shaped by the functional requirements for effi cient replication, which lead to strand bias as commonly characterized by the excess of guanines over cytosines in the leading strand. Gene structures are also highly organized within bacterial genomes as a result of such functional constraints, displaying characteristic positioning and structuring along the genome. Here we analyze the gene structures in completely sequenced bacterial chromosomes to observe the positional constraints on gene orientation, length, and codon usage with regard to the positions of replication origin and terminus. Selection on these gene features is different in regions surrounding the terminus of replication from the rest of the genome, but the selection could be either positive or negative depending on the species, and these positional effects are partly attributed to the A-T enrichment near the terminus. Characteristic gene structuring relative to the position of replication origin and terminus is commonly observed among most bacterial species with circular chromosomes, and therefore we argue that the highly organized gene positioning as well as the strand bias should be considered for genomics studies of bacteria.

Original languageEnglish
Pages (from-to)279-286
Number of pages8
JournalEvolutionary Bioinformatics
Volume3
Publication statusPublished - 2007 Oct 9

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Bacterial Genomes
Transcription
positioning
genome
transcription (genetics)
Genes
gene
Bacterial Chromosomes
replication origin
chromosome
Replication Origin
genes
Chromosomes
chromosomes
Genome
cytosine
Cytosine
guanine
Guanine
Genomics

Keywords

  • DNA replication
  • GC skew
  • Genome organization
  • Replicational selection

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Computer Science Applications
  • Genetics

Cite this

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