| [1] | Danhorn T, Fuqua C (2007) Biofilm formation by plant-associated bacteria. Annu Rev Microbiol 61: 401–422. doi: 10.1146/annurev.micro.61.080706.093316
|
| [2] | Rodríguez-Navarro DN, Dardanelli MS, Ruiz-Sainz JE (2007) Attachment of bacteria to the roots of higher plants. FEMS Microbiol Lett 272: 127–136. doi: 10.1111/j.1574-6968.2007.00761.x
|
| [3] | Yousef-Coronado F, Travieso ML, Espinosa-Urgel M (2008) Different, overlapping mechanisms for colonization of abiotic and plant surfaces by Pseudomonas putida. FEMS Microbiol Lett 288: 118–124. doi: 10.1111/j.1574-6968.2008.01339.x
|
| [4] | Ross P, Weinhouse H, Aloni Y, Michaeli D, Weinbergerohana P, et al. (1987) Regulation of Cellulose Synthesis in Acetobacter xylinum by Cyclic Diguanylic Acid. Nature 325: 279–281. doi: 10.1038/325279a0
|
| [5] | R？mling U, Galperin MY, Gomelsky M (2013) Cyclic di-GMP: the first 25 years of a universal bacterial second messenger. Microbiol Mol Biol Rev 77: 1–52. doi: 10.1128/mmbr.00043-12
|
| [6] | Galperin MY, Nikolskaya AN, Koonin EV (2001) Novel domains of the prokaryotic two-component signal transduction systems. FEMS Microbiol Lett 203: 11–21. doi: 10.1111/j.1574-6968.2001.tb10814.x
|
| [7] | Paul R, Weiser S, Amiot NC, Chan C, Schirmer T, et al. (2004) Cell cycle-dependent dynamic localization of a bacterial response regulator with a novel di-guanylate cyclase output domain. Genes Dev 18: 715–727. doi: 10.1101/gad.289504
|
| [8] | Schmidt AJ, Ryjenkov DA, Gomelsky M (2005) The ubiquitous protein domain EAL is a cyclic diguanylate-specific phosphodiesterase: enzymatically active and inactive EAL domains. J Bacteriol 187: 4774–4781. doi: 10.1128/jb.187.14.4774-4781.2005
|
| [9] | Ryan RP, Fouhy Y, Lucey JF, Dow JM (2006) Cyclic di-GMP signaling in bacteria: recent advances and new puzzles. J Bacteriol 188: 8327–8334. doi: 10.1128/jb.01079-06
|
| [10] | Boyd CD, O’Toole GA (2012) Second messenger regulation of biofilm formation: breakthroughs in understanding c-di-GMP effector systems. Annu Rev Cell Dev Biol 28: 439–462. doi: 10.1146/annurev-cellbio-101011-155705
|
| [11] | Hengge R (2009) Principles of c-di-GMP signalling in bacteria. Nat Rev Microbiol 7: 263–273. doi: 10.1038/nrmicro2109
|
| [12] | Jenal U, Malone J (2006) Mechanisms of cyclic-di-GMP signaling in bacteria. Annu Rev Genet 40: 385–407. doi: 10.1146/annurev.genet.40.110405.090423
|
| [13] | R？mling U, Amikam D (2006) Cyclic di-GMP as a second messenger. Curr Opin Microbiol 9: 218–228. doi: 10.1016/j.mib.2006.02.010
|
| [14] | Kulasakara H, Lee V, Brencic A, Liberati N, Urbach J, et al. (2006) Analysis of Pseudomonas aeruginosa diguanylate cyclases and phosphodiesterases reveals a role for bis-(3′-5′)-cyclic-GMP in virulence. Proc Natl Acad Sci U S A 103: 2839–2844. doi: 10.1073/pnas.0511090103
|
| [15] | Cotter PA, Stibitz S (2007) c-di-GMP-mediated regulation of virulence and biofilm formation. Curr Opin Microbiol 10: 17–23. doi: 10.1016/j.mib.2006.12.006
|
| [16] | Ryan RP, Fouhy Y, Lucey JF, Jiang BL, He YQ, et al. (2007) Cyclic di-GMP signalling in the virulence and environmental adaptation of Xanthomonas campestris. Mol Microbiol 63: 429–442. doi: 10.1111/j.1365-2958.2006.05531.x
|
