细菌四类胞外感觉结构域的概述

doi:10.14088/j.cnki.issn0439-8114.2022.11.030

摘要/Abstract

摘要： 细菌通过信号转导网络系统感知外界的环境变化,并通过调节自身基因表达,控制菌体的行为、代谢以及发育等。细菌和古细菌大多数使用双组分转导系统和化学传感系统感知环境变化。基于基因组研究发现在细菌的双组份转导系统和化学传感系统中存在多种不同的胞外结构域,这些胞外结构域能感知胞外信号,对细菌的各种生理功能具有重要作用。介绍了Cache结构域、CHASE结构域、NIT结构域以及4HB结构域这4类胞外感觉结构域的结构特性以及功能,为胞外感觉结构域的分类以及识别信号的位点提供借鉴。

关键词: 信号转导, 双组份系统, 化学传感系统, 胞外感觉结构域

Abstract: Bacteria perceive environmental changes through the signal transduction network system, and control bacterial behavior, metabolism and development by regulating their own gene expression. Most bacteria and archaea use two-component transduction system and chemical sensing system to perceive environmental changes. In recent years, based on genome research, it has been found that there are many different extracellular domains in bacterial two-component transduction system and chemical sensing system. These extracellular domains can sense extracellular signals and play an important role in various physiological functions of bacteria. The structural characteristics and functions of Cache domain, CHASE domain, NIT domain and 4HB domain were introduced to provide a reference for the classification of extracellular sensory domains and the identification of signal sites.

Key words: signal transduction, two-component system, chemical sensing system, extracellular sensory domain

中图分类号:

许阳阳, 袁文肃. 细菌四类胞外感觉结构域的概述[J]. 湖北农业科学, 2022, 61(11): 149-157.

XU Yang-yang, YUAN Wen-su. Overview of four kinds of extracellular sensory domains in bacteria[J]. HUBEI AGRICULTURAL SCIENCES, 2022, 61(11): 149-157.

