参考文献/References:
[1] PURCELL E B. Second messenger signaling in Clostri-dioides difficile [J].Current Opinion in Microbiology,2022,65:138-144.
[2] HENGGE R,H?USSLER S,PRUTEANU M,et al.Recent advances and current trends in nucleotide second messenger signaling in bacteria [J].Journal of Molecular Biology,2019,431(5):908-927.
[3] ROSS P,WEINHOUSE H,ALONI Y,et al.Regulation of cellulose synthesis in Acetobacter xylinum by cyclic diguanylic acid [J].Nature,1987,325(6101):279-281.
[4] JENAL U,REINDERS A,LORI C.Cyclic di-GMP:second messenger extraordinaire [J].Nature Reviews Microbiology,2017,15(5):271-284.
[5] 程寿廷,王芳芳,钱韦.鉴定cyclic di-GMP效应蛋白:高通量筛选策略与实验验证方法 [J].生物工程学报,2017,33(9):1376-1389.
[6] SESHASAYEE A S,FRASER G M,LUSCOMBE N M.Comparative genomics of cyclic-di-GMP signalling in bacteria: post-translational regulation and catalytic activity [J].Nucleic Acids Research,2010,38(18):5970-5981.
[7] DE N,PIRRUCCELLO M,KRASTEVA P V,et al.Phosphorylation-independent regulation of the diguanylate cyclase WspR [J].PLoS Biology,2008,6(3):e67.
[8] ZAHRINGER F,LACANNA E,JENAL U,et al.Structure and signaling mechanism of a zinc-sensory diguanylate cyclase [J].Structure,2013,21(7):1149-1157.
[9] 匡素芳,彭仁.赤红球菌二鸟苷酸环化酶基因的克隆、信息学分析和转录变化研究 [J].基因组学与应用生物学,2020,39(3):1128-1136.
[10] BARENDS T R,HARTMANN E,GRIESE J J,et al.Structure and mechanism of a bacterial light-regulated cyclic nucleotide phosphodiesterase [J].Nature,2009,459(7249):1015-1018.
[11] WINKLER A,UDVARHELYI A,HARTMANN E,et al.Characterization of elements involved in allosteric light regulation of phosphodiesterase activity by comparison of different functional BlrP1 states [J].Journal of Molecular Biology,2014,426(4):853-868.
[12] CHRISTEN M,CHRISTEN B,FOLCHER M,et al.Identification and characterization of a cyclic di-GMP-specific phosphodiesterase and its allosteric control by GTP [J].Journal of Biological Chemistry,2005,280(35):30829-30837.
[13] BELLINI D,CALY D L,McCARTHY Y,et al.Crystal structure of an HD-GYP domain cyclic-di-GMP phospho-diesterase reveals an enzyme with a novel trinuclear catalytic iron centre [J].Molecular Microbiology,2014,91(1):26-38.
[14] COHEN D,MECHOLD U,NEVENZAL H,et al.Oligoribonuclease is a central feature of cyclic diguanylate signaling in Pseudomonas aeruginosa [J].Proceedings of the National Academy of Sciences of the United States of America,2015,112(36):11359-11364.
[15] VALENTINI M,FILLOUX A.Biofilms and cyclic di-GMP(c-di-GMP)signaling: lessons from Pseudomonas aeruginosa and otherbacteria [J].Journal of Biological Chemi-stry,2016,291(24):12547-12555.
[16] SARENKO O,KLAUCK G,WILKE F M,et al.More than enzymes that make or break cyclic di-GMP-local signaling in the interactome of GGDEF/EAL domain proteins of Escherichia coli [J].mBio,2017,8(5):e01639-17.
[17] KUANG Sufang,YUAN Yuan,WU Zhonghao,et al.Expression, purification and characterization of diguanylate cyclase from Rhodococcus ruber [J].Protein Expression and Purification,2019,163:105441.
[18] 李新风,陈芳,肖金凤,等.环二鸟苷单磷酸核糖开关的结构与功能 [J].生物工程学报,2017,33(9):1357-1368.
[19] SUDARSAN N,LEE E R,WEINBERG Z,et al.Riboswitches in eubacteria sense the second messenger cyclic di-GMP [J].Science, 2008,321(5887):411-413.
[20] LLIBIS V,DELéPINE B,FAULON J L.Sensing new chemicals with bacterial transcription factors [J].Current Opinion in Microbiology,2016,33:105-112.
[21] CAO Jianqian,YAO Yongpeng,FAN Keqiang,et al.Harnessing a previously unidentified capability of bacterial allosteric transcription factors for sensing diverse small mo-lecules in vitro [J].Science Advances,2018,4(11):eaau4602.
[22] TSCHOWRI N,SCHUMACHER M A,SCHLIMPERT S,et al.Tetrameric c-di-GMP mediates effective transcription factor dimerization to control Streptomyces development [J].Cell,2014,158(5):1136-1147.
[23] CHEANG Q W,XIN Lingyu,CHEA R Y F,et al.Emerging paradigms for PilZ domain-mediated c-di-GMP signaling [J].Biochemical Society Transactions,2019,47(1):381-388.
[24] BAKER A E,DIEPOLD A,KUCHMA S L,et al.PilZ Domain protein FlgZ mediates cyclic di-GMP-dependent swarming motility control in Pseudomonas aeruginosa [J].Journal of Bacteriology,2016,198(13):1837-1846.
