Abstract
The antibiotic pyrrolnitrin (PRN) is a tryptophan-derived secondary metabolite that plays an important role in the biocontrol of plant diseases due to its broad-spectrum of antimicrobial activities. The PRN biosynthetic gene cluster remains to be characterised in Serratia plymuthica, though it is highly conserved in PRN-producing bacteria. To better understand PRN biosynthesis and its regulation in Serratia, the prnABCD operon from S. plymuthica G3 was cloned, sequenced and expressed in Escherichia coli DH5α. Furthermore, an engineered strain prnind which is a conditional mutant of G3 prnABCD under the control of the Ptac promoter was constructed. This mutant was able to overproduce PRN with isopropylthiogalactoside (IPTG) induction by overexpressing prnABCD, whilst behaving as a conditional mutant of G3 prnABCD in the absence of IPTG. These results confirmed that prnABCD is responsible for PRN biosynthesis in strain G3. Further experiments involving lux-/dsRed-based promoter fusions, combined with site-directed mutagenesis of the putative σS extended -10 region in the prnA promoter, and liquid chromatography-mass spectrometry (LC-MS) analysis extended our previous knowledge about G3, revealing that quorum sensing (QS) regulates PRN biosynthesis through cross talk with RpoS, which may directly activated prnABCD transcription. These findings suggest that PRN in S. plymuthica G3 is produced in a tightly controlled manner, and has diverse functions, such as modulation of cell motility, in addition to antimicrobial activities. Meanwhile, the construction of inducible mutants could be a powerful tool to improve PRN production, beyond its potential use for the investigation of the biological function of PRN.
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References
Arima K, Imanaka H, Kousaka M, Fukuta A, Tamura G (1964) Pyrrolnitrin, a new antibiotic substance, produced by Pseudomonas. Agric Biol Chem 28(8):575–576
Atkinson S, Chang CY, Patrick HL, Buckley CM, Wang Y, Sockett RE, Cámara M, Williams P (2008) Functional interplay between the Yersinia pseudotuberculosis YpsRI and YtbRI quorum sensing systems modulates swimming motility by controlling expression of flhDC and fliA. Mol Microbiol 69:137–151
Ausubel FM, BrentR KRE, Moore DD, Seidman JG, Smith JA, Struhl K (1994) Current protocols in molecular biology. John Wiley & Sons Inc., NY
Becker G, Hengge-Aronis R (2001) What makes an Escherichia coli promoter sigma(S) dependent? Role of the -13/-14 nucleotide promoter positions and region 2.5 of sigma (S). Mol Microbiol 39(5):1153–1165
Chernin L, Brandis A, Ismailov Z, Chet I (1996) Pyrrolnitrin production by an Enterobacter agglomerans strain with a broad spectrum of antagonistic activity towards fungal and bacterial phytopathogens. Curr Microbiol 32:208–212
Chet I, Chernin L (2002) Biocontrol, microbiol agents in soil. In: Bitton G (ed) Encyclopedia of environmental microbiology. Join Willey & Sons Inc., New York, pp 450–465
Combes-Meynet E, Pothier JF, Moënne-Loccoz Y, Prigent-Combaret C (2011) The Pseudomonas secondary metabolite 2,4-diacetylphloroglucinol is a signal inducing rhizoplane expression of Azospirillum genes involved in plant-growth promotion. Mol Plant-Microbe Interact 24(2):271–284
Costa R, van Aarle IM, Mendes R, van Elsas JD (2009) Genomics of pyrrolnitrin biosynthetic loci: evidence for conservation and whole-operon mobility within gram-negative bacteria. Environ Microbiol 211:159–175
Dennis JJ, Zylstra GJ (1998) Plasposons: modular self-cloning minitransposon derivatives for rapid genetic analysis of gram-negative bacterial genomes. Appl Environ Microbiol 64:2710–2715
de Vleeschauwer D, Höfte M (2007) Using Serratia plymuthica to control fungal pathogens of plant. CAB Rev 2:046
Di Santo R, Costi R, Artico M, Massa S, Lampis G, Deidda D, Pompei R (1998) Pyrrolnitrin and related pyrroles endowed with antibacterial activities against Mycobacterium tuberculosis. Bioorg Med Chem Lett 8(20):2931–2936
