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Rueda-Mejia MP, Nägeli L, Lutz S, Hayes RD, Varadarajan AR, Grigoriev IV, Ahrens CH, Freimoser FM. Genome, transcriptome and secretome analyses of the antagonistic, yeast-like fungus Aureobasidium pullulans to identify potential biocontrol genes. MICROBIAL CELL 2021; 8:184-202. [PMID: 34395586 PMCID: PMC8329847 DOI: 10.15698/mic2021.08.757] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 05/21/2021] [Accepted: 05/26/2021] [Indexed: 12/27/2022]
Abstract
Aureobasidium pullulans is an extremotolerant, cosmopolitan yeast-like fungus that successfully colonises vastly different ecological niches. The species is widely used in biotechnology and successfully applied as a commercial biocontrol agent against postharvest diseases and fireblight. However, the exact mechanisms that are responsible for its antagonistic activity against diverse plant pathogens are not known at the molecular level. Thus, it is difficult to optimise and improve the biocontrol applications of this species. As a foundation for elucidating biocontrol mechanisms, we have de novo assembled a high-quality reference genome of a strongly antagonistic A. pullulans strain, performed dual RNA-seq experiments, and analysed proteins secreted during the interaction with the plant pathogen Fusarium oxysporum. Based on the genome annotation, potential biocontrol genes were predicted to encode secreted hydrolases or to be part of secondary metabolite clusters (e.g., NRPS-like, NRPS, T1PKS, terpene, and β-lactone clusters). Transcriptome and secretome analyses defined a subset of 79 A. pullulans genes (among the 10,925 annotated genes) that were transcriptionally upregulated or exclusively detected at the protein level during the competition with F. oxysporum. These potential biocontrol genes comprised predicted secreted hydrolases such as glycosylases, esterases, and proteases, as well as genes encoding enzymes, which are predicted to be involved in the synthesis of secondary metabolites. This study highlights the value of a sequential approach starting with genome mining and consecutive transcriptome and secretome analyses in order to identify a limited number of potential target genes for detailed, functional analyses.
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Affiliation(s)
- Maria Paula Rueda-Mejia
- Agroscope, Research Division Plant Protection, Müller-Thurgau-Strasse 29, 8820 Wädenswil, Switzerland
| | - Lukas Nägeli
- Agroscope, Research Division Plant Protection, Müller-Thurgau-Strasse 29, 8820 Wädenswil, Switzerland
| | - Stefanie Lutz
- Agroscope, Competence Division Method Development and Analytics, Müller-Thurgau-Strasse 29, 8820, Wädenswil, Switzerland
| | - Richard D Hayes
- U.S. Department of Energy Joint Genome Institute (JGI), Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, California 94720, USA
| | - Adithi R Varadarajan
- Agroscope, Competence Division Method Development and Analytics, Müller-Thurgau-Strasse 29, 8820, Wädenswil, Switzerland
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute (JGI), Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, California 94720, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Koshland Hall, Berkeley, CA, USA
| | - Christian H Ahrens
- Agroscope, Competence Division Method Development and Analytics, Müller-Thurgau-Strasse 29, 8820, Wädenswil, Switzerland.,SIB, Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Florian M Freimoser
- Agroscope, Research Division Plant Protection, Müller-Thurgau-Strasse 29, 8820 Wädenswil, Switzerland
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Sui Y, Wisniewski M, Droby S, Piombo E, Wu X, Yue J. Genome Sequence, Assembly, and Characterization of the Antagonistic Yeast Candida oleophila Used as a Biocontrol Agent Against Post-harvest Diseases. Front Microbiol 2020; 11:295. [PMID: 32158440 PMCID: PMC7052047 DOI: 10.3389/fmicb.2020.00295] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 02/10/2020] [Indexed: 11/29/2022] Open
Abstract
Candida oleophila is an effective biocontrol agent used to control post-harvest diseases of fruits and vegetables. C. oleophila I-182 was the active agent used in the first-generation yeast-based commercial product, Aspire®, for post-harvest disease management. Several action modes, like competition for nutrients and space, induction of pathogenesis-related genes in host tissues, and production of extracellular lytic enzymes, have been demonstrated for the biological control activity exhibited by C. oleophila through which it inhibits post-harvest pathogens. In the present study, the whole genome of C. oleophila I-182 was sequenced using PacBio and Illumina shotgun sequencing technologies, yielding an estimated genome size of 14.73 Mb. The genome size is similar in length to that of the model yeast strain Saccharomyces cerevisiae S288c. Based on the assembled genome, protein-coding sequences were identified and annotated. The predicted genes were further assigned with gene ontology terms and clustered in special functional groups. A comparative analysis of C. oleophila proteome with the proteomes of 11 representative yeasts revealed 2 unique and 124 expanded families of proteins in C. oleophila. Availability of the genome sequence will facilitate a better understanding the properties of biocontrol yeasts at the molecular level.