| [17] | Tamayo R, Pratt JT, Camilli A (2007) Roles of cyclic diguanylate in the regulation of bacterial pathogenesis. Annu Rev Microbiol 61: 131–148. doi: 10.1146/annurev.micro.61.080706.093426
|
| [18] | Jimenez PN, Koch G, Thompson JA, Xavier KB, Cool RH, et al. (2012) The multiple signaling systems regulating virulence in Pseudomonas aeruginosa. Microbiol Mol Biol Rev 76: 46–65. doi: 10.1128/mmbr.05007-11
|
| [19] | Beringer JE (1974) R Factor Transfer in Rhizobium-Leguminosarum. J Gen Microbiol 84: 188–198. doi: 10.1099/00221287-84-1-188
|
| [20] | Robertsen BK, Aman P, Darvill AG, Mcneil M, Albersheim P (1981) The Structure of Acidic Extracellular Polysaccharides Secreted by Rhizobium-Leguminosarum and Rhizobium-Trifolii. Plant Physiol 67: 389–400. doi: 10.1104/pp.67.3.389
|
| [21] | Huynh TV, Dahlbeck D, Staskawicz BJ (1989) Bacterial blight of soybean: regulation of a pathogen gene determining host cultivar specificity. Science 245: 1374–1377. doi: 10.1126/science.2781284
|
| [22] | Blatny JM, Brautaset T, Winther-Larsen HC, Haugan K, Valla S (1997) Construction and use of a versatile set of broad-host-range cloning and expression vectors based on the RK2 replicon. Appl Environ Microbiol 63: 370–9. doi: 10.1006/plas.1997.1294
|
| [23] | Choi KH, Kumar A, Schweizer HP (2006) A 10-min method for preparation of highly electrocompetent Pseudomonas aeruginosa cells: application for DNA fragment transfer between chromosomes and plasmid transformation. J Microbiol Methods 64: 391–397. doi: 10.1016/j.mimet.2005.06.001
|
| [24] | Demarre G, Guerout AM, Matsumoto-Mashimo C, Rowe-Magnus DA, Marliere P, et al. (2005) A new family of mobilizable suicide plasmids based on broad host range R388 plasmid (IncW) and RP4 plasmid (IncPalpha) conjugative machineries and their cognate Escherichia coli host strains. Res Microbiol 156: 245–255. doi: 10.1016/j.resmic.2004.09.007
|
| [25] | Pérez-Mendoza D, Sepúlveda E, Pando V, Mu？oz S, Nogales J, et al. (2005) Identification of the rctA gene, which is required for repression of conjugative transfer of rhizobial symbiotic megaplasmids. J Bacteriol 187: 7341–7350. doi: 10.1128/jb.187.21.7341-7350.2005
|
| [26] | Sch？fer A, Tauch A, J？ger W, Kalinowski J, Thierbach G, et al. (1994) Small mobilizable multi-purpose cloning vectors derived from the Escherichia coli plasmids pK18 and pK19: selection of defined deletions in the chromosome of Corynebacterium glutamicum. Gene 145: 69–73. doi: 10.1016/0378-1119(94)90324-7
|
| [27] | Vargas P, Felipe A, Michan C, Gallegos MT (2011) Induction of Pseudomonas syringae pv. tomato DC3000 MexAB-OprM multidrug efflux pump by flavonoids is mediated by the repressor PmeR. Mol Plant Microbe Interact 24: 1207–1219. doi: 10.1094/mpmi-03-11-0077
|
| [28] | Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25: 402–408. doi: 10.1006/meth.2001.1262
|
| [29] | Soto MJ, Fernández-Pascual M, Sanjuan J, Olivares J (2002) A fadD mutant of Sinorhizobium meliloti shows multicellular swarming migration and is impaired in nodulation efficiency on alfalfa roots. Mol Microbiol 43: 371–82. doi: 10.1046/j.1365-2958.2002.02749.x
|
| [30] | Amikam D, Steinberger O, Shkolnik T, Ben-Ishai Z (1995) The novel cyclic dinucleotide 3′-5′ cyclic diguanylic acid binds to p21ras and enhances DNA synthesis but not cell replication in the Molt 4 cell line. Biochem J 311: 921–927.
