1
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Vincent CV, Bignell DRD. Regulation of virulence mechanisms in plant-pathogenic Streptomyces. Can J Microbiol 2024; 70:199-212. [PMID: 38190652 DOI: 10.1139/cjm-2023-0171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Streptomyces have a uniquely complex developmental life cycle that involves the coordination of morphological differentiation with the production of numerous bioactive specialized metabolites. The majority of Streptomyces spp. are soil-dwelling saprophytes, while plant pathogenicity is a rare attribute among members of this genus. Phytopathogenic Streptomyces are responsible for economically important diseases such as common scab, which affects potato and other root crops. Following the acquisition of genes encoding virulence factors, Streptomyces pathogens are expected to have specifically adapted their regulatory pathways to enable transition from a primarily saprophytic to a pathogenic lifestyle. Investigations of the regulation of pathogenesis have primarily focused on Streptomyces scabiei and the principal pathogenicity determinant thaxtomin A. The coordination of growth and thaxtomin A production in this species is controlled in a hierarchical manner by cluster-situated regulators, pleiotropic regulators, signalling and plant-derived molecules, and nutrients. Although the majority of phytopathogenic Streptomyces produce thaxtomins, many also produce additional virulence factors, and there are scab-causing pathogens that do not produce thaxtomins. The development of effective control strategies for common scab and other Streptomyces plant diseases requires a more in-depth understanding of the genetic and environmental factors that modulate the plant pathogenic lifestyle of these organisms.
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Affiliation(s)
- Corrie V Vincent
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Dawn R D Bignell
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
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2
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Soares NR, Huguet-Tapia JC, Guan D, Clark CA, Yang KT, Kluchka OR, Thombal RS, Kartika R, Badger JH, Pettis GS. Comparative genomics of the niche-specific plant pathogen Streptomyces ipomoeae reveal novel genome content and organization. Appl Environ Microbiol 2023; 89:e0030823. [PMID: 38009923 PMCID: PMC10734452 DOI: 10.1128/aem.00308-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 09/28/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE While most plant-pathogenic Streptomyces species cause scab disease on a variety of plant hosts, Streptomyces ipomoeae is the sole causative agent of soil rot disease of sweet potato and closely related plant species. Here, genome sequencing of virulent and avirulent S. ipomoeae strains coupled with comparative genomic analyses has identified genome content and organization features unique to this streptomycete plant pathogen. The results here will enable future research into the mechanisms used by S. ipomoeae to cause disease and to persist in its niche environment.
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Affiliation(s)
- Natasha R. Soares
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | | | - Dongli Guan
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Christopher A. Clark
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - Kuei-Ting Yang
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Olivia R. Kluchka
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Raju S. Thombal
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Rendy Kartika
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Jonathan H. Badger
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Gregg S. Pettis
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
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3
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Kerff F, Jourdan S, Francis IM, Deflandre B, Ribeiro Monteiro S, Stulanovic N, Loria R, Rigali S. Common scab disease: structural basis of elicitor recognition in pathogenic Streptomyces species. Microbiol Spectr 2023; 11:e0197523. [PMID: 37791952 PMCID: PMC10714786 DOI: 10.1128/spectrum.01975-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 08/21/2023] [Indexed: 10/05/2023] Open
Abstract
IMPORTANCE Common scab is a disease caused by a few Streptomyces species that affects important root and tuber crops including potato, beet, radish, and parsnip, resulting in major economic losses worldwide. In this work, we unveiled the molecular basis of host recognition by these pathogens by solving the structure of the sugar-binding protein CebE of Streptomyces scabiei in complex with cellotriose, the main elicitor of the pathogenic lifestyle of these bacteria. We further revealed that the signaling pathway from CebE-mediated transport of cellotriose is conserved in all pathogenic species except Streptomyces ipomoeae, which causes soft rot disease in sweet potatoes. Our work also provides the structural basis of the uptake of cellobiose and cellotriose in saprophytic Streptomyces species, the first step activating the expression of the enzymatic system degrading the most abundant polysaccharide on earth, cellulose.
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Affiliation(s)
- Frédéric Kerff
- InBioS–Center for Protein Engineering, Institut de Chimie B6a, University of Liège, Liège, Belgium
| | - Samuel Jourdan
- InBioS–Center for Protein Engineering, Institut de Chimie B6a, University of Liège, Liège, Belgium
| | - Isolde M. Francis
- Department of Biology, California State University, Bakersfield, California, USA
| | - Benoit Deflandre
- InBioS–Center for Protein Engineering, Institut de Chimie B6a, University of Liège, Liège, Belgium
| | - Silvia Ribeiro Monteiro
- InBioS–Center for Protein Engineering, Institut de Chimie B6a, University of Liège, Liège, Belgium
| | - Nudzejma Stulanovic
- InBioS–Center for Protein Engineering, Institut de Chimie B6a, University of Liège, Liège, Belgium
| | - Rosemary Loria
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Sébastien Rigali
- InBioS–Center for Protein Engineering, Institut de Chimie B6a, University of Liège, Liège, Belgium
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4
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Haq IU, Mukhtar Z, Anwar-Ul-Haq M, Liaqat S. Deciphering host-pathogen interaction during Streptomyces spp. infestation of potato. Arch Microbiol 2023; 205:222. [PMID: 37149838 DOI: 10.1007/s00203-023-03560-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 04/16/2023] [Accepted: 04/18/2023] [Indexed: 05/08/2023]
Abstract
Potato crop, currently, is the staple food crop of about 1.3 billion global population. Potato is attaining even more admiration globally day by day owing to its public acceptability. However, potato sustainable production is distinctly challenged by multiple factors like diseases, pests and climate change etc. Among diseases, common scab is one of the prime threats to potato crop due to its soil-borne nature and versatility in phytotoxins' secretion. Common scab is caused multiple number of phytopathogenic streptomyces strains. Despite extensive research programs, researchers are still unable to identify a significant solution to this threat that is proliferating exceptional rate across the globe. To develop feasible remedies, adequate information regarding host-pathogen interaction should be available. This review possesses insights on existing pathogenic species, the evolution of novel pathogenic streptomyces spp. and phytotoxins produced by the pathogenic strains. Furthermore, which type of physiological, biochemical and genetic activities occur during pathogen's infestation of the host are also canvassed.
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Affiliation(s)
- Ihtisham Ul Haq
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan.
- Ayub Agricultural Research Institute, Faisalabad, Pakistan.
| | - Zahid Mukhtar
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | | | - Sana Liaqat
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
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5
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Role of Alternative Elicitor Transporters in the Onset of Plant Host Colonization by Streptomyces scabiei 87-22. BIOLOGY 2023; 12:biology12020234. [PMID: 36829511 PMCID: PMC9953190 DOI: 10.3390/biology12020234] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/26/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023]
Abstract
Plant colonization by Streptomyces scabiei, the main cause of common scab disease on root and tuber crops, is triggered by cello-oligosaccharides, cellotriose being the most efficient elicitor. The import of cello-oligosaccharides via the ATP-binding cassette (ABC) transporter CebEFG-MsiK induces the production of thaxtomin phytotoxins, the central virulence determinants of this species, as well as many other metabolites that compose the 'virulome' of S. scabiei. Homology searches revealed paralogues of the CebEFG proteins, encoded by the cebEFG2 cluster, while another ABC-type transporter, PitEFG, is encoded on the pathogenicity island (PAI). We investigated the gene expression of these candidate alternative elicitor importers in S. scabiei 87-22 upon cello-oligosaccharide supply by transcriptomic analysis, which revealed that cebEFG2 expression is highly activated by both cellobiose and cellotriose, while pitEFG expression was barely induced. Accordingly, deletion of pitE had no impact on virulence and thaxtomin production under the conditions tested, while the deletion of cebEFG2 reduced virulence and thaxtomin production, though not as strong as the mutants of the main cello-oligosaccharide transporter cebEFG1. Our results thus suggest that both ceb clusters participate, at different levels, in importing the virulence elicitors, while PitEFG plays no role in this process under the conditions tested. Interestingly, under more complex culture conditions, the addition of cellobiose restored thaxtomin production when both ceb clusters were disabled, suggesting the existence of an additional mechanism that is involved in sensing or importing the elicitor of the onset of the pathogenic lifestyle of S. scabiei.
