Relative entropy differences in bacterial chromosomes, plasmids, phages and genomic islands

Abstract

BackgroundWe sought to assess whether the concept of relative entropy (information capacity), could aid our understanding of the process of horizontal gene transfer in microbes. We analyzed the differences in information capacity between prokaryotic chromosomes, genomic islands (GI), phages, and plasmids. Relative entropy was estimated using the Kullback-Leibler measure.ResultsRelative entropy was highest in bacterial chromosomes and had the sequence chromosomes > GI > phage > plasmid. There was an association between relative entropy and AT content in chromosomes, phages, plasmids and GIs with the strongest association being in phages. Relative entropy was also found to be lower in the obligate intracellular Mycobacterium leprae than in the related M. tuberculosis when measured on a shared set of highly conserved genes.ConclusionsWe argue that relative entropy differences reflect how plasmids, phages and GIs interact with microbial host chromosomes and that all these biological entities are, or have been, subjected to different selective pressures. The rate at which amelioration of horizontally acquired DNA occurs within the chromosome is likely to account for the small differences between chromosomes and stably incorporated GIs compared to the transient or independent replicons such as phages and plasmids.

Positive correlations between genomic %AT and genome size within strains of bacterial species

“…In accordance with what was observed in general (Bohlin et al, 2012), we see in Fig. 3 a decrease in relative entropy with respect to genomic %AT for most species.…”

Amino Acid Usage Is Asymmetrically Biased in AT- and GC-Rich Microbial Genomes

“…Going from AT-rich to GC-rich and larger populations, proteins from prokaryotes become progressively more hydrophobic which points to increased selective pressure [27]. A previous study conducted by some of us, found that KL estimated from the DNA sequences of plasmids and phages was, in accordance with microbes, associated with AT content, but exhibited on average significantly lower KL than microbes, with plasmids having the lowest KL of all [11]. We therefore speculate that KL differences may be maintained by the sum of selective pressures the organism has been subjected to over generations and manifested through genomic %AT and amino acid usage bias, since proteins are in fact communicating with the extracellular environment [25].…”

“…The concept of relative entropy is a cornerstone in information theory where it designates the divergence of one quantity measured against another [11], [16]. We use relative entropy to assess the information potential of codon (trinucleotide) frequencies.…”

“…Relative entropy was measured using the Kullback-Leibler divergence of genomic codon frequencies versus estimated codon frequencies [11], i.e. F i (XYZ)∼F i (X)F i (Y)F i (Z) , F i being a frequency function for a genome i and X , Y and Z respective nucleotides {A, G, C, T} of a codon XYZ : …”

“…High values of AAUB (or CUB) is interpreted as one or more amino acids (or codons) being preferred (or avoided) over the remaining, while low values of AAUB (or CUB) is understood as a more balanced genomic amino acid (or codon) preference. In addition, we discuss possible influences on amino acid- and codon-usage from purifying selection, random mutations and selective pressures in general using the concept of relative entropy [11]. This was carried out by first downloading 2032 microbial genomes from GenBank (See Table S1) (http://www.ncbi.nlm.nih.gov/genome/) and then analyzing both amino acid- and codon frequencies using principal component analysis (PCA).…”