G-Quadruplex Structures in Bacteria: Biological Relevance and Potential as an Antimicrobial Target

Abstract

DNA strands consisting of multiple runs of guanines can adopt a noncanonical, four-stranded DNA secondary structure known as G-quadruplex or G4 DNA. G4 DNA is thought to play an important role in transcriptional and translational regulation of genes, DNA replication, genome stability, and oncogene expression in eukaryotic genomes. In other organisms, including several bacterial pathogens and some plant species, the biological roles of G4 DNA and G4 RNA are starting to be explored. Recent investigations showed that G4 DNA and G4 RNA are generally conserved across plant species. In silico analyses of several bacterial genomes identified putative guanine-rich, G4 DNA-forming sequences in promoter regions. The sequences were particularly abundant in certain gene classes, suggesting that these highly diverse structures can be employed to regulate the expression of genes involved in secondary metabolite synthesis and signal transduction. Furthermore, in the pathogen Mycobacterium tuberculosis, the distribution of G4 motifs and their potential role in the regulation of gene transcription advocate for the use of G4 ligands to develop novel antitubercular therapies. In this review, we discuss the various roles of G4 structures in bacterial DNA and the application of G4 DNA as inhibitors or therapeutic agents to address bacterial pathogens.

Keywords: G-quadruplex; antigenic variation; aptamers; homologous recombination; host-pathogen interaction; transcriptional and translational regulation.

FIG 1

Schematic categorization of G4 DNA based on DNA strands. (A) Intramolecular type of G4 DNA (involving only one DNA strand in the formation of the quadruplex structure). (B) Intermolecular type of G4 DNA (involving two or more DNA strands in the formation of the quadruplex structure). The direction of the DNA strands is indicated by arrowheads.

FIG 2

Graphical diagram representing the regulatory role of G-quadruplex sequences in replication and transcription (by either inhibiting or promoting expression). The presence of secondary structure G4 DNA stalls DNA replication in many bacterial species, while the destabilization of G4 DNA in the presence of helicase enzymes Rec Q, Rec A, and UvrD (studied in E. coli) and UvrD1, UvrD2, and DinG (investigated in M. tuberculosis) and topoisomerase DraTopoIB of M. tuberculosis results into the resumption of stalled DNA replication. The transcriptional regulation of many genes is observed to be either continued or hindered by G4 DNA in many bacteria. With the use of certain ligands such as NMM and TMPyP4, G4 DNA is stabilized and transcription of genes such as recA, recO, recF, recR, and recQ in D. radiodurans, espK, espB, and cyp51 in M. tuberculosis, and nasT in P. denitrificans is observed to be obstructed.

FIG 3

G-quadruplex-mediated regulatory mechanism of radioresistance in D. radiodurans.

FIG 4

Effects of G-quadruplexes with respect to positioning and strand orientation. (A) G4 DNA formed in different regions on the sense and antisense strands. (B) The presence of G4 quadruplexes on the sense strand leads to inhibition of gene expression by formation of a DNA-RNA hybrid. (C) In the presence of these secondary structures on the antisense strand, both mRNA expression and inhibition occur. In the presence of transcription factors (TFs) and RNAP in the upstream or downstream promoter region, near the 5′ UTR of mRNA, or within genes, mRNA expression is downregulated; the presence of a G-quadruplex in the 3′ UTR of mRNA shows no significant effect. RNAPs can also upregulate gene expression. (D) G4 sequences present in the 5′ UTR of mRNA, in the gene body, within genes, and in the 3′ UTR of mRNA can either inhibit, upregulate, or downregulate protein expression. P, promoter.