Long-range periodic patterns in microbial genomes indicate significant multi-scale chromosomal organization.

TitleLong-range periodic patterns in microbial genomes indicate significant multi-scale chromosomal organization.
Publication TypeJournal Article
Year of Publication2006
AuthorsAllen TE, Price ND, Joyce AR, Palsson BØ
JournalPLoS Comput Biol
Volume2
Issue1
Paginatione2
Date Published2006 Jan
ISSN1553-7358
KeywordsBacterial Proteins, Base Sequence, Cell Shape, Chromosomes, Bacterial, Databases, Genetic, Evolution, Molecular, Gene Expression Regulation, Bacterial, Genome, Bacterial, Nuclear Proteins, Species Specificity
Abstract

Genome organization can be studied through analysis of chromosome position-dependent patterns in sequence-derived parameters. A comprehensive analysis of such patterns in prokaryotic sequences and genome-scale functional data has yet to be performed. We detected spatial patterns in sequence-derived parameters for 163 chromosomes occurring in 135 bacterial and 16 archaeal organisms using wavelet analysis. Pattern strength was found to correlate with organism-specific features such as genome size, overall GC content, and the occurrence of known motility and chromosomal binding proteins. Given additional functional data for Escherichia coli, we found significant correlations among chromosome position dependent patterns in numerous properties, some of which are consistent with previously experimentally identified chromosome macrodomains. These results demonstrate that the large-scale organization of most sequenced genomes is significantly nonrandom, and, moreover, that this organization is likely linked to genome size, nucleotide composition, and information transfer processes. Constraints on genome evolution and design are thus not solely dependent upon information content, but also upon an intricate multi-parameter, multi-length-scale organization of the chromosome.

DOI10.1371/journal.pcbi.0020002
PubMed URLhttp://www.ncbi.nlm.nih.gov/pubmed/16410829?dopt=Abstract
PMCPMC1326223
Alternate JournalPLoS Comput. Biol.
PubMed ID16410829