The Wsp intermembrane complex mediates metabolic control of the swim-attach decision of Pseudomonas putida
Ángeles Hueso-Gil
Systems Biology Department, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, Madrid, 28049 Spain
Search for more papers by this authorCorresponding Author
Belén Calles
Systems Biology Department, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, Madrid, 28049 Spain
For correspondence. E-mail [email protected]; Tel. +34 91-585 4536; Fax +34 91-585 4506.
E-mail [email protected].
Search for more papers by this authorCorresponding Author
Víctor de Lorenzo
Systems Biology Department, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, Madrid, 28049 Spain
For correspondence. E-mail [email protected]; Tel. +34 91-585 4536; Fax +34 91-585 4506.
E-mail [email protected].
Search for more papers by this authorÁngeles Hueso-Gil
Systems Biology Department, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, Madrid, 28049 Spain
Search for more papers by this authorCorresponding Author
Belén Calles
Systems Biology Department, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, Madrid, 28049 Spain
For correspondence. E-mail [email protected]; Tel. +34 91-585 4536; Fax +34 91-585 4506.
E-mail [email protected].
Search for more papers by this authorCorresponding Author
Víctor de Lorenzo
Systems Biology Department, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, Madrid, 28049 Spain
For correspondence. E-mail [email protected]; Tel. +34 91-585 4536; Fax +34 91-585 4506.
E-mail [email protected].
Search for more papers by this authorSummary
Pseudomonas putida is a microorganism of biotechnological interest that—similar to many other environmental bacteria—adheres to surfaces and forms biofilms. Although various mechanisms contributing to the swim-attach decision have been studied in this species, the role of a 7-gene operon homologous to the wsp cluster of Pseudomonas aeruginosa—which regulates cyclic di-GMP (cdGMP) levels upon surface contact—remained to be investigated. In this work, the function of the wsp operon of P. putida KT2440 has been characterized through inspection of single and multiple wsp deletion variants, complementation with Pseudomonas aeruginosa's homologues, combined with mutations of regulatory genes fleQ and fleN and removal of the flagellar regulator fglZ. The ability of the resulting strains to form biofilms at 6 and 24 h under three different carbon regimes (citrate, glucose and fructose) revealed that the Wsp complex delivers a similar function to both Pseudomonas species. In P. putida, the key components include WspR, a protein that harbours the domain for producing cdGMP, and WspF, which controls its activity. These results not only contribute to a deeper understanding of the network that regulates the sessile-planktonic decision of P. putida but also suggest strategies to exogenously control such a lifestyle switch.
Supporting Information
Filename | Description |
---|---|
emi15126-sup-0001-supinfo.pdfPDF document, 3.9 MB | Table S1 Escherichia coli and Pseudomonas strains used in this work Table S2: Plasmids built and used in this work Table S3: Primers designed for wsp experiments Table S4: Statistical test for Cristal Violet results of wsp mutants at 6 h. Table S5: Statistical test for Cristal Violet results of wsp mutants at 24 h. Table S6: Statistical test for Cristal Violet results of wspF and wspR mutants transformed with pYljH and pYedQ respectively at 6 h. Table S7: Statistical test for Cristal Violet results of wspF and wspR mutants transformed with pYljH and pYedQ respectively at 24 h. Table S8: Statistical test for Cristal Violet results of wsp complementations with P. aeruginosa genes at 6 h. Table S9: Statistical test for Cristal Violet results of wsp complementations with P. aeruginosa genes at 24 h. Table S10: Statistical test for Cristal Violet results of wspF, flgZ, fleQ and fleN single, double and triple mutants at 6 h. Table S11: Statistical test for Cristal Violet results of wspF, flgZ, fleQ and fleN single, double and triple mutants at 24 h. Fig. S1: Colony morphology and swimming ability for P. putida wsp mutants and their complementation with orthologous genes from P. aeruginosa Fig. S2: Colony morphology and swimming ability of strains lacking transcription factors FleQ and FleN and for the regulator FlgZ, associated to wspF mutant |
Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
REFERENCES
- Amikam, D., and Galperin, M.Y. (2006) PilZ domain is part of the bacterial c-di-GMP binding protein. Bioinformatics 22: 3–6.
- Aparicio, T., de Lorenzo, V., and Martinez-Garcia, E. (2019) CRISPR/Cas9-enhanced ssDNA recombineering for Pseudomonas putida. J Microbial Biotechnol 12: 1076–1089.
