Genomes are covered with ubiquitous 11 bp periodic patterns, the "class A flexible patterns"

Abstract

BackgroundThe genomes of prokaryotes and lower eukaryotes display a very strong 11 bp periodic bias in the distribution of their nucleotides. This bias is present throughout a given genome, both in coding and non-coding sequences. Until now this bias remained of unknown origin.ResultsUsing a technique for analysis of auto-correlations based on linear projection, we identified the sequences responsible for the bias. Prokaryotic and lower eukaryotic genomes are covered with ubiquitous patterns that we termed "class A flexible patterns". Each pattern is composed of up to ten conserved nucleotides or dinucleotides distributed into a discontinuous motif. Each occurrence spans a region up to 50 bp in length. They belong to what we named the "flexible pattern" type, in that there is some limited fluctuation in the distances between the nucleotides composing each occurrence of a given pattern. When taken together, these patterns cover up to half of the genome in the majority of prokaryotes. They generate the previously recognized 11 bp periodic bias.ConclusionJudging from the structure of the patterns, we suggest that they may define a dense network of protein interaction sites in chromosomes.

Bacteria as computers making computers

“…A wealth of studies have explored the variety of constraints that operate on DNA: supercoiling, domain structure and attachment to specific sites ( Haran et al , 1994 ; Pedersen et al , 2000 ; Tolstorukov et al , 2005 ; Zimmerman, 2006 ). There are some indications that these physical constraints are reflected in the genome sequence in the form of fuzzy motifs (named ‘flexible motifs of type A’) that constrain a considerable amount of the DNA sequence ( Larsabal & Danchin, 2005 ).…”

Profile-Statistical Periodicity of DNA Coding Regions

“… 14 In practice, in the absence of weak periodicity in a sequence that is not an approximate tandem repeat, a high index of heterogeneity and a Fourier spectrum with a dominant peak may be observed. It is incorrect in this case to use the term ‘latent periodicity’, until the discovery of a pattern indicating some new type of periodicity, for example, such as the flexible patterns 17 of 11th nucleotide periodicity in the genomes of prokaryotes and low eukaryotes.…”

The Cellular Chassis as the Basis for New Functionalities: Shortcomings and Requirements

“…Once within the syncytium, the genetic program directs synthesis of proteins that condense DNA, making it fit to the size of a single hosting cell (Fig. 2, adapted from reference Larsabal and Danchin 2005).…”

“…2 DNA condensation. The genome DNA molecule is seeded with nucleotides that create binding sites for DNA binding proteins that result in DNA condensation (Larsabal and Danchin 2005), a process that allows the DNA molecule to be folded within a small space algorithms, depending on highly specific functionalities that will define the type of computer: mainframe, for heavy computation, desktop for versatile use, PC for travel etc. Novel uses have been created with smart phones and tablets.…”