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Morgan GL, Li K, Crawford DM, Aubé J, Li B. Enzymatic Synthesis of Diverse Heterocycles by a Noncanonical Nonribosomal Peptide Synthetase. ACS Chem Biol 2021; 16:2776-2786. [PMID: 34767712 DOI: 10.1021/acschembio.1c00623] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nonribosomal peptide synthetases (NRPSs) are typically multimodular enzymes that assemble amino acids or carboxylic acids into complex natural products. Here, we characterize a monomodular NRPS, PvfC, encoded by the Pseudomonas virulence factor (pvf) gene cluster that is essential for virulence and signaling in different bacterial species. PvfC exhibits a unique adenylation-thiolation-reductase (ATR) domain architecture that is understudied in bacteria. We show that the activity of PvfC is essential in the production of seven leucine-derived heterocyclic natural products, including two pyrazines, a pyrazinone, and a rare disubstituted imidazole, as well as three pyrazine N-oxides that require an additional N-oxygenation step. Mechanistic studies reveal that PvfC, without a canonical peptide-forming domain, makes a dipeptide aldehyde intermediate en route to both the pyrazinone and imidazole. Our work identifies a novel biosynthetic route for the production of pyrazinones, an emerging class of signaling molecules and virulence factors. Our discovery also showcases the ability of monomodular NRPSs to generate amino acid- and dipeptide-aldehydes that lead to diverse natural products. The diversity-prone biosynthesis by the pvf-encoded enzymes sets the stage for further understanding the functions of pvf in bacterial cell-to-cell signaling.
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Affiliation(s)
- Gina L. Morgan
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Kelin Li
- The Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Drake M. Crawford
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jeffrey Aubé
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- The Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Bo Li
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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Gastélum G, Rocha J. La milpa como modelo para el estudio de la microbiodiversidad e interacciones planta-bacteria. TIP REVISTA ESPECIALIZADA EN CIENCIAS QUÍMICO-BIOLÓGICAS 2020. [DOI: 10.22201/fesz.23958723e.2020.0.254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
La microbiología agrícola busca reemplazar a los agroquímicos por microorganismos o sus productos como agentes de control biológico, debido a que el uso de tecnologías de la revolución verde tiene efectos negativos sobre el ambiente, los productores y sus familias, los consumidores y la salud de los cultivos. Sin embargo, el conocimiento actual acerca de las interacciones benéficas planta-bacteria en ambientes complejos es limitado e insuficiente, para lograr el éxito esperado de los productos biológicos. Las milpas son agroecosistemas tradicionales donde se cultivan diversas variedades de maíz nativo con otras especies asociadas; no se utiliza riego, ni labranza y aunque su aplicación va en aumento, comúnmente no se utilizan agroquímicos; por esto, la milpa representa una fuente de conocimiento sobre prácticas sustentables. Recientemente, se han descrito cambios en las comunidades microbianas de los sistemas agrícolas a causa de la modernización y a la domesticación de las plantas. En la milpa, también se han identificado interacciones benéficas planta-bacteria que parecen haberse perdido en los cultivos modernos. En esta revisión, discutimos las estrategias clásicas y modernas de la microbiología agrícola que pueden ser aplicadas en el estudio de la milpa. El establecimiento de la milpa como modelo de estudio de las interacciones planta-bacteria puede resultar en la generación del conocimiento necesario para disminuir el uso de agroquímicos en los sistemas agrícolas modernos, así como evitar su creciente uso en las milpas.
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Draft Genome Sequence of Cyclic Lipopeptide Producer Pseudomonas sp. Strain SWRI103, Isolated from Wheat Rhizosphere. Microbiol Resour Announc 2020; 9:9/27/e00538-20. [PMID: 32616641 PMCID: PMC7330243 DOI: 10.1128/mra.00538-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The draft genome sequence of wheat rhizosphere isolate Pseudomonas sp. strain SWRI103 is reported. This strain carries several gene clusters encoding nonribosomal peptide synthetases (NRPSs), including a system for cyclic lipopeptide (CLP) production, and genes for carotenoid biosynthesis. The draft genome sequence of wheat rhizosphere isolate Pseudomonas sp. strain SWRI103 is reported. This strain carries several gene clusters encoding nonribosomal peptide synthetases (NRPSs), including a system for cyclic lipopeptide (CLP) production, and genes for carotenoid biosynthesis.
