G-quadruplex forming structural motifs in the genome of Deinococcus radiodurans and their regulatory roles in promoter functions

Abstract

Deinococcus radiodurans displays compromised radioresistance in the presence of guanine quadruplex (G4)-binding drugs (G4 drugs). Genome-wide scanning showed islands of guanine runs (G-motif) in the upstream regions of coding sequences as well as in the structural regions of many genes, indicating a role for G4 DNA in the regulation of genome functions in this bacterium. G-motifs present upstream to some of the DNA damage-responsive genes like lexA, pprI, recF, recQ, mutL and radA were synthesized, and the formation of G4 DNA structures was probed in vitro. The G-motifs present at the 67th position upstream to recQ and at the 121st position upstream to mutL produced parallel and mixed G4 DNA structures, respectively. Expression of β-galactosidase under recQ and mutL promoters containing respective G-motifs was inhibited by G4 drugs under normal growth conditions in D. radiodurans. However, when such cells were exposed to γ radiation, mutL promoter activity was stimulated while recQ promoter activity was inhibited in the presence of G4 drugs. Deletion of the G-motif from the recQ promoter could relax it from G4 drug repression. D. radiodurans cells treated with G4 drug showed reduction in recQ expression and γ radiation resistance, indicating an involvement of G4 DNA in the radioresistance of this bacterium. These results suggest that G-motifs from D. radiodurans genome form different types of G4 DNA structures at least in vitro, and the recQ and mutL promoters seem to be differentially regulated at the levels of G4 DNA structures.

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] .…”

DrRecQ regulates guanine quadruplex DNA structure dynamics and its impact on radioresistance in Deinococcus radiodurans

“…A), if have impacted the D10 value in response to gamma radiation in respective samples cannot be ruled out. Earlier studies have shown that NMM can affect radioresistance in D. radiodurans by affecting the expression of several DNA repair genes (Beaume et al , ; Kota et al , ). These results together suggest a possible role of RecQ in the regulation of G4 dynamics during growth in D. radiodurans .…”

“…Despite, its genome shows both qualitative and quantitative changes in response to gamma radiation by a mechanism uncharacterized yet. The genome wide scanning shows that this bacterium contains a very high density of G4 DNA motifs in genome, which plays significant roles in regulation of promoter activity of DNA repair genes (Kota et al , ). A relatively higher sensitivity of D. radiodurans to NMM under gamma stressed conditions as compared to normal growth conditions indicating a significant role of G4 DNA in radioresistance and the density of G4 DNA structure in the genome of this bacterium differs between these two growth conditions.…”

“…The GC‐rich genome of this bacterium has numerous islands of guanine repeats located both in the structural and regulatory regions of many genes including those encode for DNA repair proteins (Beaume et al , ). Our earlier studies showed that some of these repeats could form G4 DNA structures in vitro (Kota et al , ). Further, the involvement of G4 DNA in regulation of expression of DNA repair genes and radioresistance has been reported in D. radiodurans .…”

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

“…Deinococcus radiodurans is an extremophilic bacterium tolerant to ionizing radiations such as gamma rays and UV rays. Beaume et al analyzed the promoters of D. radiodurans and found that G4 motifs were particularly enriched within the 200 bp upstream region in genes that confer radiation resistance; these include recA, recF, recO, recR, recQ, and mutL, all of which are involved in recombinational DNA repair [86,87]. Interestingly, the addition of an intracellular G4-binding ligand led to a marked reduction in the expression of genes associated with radiation resistance, thus rendering D. radiodurans sensitive to radiation.…”