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Liu J, Wang Y, He H, Dong S, Tang L, Yang E, Wang W, Zhang B. The leucine-responsive regulatory protein SCAB_Lrp modulates thaxtomin biosynthesis, pathogenicity, and morphological development in Streptomyces scabies. MOLECULAR PLANT PATHOLOGY 2023; 24:167-178. [PMID: 36478143 PMCID: PMC9831280 DOI: 10.1111/mpp.13285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 11/16/2022] [Accepted: 11/20/2022] [Indexed: 06/17/2023]
Abstract
Streptomyces scabies is the best-characterized plant-pathogenic streptomycete, which is a special species among the large genus Streptomyces. The pathogenicity of S. scabies relies on the production of the secondary metabolite thaxtomin A. Little is known about the molecular mechanisms underlying the regulation of thaxtomin biosynthesis in S. scabies beyond the pathway-specific activator TxtR and the cellulose utilization repressor CebR. The leucine-responsive regulatory protein (Lrp) family modulates secondary metabolism in nonpathogenic streptomycetes. However, the regulatory relationship between the Lrp and pathogenic streptomycetes remains unknown. In this study, we demonstrated that SCAB_Lrp (SCAB_77931) from S. scabies significantly affects thaxtomin biosynthesis, pathogenicity, and morphological development. SCAB_Lrp deletion resulted in a dramatic decline in thaxtomin A production and a low-virulence phenotype of S. scabies. An in-depth dissection of the regulatory mechanism of SCAB_Lrp revealed that it positively regulates the transcription of the thaxtomin biosynthetic gene cluster by directly binding to the promoter of the cluster-situated regulator gene txtR. SCAB_Lrp also controls the morphological development of S. scabies by directly activating the transcription of amfC, whiB, and ssgB. SCAB_Lrp directly controls the transcription of its own gene by binding a specific sequence (5'-GGACAGTCGCCGTGCTACG-3'). Moreover, phenylalanine and methionine have been characterized as SCAB_Lrp effectors by strengthening the binding affinity and complex status between SCAB_Lrp and DNA. Our findings characterize a multifunctional regulatory protein, SCAB_Lrp, that controls secondary metabolism, pathogenicity, and sporulation in S. scabies and provide new insights into the complex regulatory network that modulates thaxtomin phytotoxins in pathogenic Streptomyces.
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Affiliation(s)
- Jing Liu
- School of Life SciencesAnhui Agricultural UniversityHefeiChina
| | - Yunxia Wang
- School of Life SciencesAnhui Agricultural UniversityHefeiChina
| | - Haoyang He
- School of Life SciencesAnhui Agricultural UniversityHefeiChina
| | - Shengnan Dong
- School of Life SciencesAnhui Agricultural UniversityHefeiChina
| | - Lijuan Tang
- Institute of Physical Science and Information Technology, School of Life SciencesAnhui UniversityHefeiChina
| | - Endong Yang
- School of Life SciencesAnhui Agricultural UniversityHefeiChina
| | - Weiyun Wang
- School of Life SciencesAnhui Agricultural UniversityHefeiChina
| | - Buchang Zhang
- Institute of Physical Science and Information Technology, School of Life SciencesAnhui UniversityHefeiChina
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7
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Isayenka I, Beaudoin N. The Streptomyces scabiei Pathogenicity Factor Thaxtomin A Induces the Production of Phenolic Compounds in Potato Tubers. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11233216. [PMID: 36501257 PMCID: PMC9737112 DOI: 10.3390/plants11233216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/15/2022] [Accepted: 11/23/2022] [Indexed: 05/27/2023]
Abstract
The phytotoxin thaxtomin A (TA) is the key pathogenicity factor synthesized by the bacteria Streptomyces scabiei, the main causal agent of common scab of potato (Solanum tuberosum L.). TA treatment of potato tuber flesh produces a brown color that was attributed to necrosis. The intensity of TA-induced browning was generally thought to correlate with potato sensitivity to the disease. In this study, we found that TA-induced browning was much more intense in the potato tuber flesh of the common scab moderately resistant variety Russet Burbank (RB) than that observed in tubers of the disease-susceptible variety Yukon Gold (YG). However, there was no significant difference in the level of TA-induced cell death detected in both varieties, suggesting that tubers response to TA does not correlate with the level of sensitivity to common scab. TA-treated potato tuber tissues accumulated significantly higher levels of phenolic compounds than untreated controls, with a higher phenol content detected in RB TA-treated tissues than in those of YG. Browning was associated with a significant induction of the expression of genes of the phenylpropanoid pathway in RB tubers, indicating that TA activated this metabolic pathway. These results suggest that tuber flesh browning induced by TA is due to the accumulation of phenolic compounds. These phenolics may play a role in the protection of potato tubers against S. scabiei.
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8
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Clarke CR, Kramer CG, Kotha RR, Luthria DL. The Phytotoxin Thaxtomin A Is the Primary Virulence Determinant for Scab Disease of Beet, Carrot, and Radish Caused by Streptomyces scabiei. PHYTOPATHOLOGY 2022; 112:2288-2295. [PMID: 35694886 DOI: 10.1094/phyto-03-22-0072-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Several species of Streptomyces cause common scab, a major disease of potato, primarily through the phytotoxic effects of the phytotoxin thaxtomin A. Several phytopathogenic Streptomyces species have also been implicated as the causative agents of scab diseases of taproot crops including beet, carrot, radish, parsnip, and turnip. But the molecular mechanisms employed by Streptomyces to infect these crops is unknown. In this work, we tested the hypothesis that thaxtomin A biosynthesis is also necessary for Streptomyces-caused scab of beet, carrot, radish, and turnip. Thaxtomin A induced plant stunting and cell death of all four of these species. Streptomyces mutants in which the transcriptional regulator of thaxtomin A biosynthesis is disrupted were nonvirulent on all four crops, and complementation of the transcriptional regulator rescued thaxtomin A biosynthesis and plant pathogenicity to wild-type levels. These results demonstrate that thaxtomin A is the primary virulence determinant of scab disease of these other crops.
