[1] BRIDGES A A, PRENTICE J A, WINGREEN N S, et al.Signal transduction network principles underlying bacterial collective behaviors[J].Annual Review of Microbiology, 2022, 76:235-257.
[2] HENGGE R, PRUTEANU M, STÜLKE J, et al.Recent advances and perspectives in nucleotide second messenger signaling in bacteria[J].microLife, 2023, 4:uqad015.
[3] COMMICHAU F M, DICKMANNS A, GUNDLACH J, et al.A jack of all trades:The multiple roles of the unique essential second messenger cyclic di-AMP[J].Molecular Microbiology, 2015, 97(2):189-204.
[4] DA PURIFICAÇÃO A D, DE AZEVEDO N M, DE ARAUJO G G, et al.The world of cyclic dinucleotides in bacterial behavior[J].Molecules, 2020, 25(10):2462.
[5] LU Z Z, FU Y Q, ZHOU X Y, et al.Cyclic dinucleotides mediate bacterial immunity by dinucleotide cyclase in Vibrio[J].Frontiers in Microbiology, 2022, 13:1065945.
[6] LOWEY B, KRANZUSCH P J.CD-NTases and nucleotide second messenger signaling[J].Current Biology, 2020, 30(19):R1106-R1108.
[7] 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.
[8] RÖMLING U, GALPERIN M Y, GOMELSKY M.Cyclic di-GMP:The first 25 years of a universal bacterial second messenger[J].Microbiology and Molecular Biology Reviews,2013, 77(1):1-52.
[9] WITTE G, HARTUNG S, BÜTTNER K, et al.Structural biochemistry of a bacterial checkpoint protein reveals diadenylate cyclase activity regulated by DNA recombination intermediates[J].Molecular Cell, 2008, 30(2):167-178.
[10] 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.
[11] HERZBERG C, MEIßNER J, WARNEKE R, et al.The many roles of cyclic di-AMP to control the physiology of Bacillus subtilis[J].microLife, 2023, 4:uqad043.
[12] YAN H B, CHEN W X.The promise and challenges of cyclic dinucleotides as molecular adjuvants for vaccine development[J].Vaccines, 2021, 9(8):917.
[13] CANCINO-DIAZ M E, GUERRERO-BARAJAS C, BETANZOS-CABRERA G, et al.Nucleotides as bacterial second messengers[J].Molecules, 2023, 28(24):7996.
[14] SMITH K D, STROBEL S A.Interactions of the c-di-GMP riboswitch with its second messenger ligand[J].Biochemical Society Transactions, 2011, 39(2):647-651.
[15] 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.
LI X F, CHEN F, XIAO J F, et al.Structure and function of c-di-GMP riboswitches[J].Chinese Journal of Biotechnology, 2017, 33(9):1357-1368
[16] GARST A D, BATEY R T.A switch in time:Detailing the life of a riboswitch[J].Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms, 2009, 1789(9-10):584-591.
[17] SMITH K D, LIPCHOCK S V, AMES T D, et al.Structural basis of ligand binding by a c-di-GMP riboswitch[J].Nature Structural & Molecular Biology, 2009, 16(12):1218-1223.
[18] RICHARDS J, BELASCO J G.Riboswitch control of bacterial RNA stability[J].Molecular Microbiology, 2021, 116(2):361-365.
[19] LUO Y L, CHEN B, ZHOU J, et al.E88, a new cyclic-di-GMP class I riboswitch aptamer from Clostridium tetani, has a similar fold to the prototypical class I riboswitch, Vc2, but differentially binds to c-di-GMP analogs[J].Molecular BioSystems, 2014, 10(3):384-390.
[20] MCKEE R W, HARVEST C K, TAMAYO R.Cyclic diguanylate regulates virulence factor genes via multiple riboswitches in Clostridium difficile[J].mSphere, 2018, 3(5):e00423-18.
[21] HENGGE R, GRÜNDLING A, JENAL U, et al.Bacterial signal transduction by cyclic di-GMP and other nucleotide second messengers[J].Journal of Bacteriology, 2016, 198(1):15-26.
[22] XIONG Z Q, FAN Y Z, SONG X, et al.The second messenger c-di-AMP mediates bacterial exopolysaccharide biosynthesis:A review[J].Molecular Biology Reports, 2020, 47(11):9149-9157.