- Baker, A.E., Diepold, A., Kuchma, S.L., Scott, J.E., Ha, D.G., Orazi, G., et al. (2016) PilZ domain protein FlgZ mediates cyclic Di-GMP-dependent swarming motility control in Pseudomonas aeruginosa. J Bacteriol 198: 1837–1846.
- Baraquet, C., Murakami, K., Parsek, M.R., and Harwood, C.S. (2012) The Fle Q protein from Pseudomonas aeruginosa functions as both a repressor and an activator to control gene expression from the pel operon promoter in response to c-di-GMP. Nucleic Acids Res 40: 7207–7218.
- Benedetti, I., de Lorenzo, V., and Nikel, P.I. (2016) Genetic programming of catalytic pseudomonas putida biofilms for boosting biodegradation of haloalkanes. Metab Eng 33: 109–118.
- Blanco-Romero, E., Redondo-Nieto, M., Martinez-Granero, F., Garrido-Sanz, D., Ramos-Gonzalez, M.I., Martin, M., and Rivilla, R. (2018) Genome-wide analysis of the FleQ direct regulon in Pseudomonas fluorescens F113 and pseudomonas putida KT2440. Sci Rep 8: 018–31371.
- Boehm, A., Kaiser, M., Li, H., Spangler, C., Kasper, C.A., Ackermann, M., et al. (2010) Second messenger-mediated adjustment of bacterial swimming velocity. Cell 141: 107–116.
- Chavarría, M., Kleijn, R.J., Sauer, U., Pflüger-Grau, K., de Lorenzo, V. (2012) Regulatory tasks of the phosphoenolpyruvate-phosphotransferase system of Pseudomonas putida in central carbon metabolism. mBio 3: e00028-12.
- da Costa Vasconcelos, F.N., Maciel, N.K., Favaro, D.C., de Oliveira, L.C., Barbosa, A.S., Salinas, R.K., et al. (2017) Structural and enzymatic characterization of a cAMP-dependent Diguanylate cyclase from pathogenic Leptospira species. J Mol Biol 429: 2337–2352.
- Dahlstrom, K.M., and O'Toole, G.A. (2017) A symphony of cyclases: specificity in diguanylate cyclase signaling. Annu Rev Microbiol 71: 179–195.
- Dahlstrom, K.M., Collins, A.J., Doing, G., Taroni, J.N., Gauvin, T.J., Greene, C.S., et al. (2018) A multimodal strategy used by a large c-di-GMP network. J Bacteriol 200: 00703–00717.
- Dasgupta, N., Arora, S.K., and Ramphal, R. (2000) fleN, a gene that regulates flagellar number in Pseudomonas aeruginosa. J Bacteriol 182: 357–364.
- De, N., Pirruccello, M., Krasteva, P.V., Bae, N., Raghavan, R.V., and Sondermann, H. (2008) Phosphorylation-independent regulation of the diguanylate cyclase WspR. PLoS Biol 6: 0060067.
- Gulez, G., Altıntaş, A., Fazli, M., Dechesne, A., Workman, C.T., Tolker-Nielsen, T., and Smets, B.F. (2014) Colony morphology and transcriptome profiling of pseudomonas putida KT2440 and its mutants deficient in alginate or all EPS synthesis under controlled matric potentials. Microbiology 3: 457–469.
- Guvener, Z.T., and Harwood, C.S. (2007) Subcellular location characteristics of the Pseudomonas aeruginosa GGDEF protein, WspR, indicate that it produces cyclic-di-GMP in response to growth on surfaces. Mol Microbiol 66: 1459–1473.
- Ha, D.G., and O'Toole, G.A. (2015) C-di-GMP and its effects on biofilm formation and dispersion: a Pseudomonas aeruginosa review. Microbiol Spectr 3: Mb-0003-2014.
- Hickman, J.W., Tifrea, D.F., and Harwood, C.S. (2005) A chemosensory system that regulates biofilm formation through modulation of cyclic diguanylate levels. Proc Natl Acad Sci U S A 102: 14422–14427.
- Hoiby, N., Flensborg, E.W., Beck, B., Friis, B., Jacobsen, S.V., and Jacobsen, L. (1977) Pseudomonas aeruginosa infection in cystic fibrosis. Diagnostic and prognostic significance of Pseudomonas aeruginosa precipitins determined by means of crossed immunoelectrophoresis. Scand J Respir Dis 58: 65–79.
- Huang, C.J., Wang, Z.C., Huang, H.Y., Huang, H.D., and Peng, H.L. (2013) YjcC, a c-di-GMP phosphodiesterase protein, regulates the oxidative stress response and virulence of Klebsiella pneumoniae CG43. PLoS One 8: e66740.
