Novel domains of the prokaryotic two-component signal transduction systems.

By Michael Y. Galperin, Anastasia N. Nikolskaya, Eugene V. Koonin. FEMS Microbiology Letters, 2001

682 citations recorded by the source corpus.

The archetypal two-component signal transduction systems include a sensor histidine kinase and a response regulator, which consists of a receiver CheY-like domain and a DNA-binding domain. Sequence analysis of the sensor kinases and response regulators encoded in complete bacterial and archaeal genomes revealed complex domain architectures for many of them and allowed the identification of several novel conserved domains, such as PAS, GAF, HAMP, GGDEF, EAL, and HD-GYP. All of these domains are widely represented in bacteria, including 19 copies of the GGDEF domain and 17 copies of the EAL domain encoded in the Escherichia coli genome. In contrast, these novel signaling domains are much less abundant in bacterial parasites and in archaea, with none at all found in some archaeal species. This skewed phyletic distribution suggests that the newly discovered complexity of signal transduction systems emerged early in the evolution of bacteria, with subsequent massive loss in parasites and some horizontal dissemination among archaea. Only a few proteins containing these domains have been studied experimentally, and their exact biochemical functions remain obscure; they may include transformations of novel signal molecules, such as the recently identified cyclic diguanylate. Recent experimental data provide the first direct evidence of the participation of these domains in signal transduction pathways, including regulation of virulence genes and extracellular enzyme production in the human pathogens Bordetella pertussis and Borrelia burgdorferi and the plant pathogen Xanthomonas campestris. Gene-neighborhood analysis of these new domains suggests their participation in a variety of processes, from mercury and phage resistance to maintenance of virulence plasmids. It appears that the real picture of the complexity of phosphorelay signal transduction in prokaryotes is only beginning to unfold.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/b46a996a48a1e4fb677d2b0cd1cb1186cf14cbb5

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Citations in the corpus

PilZ domain is part of the bacterial c-di-GMP binding protein (2006, background): “However, except for cellulose synthase, no protein has been shown to bind c-di-GMP and the targets for c-di-GMP action remain unknown.”
Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris (2004, background): “palustris has 451 potential regulatory and signaling genes, many of which encode multiple domain motifs ( Table 2 ; see Supplementary Table 2 online for a complete list”
Cell cycle-dependent dynamic localization of a bacterial response regulator with a novel di-guanylate cyclase output domain. (2004, background): “Although the nature of the signals is unclear in most cases, it has been well defined for others, like the PAS domain or hemerythrin (Gong et al. 1998; Terwilliger 1998).”
C‐di‐GMP: the dawning of a novel bacterial signalling system (2005, background): “Whether HD-GYP has c-di-GMP hydrolase activity remains to be tested but other bacteria, including Treponema pallidum , Campylobacter jejuni and several other important human pathogens, have a protein with a GGDEF domain but do not have proteins with either EAL or HD-GYP domains.”
CONSEJO SUPERIOR DE INVESTIGACIONES CIENTÍFICAS (2009, background): “Aunque estos dominios tengan una longitud comprendida entre 170 y 240 aminoácidos (Galperin et al., 2001; Römling et al., 2005), la nomenclatura proviene de la conservación aminoacídica de sus centros activos.”
Principles of c-di-GMP signalling in bacteria (2009, background): “Similarly to histidine sensor kinases of two-component systems, most GGDEF, EAL and HD-GYP domains are linked to various N-terminal sensory input domains, suggesting that numerous environmental and cellular signals are integrated into the c-di-GMP signalling networ”
Involvement of Nitric Oxide in Biofilm Dispersal of Pseudomonas aeruginosa (2006, background): “Several signal transduction pathways are known to regulate the activities of these GGDEF and EAL domains, including sensing of oxygen, pH, temperature, and other environmental stimuli (22, 51, 56).”
GGDEF and EAL domains inversely regulate cyclic di‐GMP levels and transition from sessility to motility (2004, background): “The mass sequencing of bacterial genomes detected an abundance of genes encoding proteins containing domains of unknown function (Galperin et al ., 2001), whereby the GGDEF [also called DUF (Domain of unknown function) 1] and the EAL (DUF2) domains are especially abundant.”
The Evolution of Two-Component Signal Transduction Systems (2012, background): “Most kinases also have at least one domain between the transmembrane and DHp domains, with PAS, HAMP, and GAF domains by far the most common (23).”
WebLogo: a sequence logo generator. (2004, background): “Protein logos can illuminate patterns of amino acid conservation that are often of structural or functional importance (Galperin et al. 2001; Rig-den et al. 2003).”
Cyclic Nucleotide Phosphodiesterases: Molecular Regulation to Clinical Use (2006, background): “The first is a “REC domain” homologous to the “receiver” domains of bacterial two-component signaling systems (Galperin et al., 2001).”
ROS as signalling molecules: mechanisms that generate specificity in ROS homeostasis (2007, background): “…and Mak3 might actually not sense H 2 O 2 , but instead might respond to some as-yet-undefined metabolic cues because they contain PAS/PAC domains 129,130 . ctt1 , cytosolic catalase-1; gpx1 , glutathione peroxidase-1; Mpr1, stress-response regulatory protein; srx1 , sulphiredoxin-1; trx2 ,…”