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Affiliation(s)
- Christopher R Clarke
- Genetic Improvement for Fruits and Vegetables Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD
| | - Charles G Kramer
- Genetic Improvement for Fruits and Vegetables Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD
| | - Raghavendhar R Kotha
- Food Composition and Methods Development Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD
| | - Devanand L Luthria
- Food Composition and Methods Development Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD
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9
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Lee HY, Yoon CK, Cho YJ, Lee JW, Lee KA, Lee WJ, Seok YJ. A mannose-sensing AraC-type transcriptional activator regulates cell-cell aggregation of Vibrio cholerae. NPJ Biofilms Microbiomes 2022; 8:65. [PMID: 35987769 PMCID: PMC9392796 DOI: 10.1038/s41522-022-00331-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 08/03/2022] [Indexed: 11/18/2022] Open
Abstract
In addition to catalyzing coupled transport and phosphorylation of carbohydrates, the phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) regulates various physiological processes in most bacteria. Therefore, the transcription of genes encoding the PTS is precisely regulated by transcriptional regulators depending on substrate availability. As the distribution of the mannose-specific PTS (PTSMan) is limited to animal-associated bacteria, it has been suggested to play an important role in host-bacteria interactions. In Vibrio cholerae, mannose is known to inhibit biofilm formation. During host infection, the transcription level of the V. cholerae gene encoding the putative PTSMan (hereafter referred to as manP) significantly increases, and mutations in this gene increase host survival rate. Herein, we show that an AraC-type transcriptional regulator (hereafter referred to as ManR) acts as a transcriptional activator of the mannose operon and is responsible for V. cholerae growth and biofilm inhibition on a mannose or fructose-supplemented medium. ManR activates mannose operon transcription by facilitating RNA polymerase binding to the promoter in response to mannose 6-phosphate and, to a lesser extent, to fructose 1-phosphate. When manP or manR is impaired, the mannose-induced inhibition of biofilm formation was reversed and intestinal colonization was significantly reduced in a Drosophila melanogaster infection model. Our results show that ManR recognizes mannose and fructose in the environment and facilitates V. cholerae survival in the host.
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Affiliation(s)
- Hye-Young Lee
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Chang-Kyu Yoon
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Yong-Joon Cho
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jin-Woo Lee
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kyung-Ah Lee
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Won-Jae Lee
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Yeong-Jae Seok
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul, 08826, Republic of Korea.
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, Republic of Korea.
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10
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Zhao X, Zong Y, Wei W, Lou C. Multiplexed Promoter Engineering for Improving Thaxtomin A Production in Heterologous Streptomyces Hosts. Life (Basel) 2022; 12:689. [PMID: 35629358 PMCID: PMC9146380 DOI: 10.3390/life12050689] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/27/2022] [Accepted: 04/30/2022] [Indexed: 11/17/2022] Open
Abstract
Thaxtomin A is a potent bioherbicide in both organic and conventional agriculture; however, its low yield hinders its wide application. Here, we report the direct cloning and heterologous expression of the thaxtomin A gene cluster in three well-characterized Streptomyces hosts. Then, we present an efficient, markerless and multiplex large gene cluster editing method based on in vitro CRISPR/Cas9 digestion and yeast homologous recombination. With this method, we successfully engineered the thaxtomin A cluster by simultaneously replacing the native promoters of the txtED operon, txtABH operon and txtC gene with strong constitutive promoters, and the yield of thaxtomin A improved to 289.5 µg/mL in heterologous Streptomyces coelicolor M1154. To further optimize the biosynthetic pathway, we used constraint-based combinatorial design to build 27 refactored gene clusters by varying the promoter strength of every operon, and the highest titer of thaxtomin A production reached 504.6 μg/mL. Taken altogether, this work puts forward a multiplexed promoter engineering strategy to engineer secondary metabolism gene clusters for efficiently improving fermentation titers.
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Affiliation(s)
- Xuejin Zhao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (X.Z.); (Y.Z.); (W.W.)
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yeqing Zong
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (X.Z.); (Y.Z.); (W.W.)
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100149, China
| | - Weijia Wei
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (X.Z.); (Y.Z.); (W.W.)
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100149, China
| | - Chunbo Lou
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100149, China
- Center for Cell and Gene Circuit Design, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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11
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Nigericin and Geldanamycin Are Phytotoxic Specialized Metabolites Produced by the Plant Pathogen
Streptomyces
sp. 11-1-2. Microbiol Spectr 2022; 10:e0231421. [PMID: 35225656 PMCID: PMC9045263 DOI: 10.1128/spectrum.02314-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Plant pathogens use a variety of mechanisms, including the production of phytotoxic specialized metabolites, to establish an infection of host tissue. Although thaxtomin A is considered the key phytotoxin involved in the development of potato scab disease, there is increasing evidence that other phytotoxins can play a role in disease development in some instances.
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12
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Deflandre B, Stulanovic N, Planckaert S, Anderssen S, Bonometti B, Karim L, Coppieters W, Devreese B, Rigali S. The virulome of Streptomyces scabiei in response to cello-oligosaccharide elicitors. Microb Genom 2022; 8. [PMID: 35040428 PMCID: PMC8914351 DOI: 10.1099/mgen.0.000760] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The development of spots or lesions symptomatic of common scab on root and tuber crops is caused by few pathogenic Streptomyces with Streptomyces scabiei 87–22 as the model species. Thaxtomin phytotoxins are the primary virulence determinants, mainly acting by impairing cellulose synthesis, and their production in S. scabiei is in turn boosted by cello-oligosaccharides released from host plants. In this work we aimed to determine which molecules and which biosynthetic gene clusters (BGCs) of the specialized metabolism of S. scabiei 87–22 show a production and/or a transcriptional response to cello-oligosaccharides. Comparative metabolomic analyses revealed that molecules of the virulome of S. scabiei induced by cellobiose and cellotriose include (i) thaxtomin and concanamycin phytotoxins, (ii) desferrioxamines, scabichelin and turgichelin siderophores in order to acquire iron essential for housekeeping functions, (iii) ectoine for protection against osmotic shock once inside the host, and (iv) bottromycin and concanamycin antimicrobials possibly to prevent other microorganisms from colonizing the same niche. Importantly, both cello-oligosaccharides reduced the production of the spore germination inhibitors germicidins thereby giving the ‘green light’ to escape dormancy and trigger the onset of the pathogenic lifestyle. For most metabolites - either with induced or reduced production - cellotriose was revealed to be a slightly stronger elicitor compared to cellobiose, supporting an earlier hypothesis which suggested the trisaccharide was the real trigger for virulence released from the plant cell wall through the action of thaxtomins. Interestingly, except for thaxtomins, none of these BGCs’ expression seems to be under direct control of the cellulose utilization repressor CebR suggesting the existence of a yet unknown mechanism for switching on the virulome. Finally, a transcriptomic analysis revealed nine additional cryptic BGCs that have their expression awakened by cello-oligosaccharides, suggesting that other and yet to be discovered metabolites could be part of the virulome of S. scabiei.
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Affiliation(s)
- Benoit Deflandre
- InBioS-Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, B-4000, Liège, Belgium
| | - Nudzejma Stulanovic
- InBioS-Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, B-4000, Liège, Belgium
| | - Sören Planckaert
- Laboratory for Microbiology, Department of Biochemistry and Microbiology, Ghent University, B-9000, Ghent, Belgium
| | - Sinaeda Anderssen
- InBioS-Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, B-4000, Liège, Belgium
| | - Beatrice Bonometti
- InBioS-Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, B-4000, Liège, Belgium
| | - Latifa Karim
- Genomics Platform, GIGA, University of Liège, B-4000, Liège, Belgium
| | - Wouter Coppieters
- Genomics Platform, GIGA, University of Liège, B-4000, Liège, Belgium
| | - Bart Devreese
- Laboratory for Microbiology, Department of Biochemistry and Microbiology, Ghent University, B-9000, Ghent, Belgium
| | - Sébastien Rigali
- InBioS-Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, B-4000, Liège, Belgium
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13
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Old Enzyme, New Role: The β-Glucosidase BglC of Streptomyces scabiei Interferes with the Plant Defense Mechanism by Hydrolyzing Scopolin. BIOPHYSICA 2021. [DOI: 10.3390/biophysica2010001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The beta-glucosidase BglC fulfills multiple functions in both primary metabolism and induction of pathogenicity of Streptomyces scabiei, the causative agent of common scab in root and tuber crops. Indeed, this enzyme hydrolyzes cellobiose and cellotriose to feed glycolysis with glucose directly and modifies the intracellular concentration of these cello-oligosaccharides, which are the virulence elicitors. The inactivation of bglC led to unexpected phenotypes such as the constitutive overproduction of thaxtomin A, the main virulence determinant of S. scabiei. In this work, we reveal a new target substrate of BglC, the phytoalexin scopolin. Removal of the glucose moiety of scopolin generates scopoletin, a potent inhibitor of thaxtomin A production. The hydrolysis of scopolin by BglC displayed substrate inhibition kinetics, which contrasts with the typical Michaelis–Menten saturation curve previously observed for the degradation of its natural substrate cellobiose. Our work, therefore, reveals that BglC targets both cello-oligosaccharide elicitors emanating from the hosts of S. scabiei, and the scopolin phytoalexin generated by the host defense mechanisms, thereby occupying a key position to fine-tune the production of the main virulence determinant thaxtomin A.