- Huangyutitham, V., Guvener, Z.T., and Harwood, C.S. (2013) Subcellular clustering of the phosphorylated WspR response regulator protein stimulates its diguanylate cyclase activity. MBio 4: e00242-13.
- Hueso-Gil, Á., Calles, B., O'Toole, G.A., and de Lorenzo, V. (2020) Gross transcriptomic analysis of pseudomonas putida for diagnosing environmental shifts. J Microbial Biotechnol 13: 263–273.
- Jimenez-Fernandez, A., Lopez-Sanchez, A., Jimenez-Diaz, L., Navarrete, B., Calero, P., Platero, A.I., and Govantes, F. (2016) Complex interplay between FleQ, cyclic diguanylate and multiple sigma factors coordinately regulates flagellar motility and biofilm development in Pseudomonas putida. PLoS One 11: e0163142.
- Kim, J., Kim, Y., Park, J., Anderson, A., and Kim, Y. (2014) The global regulator GacS regulates biofilm formation in Pseudomonas chlororaphis O6 differently with carbon source. Can J Microbiol 60: 133–138.
- Kivisaar, M. (2020) Narrative of a versatile and adept species pseudomonas putida. J Med Microbiol 69: 324–338.
- Liu, Y., Shi, H., Wang, Z., Huang, X., and Zhang, X. (2018) Pleiotropic control of antibiotic biosynthesis, flagellar operon expression, biofilm formation, and carbon source utilization by RpoN in pseudomonas protegens H78. Appl Microbiol Biotechnol 102: 9719–9730.
- Maniatis, F.a.S. (1982) Molecular cloning: A laboratory manual, Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
- Martinez-Garcia, E., and de Lorenzo, V. (2011) Engineering multiple genomic deletions in gram-negative bacteria: analysis of the multi-resistant antibiotic profile of pseudomonas putida KT2440. Environ Microbiol 13: 2702–2716.
- Martínez-Gil, M., Ramos-González, M.I., and Espinosa-Urgel, M. (2014) Roles of cyclic Di-GMP and the Gac system in transcriptional control of the genes coding for the pseudomonas putida adhesins LapA and LapF. J Bacteriol 196: 1484–1495.
- Martinez-Granero, F., Navazo, A., Barahona, E., Redondo-Nieto, M., Gonzalez de Heredia, E., Baena, I., et al. (2014) Identification of flgZ as a flagellar gene encoding a PilZ domain protein that regulates swimming motility and biofilm formation in pseudomonas. PLoS One 9: e87608.
- Molina-Henares, M.A., Ramos-Gonzalez, M.I., Daddaoua, A., Fernandez-Escamilla, A.M., and Espinosa-Urgel, M. (2017) FleQ of pseudomonas putida KT2440 is a multimeric cyclic diguanylate binding protein that differentially regulates expression of biofilm matrix components. Res Microbiol 168: 36–45.
- Nelson K.E., Weinel C., Paulsen I.T., Dodson R.J., Hilbert H., Martins dos Santos V.A.P., et al. (2002). Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environ Microbiol, 4, 799–808.
- Newell, P.D., Boyd, C.D., Sondermann, H., and O'Toole, G.A. (2011) A c-di-GMP effector system controls cell adhesion by inside-out signaling and surface protein cleavage. PLoS Biol 9: e1000587.
- Nie, H., Xiao, Y., Liu, H., He, J., Chen, W., and Huang, Q. (2017) FleN and FleQ play a synergistic role in regulating lapA and bcs operons in pseudomonas putida KT2440. Environ Microbiol Rep 9: 571–580.
- Nielsen, L., Li, X., and Halverson, L.J. (2011) Cell-cell and cell-surface interactions mediated by cellulose and a novel exopolysaccharide contribute to pseudomonas putida biofilm formation and fitness under water-limiting conditions. Environ Microbiol 13: 1342–1356.
- Nikel, P.I., and de Lorenzo, V. (2018) Pseudomonas putida as a functional chassis for industrial biocatalysis: from native biochemistry to trans-metabolism. Metab Eng 50: 142–155.
- Nikel, P.I., Chavarria, M., Fuhrer, T., Sauer, U., and de Lorenzo, V. (2015) Pseudomonas putida KT2440 strain metabolizes glucose through a cycle formed by enzymes of the Entner-Doudoroff, Embden-Meyerhof-Parnas, and pentose phosphate pathways. J Biol Chem 290: 25920–25932.