[23] JENAL U, REINDERS A, LORI C.Cyclic di-GMP:Second messenger extraordinaire[J].Nature Reviews Microbiology, 2017, 15(5):271-284.
[24] 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.
[25] LEE E R, BAKER J L, WEINBERG Z, et al.An allosteric self-splicing ribozyme triggered by a bacterial second messenger[J].Science, 2010, 329(5993):845-848.
[26] WEINBERG Z, NELSON J W, LÜNSE C E, et al.Bioinformatic analysis of riboswitch structures uncovers variant classes with altered ligand specificity[J].Proceedings of the National Academy of Sciences of the United States of America, 2017, 114(11):E2077-E2085
[27] MEIBOM K L, BLOKESCH M, DOLGANOV N A, et al.Chitin induces natural competence in Vibrio cholerae[J].Science, 2005, 310(5755):1824-1827.
[28] KULSHINA N, BAIRD N J, FERRÉ-D’AMARÉ A R.Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch[J].Nature Structural & Molecular Biology, 2009, 16(12):1212-1217.
[29] WOOD S, FERRÉ-D’AMARÉ A R, RUEDA D.Allosteric tertiary interactions preorganize the c-di-GMP riboswitch and accelerate ligand binding[J].ACS Chemical Biology, 2012, 7(5):920-927.
[30] SMITH K D, SHANAHAN C A, MOORE E L, et al.Structural basis of differential ligand recognition by two classes of bis-(3’-5’)-cyclic dimeric guanosine monophosphate-binding riboswitches[J].Proceedings of the National Academy of Sciences of the United States of America, 2011, 108(19):7757-7762.
[31] INUZUKA S, NISHIMURA K I, KAKIZAWA H, et al.Mutational analysis of structural elements in a class-I cyclic di-GMP riboswitch to elucidate its regulatory mechanism[J].Journal of Biochemistry, 2016, 160(3):153-162.
[32] CHEN A G Y, SUDARSAN N, BREAKER R R.Mechanism for gene control by a natural allosteric group Ⅰ ribozyme[J].RNA, 2011, 17(11):1967-1972.
[33] PURSLEY B R, MAIDEN M M, HSIEH M L, et al.Cyclic di-GMP regulates TfoY in Vibrio cholerae to control motility by both transcriptional and posttranscriptional mechanisms[J].Journal of Bacteriology, 2018, 200(7):e00578-17.
[34] LIAO H B, YAN X D, WANG C Y, et al.Cyclic di-GMP as an antitoxin regulates bacterial genome stability and antibiotic persistence in biofilms[J].eLife, 2024, 13:RP99194.
[35] HWANG Y, HARSHEY R M.A second role for the second messenger cyclic-di-GMP in E.coli:Arresting cell growth by altering metabolic flow[J].mBio, 2023, 14(2):e00619-23.
[36] BORDELEAU E, PURCELL E B, LAFONTAINE D A, et al.Cyclic di-GMP riboswitch-regulated type IV pili contribute to aggregation of Clostridium difficile[J].Journal of Bacteriology, 2015, 197(5):819-832.
[37] ANGELONI J, DONG Y Q, WANG Z N, et al.Bacterial second messenger 3′, 5′-cyclic diguanylate attracts Caenorhabditis elegans and suppresses its immunity[J].Communications Biology, 2020, 3:700.
[38] HOMMA M, KOJIMA S.Roles of the second messenger c-di-GMP in bacteria:Focusing on the topics of flagellar regulation and Vibrio spp[J].Genes to Cells, 2022, 27(3):157-172.
[39] PURCELL E B.Second messenger signaling in Clostridioides difficile[J].Current Opinion in Microbiology, 2022, 65:138-144.
[40] CAFARDI V, BIAGINI M, MARTINELLI M, et al.Identification of a novel zinc metalloprotease through a global analysis of Clostridium difficile extracellular proteins[J].PLoS One, 2013, 8(11):e81306.
[41] BARKETI-KLAI A, HOYS S, LAMBERT-BORDES S, et al.Role of fibronectin-binding protein A in Clostridium difficile intestinal colonization[J].Journal of Medical Microbiology, 2011, 60(8):1155-1161.