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Liu L, Hao L, Liu N, Zhao Y, Zhong N, Zhao P. iTRAQ-Based Proteomics Analysis of Response to Solanum tuberosum Leaves Treated with the Plant Phytotoxin Thaxtomin A. Int J Mol Sci 2021; 22:ijms222112036. [PMID: 34769466 PMCID: PMC8585116 DOI: 10.3390/ijms222112036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/30/2021] [Accepted: 11/04/2021] [Indexed: 11/16/2022] Open
Abstract
Thaxtomin A (TA) is a phytotoxin secreted by Streptomyces scabies that causes common scab in potatoes. However, the mechanism of potato proteomic changes in response to TA is barely known. In this study, the proteomic changes in potato leaves treated with TA were determined using the Isobaric Tags for Relative and Absolute Quantitation (iTRAQ) technique. A total of 693 proteins were considered as differentially expressed proteins (DEPs) following a comparison of leaves treated with TA and sterile water (as a control). Among the identified DEPs, 460 and 233 were upregulated and downregulated, respectively. Based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, many DEPs were found to be involved in defense and stress responses. Most DEPs were grouped in carbohydrate metabolism, amino acid metabolism, energy metabolism, and secondary metabolism including oxidation-reduction process, response to stress, plant-pathogen interaction, and plant hormone signal transduction. In this study, we analyzed the changes in proteins to elucidate the mechanism of potato response to TA, and we provided a molecular basis to further study the interaction between plant and TA. These results also offer the option for potato breeding through analysis of the resistant common scab.
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Affiliation(s)
- Lu Liu
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China;
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Liaoyang Hao
- School of Agriculture, Ningxia University, Yinchuan 750021, China; (L.H.); (Y.Z.)
| | - Ning Liu
- National Engineering Research Center for Vegetables (Beijing Vegetable Research Center), Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China;
| | - Yonglong Zhao
- School of Agriculture, Ningxia University, Yinchuan 750021, China; (L.H.); (Y.Z.)
| | - Naiqin Zhong
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Engineering Laboratory for Advanced Microbial Technology of Agriculture, Chinese Academy of Sciences, Beijing 100101, China
- The Enterprise Key Laboratory of Advanced Technology for Potato Fertilizer and Pesticide, Hulunbuir 021000, China
- Correspondence: (N.Z.); (P.Z.)
| | - Pan Zhao
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Engineering Laboratory for Advanced Microbial Technology of Agriculture, Chinese Academy of Sciences, Beijing 100101, China
- The Enterprise Key Laboratory of Advanced Technology for Potato Fertilizer and Pesticide, Hulunbuir 021000, China
- Correspondence: (N.Z.); (P.Z.)
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Li Z, Huang P, Wang M, Wang X, Wang L, Kong D, Niu G. Stepwise increase of thaxtomins production in Streptomyces albidoflavus J1074 through combinatorial metabolic engineering. Metab Eng 2021; 68:187-198. [PMID: 34673237 DOI: 10.1016/j.ymben.2021.10.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/23/2021] [Accepted: 10/16/2021] [Indexed: 11/30/2022]
Abstract
Herbicide-resistance in weeds has become a serious threat to agriculture across the world. Thus, there is an urgent need for the discovery and development of herbicides with new modes of action. Thaxtomin phytotoxins are a group of nitrated diketopiperazines produced by potato common scab-causing phytopathogen Streptomyces scabies and other actinobacterial pathogens. They are generally considered to function as inhibitors of cellulose synthesis in plants, and thus have great potential to be used as natural herbicides. Generation of an overproducing strain is crucial for the scale-up production of thaxtomins and their wide use in agriculture. In the present study, we employed a stepwise strategy by combining heterologous expression, repressor deletion, activator overexpression, and optimization of fermentation media for high-level production of thaxtomins. The maximum yield of 728 mg/L thaxtomins was achieved with engineered Streptomyces albidoflavus J1074 strains in shake-flask cultures, and it was approximately 36-fold higher than S. albidoflavus J1074 carrying the unmodified cluster. Moreover, the yield of thaxtomins could reach 1973 mg/L when the engineered strain was cultivated in a small-scale stirred-tank bioreactor. This is the highest titer reported to date, representing a significant leap forward for the scale-up production of thaxtomins. Our study presents a robust, easy-to-use system that will be broadly useful for improving titers of bioactive compounds in many Streptomyces species.
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Affiliation(s)
- Zhilei Li
- Biotechnology Research Center, Southwest University, Chongqing, 400715, China; Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Southwest University, Chongqing, 400715, China; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Pengju Huang
- Biotechnology Research Center, Southwest University, Chongqing, 400715, China; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Meiyan Wang
- Biotechnology Research Center, Southwest University, Chongqing, 400715, China; Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Southwest University, Chongqing, 400715, China; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Xia Wang
- Biotechnology Research Center, Southwest University, Chongqing, 400715, China; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Linqi Wang
- Biotechnology Research Center, Southwest University, Chongqing, 400715, China; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Dekun Kong
- Biotechnology Research Center, Southwest University, Chongqing, 400715, China; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Guoqing Niu
- Biotechnology Research Center, Southwest University, Chongqing, 400715, China; Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Southwest University, Chongqing, 400715, China; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China.
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Sahebi M, Tarighi S, Taheri P. The Arac-like transcriptional regulator YqhC is involved in pathogenicity of Erwinia amylovora. J Appl Microbiol 2021; 132:1319-1329. [PMID: 34480830 DOI: 10.1111/jam.15286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/28/2021] [Accepted: 08/30/2021] [Indexed: 11/29/2022]
Abstract
AIMS This study aimed to identify virulence-associated genes and functions that affect disease development on pear caused by Erwinia amylovora EaUMG3 isolated from Iran. METHODS AND RESULTS A mini-Tn5 transposon library was generated in EaUMG3. An E. amylovora mutant that had lost its ability to cause lesions on immature pear fruits, was selected for further analysis. This mutant was shown to have a transposon insertion in yqhC, a gene belongs to the AraC family of transcriptional regulators. A mutant of the wild-type EaUMG3 carrying an unmarked deletion of the yqhC gene was created using pDMS197. The Ea∆yqhC mutant showed reduced disease progression on immature pear fruits and pear plants, reduced motility and significantly lower levels of the virulence factors siderophore and amylovoran. Complementation with yqhC cloned in pBBR1MCS restored disease progression and the level of virulence factors to near wild type. CONCLUSION YqhC transcriptional regulator is necessary for full virulence of E. amylovora. In addition, this regulator affects virulence factors such as siderophore production, amylovoran production, and motility. SIGNIFICANCE AND IMPACT OF STUDY The identification of a novel transcriptional regulator with strong impact in the pathogenesis of E. amylovora, an organism causing significant economic losses in fruit production.