- Nikel, P.I., Chavarria, M., Danchin, A., and de Lorenzo, V. (2016) From dirt to industrial applications: pseudomonas putida as a synthetic biology chassis for hosting harsh biochemical reactions. Curr Opin Chem Biol 34: 20–29.
- Nilsson, M., Chiang, W.C., Fazli, M., Gjermansen, M., Givskov, M., and Tolker-Nielsen, T. (2011) Influence of putative exopolysaccharide genes on pseudomonas putida KT2440 biofilm stability. Environ Microbiol 13: 1357–1369.
- O'Connor, J.R., Kuwada, N.J., Huangyutitham, V., Wiggins, P.A., and Harwood, C.S. (2012) Surface sensing and lateral subcellular localization of WspA, the receptor in a chemosensory-like system leading to c-di-GMP production. Mol Microbiol 86: 720–729.
- O'Toole, G.A., and Kolter, R. (1998) Flagellar and twitching motility are necessary for Pseudomonas aeruginosa biofilm development. Mol Microbiol 30: 295–304.
- Pemmaraju, S.C., Pruthi, P.A., Prasad, R., and Pruthi, V. (2016) Modulation of Candida albicans biofilm by different carbon sources. Mycopathologia 181: 341–352.
- Ramos, A., Boels, I.C., de Vos, W.M., and Santos, H. (2001) Relationship between glycolysis and exopolysaccharide biosynthesis in Lactococcus lactis. Appl Environ Microbiol 67: 33–41.
- Reeves, P.R., Hobbs, M., Valvano, M.A., Skurnik, M., Whitfield, C., Coplin, D., et al. (1996) Bacterial polysaccharide synthesis and gene nomenclature. Trends Microbiol 4: 495–503.
- Romling, U., Galperin, M.Y., and Gomelsky, M. (2013) Cyclic di-GMP: the first 25 years of a universal bacterial second messenger. Microbiol Mol Biol Rev 77: 1–52.
- Ryjenkov, D.A., Simm, R., Romling, U., and 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.
- Schirmer, T. (2016) C-di-GMP synthesis: structural aspects of evolution, catalysis and regulation. J Mol Biol 428: 3683–3701.
- Silva-Rocha, R., Martinez-Garcia, E., Calles, B., Chavarria, M., Arce-Rodriguez, A., de Las Heras, A., et al. (2013) The standard European vector architecture (SEVA): a coherent platform for the analysis and deployment of complex prokaryotic phenotypes. Nucleic Acids Res 41: 23.
- Simm, R., Morr, M., Kader, A., Nimtz, M., and Romling, U. (2004) GGDEF and EAL domains inversely regulate cyclic di-GMP levels and transition from sessility to motility. Mol Microbiol 53: 1123–1134.
- Su, T., Liu, S., Wang, K., Chi, K., Zhu, D., Wei, T., et al. (2015) The REC domain mediated dimerization is critical for FleQ from Pseudomonas aeruginosa to function as a c-di-GMP receptor and flagella gene regulator. J Struct Biol 192: 1–13.
- Sutrina, S., Callender, S., Grazette, T., Scantlebury, P., O'Neal, S., Thomas, K., et al. (2019) The quantity and distribution of biofilm growth of Escherichia coli strain ATCC 9723 depends on the carbon/energy source. Microbiology 165: 47–64.
- Wadia, R. (2019) Biofilm as a risk factor in implant treatment. Br Dent J 227: 1041–1041.
- Wan, N., Wang H., Ng Chun K., Mukherjee M., Ren D., Cao B., Tang Y. J. (2018). Bacterial Metabolism During Biofilm Growth Investigated by 13C Tracing. Frontiers in Microbiology, 9, 2657. http://dx.doi.org/10.3389/fmicb.2018.02657.
- Wang, Y., Li, Y., Wang, J., and Wang, X. (2018) FleQ regulates both the type VI secretion system and flagella in pseudomonas putida. Biotechnol Appl Biochem 65: 419–427.
- Willias, S., Chauhan, S., Lo, C., Chain, P., and Motin, V. (2015) CRP-mediated carbon catabolite regulation of Yersinia pestis biofilm formation is enhanced by the carbon storage regulator protein, CsrA. PLoS One 10: e0135481.
- Xiao, Y., Nie, H., Liu, H., Luo, X., Chen, W., and Huang, Q. (2016) C-di-GMP regulates the expression of lapA and bcs operons via FleQ in Pseudomonas putida KT2440. Environ Microbiol Rep 8: 659–666.