Poussier S, Thoquet P, Trigalet-Demery D, Barthet S, Meyer D, Arlat
M, Trigalet A (2003) Host plant-dependent phenotypic reversion of
Ralstonia solanacearum from non-pathogenic to pathogenic forms
via alterations in the phcA gene. Mol Microbiol 49:991–1003
Rainey FA et al (2005) Extensive diversity of ionizing-radiation-resistant bacteria recovered from Sonoran Desert soil and description of
nine new species of the genus Deinococcus obtained from a single
soil sample. Appl Environ Microbiol 71:5225–5235
Ranjard L, Lignier L, Chaussod R (2006) Cumulative effects of shortterm polymetal contamination on soil bacterial community structure. Appl Environ Microbiol 72:1684–1687
Reeve JN, Bailey KA, Li WT, Marc F, Sandman K, Soares DJ (2004)
Archaeal histones: structures, stability and DNA binding. Biochem
Soc Trans 32:227–230
Ryjenkov DA, Tarutina M, Moskvin OV, Gomelsky M (2005) Cyclic
diguanylate is a ubiquitous signaling molecule in bacteria: insights
into biochemistry of the GGDEF protein domain. J Bacteriol
187:1792–1798
Santos CL, Tavares F, Thioulouse J, Normand P (2009) A
phylogenomic analysis of bacterial helix-turn-helix transcription
factors. FEMS Microbiol Rev 33:411–429
Schenk ST, Stein E, Kogel KH, Schikora A (2012) Arabidopsis growth
and defense are modulated by bacterial quorum sensing molecules.
Plant Sig Beh 7:178–181
Schloss PD, Handelsman J (2006) Toward a census of bacteria in soil.
PLoS Comput Biol 2:e92
Schuhegger R et al (2006) Induction of systemic resistance in tomato by
N-acyl-L-homoserine lactone-producing rhizosphere bacteria. Plant
Cell Environ 29:909–918
Schuster M, Lostroh CP, Ogi T, Greenberg EP (2003) Identification,
timing, and signal specificity of Pseudomonas aeruginosa
quorum-controlled genes: a transcriptome analysis. J Bacteriol
185:2066–2079
Sharif DI, Gallon J, Smith CJ, Dudley E (2008) Quorum sensing in
Cyanobacteria: N-octanoyl-homoserine lactone release and
response, by the epilithic colonial cyanobacterium Gloeothece
PCC6909. ISME J 2:1171–1182
Shen B (2003) Polyketide biosynthesis beyond the type I, II and III
polyketide synthase paradigms. Curr Opin Chem Biol 7:285–295
Simm R, Morr M, Kader A, Nimtz M, Romling U (2004) GGDEF and
EAL domains inversely regulate cyclic 360 di-GMP levels and
transition from sessility to motility. Mol Microbiol 53:1123–1134
Singer GA, Hickey DA (2003) Thermophilic prokaryotes have
characteristic patterns of codon usage, amino acid composition
and nucleotide content. Gene 317:39–47
Sio CF et al (2006) Quorum quenching by an N-acylhomoserine lactone
acylase from Pseudomonas aeruginosa PAO1. Infect Immun
74:1673–1682
Smith RS, Harris SG, Phipps R, Iglewski B (2002) The Pseudomonas
aeruginosa quorum-sensing molecule N-(3-oxododecanoyl)
homoserine lactone contributes to virulence and induces inflammation in vivo. J Bacteriol 184:1132–1139
Stack D, Neville C, Doyle S (2007) Nonribosomal peptide synthesis
in Aspergillus fumigatus and other fungi. Microbiology 153:1297–1306
Stock AM, Robinson VL, Goudreau PN (2000) Two-component signal
transduction. Annu Rev Biochem 69:183–215
Suar M, van der Meer JR, Lawlor K, Holliger C, Lal R (2004) Dynamics
of multiple lin gene expression in Sphingomonas paucimobilis B90A
in response to different hexachlorocyclohexane isomers. Appl Environ Microbiol 70:6650–6656
Subramoni S, Gonzalez JF, Johnson A, Pe ´chy-Tarr M, Rochat L,
Paulsen I, Loper JE, Keel C, Venturi V (2011) Bacterial subfamily
