Identification and classification of a two-component system based on domain structures in bacteria and differences in domain structure between gram-positive and gram-negative bacteria

Sangwan Kim, Hideki Hirakawa, Shigeru Muta, Satoru Kuhara

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Genome sequencing has revealed many pairs of proteins termed two-component systems (TCSs) in bacteria. Each pair consists of a sensor or histidine kinase (HK) and an effector or response regulator (RR). The HK is usually a membrane-spanning protein that senses specific environmental parameters and communicates this information to the cytoplasmic RR protein through phosphotransfer reactions to cope with a variety of environmental stresses, including osmotic pressure, nitrogen lack, phosphoric acid lack, and the presence of oxygen. Furthermore, some proteins have been identified as hybrid kinases composed of HK and RR. We identified the domain structures of 360 bacteria and 43 archaea by domain search against the PFAM database using HMMER. We then classified 8,573 HK, 10,807 RR, and 2,477 hybrid kinases. In addition, we identified specific domains among phylogenic clusters based on differences in domain structure of TCS genes applying the Signal-to-Noise ratio.

Original languageEnglish
Pages (from-to)716-720
Number of pages5
JournalBioscience, Biotechnology and Biochemistry
Volume74
Issue number4
DOIs
Publication statusPublished - May 3 2010

Fingerprint

Gram-Negative Bacteria
Bacteria
Phosphotransferases
Histidine
Gene Components
Proteins
Archaea
Osmotic Pressure
Signal-To-Noise Ratio
Genes
Membrane Proteins
Nitrogen
Genome
Databases
Oxygen
Histidine Kinase
Signal to noise ratio
Membranes
Sensors

All Science Journal Classification (ASJC) codes

  • Analytical Chemistry
  • Biotechnology
  • Biochemistry
  • Applied Microbiology and Biotechnology
  • Molecular Biology
  • Organic Chemistry

Cite this

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