[25] ROELOFS K G,JONES C J,HELMAN S R,et al.Syste-matic identification of cyclic-di-GMP binding proteins in Vibrio cholera ereveals a novel class of cyclic-di-GMP-binding ATPases associated with type II secretion systems [J].PLoS Pathogens,2015,11(10):e1005232.
[26] LORI C,OZAKI S,STEINER S,et al.Cyclic di-GMP acts as a cell cycle oscillator to drive chromosome replication [J].Nature, 2015,523(7559):236-239.
[27] NEWELL P D,MONDS R D,O’TOOLE G A.LapD is a bis-(3’,5’)-cyclic dimeric GMP-binding protein that re-gulates surface attachment by Pseudomonas fluorescens Pf0-1 [J].Proceedings of the National Academy of Sciences of the United States of America,2009,106(9):3461-3466.
[28] YUAN Yuan,ZHANG Fan,AI Lei,et al.Insight into the role of a novel c-di-GMP effector protein in Rhodococcus ruber [J].Biochemical and Biophysical Research Communications,2022,608:177-182.
[29] LEE V T,MATEWISH J M,KESSLER J L,et al.A cyclic-di-GMP receptor required for bacterial exopolysaccharide production [J].Molecular Microbiology,2007,65:1474-1484.
[30] XU Linghui,VENKATARAMANI P,DING Yichen,et al.A cyclic di-GMP-binding adaptor protein interacts with histidine kinase to regulate twocomponent signaling[J].Journal of Biological Chemistry,2016,291:16112-16123.
[31] BEYHAN S,TISCHLER A D,CAMILLI A,et al.Transcriptome and phenotypic responses of Vibrio cholerae to increased cyclic di-GMP level [J].Journal of Bacteriology,2006,188:3600-3613.
[32] YILDIZ F H,VISICK K L.Vibrio biofilms: so much the same yet so different [J].Trends in Microbiology,2009,17:109-118.
[33] SCHUMACHER M A,ZENG Wenjie.Structures of the activator of K.pneumonia biofilm formation, MrkH, indicates PilZ domains involved in c-di-GMP and DNA bin-ding [J].Proceedings of the National Academy of Sciences of the United States of America,2016,113(36):10067-10072.
[34] DORADO-MORALES P,MARTINEZ I,RIVERO-BUCETA V,et al.Elevated c-di-GMP levels promote biofilm formation and biodesulfurization capacity of Rhodococcus erythropolis [J].Microbial Biotechnology,2021,14(3):923-937.
[35] VALENTINI M,FILLOUX A.Multiple roles of c-di-GMP signaling in bacterial pathogenesis [J].Annual Review of Microbiology, 2019,73:387-406.
[36] MCKEE R W,MANGALEA M R,PURCELL E B,et al.The second messenger cyclic Di-GMP regulates clostridium difficile toxinproduction by controlling expression of sigD [J].Journal of Bacteriology,2013,195:5174-5185.
[37] EL MEOUCHE I,PELTIER J,MONOT M,et al.Characterization of the SigD regulon of C. difficile and its positive control of toxin production through the regulation of tcdR [J].PLoS One,2013,8:e83748.
[38] WANG Zhuo,XIE Xiaorong,SHANG Daohan,et al.A c-di-GMP signaling cascade controls motility,biofilm formation,and virulence in Burkholderia thailandensis [J].Applied and Environmental Microbiology,2022,88(7):e0252921.
[39] LI Shuyu,SUN Hengxi,LI Jianghan,et al.Autoinducer-2 and bile salts induce c-di-GMP synthesis to repress the T3SS via a T3SS chaperone [J].Nature Communication,2022,13(1):6684.
[40] CROXEN M A,FINLAY B B.Molecular mechanisms of Escherichia coli pathogenicity [J].Nature Reviews Microbiology,2009,8(1):26-38.
[41] ZHANG Si,WANG Jingting,FAN Yu,et al.YciR, a specific 3’-phosphodiesterase, plays a role in the pathogenesis of uropathogenic Escherichia coli CFT073 [J].Frontiers in Microbiology,2022,13:910906.
[42] SPRECHER K S,HUG I,NESPER J,et al.Cohesive pro-perties of the Caulobacter crescentus holdfast adhesin are regulated by a novel c-di-GMP effector protein [J].mBio,2017,8(2):e00294.
[43] ABEL S,BUCHER T,NICOLLIER M,et al.Bi-modal distribution of the second messenger c-di-GMP controls cell fate and asymmetry during the caulobacter cell cycle [J].PLoS Genetics,2013,9(9):e1003744.
[44] SKOTNICKA D,STEINCHEN W,SZADKOWSKI D,et al.CdbA is a DNA-binding protein and c-di-GMP receptor important for nucleoid organization and segregation in Myxococcus xanthus [J].Nature Communication,2020,11(1):1791.
[45] MUSHNIKOV N V,FOMICHEVA A,GOMELSKY M,et al.Inducible asymmetric cell division and cell differentiation in a bacterium [J].Nature Chemical Biology,2019,15(9):925-931.
[46] HENGGE R.High-specificity local and global c-di-GMP signaling [J].Trends in Microbiology,2021,29(11):993-1003.
[47] SRIVASTAVA D,WATERS C M.A tangled web: regulatory connections between quorum sensing and cyclic Di-GMP[J].Journal of Bacteriology,2012,194(17):4485-4493.
[48] KALIA D,MEREY G,NAKAYAMA S,et al.Nucleotide,c-di-GMP,c-di-AMP,cGMP,cAMP,(p)ppGpp signaling in bacteria and implications in pathogenesis [J].Chemical Society Reviews,2013,42(1):305-341.