of LuxR regulators that respond to plant compounds. Appl Environ
Microbiol 77:4579–4588
Suzuki K, Babitzke P, Kushner SR, Romeo T (2006) Identification of a
novel regulatory protein (CSRD) That the targets Global Regulatory
RNAs CsrB and CSRC for degradation by RNase E. Genes Dev
20:2605–2617
Tamayo R, Pratt JT, Camilli A (2007) Roles of cyclic diguanylate
in the regulation of bacterial pathogenesis. Annu Rev Microbiol
61:131–148
Tekaia F, Yeramian E, Dujon B (2002) Amino acid composition of
genomes, lifestyles of organisms, and evolutionary trends: a global
picture with correspondence analysis. Gene 297:51–60
Teplitski M et al (2004) Chlamydomonas reinhardtii secretes
compounds that mimic bacterial signals and interfere with quorum
sensing regulation in bacteria. Plant Physiol 134:137–146
Tischler AD, Camilli A (2005) Cyclic diguanylate regulates Vibrio
cholerae virulence gene expression. Infect Immun 73:5873–5882
Torsvik V, Ovreas L, Thingstad TF (2002) Prokaryotic diversitymagnitude, dynamics, and controlling factors. Science 296:1064–1066
Turick CE, Knox AS, Leverette CL, Kritzas YG (2008) In situ uranium
stabilization by microbial metabolites. J Environ Radioactiv
99:890–899
Uroz S, Dessaux Y, Oger P (2009) Quorum sensing and quorum
quenching: the yin and yang of bacterial communication.
Chembiochem 10:205–216
van den Broek D, Chin AWTF, Bloemberg GV, Lugtenberg BJ (2005)
Molecular nature of spontaneous modifications in gacS which cause
colony phase variation in Pseudomonas sp. strain PCL1171.
J Bacteriol 187:593–600
van der Woude MW, Baumler AJ (2004) Phase and antigenic variation
in bacteria. Clin Microbiol Rev 17:581–611
van Ham SM, van Alphen L, Mooi FR, van Putten JP (1993) Phase
variation of H. influenzae fimbriae: transcriptional control of two
divergent genes through a variable combined promoter region. Cell
73:1187–1196
Van Houdt R, Aertsen A, Moons P, Vanoirbeek K, Michiels CW (2006)
N-acyl-L-homoserine lactone signal interception by Escherichia
coli. FEMS Microbiol Lett 256:83–89
van Keulen G, Hopwood DA, Dijkhuizen L, Sawers RG (2005) Gas
vesicles in actinomycetes: old buoys in novel habitats? Trends
Microbiol 13:350–354
Vial L et al (2006) Phase variation and genomic architecture changes in
Azospirillum. J Bacteriol 188:5364–5373
Vial L, Lepine F, Milot S, Groleau MC, Dekimpe V, Woods DE, Deziel
E (2008) Burkholderia pseudomallei, B. thailandensis, and
B. ambifaria produce 4-hydroxy- 2-alkylquinoline analogues with
a methyl group at the 3 position that is required for quorum-sensing
regulation. J Bacteriol 190:5339–5352
Vogel J, Bartels V, Tang TH, Churakov G, Slagter-Jager JG,
Huttenhofer A, Wagner EG (2003) RNomics in Escherichia coli
detects new sRNA species and data and identify parallel transcriptional output in bacteria. Nucleic Acids Res 31:6435–6443
von Rad U et al (2008) Response of Arabidopsis thaliana to
N-hexanoyl-DL-homoserine-lactone, a bacterial quorum sensing
molecule produced in the rhizosphere. Planta 229:73–85
Wadhams GH, Armitage JP (2004) Making sense of it all: bacterial
chemotaxis. Nat Rev Mol Cell Biol 5:1024–1037
Waite RD, Struthers JK, Dowson CG (2001) Spontaneous sequence
duplication within an open reading frame of the pneumococcal type
3 capsule locus causes high-frequency phase variation. Mol
Microbiol 42:1223–1232
Walsby AE (1978) The gas vesicles of aquatic prokaryotes. In:
Relations between structure and function in the prokaryotic cells.
Symposium of Society for General Microbiology, vol. 28.