[42] HENSBERGEN P J, KLYCHNIKOV O I, BAKKER D, et al.Clostridium difficile secreted Pro-Pro endopeptidase PPEP-1 (ZMP1/CD2830) modulates adhesion through cleavage of the collagen binding protein CD2831[J].FEBS Letters, 2015, 589(24 PartB):3952-3958.
[43] SOUTOURINA O A, MONOT M, BOUDRY P, et al.Genome-wide identification of regulatory RNAs in the human pathogen Clostridium difficile[J].PLoS Genetics, 2013, 9(5):e1003493.
[44] PURCELL E B, TAMAYO R.Cyclic diguanylate signaling in Gram-positive bacteria[J].FEMS Microbiology Reviews, 2016, 40(5):753-773.
[45] PURCELL E B, MCKEE R W, MCBRIDE S M, et al.Cyclic diguanylate inversely regulates motility and aggregation in Clostridium difficile[J].Journal of Bacteriology, 2012, 194(13):3307-3316.
[46] SRIVASTAVA D, HSIEH M L, KHATAOKAR A, et al.Cyclic di-GMP inhibits Vibrio cholerae motility by repressing induction of transcription and inducing extracellular polysaccharide production[J].Molecular Microbiology, 2013, 90(6):1262-1276.
[47] MEEHAN R E, TORGERSON C D, GAFFNEY B L, et al.Nuclease-resistant c-di-AMP derivatives that differentially recognize RNA and protein receptors[J].Biochemistry, 2016, 55(6):837-849.
[48] CORRIGAN R M, GRÜNDLING A.Cyclic di-AMP:Another second messenger enters the fray[J].Nature Reviews Microbiology, 2013, 11(8):513-524.
[49] MUDGAL S, MANIKANDAN K, MUKHERJEE A, et al.Cyclic di-AMP:Small molecule with big roles in bacteria[J].Microbial Pathogenesis, 2021, 161:105264.
[50] HE J, YIN W, GALPERIN M Y, et al.Cyclic di-AMP, a second messenger of primary importance:Tertiary structures and binding mechanisms[J].Nucleic Acids Research, 2020, 48(6):2807-2829.
[51] BARRICK J E, CORBINO K A, WINKLER W C, et al.New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control[J].Proceedings of the National Academy of Sciences of the United States of America, 2004, 101(17):6421-6426.
[52] BLOCK K F, HAMMOND M C, BREAKER R R.Evidence for widespread gene control function by the ydaO Riboswitch candidate[J].Journal of Bacteriology, 2010, 192(15):3983-3989.
[53] NELSON J W, SUDARSAN N, FURUKAWA K, et al.Riboswitches in eubacteria sense the second messenger c-di-AMP[J].Nature Chemical Biology, 2013, 9(12):834-839.
[54] JONES C P, FERRÉ-D’AMARÉ A R.Crystal structure of a c-di-AMP riboswitch reveals an internally pseudo-dimeric RNA[J].The EMBO Journal, 2014, 33(22):2692-2703.
[55] GAO A, SERGANOV A.Structural insights into recognition of c-di-AMP by the ydaO riboswitch[J].Nature Chemical Biology, 2014, 10(9):787-792.
[56] ZARRELLA T M, BAI G C.The many roles of the bacterial second messenger cyclic di-AMP in adapting to stress cues[J].Journal of Bacteriology, 2020, 203(1):e00348-20.
[57] FAHMI T, PORT G, CHO K.C-di-AMP:An essential molecule in the signaling pathways that regulate the viability and virulence of gram-positive bacteria[J].Genes, 2017, 8(8):197.
[58] STÜLKE J, KRÜGER L.Cyclic di-AMP signaling in bacteria[J].Annual Review of Microbiology, 2020, 74:159-179.
[59] WANG X, CAI X, MA H D, et al.A c-di-AMP riboswitch controlling kdpFABC operon transcription regulates the potassium transporter system in Bacillus thuringiensis[J].Communications Biology, 2019, 2:151.
[60] DÜCHS M J, KRATZER R F, VIEYRA-GARCIA P, et al.Riboswitch-controlled IL-12 gene therapy reduces hepatocellular cancer in mice[J].Frontiers in Immunology, 2024, 15:1360063.