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

• Published in: Bioscience, biotechnology, and biochemistry biotechnology, and biochemistry, 2010, Vol.74 (4), p.716-720
• Main Authors: Kim, S., Kyushu Univ., Fukuoka (Japan), Hirakawa, H, Muta, S, Kuhara, S
• Format: Article
• Language: English
• Subjects: Archaea; Archaea - genetics; Archaea - metabolism; Bacteria - genetics; Bacteria - metabolism; BACTERIA GRAM NEGATIVA; BACTERIA GRAM POSITIVA; BACTERIE GRAM NEGATIF; BACTERIE GRAM POSITIF; Biological and medical sciences; CELL MEMBRANES; Chromosome Mapping; CLASIFICACION; CLASSIFICATION; domain structure; ESTRES; evolutional adaptation; Fundamental and applied biological sciences. Psychology; GENE; GENES; GRAM NEGATIVE BACTERIA; GRAM POSITIVE BACTERIA; Gram-Negative Bacteria - genetics; Gram-Negative Bacteria - metabolism; Histidine Kinase; http://www.fao.org/aos/agrovoc#c_1653; http://www.fao.org/aos/agrovoc#c_27583; http://www.fao.org/aos/agrovoc#c_3214; http://www.fao.org/aos/agrovoc#c_3352; http://www.fao.org/aos/agrovoc#c_3353; http://www.fao.org/aos/agrovoc#c_3791; http://www.fao.org/aos/agrovoc#c_7452; http://www.fao.org/aos/agrovoc#c_9693; IDENTIFICACION; IDENTIFICATION; MEMBRANAS CELULARES; MEMBRANE CELLULAIRE; Membrane Proteins - genetics; Membrane Proteins - metabolism; NUCLEOTIDE SEQUENCE; Phylogeny; Protein Kinases; SECUENCIA NUCLEOTIDICA; SEQUENCE NUCLEOTIDIQUE; Signal Transduction - genetics; Signal Transduction - physiology; signal-to-noise ratio; STRESS; two-component system (TCS)
• ISSN: 0916-8451; 1347-6947
• DOI: 10.1271/bbb.90746

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.