Cambridge/New York: Published for the Society for General
Microbiology, Cambridge University Press, pp 327–358
Walsby AE (1994) Gas vesicles. Microbiol Rev 58:94–144
Wassarman KM, Repoila F, Rosenow C, Storz G, Gottesman S (2001)
Identification of novel small RNAs using comparative genomics
and microarrays. Genes Dev 15:1637–1651
350
P. Normand et al.
M, Trigalet A (2003) Host plant-dependent phenotypic reversion of
Ralstonia solanacearum from non-pathogenic to pathogenic forms
via alterations in the phcA gene. Mol Microbiol 49:991–1003
Rainey FA et al (2005) Extensive diversity of ionizing-radiation-resistant bacteria recovered from Sonoran Desert soil and description of
nine new species of the genus Deinococcus obtained from a single
soil sample. Appl Environ Microbiol 71:5225–5235
Ranjard L, Lignier L, Chaussod R (2006) Cumulative effects of shortterm polymetal contamination on soil bacterial community structure. Appl Environ Microbiol 72:1684–1687
Reeve JN, Bailey KA, Li WT, Marc F, Sandman K, Soares DJ (2004)
Archaeal histones: structures, stability and DNA binding. Biochem
Soc Trans 32:227–230
Ryjenkov DA, Tarutina M, Moskvin OV, Gomelsky M (2005) Cyclic
diguanylate is a ubiquitous signaling molecule in bacteria: insights
into biochemistry of the GGDEF protein domain. J Bacteriol
187:1792–1798
Santos CL, Tavares F, Thioulouse J, Normand P (2009) A
phylogenomic analysis of bacterial helix-turn-helix transcription
factors. FEMS Microbiol Rev 33:411–429
Schenk ST, Stein E, Kogel KH, Schikora A (2012) Arabidopsis growth
and defense are modulated by bacterial quorum sensing molecules.
Plant Sig Beh 7:178–181
Schloss PD, Handelsman J (2006) Toward a census of bacteria in soil.
PLoS Comput Biol 2:e92
Schuhegger R et al (2006) Induction of systemic resistance in tomato by
N-acyl-L-homoserine lactone-producing rhizosphere bacteria. Plant
Cell Environ 29:909–918
Schuster M, Lostroh CP, Ogi T, Greenberg EP (2003) Identification,
timing, and signal specificity of Pseudomonas aeruginosa
quorum-controlled genes: a transcriptome analysis. J Bacteriol
185:2066–2079
Sharif DI, Gallon J, Smith CJ, Dudley E (2008) Quorum sensing in
Cyanobacteria: N-octanoyl-homoserine lactone release and
response, by the epilithic colonial cyanobacterium Gloeothece
PCC6909. ISME J 2:1171–1182
Shen B (2003) Polyketide biosynthesis beyond the type I, II and III
polyketide synthase paradigms. Curr Opin Chem Biol 7:285–295
Simm R, Morr M, Kader A, Nimtz M, Romling U (2004) GGDEF and
EAL domains inversely regulate cyclic 360 di-GMP levels and
transition from sessility to motility. Mol Microbiol 53:1123–1134
Singer GA, Hickey DA (2003) Thermophilic prokaryotes have
characteristic patterns of codon usage, amino acid composition
and nucleotide content. Gene 317:39–47
Sio CF et al (2006) Quorum quenching by an N-acylhomoserine lactone
acylase from Pseudomonas aeruginosa PAO1. Infect Immun
74:1673–1682
Smith RS, Harris SG, Phipps R, Iglewski B (2002) The Pseudomonas
aeruginosa quorum-sensing molecule N-(3-oxododecanoyl)
homoserine lactone contributes to virulence and induces inflammation in vivo. J Bacteriol 184:1132–1139
Stack D, Neville C, Doyle S (2007) Nonribosomal peptide synthesis
in Aspergillus fumigatus and other fungi. Microbiology 153:1297–1306
Stock AM, Robinson VL, Goudreau PN (2000) Two-component signal
transduction. Annu Rev Biochem 69:183–215
Suar M, van der Meer JR, Lawlor K, Holliger C, Lal R (2004) Dynamics
of multiple lin gene expression in Sphingomonas paucimobilis B90A
in response to different hexachlorocyclohexane isomers. Appl Environ Microbiol 70:6650–6656
Subramoni S, Gonzalez JF, Johnson A, Pe ´chy-Tarr M, Rochat L,
Paulsen I, Loper JE, Keel C, Venturi V (2011) Bacterial subfamily
of LuxR regulators that respond to plant compounds. Appl Environ