参考文献

[1] COMBARNOUS Y,NGUYEN T M D. Cell communications among microorganisms, plants, and animals: Origin, evolution, and interplays[J].Int J Mol Sci,2020,21(21):8052.
[2] ORTEGA A, ZHULIN L B, KRELL T.Sensory repertoire of bacterial chemoreceptors[J]. Microbiology and molecular biology reviews,2017,81(4):e00033-17.
[3] GUSHCHIN I, MELNIKOV I, POLOVINKIN V,et al.Mechanism of transmembrane signaling by sensor histidine kinases[J].Science,2017,356(6342):6345.
[4] HOCH J A.Two-component and phosphorelay signal transduction[J].Current opinion in microbiology,2000,3(2):165-170.
[5] HOCH J A,VARUGHESE K I.Keeping signals straight in phosphorelay signal transduction[J]. Journal of bacteriology,2001,183(17):4941-4949.
[6] STOCK A M,ROBINSON V L,GOUDREAU P N.Two-component signal transduction[J].Annual review of biochemistry,2010,13(2):113-115.
[7] WEST A H,STOCK A M.Histidine kinases and response regulator proteins in two-component signaling systems[J].Trends in biochemical sciences,2001,26(6):369-376.
[8] KILMURY S L N,BURROWS L L. The Pseudomonas aeruginosa PilSR two-component system regulates both twitching and swimming motilities[J].Motility,2018,9(4):1310-1318.
[9] PAPON N,STOCK A M.What do archaeal and eukaryotic histidine kinases sense?[J].Floor research,2019,8:2145-2153.
[10] MUOK A R, BRIEGEL A,CRANE B R.Regulation of the chemotaxis histidine kinase CheA: A structural perspective[J].Biochim Biophys Acta Biomembr,2020,1862(1):183030.
[11] DING X Y,HE Q, SHEN F L, et al.Regulatory role of an interdomain linker in the bacterial chemotaxis histidine kinase CheA[J].Journal of bacteriology,2018,200(10):e00052-18.
[12] BI S Y,LAI L H.Bacterial chemoreceptors and chemoeffectors[J]. Cell Mol Life Sci,2015,72(4):691-708.
[13] UD-DIN A I M S,ROUJEINIKOVA A. Methyl-accepting chemotaxis proteins:A core sensing element in prokaryotes and archaea[J].Cell Mol Life Sci,2017,74(18):3293-3303.
[14] O'NEAL L,GULLETT J M,AKSENOVA A,et al. Distinct chemotaxis protein paralogs assemble into chemoreceptor signaling arrays to coordinate signaling output[J].MBio,2019,24;10(5):e01757-19.
[15] HUANG Z W,PAN X Y,XU N,et al.Bacterial chemotaxis coupling protein: Structure, function and diversity[J].Microbiol Res,2019,219:40-48.
[16] PONTING C P, ARAVIND L.PAS: A multifunctional domain family comes to light[J].Current biology,1997,7(11):R674-R677.
[17] TAYLOR B L,ZHULIN I B.PAS domains: Internal sensors of oxygen, redox potential, and light[J].Microbiol Mol Biol Rev,1999, 63(2):479.
[18] SOBRAN M A,COTTER P A.The BvgS pas domain, an independent sensory perception module in the bordetella bronchiseptica BvgAS phosphorelay[J].Journal of bacteriology,2019,201(17):e00286-19.
[19] ADHIKARI A,BISWAS S,MUKHERJEE A,et al.PAS domain-containing phosphoglycerate kinase deficiency in Leishmania major results in increased autophagosome formation and cell death[J].Biochem J,2019,476(8):1303-1321.
[20] ZHULIN I B.A novel phototaxis receptor hidden in the cyanobacterial genome[J].Journal of molecular microbiology & biotechnology,2000,2(4):491-493.
[21] CHEN H J, LI N,YE L,et al.The GDP-switched GAF domain of DcpA modulates the concerted synthesis/hydrolysis of c-di-GMP in Mycobacterium smegmatis[J].Biochem J,2018,475(7):1295-1308.
[22] WILLIAMS S B,STEWART V.Functional similarities among two-component sensors and methyl-accepting chemotaxis proteins suggest a role for linker region amphipathic helices in transmembrane signal transduction[J].Molecular microbiology,2010,33(6):1093-1102.
[23] FLACK C E, PARKINSON J S.A zipped-helix cap potentiates HAMP domain control of chemoreceptor signaling[J].Proceedings of the national academy of ences of the United States of America,2018,115(15): 3519-3528.
[24] ZHULIN I B.The superfamily of chemotaxis transducers: From physiology to genomics and back[J]. Adv Microb Physiol,2001,45:157-198.
[25] KRELL T,LACAL J,MUÑOZ -MARTÍNEZ F, et al. Diversity at its best: Bacterial taxis[J]. Environ Microbiol,2011,13(5):1115-1124.
