Genomic and transcriptomic analysis of the streptomycin-dependent Mycobacterium tuberculosis strain 18b

BMC Genomics. 2016 Mar 5;17:190. doi: 10.1186/s12864-016-2528-2.

Abstract

Background: The ability of Mycobacterium tuberculosis to establish a latent infection (LTBI) in humans confounds the treatment of tuberculosis. Consequently, there is a need to discover new therapeutic agents that can kill M. tuberculosis both during active disease and LTBI. The streptomycin-dependent strain of M. tuberculosis, 18b, provides a useful tool for this purpose since upon removal of streptomycin (STR) it enters a non-replicating state that mimics latency both in vitro and in animal models.

Results: The 4.41 Mb genome sequence of M. tuberculosis 18b was determined and this revealed the strain to belong to clade 3 of the ancient ancestral lineage of the Beijing family. STR-dependence was attributable to insertion of a single cytosine in the 530 loop of the 16S rRNA and to a single amino acid insertion in the N-terminal domain of initiation factor 3. RNA-seq was used to understand the genetic programme activated upon STR-withdrawal and hence to gain insight into LTBI. This revealed reconfiguration of gene expression and metabolic pathways showing strong similarities between non-replicating 18b and M. tuberculosis residing within macrophages, and with the core stationary phase and microaerophilic responses.

Conclusion: The findings of this investigation confirm the validity of 18b as a model for LTBI, and provide insight into both the evolution of tubercle bacilli and the functioning of the ribosome.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Comparative Genomic Hybridization
  • Genome, Bacterial*
  • High-Throughput Nucleotide Sequencing
  • INDEL Mutation
  • Models, Molecular
  • Molecular Sequence Annotation
  • Mycobacterium tuberculosis / classification
  • Mycobacterium tuberculosis / drug effects
  • Mycobacterium tuberculosis / genetics*
  • Phylogeny
  • Polymorphism, Single Nucleotide
  • Protein Structure, Tertiary
  • RNA, Bacterial / genetics
  • RNA, Ribosomal, 16S / genetics
  • Ribosome Subunits, Small, Bacterial / genetics
  • Sequence Analysis, RNA
  • Streptomycin / pharmacology*
  • Transcriptome*

Substances

  • RNA, Bacterial
  • RNA, Ribosomal, 16S
  • Streptomycin