Microbiol 77:4579–4588
Suzuki K, Babitzke P, Kushner SR, Romeo T (2006) Identification of a
novel regulatory protein (CSRD) That the targets Global Regulatory
RNAs CsrB and CSRC for degradation by RNase E. Genes Dev
20:2605–2617
Tamayo R, Pratt JT, Camilli A (2007) Roles of cyclic diguanylate
in the regulation of bacterial pathogenesis. Annu Rev Microbiol
61:131–148
Tekaia F, Yeramian E, Dujon B (2002) Amino acid composition of
genomes, lifestyles of organisms, and evolutionary trends: a global
picture with correspondence analysis. Gene 297:51–60
Teplitski M et al (2004) Chlamydomonas reinhardtii secretes
compounds that mimic bacterial signals and interfere with quorum
sensing regulation in bacteria. Plant Physiol 134:137–146
Tischler AD, Camilli A (2005) Cyclic diguanylate regulates Vibrio
cholerae virulence gene expression. Infect Immun 73:5873–5882
Torsvik V, Ovreas L, Thingstad TF (2002) Prokaryotic diversitymagnitude, dynamics, and controlling factors. Science 296:1064–1066
Turick CE, Knox AS, Leverette CL, Kritzas YG (2008) In situ uranium
stabilization by microbial metabolites. J Environ Radioactiv
99:890–899
Uroz S, Dessaux Y, Oger P (2009) Quorum sensing and quorum
quenching: the yin and yang of bacterial communication.
Chembiochem 10:205–216
van den Broek D, Chin AWTF, Bloemberg GV, Lugtenberg BJ (2005)
Molecular nature of spontaneous modifications in gacS which cause
colony phase variation in Pseudomonas sp. strain PCL1171.
J Bacteriol 187:593–600
van der Woude MW, Baumler AJ (2004) Phase and antigenic variation
in bacteria. Clin Microbiol Rev 17:581–611
van Ham SM, van Alphen L, Mooi FR, van Putten JP (1993) Phase
variation of H. influenzae fimbriae: transcriptional control of two
divergent genes through a variable combined promoter region. Cell
73:1187–1196
Van Houdt R, Aertsen A, Moons P, Vanoirbeek K, Michiels CW (2006)
N-acyl-L-homoserine lactone signal interception by Escherichia
coli. FEMS Microbiol Lett 256:83–89
van Keulen G, Hopwood DA, Dijkhuizen L, Sawers RG (2005) Gas
vesicles in actinomycetes: old buoys in novel habitats? Trends
Microbiol 13:350–354
Vial L et al (2006) Phase variation and genomic architecture changes in
Azospirillum. J Bacteriol 188:5364–5373
Vial L, Lepine F, Milot S, Groleau MC, Dekimpe V, Woods DE, Deziel
E (2008) Burkholderia pseudomallei, B. thailandensis, and
B. ambifaria produce 4-hydroxy- 2-alkylquinoline analogues with
a methyl group at the 3 position that is required for quorum-sensing
regulation. J Bacteriol 190:5339–5352
Vogel J, Bartels V, Tang TH, Churakov G, Slagter-Jager JG,
Huttenhofer A, Wagner EG (2003) RNomics in Escherichia coli
detects new sRNA species and data and identify parallel transcriptional output in bacteria. Nucleic Acids Res 31:6435–6443
von Rad U et al (2008) Response of Arabidopsis thaliana to
N-hexanoyl-DL-homoserine-lactone, a bacterial quorum sensing
molecule produced in the rhizosphere. Planta 229:73–85
Wadhams GH, Armitage JP (2004) Making sense of it all: bacterial
chemotaxis. Nat Rev Mol Cell Biol 5:1024–1037
Waite RD, Struthers JK, Dowson CG (2001) Spontaneous sequence
duplication within an open reading frame of the pneumococcal type
3 capsule locus causes high-frequency phase variation. Mol
Microbiol 42:1223–1232
Walsby AE (1978) The gas vesicles of aquatic prokaryotes. In:
Relations between structure and function in the prokaryotic cells.
Symposium of Society for General Microbiology, vol. 28.
Cambridge/New York: Published for the Society for General
Microbiology, Cambridge University Press, pp 327–358
Walsby AE (1994) Gas vesicles. Microbiol Rev 58:94–144
Wassarman KM, Repoila F, Rosenow C, Storz G, Gottesman S (2001)
Identification of novel small RNAs using comparative genomics
and microarrays. Genes Dev 15:1637–1651
350
P. Normand et al.