G-quadruplex prediction in E. coli genome reveals a conserved putative G-quadruplex-Hairpin-Duplex switch.
Many studies show that short non-coding sequences are widely conserved among regulatory elements. More and more conserved sequences are being discovered since the development of next generation sequencing technology. A common approach to identify conserved sequences with regulatory roles relies on topological changes such as hairpin formation at the DNA or RNA level. G-quadruplexes, non-canonical nucleic acid topologies with little established biological roles, are increasingly considered for conserved regulatory element discovery. Since the tertiary structure of G-quadruplexes is strongly dependent on the loop sequence which is disregarded by the generally accepted algorithm, we hypothesized that G-quadruplexes with similar topology and, indirectly, similar interaction patterns, can be determined using phylogenetic clustering based on differences in the loop sequences. Phylogenetic analysis of 52 G-quadruplex forming sequences in the Escherichia coli genome revealed two conserved G-quadruplex motifs with a potential regulatory role. Further analysis revealed that both motifs tend to form hairpins and G quadruplexes, as supported by circular dichroism studies. The phylogenetic analysis as described in this work can greatly improve the discovery of functional G-quadruplex structures and may explain unknown regulatory patterns.
Berlin Institute for Medical Systems Biology, Max Delbrück Center, 13125 Berlin, Germany.|School of Medicine, Istanbul Medeniyet University, 34000 Istanbul, Turkey.
Oktay I
http://orcid.org/0000-0002-8733-0920
OI
Kaplan
Department of Biology, Osmangazi University, Eskisehir, 26480, Turkey.
Burak
B
Berber
School of Medicine, Istanbul Kemerburgaz University, 34217, Turkey.
Nezih
N
Hekim
Department of Biomedical Engineering, Izmir University of Economics, Izmir, 35330, Turkey osman.doluca@iue.edu.tr doluca.osman@gmail.com.
Osman
http://orcid.org/0000-0003-0412-6148
O
Doluca
D016384:Consensus Sequence; D017124:Conserved Sequence; D004269:DNA, Bacterial / Q000737:chemistry* / Q000235:genetics*; D004926:Escherichia coli / Q000145:classification / Q000235:genetics*; D054856:G-Quadruplexes; D063990:Gene Ontology; D016680:Genome, Bacterial; D055029:Inverted Repeat Sequences; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs; D010802:Phylogeny; D056510:Position-Specific Scoring Matrices
D004269:DNA, Bacterial