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Tahir M, Naeem M, Shahid M, Khalid U, Farooq A, Ahmad N, Ahmad I, Arshad M, Waqar A. Inoculation of
pqq
E gene inhabiting
Pantoea
and
Pseudomonas
strains improves the growth and grain yield of wheat with a reduced amount of chemical fertilizer. J Appl Microbiol 2020; 129:575-589. [DOI: 10.1111/jam.14630] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 01/14/2020] [Accepted: 02/28/2020] [Indexed: 02/05/2023]
Affiliation(s)
- M. Tahir
- Department of Environmental Sciences COMSATS University Islamabad Vehari Campus Pakistan
| | - M.A. Naeem
- Department of Environmental Sciences COMSATS University Islamabad Vehari Campus Pakistan
| | - M. Shahid
- Department of Bioinformatics and Biotechnology Government College University Faisalabad Pakistan
| | - U. Khalid
- Department of Agronomy Bahauddin Zakariya University Multan Punjab Pakistan
| | - A.B.U. Farooq
- Department of Environmental Sciences COMSATS University Islamabad Vehari Campus Pakistan
| | - N. Ahmad
- Department of Environmental Sciences COMSATS University Islamabad Vehari Campus Pakistan
| | - I. Ahmad
- Department of Environmental Sciences COMSATS University Islamabad Vehari Campus Pakistan
| | - M. Arshad
- Department of Biotechnology University of Okara Punjab Pakistan
| | - A. Waqar
- Department of Environmental Sciences COMSATS University Islamabad Vehari Campus Pakistan
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Naik K, Mishra S, Srichandan H, Singh PK, Sarangi PK. Plant growth promoting microbes: Potential link to sustainable agriculture and environment. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2019. [DOI: 10.1016/j.bcab.2019.101326] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Jeong JJ, Sajidah S, Oh JY, Sang MK, Kim KS, Kim KD. Complete genome sequence data of Flavobacterium anhuiense strain GSE09, a volatile-producing biocontrol bacterium isolated from cucumber ( Cucumis sativus) root. Data Brief 2019; 25:104270. [PMID: 31388522 PMCID: PMC6676235 DOI: 10.1016/j.dib.2019.104270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/09/2019] [Accepted: 07/09/2019] [Indexed: 12/16/2022] Open
Abstract
Flavobacterium anhuiense (previously identified as Flavobacterium johnsoniae) strain GSE09 is a volatile-producing bacterium that exhibits significant biocontrol activity against an oomycete pathogen, Phytophthora capsici, on pepper plants. Here, we report the complete genome sequence data of strain GSE09, isolated from surface-sterilized cucumber root. The genome consists of a circular 5,109,718-bp chromosome with a G + C content of 34.30%. A total of 4,138 complete coding sequences including 15 rRNA, 66 tRNA, 3 ncRNA, and 51 pseudogene sequences were retrieved. Thus, the genome sequence data of F. anhuiense GSE09 may facilitate the elucidation of many biological traits related to the biocontrol against plant pathogens.
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Affiliation(s)
- Jin-Ju Jeong
- Laboratory of Plant Disease and Biocontrol, Department of Biosystems and Biotechnology, Korea University, Seoul, South Korea
| | - Siti Sajidah
- Laboratory of Plant Disease and Biocontrol, Department of Biosystems and Biotechnology, Korea University, Seoul, South Korea
| | - Ji Yeon Oh
- Laboratory of Plant Disease and Biocontrol, Department of Biosystems and Biotechnology, Korea University, Seoul, South Korea
| | - Mee Kyung Sang
- Laboratory of Plant Disease and Biocontrol, Department of Biosystems and Biotechnology, Korea University, Seoul, South Korea.,Division of Agricultural Microbiology, National Academy of Agricultural Science, Rural Development Administration, Wanju, South Korea
| | - Kyoung-Su Kim
- Division of Bioresource Sciences, Bioherb Research Institute, Kangwon National University, Chuncheon, South Korea
| | - Ki Deok Kim
- Laboratory of Plant Disease and Biocontrol, Department of Biosystems and Biotechnology, Korea University, Seoul, South Korea
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Morgan GL, Kretsch AM, Santa Maria KC, Weeks SJ, Li B. Specificity of Nonribosomal Peptide Synthetases in the Biosynthesis of the Pseudomonas virulence factor. Biochemistry 2019; 58:5249-5254. [PMID: 31243997 DOI: 10.1021/acs.biochem.9b00360] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The Pseudomonas virulence factor (pvf) biosynthetic operon has been implicated in bacterial virulence and signaling. We identified 308 bacterial strains containing pvf homologues that likely produce signaling molecules with distinct structures and biological activities. Several homologues of the nonribosomal peptide synthetase (NRPS), PvfC, were biochemically characterized and shown to activate l-Val or l-Leu. The amino acid selectivity of PvfC and its homologues likely direct pvf signaling activity. We explored the natural diversity of the active site residues present in 92% of the adenylation domains of PvfC homologues and identified key residues for substrate selection and catalysis. Sequence similarity network (SSN) analysis revealed grouping of PvfC homologues that harbor the same active site residues and activate the same amino acids. Our work identified PvfC as a gatekeeper for the structure and bioactivity of the pvf-produced signaling molecules. The combination of active site residue identification and SSN analysis can improve the prediction of aliphatic amino acid substrates for NRPS adenylation domains.
