Complete genome sequencing of Shigella sp. PAMC 28760: Identification of CAZyme genes and analysis of their potential role in glycogen metabolism for cold survival adaptation

Microb Pathog. 2019 Dec;137:103759. doi: 10.1016/j.micpath.2019.103759. Epub 2019 Sep 24.

Abstract

Shigella sp. PAMC 28760 (isolated from Himantormia sp. lichen in Antarctica) is a gram-negative, non-sporulating bacterium that has cellulolytic and amylolytic characteristics as well as glycogen metabolic pathways. In this study, we isolated S. sp. PAMC 28760 from Antarctic lichen, and present the complete genome sequence with annotations describing its unique features. The genome sequence has 58.85% GC content, 4,278 coding DNA sequences, 85 tRNAs, and 22 rRNA operons. 16S rRNA gene sequence analyses revealed strain PAMC 28760 as a potentially new species of genus Shigella, showing various differences from pathogenic bacteria reported previously. dbCAN2 analyses revealed 91 genes related to carbohydrate-metabolizing enzymes. S. sp. PAMC 28760 likely degrades polysaccharide starch to obtain glucose for energy conservation. This study provides a foundation for understanding Shigella survival adaptation mechanisms under extremely cold Antarctic conditions.

Keywords: Amylolytic characteristic; Antarctic lichen; CAZyme; Genome sequencing; Shigella.

MeSH terms

  • Adaptation, Physiological
  • Antarctic Regions
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Bacterial Typing Techniques
  • Base Composition
  • Cold Temperature
  • DNA, Bacterial / genetics
  • Genes, Bacterial / genetics
  • Genome, Bacterial
  • Glycogen / metabolism*
  • Lichens / microbiology
  • Phylogeny
  • RNA, Ribosomal, 16S / genetics
  • Shigella / classification
  • Shigella / enzymology*
  • Shigella / genetics*
  • Shigella / isolation & purification*
  • Whole Genome Sequencing*

Substances

  • Bacterial Proteins
  • DNA, Bacterial
  • RNA, Ribosomal, 16S
  • Glycogen