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Affiliation(s)
- Masood Sahebi
- Department of Plant Protection, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Saeed Tarighi
- Department of Plant Protection, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Parissa Taheri
- Department of Plant Protection, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
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Planckaert S, Deflandre B, de Vries AM, Ameye M, Martins JC, Audenaert K, Rigali S, Devreese B. Identification of Novel Rotihibin Analogues in Streptomyces scabies, Including Discovery of Its Biosynthetic Gene Cluster. Microbiol Spectr 2021; 9:e0057121. [PMID: 34346752 PMCID: PMC8552735 DOI: 10.1128/spectrum.00571-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 02/01/2023] Open
Abstract
Streptomyces scabies is a phytopathogen associated with common scab disease. This is mainly attributed to its ability to produce the phytotoxin thaxtomin A, the biosynthesis of which is triggered by cellobiose. During a survey of other metabolites released in the presence of cellobiose, we discovered additional compounds in the thaxtomin-containing extract from Streptomyces scabies. Structural analysis by mass spectrometry (MS) and nuclear magnetic resonance (NMR) revealed that these compounds are amino acid sequence variants of the TOR (target of rapamycin) kinase (TORK) pathway-inhibitory lipopeptide rotihibin A, and the main compounds were named rotihibins C and D. In contrast to thaxtomin, the production of rotihibins C and D was also elicited in the presence of glucose, indicating different regulation of their biosynthesis. Through a combination of shotgun and targeted proteomics, the putative rotihibin biosynthetic gene cluster rth was identified in the publicly available genome of S. scabies 87-22. This cluster spans 33 kbp and encodes 2 different nonribosomal peptide synthetases (NRPSs) and 12 additional enzymes. Homologous rth biosynthetic gene clusters were found in other publicly available and complete actinomycete genomes. Rotihibins C and D display herbicidal activity against Lemna minor and Arabidopsis thaliana at low concentrations, shown by monitoring the effects on growth and the maximal photochemistry efficiency of photosystem II. IMPORTANCE Rotihibins A and B are plant growth inhibitors acting on the TORK pathway. We report the isolation and characterization of new sequence analogues of rotihibin from Streptomyces scabies, a major cause of common scab in potato and other tuber and root vegetables. By combining proteomics data with genomic analysis, we found a cryptic biosynthetic gene cluster coding for enzyme machinery capable of rotihibin production. This work may lead to the biotechnological production of variants of this lipopeptide to investigate the exact mechanism by which it can target the plant TORK pathway in Arabidopsis thaliana. In addition, bioinformatics revealed the existence of other variants in plant-associated Streptomyces strains, both pathogenic and nonpathogenic species, raising new questions about the actual function of this lipopeptide. The discovery of a module in the nonribosomal peptide synthetase (NRPS) that incorporates the unusual citrulline residue may improve the prediction of peptides encoded by cryptic NRPS gene clusters.
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Affiliation(s)
- Sören Planckaert
- Laboratory for Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Benoit Deflandre
- InBioS-Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, Liège, Belgium
| | | | - Maarten Ameye
- Laboratory of Applied Mycology and Phenomics, Department of Plants and Crops, Ghent University, Ghent, Belgium
| | - José C. Martins
- NMR and Structure Analysis Group, Ghent University, Ghent, Belgium
| | - Kris Audenaert
- Laboratory of Applied Mycology and Phenomics, Department of Plants and Crops, Ghent University, Ghent, Belgium
| | - Sébastien Rigali
- InBioS-Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, Liège, Belgium
| | - Bart Devreese
- Laboratory for Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
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Hudec C, Biessy A, Novinscak A, St-Onge R, Lamarre S, Blom J, Filion M. Comparative Genomics of Potato Common Scab-Causing Streptomyces spp. Displaying Varying Virulence. Front Microbiol 2021; 12:716522. [PMID: 34413844 PMCID: PMC8369830 DOI: 10.3389/fmicb.2021.716522] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 07/13/2021] [Indexed: 11/20/2022] Open
Abstract
Common scab of potato causes important economic losses worldwide following the development of necrotic lesions on tubers. In this study, the genomes of 14 prevalent scab-causing Streptomyces spp. isolated from Prince Edward Island, one of the most important Canadian potato production areas, were sequenced and annotated. Their phylogenomic affiliation was determined, their pan-genome was characterized, and pathogenic determinants involved in their virulence, ranging from weak to aggressive, were compared. 13 out of 14 strains clustered with Streptomyces scabiei, while the last strain clustered with Streptomyces acidiscabies. The toxicogenic and colonization genomic regions were compared, and while some atypical gene organizations were observed, no clear correlation with virulence was observed. The production of the phytotoxin thaxtomin A was also quantified and again, contrary to previous reports in the literature, no clear correlation was found between the amount of thaxtomin A secreted, and the virulence observed. Although no significant differences were observed when comparing the presence/absence of the main virulence factors among the strains of S. scabiei, a distinct profile was observed for S. acidiscabies. Several mutations predicted to affect the functionality of some virulence factors were identified, including one in the bldA gene that correlates with the absence of thaxtomin A production despite the presence of the corresponding biosynthetic gene cluster in S. scabiei LBUM 1485. These novel findings obtained using a large number of scab-causing Streptomyces strains are challenging some assumptions made so far on Streptomyces’ virulence and suggest that other factors, yet to be characterized, are also key contributors.
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Affiliation(s)
- Cindy Hudec
- Department of Biology, Université de Moncton, Moncton, NB, Canada
| | - Adrien Biessy
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC, Canada
| | - Amy Novinscak
- Agassiz Research and Development Centre, Agriculture and Agri-Food Canada, Agassiz, BC, Canada
| | - Renée St-Onge
- Department of Biology, Université de Moncton, Moncton, NB, Canada
| | - Simon Lamarre
- Department of Biology, Université de Moncton, Moncton, NB, Canada
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-Universität Giessen, Giessen, Germany
| | - Martin Filion
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC, Canada
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Beaudoin N, Isayenka I, Ducharme A, Massie S, Gagnon A, Hogue R, Beaulieu C, Michaud D. Habituation to thaxtomin A increases resistance to common scab in 'Russet Burbank' potato. PLoS One 2021; 16:e0253414. [PMID: 34133457 PMCID: PMC8208575 DOI: 10.1371/journal.pone.0253414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/04/2021] [Indexed: 11/19/2022] Open
Abstract
Common scab is a potato disease characterized by the formation of scab-like lesions on the surface of potato tubers. The actinobacterium Streptomyces scabiei is the main causal agent of common scab. During infection, this bacterium synthesizes the phytotoxin thaxtomin A which is essential for the production of disease symptoms. While thaxtomin A can activate an atypical programmed cell death in plant cell suspensions, it is possible to gradually habituate plant cells to thaxtomin A to provide resistance to lethal phytotoxin concentrations. Potato 'Russet Burbank' calli were habituated to thaxtomin A to regenerate the somaclone RB9 that produced tubers more resistant to common scab than those obtained from the original cultivar. Compared to the Russet Burbank cultivar, somaclone RB9 generated up to 22% more marketable tubers with an infected tuber area below the 5% threshold. Enhanced resistance was maintained over at least two years of cultivation in the field. However, average size of tubers was significantly reduced in somaclone RB9 compared to the parent cultivar. Small RB9 tubers had a thicker phellem than Russet Burbank tubers, which may contribute to improving resistance to common scab. These results show that thaxtomin A-habituation in potato is efficient to produce somaclones with increased and durable resistance to common scab.