|
| [31] | Bradford MM (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72: 248–254. doi: 10.1006/abio.1976.9999
|
| [32] | May TB, Chakrabarty AM (1994) Isolation and assay of Pseudomonas aeruginosa alginate. Methods Enzymol 235: 295–304. doi: 10.1016/0076-6879(94)35148-1
|
| [33] | Rigaud J, Puppo A (1975) Indole-3 Acetic Acid Catabolism by Soybean Bacteroids. J Gen Microbiol 88: 223–228. doi: 10.1099/00221287-88-2-223
|
| [34] | Rodríguez-Moreno L, Barcelo-Munoz A, Ramos C (2008) In vitro analysis of the interaction of Pseudomonas savastanoi pvs. savastanoi and nerii with micropropagated olive plants. Phytopathology 98: 815–822. doi: 10.1094/phyto-98-7-0815
|
| [35] | Rodríguez-Moreno L, Jimenez AJ, Ramos C (2009) Endopathogenic lifestyle of Pseudomonas savastanoi pv. savastanoi in olive knots. Microb Biotechnol 2: 476–488. doi: 10.1111/j.1751-7915.2009.00101.x
|
| [36] | Penyalver R, Garcia A, Ferrer A, Bertolini E, Quesada JM, et al. (2006) Factors affecting Pseudomonas savastanoi pv. savastanoi plant inoculations and their use for evaluation of olive cultivar susceptibility. Phytopathology 96: 313–319. doi: 10.1094/phyto-96-0313
|
| [37] | Pérez-Martínez I, Rodríguez-Moreno L, Matas IM, Ramos C (2007) Strain selection and improvement of gene transfer for genetic manipulation of Pseudomonas savastanoi isolated from olive knots. Res Microbiol 158: 60–69. doi: 10.1016/j.resmic.2006.09.008
|
| [38] | Moretti C, Ferrante P, Hosni T, Valentini F, D’Ongiha A, et al.. (2008) Characterization of Pseudomonas savastanoi pv. savastanoi strains collected from olive trees in different countries. In: Fatmi MB, Collmer A, Lacobellis N, Mansfield J, Murillo J et al.., editors. Pseudomonas syringae pathovars and related pathogens – Identification, epidemiology and genomics. Netherlands: Springer. 321–329.
|
| [39] | Hosni T, Moretti C, Devescovi G, Suarez-Moreno ZR, Fatmi MB, et al. (2011) Sharing of quorum-sensing signals and role of interspecies communities in a bacterial plant disease. ISME J 5: 1857–1870. doi: 10.1038/ismej.2011.65
|
| [40] | Aldridge P, Paul R, Goymer P, Rainey P, Jenal U (2003) Role of the GGDEF regulator PleD in polar development of Caulobacter crescentus. Mol Microbiol 47: 1695–1708. doi: 10.1046/j.1365-2958.2003.03401.x
|
| [41] | R？mling U, Gomelsky M, Galperin MY (2005) C-di-GMP: the dawning of a novel bacterial signalling system. Mol Microbiol 57: 629–639. doi: 10.1111/j.1365-2958.2005.04697.x
|
| [42] | Ryjenkov DA, Simm R, R？mling U, Gomelsky M (2006) The PilZ domain is a receptor for the second messenger c-di-GMP: the PilZ domain protein YcgR controls motility in enterobacteria. J Biol Chem 281: 30310–30314. doi: 10.1074/jbc.c600179200
