Oligonucleotide Usage Signatures of the Pseudomonas putida KT2440 Genome
Oleg Reva and Burkhard Tümmler
from: Pseudomonas: Genomics and Molecular Biology (Edited by: Pierre Cornelis). Caister Academic Press, U.K. (2008)
Abstract
Di- to pentanucleotide usage and the list of the most abundant octa- to tetradecanucleotides are useful measures of the bacterial genomic signature. The Pseudomonas putida KT2440 chromosome is characterized by strand symmetry and intra-strand parity of complementary oligonucleotides. Each tetranucleotide occurs with similar frequency on the two strands. Tetranucleotide usage is biased by G+C content and physicochemical constraints such as base stacking energy, dinucleotide propeller twist angle or trinucleotide bendability. The 105 regions with atypical oligonucleotide composition can be differentiated by their patterns of oligonucleotide usage into categories of horizontally acquired gene islands, multidomain genes or ancient regions such as genes for ribosomal proteins and RNAs. A species-specific extragenic palindromic sequence is the most common repeat in the genome that can be exploited for the typing of P. putida strains. In the coding sequence of P. putida LLL is the most abundant tripeptide read more ...
