RNA G-quadruplexes inhibit translation of the PE/PPE transcripts in Mycobacterium tuberculosis

J Biol Chem. 2024 Jan;300(1):105567. doi: 10.1016/j.jbc.2023.105567. Epub 2023 Dec 14.


The role of RNA G-quadruplexes (rG4s) in bacteria remains poorly understood. High G-quadruplex densities have been linked to organismal stress. Here we investigate rG4s in mycobacteria, which survive highly stressful conditions within the host. We show that rG4-enrichment is a unique feature exclusive to slow-growing pathogenic mycobacteria, and Mycobacterium tuberculosis (Mtb) transcripts contain an abundance of folded rG4s. Notably, the PE/PPE family of genes, unique to slow-growing pathogenic mycobacteria, contain over 50% of rG4s within Mtb transcripts. We found that RNA oligonucleotides of putative rG4s in PE/PPE genes form G-quadruplex structures in vitro, which are stabilized by the G-quadruplex ligand BRACO19. Furthermore, BRACO19 inhibits the transcription of PE/PPE genes and selectively suppresses the growth of Mtb but not Mycobacterium smegmatis or other rapidly growing bacteria. Importantly, the stabilization of rG4s inhibits the translation of Mtb PE/PPE genes (PPE56, PPE67, PPE68, PE_PGRS39, and PE_PGRS41) ectopically expressed in M. smegmatis or Escherichia coli. In addition, the rG4-mediated reduction in PE/PPE protein levels attenuates proinflammatory response upon infection of THP-1 cells. Our findings shed new light on the regulation of PE/PPE genes and highlight a pivotal role for rG4s in Mtb transcripts as regulators of post-transcriptional translational control. The rG4s in mycobacterial transcripts may represent potential drug targets for newer therapies.

Keywords: G-quadruplex; Mycobacterium tuberculosis (Mtb); PE/PPE genes; RNA G-quadruplexes (rG4s); slow-growing mycobacteria; translation.

MeSH terms

  • Bacterial Proteins* / biosynthesis
  • Bacterial Proteins* / genetics
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • G-Quadruplexes*
  • Gene Expression Regulation, Bacterial*
  • Genes, Bacterial / genetics
  • Humans
  • Inflammation / microbiology
  • Ligands
  • Mycobacterium smegmatis / drug effects
  • Mycobacterium smegmatis / genetics
  • Mycobacterium smegmatis / growth & development
  • Mycobacterium smegmatis / metabolism
  • Mycobacterium tuberculosis* / drug effects
  • Mycobacterium tuberculosis* / genetics
  • Mycobacterium tuberculosis* / growth & development
  • Mycobacterium tuberculosis* / metabolism
  • Oligoribonucleotides / genetics
  • Oligoribonucleotides / metabolism
  • Protein Biosynthesis*
  • RNA Stability
  • RNA, Bacterial* / genetics
  • RNA, Messenger* / genetics
  • THP-1 Cells
  • Transcription, Genetic / drug effects


  • Bacterial Proteins
  • Ligands
  • Oligoribonucleotides
  • RNA, Bacterial
  • RNA, Messenger