|
| [43] | Amikam D, Galperin MY (2006) PilZ domain is part of the bacterial c-di-GMP binding protein. Bioinformatics 22: 3–6. doi: 10.1093/bioinformatics/bti739
|
| [44] | Simm R, Morr M, Kader A, Nimtz M, R？mling U (2004) GGDEF and EAL domains inversely regulate cyclic di-GMP levels and transition from sessility to motility. Mol Microbiol 53: 1123–1134. doi: 10.1111/j.1365-2958.2004.04206.x
|
| [45] | Joardar V, Lindeberg M, Jackson RW, Selengut J, Dodson R, et al. (2005) Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition. J Bacteriol 187: 6488–6498. doi: 10.1128/jb.187.18.6488-6498.2005
|
| [46] | Zogaj X, Bokranz W, Nimtz M, R？mling U (2003) Production of cellulose and curli fimbriae by members of the family Enterobacteriaceae isolated from the human gastrointestinal tract. Infect Immun 71: 4151–4158. doi: 10.1128/iai.71.7.4151-4158.2003
|
| [47] | Whitney JC, Howell PL (2013) Synthase-dependent exopolysaccharide secretion in Gram-negative bacteria. Trends Microbiol 21: 63–72. doi: 10.1016/j.tim.2012.10.001
|
| [48] | Ude S, Arnold DL, Moon CD, Timms-Wilson T, Spiers AJ (2006) Biofilm formation and cellulose expression among diverse environmental Pseudomonas isolates. Environ Microbiol 8: 1997–2011. doi: 10.1111/j.1462-2920.2006.01080.x
|
| [49] | Robertson M, Hapca SM, Moshynets O, Spiers AJ (2013) Air-liquid interface biofilm formation by psychrotrophic pseudomonads recovered from spoilt meat. Antonie Van Leeuwenhoek 103: 251–259. doi: 10.1007/s10482-012-9796-x
|
| [50] | Merighi M, Lee VT, Hyodo M, Hayakawa Y, Lory S (2007) The second messenger bis-(3′-5′)-cyclic-GMP and its PilZ domain-containing receptor Alg44 are required for alginate biosynthesis in Pseudomonas aeruginosa. Mol Microbiol 65: 876–895. doi: 10.1111/j.1365-2958.2007.05817.x
|
| [51] | Starkey M, Hickman JH, Ma L, Zhang N, De LS, et al. (2009) Pseudomonas aeruginosa rugose small-colony variants have adaptations that likely promote persistence in the cystic fibrosis lung. J Bacteriol 191: 3492–3503. doi: 10.1128/jb.00119-09
|
| [52] | Albareda M, Dardanelli MS, Sousa C, Megias M, Temprano F, et al. (2006) Factors affecting the attachment of rhizospheric bacteria to bean and soybean roots. FEMS Microbiol Lett 259: 67–73. doi: 10.1111/j.1574-6968.2006.00244.x
|
| [53] | Smit G, Kijne JW, Lugtenberg BJ (1987) Involvement of both cellulose fibrils and a Ca2+-dependent adhesin in the attachment of Rhizobium leguminosarum to pea root hair tips. J Bacteriol 169: 4294–4301.