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Affiliation(s)
- Gina L Morgan
- Department of Chemistry , The University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Ashley M Kretsch
- Department of Chemistry , The University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Kevin C Santa Maria
- Department of Chemistry , The University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Savannah J Weeks
- Department of Chemistry , The University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Bo Li
- Department of Chemistry , The University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
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8
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Sun W, Alexander T, Man Z, Xiao F, Cui F, Qi X. Enhancing 2-Ketogluconate Production of Pseudomonas plecoglossicida JUIM01 by Maintaining the Carbon Catabolite Repression of 2-Ketogluconate Metabolism. Molecules 2018; 23:molecules23102629. [PMID: 30322137 PMCID: PMC6222622 DOI: 10.3390/molecules23102629] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 10/09/2018] [Accepted: 10/11/2018] [Indexed: 12/22/2022] Open
Abstract
2-Ketogluconate (2KGA) is an organic acid that is important for pharmaceutical, cosmetic, and environmental applications. Pseudomonas plecoglossicida JUIM01 strain is an important industrial 2KGA producer in China. In this paper, we found that P. plecoglossicida JUIM01 could convert glucose to 2KGA extracellularly, and the formed 2KGA was subsequently consumed after glucose was exhausted during the fermentation process. Experiments of glucose and 2KGA supplementation during fermentation process revealed that, only when glucose was exhausted, the strain started to consume the product 2KGA. Then, the mechanism of this phenomenon was investigated at transcription and protein levels, and the results indicated that P. plecoglossicida JUIM01 possesses carbon catabolite repression of 2KGA metabolism by glucose. Next, increasing the supply of glucose could attenuate 2KGA consumption and enhance the 2KGA yield from glucose. Finally, fed-batch fermentation of P. plecoglossicida JUIM01 resulted in 205.67 g/L of 2KGA with a productivity of 6.86 g/L/h and yield of 0.953 g/g glucose. These results can provide references for the industrial fermentation production of 2KGA and other fermentation products.
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Affiliation(s)
- Wenjing Sun
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China.
- Parchn Sodium Isovitamin C Co. Ltd., Dexing, 334221, China.
| | - Tjahjasari Alexander
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China.
| | - Zaiwei Man
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China.
| | - Fangfang Xiao
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China.
| | - Fengjie Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China.
- Parchn Sodium Isovitamin C Co. Ltd., Dexing, 334221, China.
| | - Xianghui Qi
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China.
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Kretsch AM, Morgan GL, Tyrrell J, Mevers E, Vallet-Gély I, Li B. Discovery of (Dihydro)pyrazine N-Oxides via Genome Mining in Pseudomonas. Org Lett 2018; 20:4791-4795. [PMID: 30073838 DOI: 10.1021/acs.orglett.8b01944] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Overexpression of the Pseudomonas virulence factor ( pvf) biosynthetic operon led to the identification of a family of pyrazine N-oxides (PNOs), including a novel dihydropyrazine N,N'-dioxide (dPNO) metabolite. The nonribosomal peptide synthetase responsible for production of (d)PNOs was characterized, and a biosynthetic pathway for (d)PNOs was proposed. This work highlights the unique chemistry catalyzed by pvf-encoded enzymes and sets the stage for bioactivity studies of the metabolites produced by the virulence pathway.
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Affiliation(s)
- Ashley M Kretsch
- Department of Chemistry , The University of North Carolina at Chapel Hill , 250 Bell Tower Road , Chapel Hill , North Carolina 27599 , United States
| | - Gina L Morgan
- Department of Chemistry , The University of North Carolina at Chapel Hill , 250 Bell Tower Road , Chapel Hill , North Carolina 27599 , United States
| | - Jillian Tyrrell
- Department of Chemistry , The University of North Carolina at Chapel Hill , 250 Bell Tower Road , Chapel Hill , North Carolina 27599 , United States
| | - Emily Mevers
- Department of Biological Chemistry and Molecular Pharmacology , Harvard Medical School , 240 Longwood Avenue , Boston , Massachusetts 02115 , United States
| | - Isabelle Vallet-Gély
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS , Univ. Paris-Sud, Université Paris-Saclay , 91198 , Gif-sur-Yvette cedex , France
| | - Bo Li
- Department of Chemistry , The University of North Carolina at Chapel Hill , 250 Bell Tower Road , Chapel Hill , North Carolina 27599 , United States
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Collazo C, Abadias M, Aguiló-Aguayo I, Alegre I, Chenoll E, Viñas I. Studies on the biocontrol mechanisms of Pseudomonas graminis strain CPA-7 against food-borne pathogens in vitro and on fresh-cut melon. Lebensm Wiss Technol 2017. [DOI: 10.1016/j.lwt.2017.02.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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11
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Abstract
Pseudomonas chlororaphis strain 189 is a potent inhibitor of the growth of the potato pathogen Phytophthora infestans We determined the complete, finished sequence of the 6.8-Mbp genome of this strain, consisting of a single contiguous molecule. Strain 189 is closely related to previously sequenced strains of P. chlororaphis.
