Assessing Diversity of DNA Structure-Related Sequence Features in Prokaryotic Genomes

Abstract

Prokaryotic genomes are diverse in terms of their nucleotide and oligonucleotide composition as well as presence of various sequence features that can affect physical properties of the DNA molecule. We present a survey of local sequence patterns which have a potential to promote non-canonical DNA conformations (i.e. different from standard B-DNA double helix) and interpret the results in terms of relationships with organisms' habitats, phylogenetic classifications, and other characteristics. Our present work differs from earlier similar surveys not only by investigating a wider range of sequence patterns in a large number of genomes but also by using a more realistic null model to assess significant deviations. Our results show that simple sequence repeats and Z-DNA-promoting patterns are generally suppressed in prokaryotic genomes, whereas palindromes and inverted repeats are over-represented. Representation of patterns that promote Z-DNA and intrinsic DNA curvature increases with increasing optimal growth temperature (OGT), and decreases with increasing oxygen requirement. Additionally, representations of close direct repeats, palindromes and inverted repeats exhibit clear negative trends with increasing OGT. The observed relationships with environmental characteristics, particularly OGT, suggest possible evolutionary scenarios of structural adaptation of DNA to particular environmental niches.

Repetitive Elements in Mycoplasma hyopneumoniae Transcriptional Regulation

“…In silico analysis revealed that the majority of the repeat sequences found were classified as palindromic elements (1,171 elements) compared with tandem repeats (144 elements). Similar results were also reported by Huang et al [36] who investigated tandem and palindromic repeats in protein-coding sequences and intergenic regions through a global analysis of more than 1,000 genomes, including Mycoplasma agalactiae , M . bovis , M .…”

“…Prokaryote genomes are extremely diverse in terms of nucleotide composition and the presence of distinct patterns of repeat sequences that could affect the physical properties of DNA molecules [36]. In this work, a global analysis of tandem and palindromic repetitive elements found in noncoding sequences of M .…”

“…[36], two types of DNA repeats were selected to be investigated in this work (tandem and palindromic elements). Tandem sequences were divided into the following: i) Simple Sequence Repeats (SSR); ii) Simple Sequence Repeats of Mononucleotides (SSRM) and iii) Direct Repeats (DR).…”

“…In the present work, SSR is defined as a sequence containing 2 to 10 repeated nucleotides as described by Huang et al [36]. The algorithms used to search for SSR were SSRLocator [37] and Simple Sequence Repeat Identification Tool (SSRIT) [38].…”

Recombinant DNA Technology: A Short Communication

“…Therefore this has been recognized as a plausible strategy for gene therapy, by removing the viral DNA and using the virus as a vehicle to deliver the therapeutic DNA. A number of viruses have been used for human gene therapy, including retrovirus, adenovirus, lentivirus, herpes simplex virus, vaccinia, pox virus, and adeno-associated virus [11,12,13].…”