|
| [54] | Williams A, Wilkinson A, Krehenbrink M, Russo DM, Zorreguieta A, et al. (2008) Glucomannan-mediated attachment of Rhizobium leguminosarum to pea root hairs is required for competitive nodule infection. J Bacteriol 190: 4706–4715. doi: 10.1128/jb.01694-07
|
| [55] | Ausmees N, Jonsson H, Hoglund S, Ljunggren H, Lindberg M (1999) Structural and putative regulatory genes involved in cellulose synthesis in Rhizobium leguminosarum bv. trifolii. Microbiology 145: 1253–1262. doi: 10.1099/13500872-145-5-1253
|
| [56] | Laus MC, van Brussel AA, Kijne JW (2005) Role of cellulose fibrils and exopolysaccharides of Rhizobium leguminosarum in attachment to and infection of Vicia sativa root hairs. Mol Plant Microbe Interact 18: 533–538. doi: 10.1094/mpmi-18-0533
|
| [57] | Fett WF, Dunn MF (1989) Exopolysaccharides produced by phytopathogenic Pseudomonas syringae pathovars in infected leaves of susceptible hosts. Plant Physiol 89: 5–9. doi: 10.1104/pp.89.1.5
|
| [58] | Yu J, Pe？aloza-Vázquez A, Chakrabarty AM, Bender CL (1999) Involvement of the exopolysaccharide alginate in the virulence and epiphytic fitness of Pseudomonas syringae pv. syringae. Mol Microbiol 33: 712–720. doi: 10.1046/j.1365-2958.1999.01516.x
|
| [59] | Matas IM, Lambertsen L, Rodriguez-Moreno L, Ramos C (2012) Identification of novel virulence genes and metabolic pathways required for full fitness of Pseudomonas savastanoi pv. savastanoi in olive (Olea europaea) knots. New Phytol 196: 1182–1196. doi: 10.1111/j.1469-8137.2012.04357.x
|
| [60] | Yi X, Yamazaki A, Biddle E, Zeng Q, Yang CH (2010) Genetic analysis of two phosphodiesterases reveals cyclic diguanylate regulation of virulence factors in Dickeya dadantii. Mol Microbiol 77: 787–800. doi: 10.1111/j.1365-2958.2010.07246.x
|
| [61] | Moscoso JA, Mikkelsen H, Heeb S, Williams P, Filloux A (2011) The Pseudomonas aeruginosa sensor RetS switches Type III and Type VI secretion via c-di-GMP signalling. Environ Microbiol 13: 3128–3138. doi: 10.1111/j.1462-2920.2011.02595.x
|
| [62] | Hickman JW, Harwood CS (2008) Identification of FleQ from Pseudomonas aeruginosa as a c-di-GMP-responsive transcription factor. Mol Microbiol 69: 376–389. doi: 10.1111/j.1365-2958.2008.06281.x
|
| [63] | Sudarsan N, Lee ER, Weinberg Z, Moy RH, Kim JN, et al. (2008) Riboswitches in eubacteria sense the second messenger cyclic di-GMP. Science 321: 411–413. doi: 10.1126/science.1159519
|
| [64] | Fang X, Gomelsky M (2010) A post-translational, c-di-GMP-dependent mechanism regulating flagellar motility. Mol Microbiol 76: 1295–1305. doi: 10.1111/j.1365-2958.2010.07179.x
|
| [65] | Navarro MV, Newell PD, Krasteva PV, Chatterjee D, Madden DR, et al. (2011) Structural basis for c-di-GMP-mediated inside-out signaling controlling periplasmic proteolysis. PLoS Biol 9: e1000588. doi: 10.1371/journal.pbio.1000588
|
| [66] | Chin KH, Lee YC, Tu ZL, Chen CH, Tseng YH, et al. (2010) The cAMP receptor-like protein CLP is a novel c-di-GMP receptor linking cell-cell signaling to virulence gene expression in Xanthomonas campestris. J Mol Biol 396: 646–662. doi: 10.1016/j.jmb.2009.11.076
|
| [67] | Pérez-Mendoza D, Coulthurst SJ, Humphris S, Campbell E, Welch M, et al. (2011) A multi-repeat adhesin of the phytopathogen, Pectobacterium atrosepticum, is secreted by a Type I pathway and is subject to complex regulation involving a non-canonical diguanylate cyclase. Mol Microbiol 82: 719–733. doi: 10.1111/j.1365-2958.2011.07849.x
|