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Affiliation(s)
- Yuan Sui
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, College of Forestry and Life Science, Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, China
| | - Michael Wisniewski
- U.S. Department of Agriculture-Agricultural Research Service, Kearneysville, WV, United States
| | - Samir Droby
- Department of Postharvest Science, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel
| | - Edoardo Piombo
- Department of Agricultural, Forestry and Food Sciences, University of Turin, Turin, Italy
| | - Xuehong Wu
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Junyang Yue
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
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Freimoser FM, Rueda-Mejia MP, Tilocca B, Migheli Q. Biocontrol yeasts: mechanisms and applications. World J Microbiol Biotechnol 2019; 35:154. [PMID: 31576429 PMCID: PMC6773674 DOI: 10.1007/s11274-019-2728-4] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 09/17/2019] [Indexed: 01/10/2023]
Abstract
Yeasts occur in all environments and have been described as potent antagonists of various plant pathogens. Due to their antagonistic ability, undemanding cultivation requirements, and limited biosafety concerns, many of these unicellular fungi have been considered for biocontrol applications. Here, we review the fundamental research on the mechanisms (e.g., competition, enzyme secretion, toxin production, volatiles, mycoparasitism, induction of resistance) by which biocontrol yeasts exert their activity as plant protection agents. In a second part, we focus on five yeast species (Candida oleophila, Aureobasidium pullulans, Metschnikowia fructicola, Cryptococcus albidus, Saccharomyces cerevisiae) that are or have been registered for the application as biocontrol products. These examples demonstrate the potential of yeasts for commercial biocontrol usage, but this review also highlights the scarcity of fundamental studies on yeast biocontrol mechanisms and of registered yeast-based biocontrol products. Yeast biocontrol mechanisms thus represent a largely unexplored field of research and plentiful opportunities for the development of commercial, yeast-based applications for plant protection exist.
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Affiliation(s)
- Florian M Freimoser
- Agroscope, Research Division Plant Protection, Müller-Thurgau-Strasse 29, 8820, Wädenswil, Switzerland.