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Improved High-Quality Draft Genome Sequence of Pseudomonas fluorescens KENGFT3. GENOME ANNOUNCEMENTS 2016; 4:4/3/e00428-16. [PMID: 27231365 PMCID: PMC4882946 DOI: 10.1128/genomea.00428-16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Pseudomonas sp. strain KENGFT3 inhibits the growth of Phytophthora infestans and is a potentially useful biopesticide for plant diseases, including potato late blight. We sequenced the 6.2-Mbp genome of this strain and assembled it into a single scaffold with 9 contigs. KENGFT3 is related to previously sequenced strains of P. fluorescens.
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Zheng D, Burr TJ. Inhibition of Grape Crown Gall by Agrobacterium vitis F2/5 Requires Two Nonribosomal Peptide Synthetases and One Polyketide Synthase. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2016; 29:109-118. [PMID: 26575143 DOI: 10.1094/mpmi-07-15-0153-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Agrobacterium vitis nontumorigenic strain F2/5 is able to inhibit crown gall disease on grapevines. The mechanism of grape tumor inhibition (GTI) by F2/5 has not been fully determined. In this study, we demonstrate that two nonribosomal peptide synthetase (NRPS) genes (F-avi3342 and F-avi5730) and one polyketide synthase gene (F-avi4330) are required for GTI. Knockout of any one of them resulted in F/25 losing GTI capacity. We previously reported that F-avi3342 and F-avi4330 but not F-avi5730 are required for induction of grape tissue necrosis and tobacco hypersensitive response. F-avi5730 is predicted to encode a single modular NRPS. It is located in a cluster that is homologous to the siderophore vicibactin biosynthesis locus in Rhizobium species. Individual disruption of F-avi5730 and two immediate downstream genes, F-avi5731 and F-avi5732, all resulted in reduced siderophore production; however, only F-avi5730 was found to be required for GTI. Complemented F-avi5730 mutant (ΔF-avi5730(+)) restored a wild-type level of GTI activity. It was determined that, over time, populations of ΔF-avi4330, ΔF-avi3342, and ΔF-avi5730 at inoculated wound sites on grapevine did not differ from those of ΔF-avi5730(+) indicating that loss of GTI was not due to reduced colonization of wound sites by mutants.
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Affiliation(s)
- Desen Zheng
- Department of Plant Pathology and Plant-Microbe Biology, New York State Agricultural Experimental Station, Cornell University, 630 W. North Street Geneva, NY 14456, U.S.A
| | - Thomas J Burr
- Department of Plant Pathology and Plant-Microbe Biology, New York State Agricultural Experimental Station, Cornell University, 630 W. North Street Geneva, NY 14456, U.S.A
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Cheng X, van der Voort M, Raaijmakers JM. Gac-mediated changes in pyrroloquinoline quinone biosynthesis enhance the antimicrobial activity of Pseudomonas fluorescens SBW25. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:139-47. [PMID: 25356880 DOI: 10.1111/1758-2229.12231] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 10/08/2014] [Indexed: 05/10/2023]
Abstract
In Pseudomonas species, production of secondary metabolites and exoenzymes is regulated by the GacS/GacA two-component regulatory system. In Pseudomonas fluorescens SBW25, mutations in the Gac-system cause major transcriptional changes and abolished production of the lipopeptide viscosin and of an exoprotease. In contrast to many other Pseudomonas species and strains, inactivation of the Gac-system in strain SBW25 significantly enhanced its antimicrobial activities against oomycete, fungal and bacterial pathogens. Here, random plasposon mutagenesis of the gacS mutant led to the identification of seven mutants with reduced or loss of antimicrobial activity. In four mutants, the plasposon insertion was located in genes of the pyrroloquinoline quinone (PQQ) biosynthesis pathway. Genetic complementation, ectopic expression, activity bioassays and Reversed-phase high-performance liquid chromatography (RP-HPLC) analyses revealed that a gacS mutation in SBW25 leads to enhanced expression of pqq genes, resulting in an increase in gluconic and 2-ketogluconic acid production, which in turn acidified the extracellular medium to levels that inhibit growth of other microorganisms. We also showed that PQQ-mediated acidification comes with a growth penalty for the gacS mutant in the stationary phase. In conclusion, PQQ-mediated acidification compensates for the loss of several antimicrobial traits in P. fluorescens SBW25 and may help gac mutants to withstand competitors.
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Affiliation(s)
- Xu Cheng
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
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