The bare necessities: Uncovering essential and condition-critical genes with transposon sequencing

Mol Oral Microbiol. 2019 Apr;34(2):39-50. doi: 10.1111/omi.12256. Epub 2019 Mar 1.

Abstract

Querying gene function in bacteria has been greatly accelerated by the advent of transposon sequencing (Tn-seq) technologies (related Tn-seq strategies are known as TraDIS, INSeq, RB-TnSeq, and HITS). Pooled populations of transposon mutants are cultured in an environment and next-generation sequencing tools are used to determine areas of the genome that are important for bacterial fitness. In this review we provide an overview of Tn-seq methodologies and discuss how Tn-seq has been applied, or could be applied, to the study of oral microbiology. These applications include studying the essential genome as a means to rationally design therapeutic agents. Tn-seq has also contributed to our understanding of well-studied biological processes in oral bacteria. Other important applications include in vivo pathogenesis studies and use of Tn-seq to probe the molecular basis of microbial interactions. We also highlight recent advancements in techniques that act in synergy with Tn-seq such as clustered regularly interspaced short palindromic repeats (CRISPR) interference and microfluidic chip platforms.

Keywords: essential genes; functional genomics; next-generation sequencing; oral microbiology; transposon sequencing.

Publication types

  • Review

MeSH terms

  • Bacteria / genetics*
  • DNA Transposable Elements / genetics*
  • Drug Delivery Systems
  • Genes, Essential / drug effects
  • Genes, Essential / genetics*
  • Genome, Bacterial
  • High-Throughput Nucleotide Sequencing / instrumentation
  • High-Throughput Nucleotide Sequencing / methods
  • Microbial Interactions / genetics
  • Mouth / microbiology*
  • Mutagenesis, Insertional
  • Phenotype
  • Sequence Analysis / instrumentation
  • Sequence Analysis / methods*
  • Sequence Analysis, DNA / instrumentation
  • Sequence Analysis, DNA / methods*

Substances

  • DNA Transposable Elements