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Affiliation(s)
- Nathalie Beaudoin
- Département de biologie, Centre SÈVE, Université de Sherbrooke, Sherbrooke, QC, Canada
- * E-mail:
| | - Iauhenia Isayenka
- Département de biologie, Centre SÈVE, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Audrey Ducharme
- Département de biologie, Centre SÈVE, Université de Sherbrooke, Sherbrooke, QC, Canada
| | | | | | - Richard Hogue
- Institut de recherche et de développement en agroenvironnement inc. (IRDA), Québec, QC, Canada
| | - Carole Beaulieu
- Département de biologie, Centre SÈVE, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Dominique Michaud
- Centre de recherche et d’innovation sur les végétaux, Université Laval, Québec, QC, Canada
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20
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Cortés-Avalos D, Martínez-Pérez N, Ortiz-Moncada MA, Juárez-González A, Baños-Vargas AA, Estrada-de Los Santos P, Pérez-Rueda E, Ibarra JA. An update of the unceasingly growing and diverse AraC/XylS family of transcriptional activators. FEMS Microbiol Rev 2021; 45:6219864. [PMID: 33837749 DOI: 10.1093/femsre/fuab020] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 03/31/2021] [Indexed: 01/09/2023] Open
Abstract
Transcriptional factors play an important role in gene regulation in all organisms, especially in Bacteria. Here special emphasis is placed in the AraC/XylS family of transcriptional regulators. This is one of the most abundant as many predicted members have been identified and more members are added because more bacterial genomes are sequenced. Given the way more experimental evidence has mounded in the past decades, we decided to update the information about this captivating family of proteins. Using bioinformatics tools on all the data available for experimentally characterized members of this family, we found that many members that display a similar functional classification can be clustered together and in some cases they have a similar regulatory scheme. A proposal for grouping these proteins is also discussed. Additionally, an analysis of surveyed proteins in bacterial genomes is presented. Altogether, the current review presents a panoramic view into this family and we hope it helps to stimulate future research in the field.
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Affiliation(s)
- Daniel Cortés-Avalos
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Noemy Martínez-Pérez
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica Yucatán, Mérida, Yucatán, México
| | - Mario A Ortiz-Moncada
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Aylin Juárez-González
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Arturo A Baños-Vargas
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Paulina Estrada-de Los Santos
- Laboratorio de Biotecnología Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Ernesto Pérez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica Yucatán, Mérida, Yucatán, México.,Facultad de Ciencias, Centro de Genómica y Bioinformática, Universidad Mayor, Santiago, Chile
| | - J Antonio Ibarra
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
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Weisberg AJ, Kramer CG, Kotha RR, Luthria DL, Chang JH, Clarke CR. A Novel Species-Level Group of Streptomyces Exhibits Variation in Phytopathogenicity Despite Conservation of Virulence Loci. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:39-48. [PMID: 33030393 DOI: 10.1094/mpmi-06-20-0164-r] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The genus Streptomyces includes several phytopathogenic species that cause common scab, a devastating disease of tuber and root crops, in particular potato. The diversity of species that cause common scab is unknown. Likewise, the genomic context necessary for bacteria to incite common scab symptom development is not fully characterized. Here, we phenotyped and sequenced the genomes of five strains from a poorly studied Streptomyces lineage. These strains form a new species-level group. When genome sequences within just these five strains are compared, there are no polymorphisms of loci implicated in virulence. Each genome contains the pathogenicity island that encodes for the production of thaxtomin A, a phytotoxin necessary for common scab. Yet, not all sequenced strains produced thaxtomin A. Strains varied from nonpathogenic to highly virulent on two hosts. Unexpectedly, one strain that produced thaxtomin A and was pathogenic on radish was not aggressively pathogenic on potato. Therefore, while thaxtomin A biosynthetic genes and production of thaxtomin A are necessary, they are not sufficient for causing common scab of potato. Additionally, results show that even within a species-level group of Streptomyces strains, there can be aggressively pathogenic and nonpathogenic strains despite conservation of virulence genes.
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Affiliation(s)
- Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, OR 97331, U.S.A
| | - Charles G Kramer
- Genetic Improvement for Fruits and Vegetables Lab, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705, U.S.A
| | - Raghavendhar R Kotha
- Food Composition and Methods Development Lab, Beltsville Human Nutrition Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705, U.S.A
| | - Devanand L Luthria
- Food Composition and Methods Development Lab, Beltsville Human Nutrition Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705, U.S.A
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, OR 97331, U.S.A
- Center for Genome Research and Biocomputing, Oregon State University, OR 97331, U.S.A
| | - Christopher R Clarke
- Genetic Improvement for Fruits and Vegetables Lab, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705, U.S.A
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Diffusible Signal Factors Act through AraC-Type Transcriptional Regulators as Chemical Cues To Repress Virulence of Enteric Pathogens. Infect Immun 2020; 88:IAI.00226-20. [PMID: 32690633 PMCID: PMC7504960 DOI: 10.1128/iai.00226-20] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/08/2020] [Indexed: 01/02/2023] Open
Abstract
Successful colonization by enteric pathogens is contingent upon effective interactions with the host and the resident microbiota. These pathogens thus respond to and integrate myriad signals to control virulence. Long-chain fatty acids repress the virulence of the important enteric pathogens Salmonella enterica and Vibrio cholerae by repressing AraC-type transcriptional regulators in pathogenicity islands. While several fatty acids are known to be repressive, we show here that cis-2-unsaturated fatty acids, a rare chemical class used as diffusible signal factors (DSFs), are highly potent inhibitors of virulence functions. We found that DSFs repressed virulence gene expression of enteric pathogens by interacting with transcriptional regulators of the AraC family. In Salmonella enterica serovar Typhimurium, DSFs repress the activity of HilD, an AraC-type activator essential to the induction of epithelial cell invasion, by both preventing its interaction with target DNA and inducing its rapid degradation by Lon protease. cis-2-Hexadecenoic acid (c2-HDA), a DSF produced by Xylella fastidiosa, was the most potent among those tested, repressing the HilD-dependent transcriptional regulator hilA and the type III secretion effector sopB >200- and 68-fold, respectively. Further, c2-HDA attenuated the transcription of the ToxT-dependent cholera toxin synthesis genes of V. cholerae c2-HDA significantly repressed invasion gene expression by Salmonella in the murine colitis model, indicating that the HilD-dependent signaling pathway functions within the complex milieu of the animal intestine. These data argue that enteric pathogens respond to DSFs as interspecies signals to identify appropriate niches in the gut for virulence activation, which could be exploited to control the virulence of enteric pathogens.
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Wang L, Wang M, Fu Y, Huang P, Kong D, Niu G. Engineered biosynthesis of thaxtomin phytotoxins. Crit Rev Biotechnol 2020; 40:1163-1171. [PMID: 32819175 DOI: 10.1080/07388551.2020.1807461] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Herbicide-resistant weeds are a growing problem worldwide. Thaxtomin phytotoxins are a group of nitrated diketopiperazines produced by the potato common scab-causing pathogen Streptomyces scabies and other actinobacterial plant pathogens. They represent a unique class of microbial natural products with distinctive structural features and promising herbicidal activity. The biosynthesis of thaxtomins proceeds through multiple steps of unusual enzymatic reactions. Advances in understanding of thaxtomins biosynthetic machinery have provided the basis for precursor-directed biosynthesis, pathway refactoring, and one-pot biocombinatorial synthesis to generate thaxtomin analogues. We herein summarize recent findings on the biosynthesis of thaxtomins and highlight recent advances in the rational generation of novel thaxtomins for the development of potent herbicidal agents.