| [68] | Pérez-Mendoza D, Coulthurst SJ, Sanjuán J, Salmond GPC (2011) N-Acetylglucosamine-dependent biofilm formation in Pectobacterium atrosepticum is cryptic and activated by elevated c-di-GMP levels. Microbiology 157: 3340–3348. doi: 10.1099/mic.0.050450-0
|
| [69] | Xu J, Kim J, Koestler BJ, Choi JH, Waters CM, et al. (2013) Genetic analysis of Agrobacterium tumefaciens unipolar polysaccharide production reveals complex integrated control of the motile-to-sessile switch. Mol Microbiol 89: 929–948. doi: 10.1111/mmi.12321
|
| [70] | Barnhart DM, Su S, Baccaro BE, Banta LM, Farrand SK (2013) CelR, an ortholog of the diguanylate cyclase PleD of Caulobacter, regulates cellulose synthesis in Agrobacterium tumefaciens. Appl Environ Microbiol 79: 7188–7202. doi: 10.1128/aem.02148-13
|
| [71] | Edmunds AC, Castiblanco LF, Sundin GW, Waters CM (2013) Cyclic Di-GMP modulates the disease progression of Erwinia amylovora. J Bacteriol 195: 2155–2165. doi: 10.1128/jb.02068-12
|
| [72] | Chatterjee S, Killiny N, Almeida RP, Lindow SE (2010) Role of cyclic di-GMP in Xylella fastidiosa biofilm formation, plant virulence, and insect transmission. Mol Plant Microbe Interact 23: 1356–1363. doi: 10.1094/mpmi-03-10-0057
|
| [73] | Matilla MA, Travieso ML, Ramos JL, Ramos-Gonzalez MI (2011) Cyclic diguanylate turnover mediated by the sole GGDEF/EAL response regulator in Pseudomonas putida: its role in the rhizosphere and an analysis of its target processes. Environ Microbiol 13: 1745–1766. doi: 10.1111/j.1462-2920.2011.02499.x
|
| [74] | Newell PD, Monds RD, O’Toole GA (2009) LapD is a bis-(3′,5′)-cyclic dimeric GMP-binding protein that regulates surface attachment by Pseudomonas fluorescens Pf0–1. Proc Natl Acad Sci U S A 106: 3461–3466. doi: 10.1073/pnas.0808933106
|
| [75] | Newell PD, Boyd CD, Sondermann H, O’Toole GA (2011) A c-di-GMP effector system controls cell adhesion by inside-out signaling and surface protein cleavage. PLoS Biol 9: e1000587. doi: 10.1371/journal.pbio.1000587
|
| [76] | Ausmees N, Mayer R, Weinhouse H, Volman G, Amikam D, et al. (2001) Genetic data indicate that proteins containing the GGDEF domain possess diguanylate cyclase activity. FEMS Microbiol Lett 204: 163–167. doi: 10.1111/j.1574-6968.2001.tb10880.x
|
| [77] | Quinto C, De La Vega H, Flores M, Leemans J, Cevallos MA, et al. (1985) Nitrogenase reductase - A functional multigene family in Rhizobium phaseoli. Proc Natl Acad Sci U S A 82: 1170–1174. doi: 10.1073/pnas.82.4.1170
|
| [78] | Leyva A, Palacios JM, Mozo T, Ruiz-Argueso T (1987) Cloning and characterization of hydrogen uptake genes from Rhizobium leguminosarum. J Bacteriol 169: 4929–4934. doi: 10.1007/978-3-642-71890-8_27
|
| [79] | Cuppels DA (1986) Generation and characterization of Tn5 insertion mutations in Pseudomonas syringae pv. tomato. Appl Environ Microbiol 51: 323–327.
|
| [80] | Taylor JD, Teverson DM, Allen DJ, Pastor-Corrales MA (1996) Identification and origin of races of Pseudomonas syringae pv. phaseolicola from Africa and other bean growing areas. Plant Pathol 45: 469–478. doi: 10.1046/j.1365-3059.1996.d01-147.x
|
| [81] | Hanahan D (1983) Studies on transformation of Escherichia coli with plasmids. J Mol Biol 166: 557–580. doi: 10.1016/s0022-2836(83)80284-8
|
| [82] | Simon R, Priefer U, Pühler A (1983) A broad host range mobilization system for in vivo genetic-engineering-transposon mutagenesis in gram-negative bacteria. Biotechnology 1: 784–791. doi: 10.1038/nbt1183-784
|
