User:Sarasunadalkilic/sandbox
Original – Response Regulator
Classification
[edit]Response regulators can be divided into at least three broad classes:[1]
- Single-domain response regulators, which contain only a receiver domain and which use protein-protein interactions to exert their downstream biological effects; for example, the chemotaxis regulator CheY.
- Response regulators with a DNA-binding effector domain, usually of helix-turn-helix architecture.
- Response regulators with effector domains that have enzymatic functions, giving rise to secondary messenger molecules such as cAMP.
More comprehensive classifications based on more detailed analysis of domain architecture are possible, and find that response regulators with DNA-binding domains are by far the most common.[2]
Edit – Response Regulator
Classification
[edit]Response regulators can be divided into at least three broad classes, based on the features of effector domains: regulators with a DNA-binding effector domain, regulators with an enzymatic effector domain, and single-domain response regulators.[1] More comprehensive classifications based on more detailed analysis of domain architecture are possible.[2] Beyond these broad categorizations, there are response regulators with other types of effector domains, including RNA-binding effector domains.
Regulators with a DNA-binding effector domain are the most common response regulators, and have direct impacts on transcription.[2] They tend to interact with their cognate regulators at an N-terminus receiver domain, and contain the DNA-binding effector towards the C-terminus. Once phosphorylated at the receiver domain, the response regulator dimerizes, gains enhanced DNA binding capacity and acts as a transcription factor.[3] The architecture of DNA binding domains are characterized as being variations on helix-turn-helix motifs. One variation, found on the response regulator OmpR of the EnvZ/OmpR two-component system and other OmpR-like response regulators, is a "winged helix" architecture.[4] OmpR-like response regulators are the largest group of response regulators and the winged helix motif is widespread. Other subtypes of DNA-binding response regulators include FixJ-like and NtrC-like regulators.[5] DNA-binding response regulators are involved in various uptake processes, including nitrate/nitrite (NarL, found in most prokaryotes).[6]
The second class of multidomain response regulators are those with enzymatic effector domains.[7] These response regulators can participate in signal transduction, and generate secondary messenger molecules. Examples include the chemotaxis regulator CheB, with a methylesterase domain that is inhibited when the response regulator is in the inactive unphosphorylated conformation. Other enzymatic response regulators include c-di-GMP phosphodiesterases (e.g. VieA in V. cholerae), protein phosphatases and histidine kinases.[7]
A relatively small number of response regulators, single-domain response regulators, only contain a receiver domain, relying on protein-protein interactions to exert their downstream biological effects.[8] The receiver domain undergoes a conformational change as it interacts with an autophosphorylated histidine kinase, and consequently the response regulator can initiate further reactions along a signaling cascade. Prominent examples include the chemotaxis regulator CheY, which interacts with flagellar motor proteins directly in its phosphorylated state.[8]
Sequencing has so far shown that the distinct classes of response regulators are unevenly distributed throughout various taxa,[9] including across domains. While response regulators with DNA-binding domains are the most common in bacteria, single-domain response regulators are more common in archaea, with other major classes of response regulators seemingly absent from archaeal genomes.
--Sarasunadalkilic (talk) 06:03, 8 October 2017 (UTC)
References
[edit]- ^ a b Galperin, MY (14 June 2005). "A census of membrane-bound and intracellular signal transduction proteins in bacteria: bacterial IQ, extroverts and introverts". BMC microbiology. 5: 35. doi:10.1186/1471-2180-5-35. PMC 1183210. PMID 15955239.
{{cite journal}}: CS1 maint: unflagged free DOI (link) - ^ a b c Galperin, MY (June 2006). "Structural classification of bacterial response regulators: diversity of output domains and domain combinations". Journal of Bacteriology. 188 (12): 4169–82. doi:10.1128/jb.01887-05. PMC 1482966. PMID 16740923. Cite error: The named reference "galperin_2006" was defined multiple times with different content (see the help page).
- ^ Barbieri, Christopher M.; Wu, Ti; Stock, Ann M. (2013-05-27). "Comprehensive Analysis of OmpR Phosphorylation, Dimerization, and DNA Binding Supports a Canonical Model for Activation". Journal of Molecular Biology. 425 (10): 1612–1626. doi:10.1016/j.jmb.2013.02.003.
- ^ Kenney, Linda J (2002-04-01). "Structure/function relationships in OmpR and other winged-helix transcription factors". Current Opinion in Microbiology. 5 (2): 135–141. doi:10.1016/S1369-5274(02)00310-7.
- ^ Rajeev, Lara; Luning, Eric G.; Dehal, Paramvir S.; Price, Morgan N.; Arkin, Adam P.; Mukhopadhyay, Aindrila (2011-10-12). "Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium". Genome Biology. 12: R99. doi:10.1186/gb-2011-12-10-r99. ISSN 1474-760X.
{{cite journal}}: CS1 maint: unflagged free DOI (link) - ^ Baikalov, Igor; Schröder, Imke; Kaczor-Grzeskowiak, Maria; Grzeskowiak, Kazimierz; Gunsalus, Robert P.; Dickerson, Richard E. "Structure of theEscherichia coliResponse Regulator NarL†,‡". Biochemistry. 35 (34): 11053–11061. doi:10.1021/bi960919o.
- ^ a b Galperin, Michael Y. (2010-4). "Diversity of Structure and Function of Response Regulator Output Domains". Current opinion in microbiology. 13 (2): 150–159. doi:10.1016/j.mib.2010.01.005. ISSN 1369-5274. PMC 3086695. PMID 20226724.
{{cite journal}}: Check date values in:|date=(help)CS1 maint: PMC format (link) - ^ a b Sarkar, Mayukh K.; Paul, Koushik; Blair, David (2010-05-18). "Chemotaxis signaling protein CheY binds to the rotor protein FliN to control the direction of flagellar rotation in Escherichia coli". Proceedings of the National Academy of Sciences. 107 (20): 9370–9375. doi:10.1073/pnas.1000935107. ISSN 0027-8424. PMID 20439729.
- ^ "Census of prokaryotic response regulators". www.ncbi.nlm.nih.gov. Retrieved 2017-10-08.