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Affiliation(s)
- Linqi Wang
- Biotechnology Research Center, Southwest University, Chongqing, China.,State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Meiyan Wang
- Biotechnology Research Center, Southwest University, Chongqing, China.,State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Yudie Fu
- Biotechnology Research Center, Southwest University, Chongqing, China.,State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Pengju Huang
- Biotechnology Research Center, Southwest University, Chongqing, China.,State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Dekun Kong
- Biotechnology Research Center, Southwest University, Chongqing, China.,State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Guoqing Niu
- Biotechnology Research Center, Southwest University, Chongqing, China.,State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China.,Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Southwest University, Chongqing, China
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24
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Vergnes S, Gayrard D, Veyssière M, Toulotte J, Martinez Y, Dumont V, Bouchez O, Rey T, Dumas B. Phyllosphere Colonization by a Soil Streptomyces sp. Promotes Plant Defense Responses Against Fungal Infection. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:223-234. [PMID: 31544656 DOI: 10.1094/mpmi-05-19-0142-r] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Streptomycetes are soil-dwelling, filamentous actinobacteria and represent a prominent bacterial clade inside the plant root microbiota. The ability of streptomycetes to produce a broad spectrum of antifungal metabolites suggests that these bacteria could be used to manage plant diseases. Here, we describe the identification of a soil Streptomyces strain named AgN23 which strongly activates a large array of defense responses when applied on Arabidopsis thaliana leaves. AgN23 increased the biosynthesis of salicylic acid, leading to the development of salicylic acid induction deficient 2 (SID2)-dependent necrotic lesions. Size exclusion fractionation of plant elicitors secreted by AgN23 showed that these signals are tethered into high molecular weight complexes. AgN23 mycelium was able to colonize the leaf surface, leading to plant resistance against Alternaria brassicicola infection in wild-type Arabidopsis plants. AgN23-induced resistance was found partially compromised in salicylate, jasmonate, and ethylene mutants. Our data show that Streptomyces soil bacteria can develop at the surface of plant leaves to induce defense responses and protection against foliar fungal pathogens, extending their potential use to manage plant diseases.
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Affiliation(s)
- Sophie Vergnes
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, France
| | - Damien Gayrard
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, France
- De Sangosse, Bonnel, 47480 Pont-Du-Casse, France
| | - Marine Veyssière
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, France
| | - Justine Toulotte
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, France
| | - Yves Martinez
- CNRS, Plateforme Imagerie-Microscopie, Fédération de Recherche FR3450, Castanet-Tolosan, France
| | - Valérie Dumont
- CRITT-Bio-industries, INSA, 135 avenue de Rangueil, 31077 Toulouse Cedex 4, France
| | - Olivier Bouchez
- INRA, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Thomas Rey
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, France
- De Sangosse, Bonnel, 47480 Pont-Du-Casse, France
| | - Bernard Dumas
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, France
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25
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Khalil M, Lerat S, Beaudoin N, Beaulieu C. The Plant Pathogenic Bacterium Streptomyces scabies Degrades the Aromatic Components of Potato Periderm via the β-Ketoadipate Pathway. Front Microbiol 2019; 10:2795. [PMID: 31866970 PMCID: PMC6904314 DOI: 10.3389/fmicb.2019.02795] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 11/18/2019] [Indexed: 11/13/2022] Open
Abstract
The outer potato periderm layer consists of dead suberized cells. Suberin, a protective biopolymer, is made of a polyaliphatic portion covalently linked to polyaromatic moieties. Evidence accumulates that Streptomyces scabies, the main causal agent of potato common scab, can degrade the suberin aliphatic part but its ability to degrade the aromatic portion has not been documented. This polyaromatic portion is mainly composed of cinnamic acids. In this study, two cinnamates (trans-ferulic or p-coumaric acids) were added to the culture medium of S. scabies strains EF-35 and 87.22. HPLC quantification revealed that both strains efficiently utilized these compounds. A proteomic study coupled with gene expression analysis led to the identification of putative catabolic pathways for cinnamates. Catabolism of both compounds appeared to occur via the β-ketoadipate pathway. Gene SCAB_15301, encoding for a putative vanillate monooxygenase, was partly deleted from S. scabies strain 87.22 genome. The mutant retained its ability to catabolize trans-ferulic acid into vanillate but lost its ability to further degrade the latter compound. When the wild-type mutant and complemented strains were grown in the presence of suberin-enriched potato periderm, accumulation of vanillic acid was observed only in the mutant culture medium. This work presents evidence that S. scabies can degrade not only the aliphatic part of suberin but also the constituents of suberin aromatic portion. This may provide ecological and pathological advantages to S. scabies as a saprophyte and pathogen.
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Affiliation(s)
- Mario Khalil
- Département de Biologie, Centre SÈVE, Université de Sherbrooke, Sherbrooke, QC, Canada
- Department of Microbiology, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Sylvain Lerat
- Département de Biologie, Centre SÈVE, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Nathalie Beaudoin
- Département de Biologie, Centre SÈVE, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Carole Beaulieu
- Département de Biologie, Centre SÈVE, Université de Sherbrooke, Sherbrooke, QC, Canada
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26
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Clarke CR, Kramer CG, Kotha RR, Wanner LA, Luthria DL, Kramer M. Cultivar Resistance to Common Scab Disease of Potato Is Dependent on the Pathogen Species. PHYTOPATHOLOGY 2019; 109:1544-1554. [PMID: 31066348 DOI: 10.1094/phyto-09-18-0368-r] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Common scab of potato is a superficial tuber disease caused by Streptomyces species that produce the phytotoxin thaxtomin. Because common scab development is highly dependent on the effects of this single toxin, the current operating paradigm in common scab pathology is that a potato cultivar resistant to one strain of the common scab pathogen is resistant to all strains. However, cultivar resistance to common scab disease identified in one breeding program is often not durable when tested in other potato breeding programs across the United States. We infected 55 potato cultivar populations with three distinct species of the common scab pathogen and identified cultivars that were resistant or susceptible to all three species and cultivars that had widely varying resistance dependent on the pathogen species. Overall lower virulence was associated with the strain that produces the least thaxtomin. This result showcases several cultivars of potato that are expected to be resistant to the majority of common scab populations but also highlights that many potato cultivars are resistant to only specific species of the pathogen. These results demonstrate that extension specialists and growers must consider their local population of the common scab pathogen when selecting which cultivars to plant for common scab resistance.
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Affiliation(s)
- Christopher R Clarke
- Genetic Improvement for Fruits and Vegetables Laboratory, Beltsville Agricultural Research Center, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD 20705
| | - Charles G Kramer
- Genetic Improvement for Fruits and Vegetables Laboratory, Beltsville Agricultural Research Center, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD 20705
| | - Raghavendhar R Kotha
- Food Composition and Methods Development Laboratory, Beltsville Human Nutrition Research Center, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD 20705
| | - Leslie A Wanner
- Genetic Improvement for Fruits and Vegetables Laboratory, Beltsville Agricultural Research Center, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD 20705
| | - Devanand L Luthria
- Food Composition and Methods Development Laboratory, Beltsville Human Nutrition Research Center, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD 20705
| | - Matthew Kramer
- Statistics Group, Northeast Area, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD 20705
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27
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Thapa SP, Davis EW, Lyu Q, Weisberg AJ, Stevens DM, Clarke CR, Coaker G, Chang JH. The Evolution, Ecology, and Mechanisms of Infection by Gram-Positive, Plant-Associated Bacteria. ANNUAL REVIEW OF PHYTOPATHOLOGY 2019; 57:341-365. [PMID: 31283433 DOI: 10.1146/annurev-phyto-082718-100124] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Gram-positive bacteria are prominent members of plant-associated microbial communities. Although many are hypothesized to be beneficial, some are causative agents of economically important diseases of crop plants. Because the features of Gram-positive bacteria are fundamentally different relative to those of Gram-negative bacteria, the evolution and ecology as well as the mechanisms used to colonize and infect plants also differ. Here, we discuss recent advances in our understanding of Gram-positive, plant-associated bacteria and provide a framework for future research directions on these important plant symbionts.