[26] ZSCHIEDRICH C P,KEIDEL V,SZURMANT H.Molecular mechanisms of two-component signal transduction[J].Journal of molecular biology,2016,428(19):3752-3775.
[27] ZHULIN I B,NIKOLSKAYA A N,GALPERIN M Y.Common extracellular sensory domains in transmembrane receptors for diverse signal transduction pathways in bacteria and archaea[J]. Journal of bacteriology,2003,185(1):285-294.
[28] BREWSTER J L,MCKELLAR J L O,FINN T J,et al. Structural basis for ligand recognition by a Cache chemosensory domain that mediates carboxylate sensing in Pseudomonas syringae[J]. Scientific reports,2016,6:35198.
[29] ANANTHARAMAN V,ARAVIND L.Cache-a signaling domain common to animal Ca²+-channel subunits and a class of prokaryotic chemotaxis receptors[J].Trends Biochem Sci,2000,25(11):535-537.
[30] UPADHYAY A A,FLEETWOOD A D,ADBALI O,et al.Cache domains that are homologous to, but different from PAS domains comprise the largest superfamily of extracellular sensors in prokaryotes[J].PLoS computational biology,2016,12(4):e1004862.
[31] CHEUNG J,HENDRICKSON W A.Sensor domains of two-component regulatory systems[J].Current opinion in microbiology,2010,13(2):116-123.
[32] YOSHITANI K,ISHII E,TANIGUCHI K,et al.Identification of an internal cavity in the PhoQ sensor domain for PhoQ activity and safa-mediated control[J].Journal of the agricultural chemical society of Japan,2019,83(4):684-694.
[33] YUAN J,JIN F,GLATTER T,et al.Osmosensing by the bacterial PhoQ/PhoP two-component system[J].Proceedings of the national academy of ences of the United States of America,2017:e10792-e10798.
[34] PAPPALARDO L,JANAUSCH I G,VIJAYAN V,et al.The NMR structure of the sensory domain of the membranous two-component fumarate sensor (Histidine protein kinase) dcus of Escherichia coli[J].Journal of biological chemistry,2003,278(40):39185-39188.
[35] KHAN M F,MACHUCA M A,RAHMAN M M,et al.Structure-activity relationship study reveals the molecular basis for specific sensing of hydrophobic amino acids by the Campylobacter jejuni chemoreceptor Tlp3[J].Biomolecules,2020,10(5):744.
[36] UD-DIN A I M S,KHAN M F,ROUJEINIKOV A A. Broad specificity of amino acid chemoreceptor CtAa of Pseudomonas fluorescens is afforded by plasticity of its amphipathic ligand-binding pocket[J].Mol Plant Microbe Interact,2020,33(4):612-623.
[37] LIU Y C,MACHUCA M A,BECKHAM S A, et al.Structural basis for amino-acid recognition and transmembrane signalling by tandem Per-Arnt-Sim (tandem PAS) chemoreceptor sensory domains[J].Acta Crystallogr D Biol Crystallogr,2015,71(Pt 10):2127-2136.
[38] RICO-JIMENEZ M,MUNOZ-MARTINEZ F,GARCIA-FONTANA C,et al.Paralogous chemoreceptors mediate chemotaxis towards protein amino acids and the non-protein amino acid gamma-aminobutyrate (GABA)[J].Mol Microbiol,2013,88(6):1230-1243.
[39] SANTOS J C,VIEIRA M L,ABENDROTH J,et al. Structural analysis of CACHE domain of the McpA chemoreceptor from Leptospira interrogans[J].Biochem Biophys Res Commun,2020,17;533(4):1323-1329.
[40] MACHUCA M A,JOHNSON K S,LIU Y C,et al. Helicobacter pylori chemoreceptor TlpC mediates chemotaxis to lactate[J].Sci Rep,2017,26;7(1):14089.
[41] BREWSTER J L, MCKELLAR J L,FINN T J, et al.Structural basis for ligand recognition by a Cache chemosensory domain that mediates carboxylate sensing in Pseudomonas syringae[J].Sci Rep, 2016,6:35198.
[42] GARCIA V,REYES-DARIAS J A,MARTIN-MORA D,et al. Identification of a Chemoreceptor for C₂ and C₃ Carboxylic Acids[J].Appl Environ Microbiol,2015,81(16):5449-5457.
[43] MARTIN-MORA D,ORTEGA Á,PEREZ-MALDONADO F J, et al. The activity of the C4-dicarboxylic acid chemoreceptor of Pseudomonas aeruginosa is controlled by chemoattractants and antagonists[J].Sci Rep,2018,8(1):2102.
[44] ANANTHARAMAN V,ARAVIND L.The CHASE domain: A predicted ligand-binding module in plant cytokinin receptors and other eukaryotic and bacterial receptors[J].Trends in biochemical sciences,2001,26(10):579-582.
[45] MOUGEL C,ZHULIN I B.CHASE: An extracellular sensing domain common to transmembrane receptors from prokaryotes, lower eukaryotes and plants[J].Trends in biochemical sciences,2001, 26(10):582-584.