Dietrich LE, Price-Whelan A, Petersen A, Whiteley M, Newman DK (2006) The phenazine pyocyanin is a terminal signalling factor in the quorum sensing network of Pseudomonas aeruginosa. Mol Microbiol 61(5):1308–1321
Hammer PE, Hill DS, Lam ST, Van Pée KH, Ligon JM (1997) Four genes from Pseudomonas fluorescens that encode the biosynthesis of pyrrolnitrin. Appl Environ Microbiol 63:2147–2154
Hammer PE, Burd W, Hill DS, Ligon JM, van Pée KH (1999) Conservation of the pyrrolnitrin biosynthetic gene cluster among six pyrrolnitrin-producing strains. FEMS Microbiol Lett 180:39–44
Haas D, Blumer C, Keel C (2000) Biocontrol ability of fluorescent pseudomonads genetically dissected: importance of positive feedback regulation. Curr Opin Biotechnol 11(3):290–297
Heeb S, Blume C, Haas D (2002) Regulatory RNA as mediator in GacA/RsmA-dependent global control of exoproduct formation in Pseudomonas fluorescens CHA0. J Bacteriol 184:1046–1056
Hill DS, Stein JI, Torkewitz NR, Morse AM, Howell CR, Pachlatko JP, Becker JO, Ligon JM (1994) Cloning of genes involved in the synthesis of pyrrolnitrin from Pseudomonas fluorescens and role of pyrrolnitrin synthesis in biological control of plant disease. Appl Environ Microbiol 60:78–85
Hwang J, Chilton WS, Benson DM (2002) Pyrrolnitrin production by Burkholderia cepacia and biocontrol of Rhizoctonia stem rot of poinsettia. Biol Control 25:56–63
Kalbe C, Marten P, Berg G (1996) Strains of the genus Serratia as beneficial rhizobacteria of oilseed rape. Microbiol Res 151:4400–4433
Kamensky M, Ovadis M, Chet I, Chernin L (2003) Soil-borne strain IC14 of Serratia plymuthica with multiple mechanisms of antifungal activity provides biocontrol of Botrytis cinerea and Sclerotinia sclerotiomm diseases. Soil Biol Biochem 35:323–331
Keum YS, Lee YJ, Lee YH, Kim JH (2009) Effects of nutrients on quorum signals and secondary metabolite productions of Burkholderia sp. O33. J Microbiol Biotechnol 19:1142–1149
Kim CH, Kim YH, Anderson AJ, Kim YC (2014) Proteomic analysis of a global regulator GacS sensor kinase in the Rhizobacterium, Pseudomonas chlororaphis O6. Plant Pathol J 30(2):220–227
Kirner S, Hammer PE, Hill DS, Altmann A, Fischer I, Weislo LJ, Lanahan M, van Pée KH, Ligon JM (1998) Functions encoded by pyrrolnitrin biosynthetic genes from Pseudomonas fluorescens. J Bacteriol 180:1939–43
Ligon JM, Hill DS, Hammer PE, Torkewitz NR, Hofmann D, Kempf H, van Pée KH (2000) Natural products with antifungal activity from Pseudomonas biocontrol bacteria. Pest Manag Sci 56(8):688–695
Liu X, Bimerew M, Ma YX, Müller H, Ovadis M, Eberl L, Berg G, Chernin L (2007) Quorum-sensing signaling is required for production of the antibiotic pyrrolnitrin in a rhizospheric biocontrol strain of Serratia plymuthica. FEMS Microbiol Lett 270:299–305
Liu X, Jia J, Atkinson S, Cámara M, Gao K, Li H, Cao J (2010) Biocontrol potential of an endophytic Serratia sp. G3 and its mode of action. World J Microbiol Biotechnol 26:465–471
Liu X, Jia J, Popat R, Ortori CA, Li J, Diggle SP, Gao K, Cámara M (2011) Characterisation of two quorum sensing systems in the endophytic Serratia plymuthica strain G3: differential control of motility and biofilm formation according to life-style. BMC Microbiol 11:26
Liu X, Wu Y, Chen Y, Xu F, Halliday N, Gao K, Chan KG, Cámara M (2016) RpoS differentially affects the general stress response and biofilm formation in the endophytic Serratia plymuthica G3. Res Microbiol 167(3):168–177
Maurhofer M, Baehler E, Notz R, Martinez V, Keel C (2004) Cross talk between 2,4-diacetylphloroglucinol-producing biocontrol pseudomonads on wheat roots. Appl Environ Microbiol 70(4):1990–1998
Milton DL, O’Toole R, Horstedt P, Wolf-Watz H (1996) Flagellin A is essential for the virulence of Vibrio anguillarum. J Bacteriol 178:1310–1319
Mozes-Koch R, Gover O, Tanne E, Peretz Y, Maori E, Chernin L, Sela I (2012) Expression of an entire bacterial operon in plants. Plant Physiol 158(4):1883–1892