| | - Maria Paula Rueda-Mejia
- Agroscope, Research Division Plant Protection, Müller-Thurgau-Strasse 29, 8820, Wädenswil, Switzerland
| | - Bruno Tilocca
- Dipartimento di Agraria, Università degli Studi di Sassari, Viale Italia 39, 07100, Sassari, Italy
- Department of Health Sciences, University "Magna Græcia" of Catanzaro, Viale Europa, 88100, Catanzaro, Italy
| | - Quirico Migheli
- Dipartimento di Agraria, Università degli Studi di Sassari, Viale Italia 39, 07100, Sassari, Italy
- Istituto Nazionale di Biostrutture e Biosistemi and NRD - Nucleo di Ricerca sulla Desertificazione, Università degli Studi di Sassari, Viale Italia 39, 07100, Sassari, Italy
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Massart S, Jijakli HM. Use of molecular techniques to elucidate the mechanisms of action of fungal biocontrol agents: a review. J Microbiol Methods 2006; 69:229-41. [PMID: 17084929 DOI: 10.1016/j.mimet.2006.09.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2006] [Revised: 09/12/2006] [Accepted: 09/12/2006] [Indexed: 11/17/2022]
Abstract
Biological control of fungal plant pathogens appears as an attractive and realistic approach, and numerous microorganisms have been identified as biocontrol agents. There have been many efforts to understand the mechanisms of action of fungal biocontrol agents. Microbiological, microscopic, and biochemical techniques applied over many years have shed light on these mechanisms without fully demonstrating them. More recently, the development of molecular techniques has yielded innovative alternative tools for understanding and demonstrating the mechanisms underlying biocontrol properties. To date, more than 70 publications describe the use of molecular techniques for this purpose. They describe work exploiting targeted or non-targeted gene isolation, gene expression profiling, gene inactivation and/or overexpression, the study of regulatory factors. This work has shed considerable light on mechanisms underlying biocontrol properties. It has also fully demonstrated a number of targeted action mechanisms of some biocontrol agents. This review describes the techniques used in such studies, with their potential and limitations. It should provide a guide for researchers wanting to study the molecular basis of the biocontrol in diverse biocontrol agents.
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Affiliation(s)
- Sébastien Massart
- Plant Pathology Unit, Faculté Universitaire des Sciences Agronomiques de Gembloux, Passage des déportés, 2-5030 Gembloux, Belgium
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Xu Z, Shih MC, Poulton JE. An extracellular exo-beta-(1,3)-glucanase from Pichia pastoris: purification, characterization, molecular cloning, and functional expression. Protein Expr Purif 2005; 47:118-27. [PMID: 16427312 DOI: 10.1016/j.pep.2005.11.025] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2005] [Revised: 11/17/2005] [Accepted: 11/17/2005] [Indexed: 11/19/2022]
Abstract
An extracellular exo-beta-(1,3)-glucanase (designated EXG1) was purified to apparent homogeneity from Pichia pastoris X-33 cultures by ammonium sulfate fractionation, ion-exchange chromatography, and gel filtration. The native enzyme is unglycosylated and monomeric with a molecular mass of approximately 47kDa. At its optimal pH of 6.0, the enzyme shows highest activity among physiological substrates toward laminarin (apparent Km, 3.5 mg/ml; Vmax, 192 micromole glucose produced/min/mg protein) but also hydrolyzes amygdalin and esculin, and the chromogenic substrates p-nitrophenyl-beta-D-glucopyranoside and p-nitrophenyl-beta-D-xylopyranoside. The P. pastoris EXG1 gene was cloned by a PCR-based strategy using genomic DNA as template. This intronless gene predicts an ORF that encodes a primary translation product of 414 amino acids. We believe that this preproprotein is processed sequentially by signal peptidase and a Kex2-like endoprotease to yield a mature protein of 392 amino acids (45,376 Da; pI, 4.46) that shares 36-64% amino acid identity with other yeast exo-beta-(1,3)-glucanases belonging to Glycoside Hydrolase Family 5. It also possesses the eight invariant residues and signature pattern [LIV]-[LIVMFYWGA](2)-[DNEQG]-[LIVMGST]-X-N-E-[PV]-[RHDNSTLIVFY] shown by all Family 5 members. Overexpression of the cloned EXG1 gene in Pichia cells, followed by Ni-CAM HC resin chromatography, yielded milligram quantities of homogeneous recombinant EXG1 in active form for further characterization studies.