[46] ZHULIN I B,NIKOLSKAYA A N,GALPERIN M Y.Common extracellular sensory domains in transmembrane receptors for diverse signal transduction pathways in bacteria and archaea[J]. Journal of bacteriology,2003,185(1):285-294.
[47] OKU S,KOMATSU A,TAJIMA T,et al.Identification of chemotaxis sensory proteins for amino acids in Pseudomonas fluorescens Pf 0-1 and their involvement in chemotaxis to tomato root exudate and root colonization[J]. Microbes Environ,2012,27(4):462-469.
[48] O'NEAL L,VO L,ALEXANDRE G. Specific root exudate compounds sensed by dedicated chemoreceptors shape Azospirillum brasilense chemotaxis in the rhizosphere[J].Appl Environ Microbiol,2020,86(15):e01026-20.
[49] HOTHORN M,DABI T,CHORY J.Structural basis for cytokinin recognition by Arabidopsis thaliana histidine kinase 4[J].Nat Chem Biol,2011,7(11):766-768.
[50] PERNISOVA M,GROCHOVA M,KONECNY T,et al.Cytokinin signalling regulates organ identity via the AHK4 receptor in Arabidopsis[J]. Development,2018,20;145(14):dev163907.
[51] CHEN P, JIAO X, ZHANG Y, et al.The crystal structure of the phytopathogenic bacterial sensor PcrK reveals different cytokinin recognition mechanism from the plant sensor AHK4[J]. J Struct Biol,2019,208(1):69-76.
[52] SHU C J,ULRICHl L E,ZHULIN I B.The NIT domain: A predicted nitrate-responsive module in bacterial sensory receptors[J]. Trends in biochemical sciences,2003,28(3):121-124.
[53] BOUDES M,LAZAR N,GRAILLE M,et al.The structure of the NasR transcription antiterminator reveals a one-component system with a NIT nitrate receptor coupled to an ANTAR RNA-binding effector[J]. Mol Microbiol,2012,85(3):431-444.
[54] GOODSON J R,ZHANG C,TRETTEL D, et al.An autoinhibitory mechanism controls RNA-binding activity of the nitrate-sensing protein NasR[J]. Mol Microbiol,2020,114(2):348-360.
[55] SHRESTHA O K,SHARMA R,TOMICZEK B,et al.Structure and evolution of the 4-helix bundle domain of Zuotin, a J-domain protein co-chaperone of Hsp70[J]. PLoS one,2019,14(5):e0217098.
[56] FALKE J, DERNBURG A F,STERNBERG D A,et al.Structure of a bacterial sensory receptor. A site-directed sulfhydryl study[J]. Journal of biological chemistry,1988,263(29):14850-14858.
[57] CHERVITZ S A, LIN C M, FALKE J J.Transmembrane signaling by the aspartate receptor: Engineered disulfides reveal static regions of the subunit interface[J]. Biochemistry,1995, 34(30):9722-9733.
[58] ULRICH L E, ZHULIN I B.Four-helix bundle: A ubiquitous sensory module in prokaryotic signal transduction[J]. Bioinformatics,2005,21(S3): 45-48.
[59] LI M,HAZELBAUER G L.Core unit of chemotaxis signaling complexes[J]. Proceedings of the national academy of sciences of the United States of America,2011,108(23):9390-9395.
[60] LIU J, HU B,MORADO D R, et al.Molecular architecture of chemoreceptor arrays revealed by cryoelectron tomography of Escherichia coli minicells[J]. Proceedings of the national academy of sciences of the United States of America,2012,109(23):8806-8807.
[61] HAZELBAUER G L,FALKE J J,PARKINSON J S.Bacterial chemoreceptors: High-performance signaling in networked arrays[J].Trends Biochem Sci,2008,33(1):9-19.
[62] HAZELBAUER G L.Bacterial chemotaxis: The early years of molecular studies[J].Annu Rev Microbiol,2012; 66:285-303.
[63] BIEMANN H P, KOSHLAND D E. Aspartate receptors of Escherichia coli and Salmonella typhimurium bind ligand with negative and half-of-the-sites cooperativity[J]. Biochemistry,1994,25; 33(3):629-634.
[64] MISE T.Structural analysis of the ligand-binding domain of the aspartate receptor tar from escherichia coli[J]. Biochemistry,2016,55(26):3708-3713.
[65] TAJIMA H,IMADA K,SAKUMA M,et al.Ligand specificity determined by differentially arranged common ligand-binding residues in bacterial amino acid chemoreceptors Tsr and Tar[J].J Biol Chem,2011,286(49):42200-42210.
[66] GAVIRA J A,MATILLA M A,FERNANDEZ M,et al.The structural basis for signal promiscuity in a bacterial chemoreceptor[J].FEBS J,2021,288(7):2294-2310.