Abstract
The role of local DNA structures in the regulation of basic cellular processes is an emerging field of research. Amongst local non-B DNA structures, the significance of G-quadruplexes was demonstrated in the last decade, and their presence and functional relevance has been demonstrated in many genomes, including humans. In this study, we analyzed the presence and locations of G-quadruplex-forming sequences by G4Hunter in all complete bacterial genomes available in the NCBI database. G-quadruplex-forming sequences were identified in all species, however the frequency differed significantly across evolutionary groups. The highest frequency of G-quadruplex forming sequences was detected in the subgroup Deinococcus-Thermus, and the lowest frequency in Thermotogae. G-quadruplex forming sequences are non-randomly distributed and are favored in various evolutionary groups. G-quadruplex-forming sequences are enriched in ncRNA segments followed by mRNAs. Analyses of surrounding sequences showed G-quadruplex-forming sequences around tRNA and regulatory sequences. These data point to the unique and non-random localization of G-quadruplex-forming sequences in bacterial genomes.
Highlights
The discovery of the B-DNA structure by Crick and Watson started a rapid growth in genetic and molecular biology research [1]
We analyzed the occurrence of putative G4 sequences (PQS) by G4Hunter in all 1627 known bacterial genomes
We analyzed the presence of PQS in bacterial genomes
Summary
The discovery of the B-DNA structure by Crick and Watson started a rapid growth in genetic and molecular biology research [1]. DNA structure, other forms of secondary structure participate in various basic processes [2]. The presence of various local DNA structures including cruciforms [3], quadruplexes [4] and triplexes [5]. G4s are secondary structures formed by guanine rich sequences which are widespread in DNA and RNA [4]. G4 formation requires the presence of monovalent cations such as Na+ and K+ [7]. Formation of this structure regulates various processes including gene expression [8], protein translation [9] and proteolysis pathways [10] in both prokaryotes
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