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Affiliation(s)
- Zhiwei Xu
- Department of Biological Sciences, University of Iowa, Iowa City, IA 52242, USA
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Bar-Shimon M, Yehuda H, Cohen L, Weiss B, Kobeshnikov A, Daus A, Goldway M, Wisniewski M, Droby S. Characterization of extracellular lytic enzymes produced by the yeast biocontrol agent Candida oleophila. Curr Genet 2004; 45:140-8. [PMID: 14716497 DOI: 10.1007/s00294-003-0471-7] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2003] [Revised: 11/04/2003] [Accepted: 11/06/2003] [Indexed: 10/26/2022]
Abstract
The yeast Candida oleophila, the base of the commercial product Aspire, is recommended for the control of postharvest decay of citrus and pome fruit. Competition for nutrients and space is believed to be the major mode of action. Involvement of fungal cell wall-degrading enzymes is also suggested to play a role in the mechanism of action of yeast antagonists. The present study showed that the yeast C. oleophila is capable of producing and secreting various cell wall-degrading enzymes, including exo-beta-1,3-glucanase, chitinase and protease. Exo-beta-1,3-glucanase and chitinase were produced and maximized in the early stages of growth, whereas protease reached a maximum level only after 6-8 days. Production of exo-beta-1,3-glucanase, chitinase and protease was stimulated by the presence of cell wall fragments of Penicillium digitatum in the growth medium, in addition to glucose. This study also provided evidence that C. oleophila is capable of secreting exo-beta-1,3-glucanase into the wounded surface of grapefruit. The role of exo-beta-1,3-glucanase ( CoEXG1) in the biocontrol activity of C. oleophila was tested using CoEXG1-knockouts and double- CoEXG1 over-producing transformants. In vitro bioassays showed that wild-type C. oleophila and exo-beta-1,3-glucanase over-expressing transformants had similar inhibitory effects on spore germination and germ-tube elongation; and both were more inhibitory to the fungus than the knockout transformant. In experiments conducted on fruit to test the biocontrol activity against infection by P. digitatum, no significant difference in inhibition was observed between transformants and untransformed C. oleophila cells at the high concentrations of cells used, whereas at a lower concentration of yeast cells the knockout transformants appeared to be less effective.
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Affiliation(s)
- Meirav Bar-Shimon
- Department of Postharvest Science, A.R.O., The Volcani Center, P.O. Box 6, 50250, Bet Dagan, Israel
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Yehuda H, Droby S, Bar-Shimon M, Wisniewski M, Goldway M. The effect of under- and overexpressed CoEXG1-encoded exoglucanase secreted by Candida oleophila on the biocontrol of Penicillium digitatum. Yeast 2003; 20:771-80. [PMID: 12845603 DOI: 10.1002/yea.1006] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The yeast, Candida oleophila, is acknowledged for its biocontrol activity against postharvest moulds. However, the mechanism of this activity is not fully understood. One of the conjectured modes of action is associated with extracellular lytic enzymes, such as beta-exoglucanase. The relationship of beta-exoglucanase in the biocontrol activity of C. oleophila was investigated by generating C. oleophila CoEXG1-knockouts and double-CoEXG1 transformants. The knockout transformants secreted 0-13% of the exoglucanase activity detected in the medium of the untransformed yeast (depending on the medium), indicating that CoEXG1 is the main gene responsible for the production of the secreted exoglucanase. Correspondingly, the double-CoEXG1 transformants secreted approximately twice as much 1,3-beta-exoglucanase as the untransformed C. oleophila. The biocontrol activity of the CoEXG1-knockout and the double-CoEXG1 transformants against Penicillium digitatum did not differ from that of the untransformed C. oleophila on kumquats. These results imply that the 1,3-beta-exoglucanase encoded by the gene CoEXG1 is not involved in the biocontrol activity of C. oleophila against P. digitatum under these experimental terms. However, these findings do not rule out the possibilities, that the participation of CoEXG1 in biocontrol is dependent on the activity of other gene products, or that its effect may be manifested under altered environmental conditions.
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Affiliation(s)
- Hila Yehuda
- Department of Molecular Genetics, MIGAL Galilee Technology Center, PO Box 831, Kiryat-Shmona 11016, Israel
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Current Awareness on Yeast. Yeast 2003. [DOI: 10.1002/yea.940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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