Investigation of a Quadruplex-Forming Repeat Sequence Highly Enriched in Xanthomonas and Nostoc sp.

Abstract

In prokaryotes simple sequence repeats (SSRs) with unit sizes of 1–5 nucleotides (nt) are causative for phase and antigenic variation. Although an increased abundance of heptameric repeats was noticed in bacteria, reports about SSRs of 6–9 nt are rare. In particular G-rich repeat sequences with the propensity to fold into G-quadruplex (G4) structures have received little attention. In silico analysis of prokaryotic genomes show putative G4 forming sequences to be abundant. This report focuses on a surprisingly enriched G-rich repeat of the type in Xanthomonas and cyanobacteria such as Nostoc. We studied in detail the genomes of Xanthomonas campestris pv. campestris ATCC 33913 (Xcc), Xanthomonas axonopodis pv. citri str. 306 (Xac), and Nostoc sp. strain PCC7120 (Ana). In all three organisms repeats are spread all over the genome with an over-representation in non-coding regions. Extensive variation of the number of repetitive units was observed with repeat numbers ranging from two up to 26 units. However a clear preference for four units was detected. The strong bias for four units coincides with the requirement of four consecutive G-tracts for G4 formation. Evidence for G4 formation of the consensus repeat sequences was found in biophysical studies utilizing CD spectroscopy. The G-rich repeats are preferably located between aligned open reading frames (ORFs) and are under-represented in coding regions or between divergent ORFs. The G-rich repeats are preferentially located within a distance of 50 bp upstream of an ORF on the anti-sense strand or within 50 bp from the stop codon on the sense strand. Analysis of whole transcriptome sequence data showed that the majority of repeat sequences are transcribed. The genetic loci in the vicinity of repeat regions show increased genomic stability. In conclusion, we introduce and characterize a special class of highly abundant and wide-spread quadruplex-forming repeat sequences in bacteria.

Mapping and characterization of G-quadruplexes in Mycobacterium tuberculosis gene promoter regions

“…In prokaryotes, G4 sequences have been reported in Escherichia coli 7,31,32 , Deinococcus radiodurans [33][34][35] Xanthomonas and Nostoc sp 36 . Evidence of bacterial enzymes that process G4s, such as Pif1 and RecQ helicases, has been provided in Escherichia coli, Clostridium difficile and Bacteroides sp [37][38][39][40][41][42] .…”

G-Quadruplexes: More Than Just a Kink in Microbial Genomes

“…and Xanthomonad spp. [97]. Bacterial SSRs are known to be implicated in antigenic and phase variation.…”

Computational understanding and experimental characterization of twice-as-smart quadruplex ligands as chemical sensors of bacterial nucleotide second messengers

“…For instance, bacterial and viral quadruplexes are now considered as valuable targets for therapeutic interventions aiming at harnessing pathogenic virulence 7 , as demonstrated by recent and elegant works from research teams of J.S. Hartig 40 41 42 and S. Richter 43 44 45 46 for instance.…”