Münch R, Hiller K, Grote A, Scheer M, Klein J, Schobert M, Jahn D (2005) Virtual footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes. Bioinformatics 21:4187–4189
Nandi M, Selin C, Brassinga AK, Belmonte MF, Fernando WG, Loewen PC, de Kievit TR (2015) Pyrrolnitrin and hydrogen cyanide production by Pseudomonas chlororaphis strain PA23 exhibits nematicidal and repellent activity against Caenorhabditis elegans. PLoS One 10(4):e0123184
Ovadis M, Liu X, Gavriel S, Ismailov Z, Chet I, Chernin L (2004) The global regulator genes from biocontrol strain Serratia plymuthica IC1270: cloning, sequencing, and functional studies. J Bacteriol 186:4986–4993
Park JY, Oh SA, Anderson AJ, Neiswender J, Kim JC, Kim YC (2011) Production of the antifungal compounds phenazine and pyrrolnitrin from Pseudomonas chlororaphis O6 is differentially regulated by glucose. Lett Appl Microbiol 52:532–537
Pierson LS 3rd, Pierson EA (2010) Metabolism and function of phenazines in bacteria: impacts on the behavior of bacteria in the environment and biotechnological processes. Appl Microbiol Biotechnol 86(6):1659–1670
Rampioni G, Pustelny C, Fletcher MP, Wright VJ, Bruce M, Rumbaugh KP, Heeb S, Cámara M, Williams P (2010) Transcriptomic analysis reveals a global alkyl-quinolone-independent regulatory role for PqsE in facilitating the environmental adaptation of Pseudomonas aeruginosa to plant and animal hosts. Environ Microbiol 12(6):1659–1673
Rutherford ST, Bassler BL (2012) Bacterial quorum sensing: its role in virulence and possibilities for its control. Cold Spring Harb Perspect Med 2(11):a012427
Sarniguet A, Kraus J, Henkels MD, Muehlchen AM, Loper JE (1995) The sigma factor sigma s affects antibiotic production and biological control activity of Pseudomonas fluorescens Pf-5. Proc Natl Acad Sci U S A 92(26):12255–12259
Schmidt S, Blom JF, Pernthaler J, Berg G, Baldwin A, Mahenthiralingam E, Eberl L (2009) Production of the antifungal compound pyrrolnitrin is quorum sensing-regulated in members of the Burkholderia cepacia complex. Environ Microbiol 11:1422–1437
Schnider U, Keel C, Blumer C, Troxler J, Défago G, Haas D (1995) Amplification of the housekeeping sigma factor in Pseudomonas fluorescens CHA0 enhances antibiotic production and improves biocontrol abilities. J Bacteriol 177(18):5387–5392
Umarov RK, Solovyev VV (2017) Prediction of prokaryotic and eukaryotic promoters using convolutional deep learning neural networks. PLoS One 12(2):e0171410
Venturi V (2006) Regulation of quorum sensing in Pseudomonas. FEMS Microbiol Rev 30(2):274–291
Weber H, Polen T, Heuveling J, Wendisch VF, Hengge R (2005) Genome-wide analysis of the general stress response network in Escherichia coli: σS-dependent genes, promoters, and sigma factor selectivity. J Bacteriol 187(5):1591–1603
West SE, Schweizer HP, Dall C, Sample AK, Runyen-Janecky LJ (1994) Construction of improved Escherichia–Pseudomonas shuttle vectors derived from pUC18/19 and sequence of the region required for their replication in Pseudomonas aeruginosa. Gene 148:81–86
Zhou M, Gao K, Zeng J, Yu X, Wu Y, Ge J, Duan Y, Liu X (2012) Role of the RNA-binding protein Hfq in Serratia plymuthica. Front Biosci E4:1263–1275
Acknowledgements
We would like to thank N. Halliday for kind assistance with LC-MS analysis.
Funding
The study was funded partially by the National Natural Science Foundation of China (grant no. 31240046), EU Marie Curie IIF project PROAGROBAC (grant no. 297882) and the Special Fund for Agro-Scientific Research in the Public Interest of China (grant no. 201503110-12).
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Liu, X., Yu, X., Yang, Y. et al. Functional identification of the prnABCD operon and its regulation in Serratia plymuthica. Appl Microbiol Biotechnol 102, 3711–3721 (2018). https://doi.org/10.1007/s00253-018-8857-0
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DOI: https://doi.org/10.1007/s00253-018-8857-0