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Affiliation(s)
- Shree P Thapa
- Department of Plant Pathology, University of California, Davis, California 95616, USA
| | - Edward W Davis
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA;
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon 97331, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331, USA
| | - Qingyang Lyu
- Department of Plant Pathology, University of California, Davis, California 95616, USA
| | - Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA;
| | - Danielle M Stevens
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA;
- Integrative Genetics and Genomics, University of California, Davis, California 95616, USA
| | - Christopher R Clarke
- Genetic Improvement for Fruits and Vegetables Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, Maryland 20705, USA
| | - Gitta Coaker
- Department of Plant Pathology, University of California, Davis, California 95616, USA
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA;
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon 97331, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331, USA
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28
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Liang F, Lin R, Yao Y, Xiao Y, Zhang M, Shi C, He X, Zhou B, Wang B. Systematic Identification of Pathogenic Streptomyces sp. AMCC400023 That Causes Common Scab and Genomic Analysis of Its Pathogenicity Island. PHYTOPATHOLOGY 2019; 109:1115-1128. [PMID: 30829555 DOI: 10.1094/phyto-07-18-0266-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Potato scab, a serious soilborne disease caused by Streptomyces spp., occurs in potato-growing areas worldwide and results in severe economic losses. In this paper, the pathogenicity of Streptomyces strain AMCC400023, isolated from potato scabs in Hebei Province, China, was verified systematically by the radish seedling test, the potato tuber slice assay, the potted back experiment, and the detection of phytotoxin thaxtomin A. Morphological, physiological, and biochemical characteristics were determined, and the 16S ribosomal RNA analyses of Streptomyces sp. AMCC400023 were carried out. To obtain the accurate taxonomic status of the pathogen strain, the whole genome was sequenced, and the phylogenetic tree among 31 Streptomyces genomes was formed. The average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH) were analyzed, and at the same time, the toxicity-related genes between Streptomyces sp. AMCC400023 and Streptomyces scabiei were compared, all based on the whole-genome level. All of the data supported that, instead of a member of S. scabiei, test strain Streptomyces sp. AMCC400023 was a distinct phytopathogen of potato common scab, which had a relatively close relationship with S. scabiei while separating clearly from S. scabiei at least in the species level of taxonomic status. The complete pathogenicity island (PAI) composition of Streptomyces sp. AMCC400023 was identified, which contained a toxin region and a colonization region. It was conjectured that the PAI of Streptomyces sp. AMCC400023 might be directly or indirectly acquired from S. scabiei 87-22 by horizontal gene transfer, or at the very least, there was a very close homologous relationship between the two pathogens as indicated by a series of analyses, such as phylogenetic relationships among 31 Streptomyces species, ANI and isDDH analyses, PAI structure mapping, thaxtomin A synthetic gene cluster tree construction, and most important, the collinearity analysis at the genome level.
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Affiliation(s)
- Feiyang Liang
- 1 Department of Microbiology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, People's Republic of China
| | - Rongshan Lin
- 1 Department of Microbiology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, People's Republic of China
| | - Yaqian Yao
- 1 Department of Microbiology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, People's Republic of China
| | | | - Mingshuo Zhang
- 1 Department of Microbiology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, People's Republic of China
| | - Chunyu Shi
- 3 Agricultural College, Shandong Agricultural University, Tai'an 271018, People's Republic of China
| | - Xiaoli He
- 1 Department of Microbiology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, People's Republic of China
| | - Bo Zhou
- 1 Department of Microbiology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, People's Republic of China
- 4 National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Tai'an 271018, People's Republic of China
| | - Bing Wang
- 1 Department of Microbiology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, People's Republic of China
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29
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Li Y, Liu J, Díaz-Cruz G, Cheng Z, Bignell DRD. Virulence mechanisms of plant-pathogenic Streptomyces species: an updated review. MICROBIOLOGY-SGM 2019; 165:1025-1040. [PMID: 31162023 DOI: 10.1099/mic.0.000818] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Gram-positive Actinobacteria from the genus Streptomyces are best known for their morphological complexity and for their ability to produce numerous bioactive specialized metabolites with useful applications in human and veterinary medicine and in agriculture. In contrast, the ability to infect living plant tissues and to cause diseases of root and tuber crops such as potato common scab (CS) is a rare attribute among members of this genus. Research on the virulence mechanisms of plant-pathogenic Streptomyces spp. has revealed the importance of the thaxtomin phytotoxins as key pathogenicity determinants produced by several species. In addition, other phytotoxic specialized metabolites may contribute to the development or severity of disease caused by Streptomyces spp., along with the production of phytohormones and secreted proteins. A thorough understanding of the molecular mechanisms of plant pathogenicity will enable the development of better management procedures for controlling CS and other plant diseases caused by the Streptomyces.
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Affiliation(s)
- Yuting Li
- Department of Biology, Memorial University of Newfoundland, St John's, NL A1B 3X9, Canada
| | - Jingyu Liu
- Department of Biology, Memorial University of Newfoundland, St John's, NL A1B 3X9, Canada
| | - Gustavo Díaz-Cruz
- Department of Biology, Memorial University of Newfoundland, St John's, NL A1B 3X9, Canada
| | - Zhenlong Cheng
- Department of Biology, Memorial University of Newfoundland, St John's, NL A1B 3X9, Canada
| | - Dawn R D Bignell
- Department of Biology, Memorial University of Newfoundland, St John's, NL A1B 3X9, Canada
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30
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A Novel AdpA Homologue Negatively Regulates Morphological Differentiation in Streptomyces xiamenensis 318. Appl Environ Microbiol 2019; 85:AEM.03107-18. [PMID: 30683747 DOI: 10.1128/aem.03107-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Accepted: 01/23/2019] [Indexed: 11/20/2022] Open
Abstract
The pleiotropic transcriptional regulator AdpA positively controls morphological differentiation and regulates secondary metabolism in most Streptomyces species. Streptomyces xiamenensis 318 has a linear chromosome 5.96 Mb in size. How AdpA affects secondary metabolism and morphological differentiation in such a naturally minimized genomic background is unknown. Here, we demonstrated that AdpA Sx , an AdpA orthologue in S. xiamenensis, negatively regulates cell growth and sporulation and bidirectionally regulates the biosynthesis of xiamenmycin and polycyclic tetramate macrolactams (PTMs) in S. xiamenensis 318. Overexpression of the adpASx gene in S. xiamenensis 318 had negative effects on morphological differentiation and resulted in reduced transcription of putative ssgA, ftsZ, ftsH, amfC, whiB, wblA1, wblA2, wblE, and a gene encoding sporulation-associated protein (sxim_29740), whereas the transcription of putative bldD and bldA genes was upregulated. Overexpression of adpASx led to significantly enhanced production of xiamenmycin but had detrimental effects on the production of PTMs. As expected, the transcriptional level of the xim gene cluster was upregulated, whereas the PTM gene cluster was downregulated. Moreover, AdpA Sx negatively regulated the transcription of its own gene. Electrophoretic mobility shift assays revealed that AdpA Sx can bind the promoter regions of structural genes of both the xim and PTM gene clusters as well as to the promoter regions of genes potentially involved in the cell growth and differentiation of S. xiamenensis 318. We report that an AdpA homologue has negative effects on morphological differentiation in S. xiamenensis 318, a finding confirmed when AdpA Sx was introduced into the heterologous host Streptomyces lividans TK24.IMPORTANCE AdpA is a key regulator of secondary metabolism and morphological differentiation in Streptomyces species. However, AdpA had not been reported to negatively regulate morphological differentiation. Here, we characterized the regulatory role of AdpA Sx in Streptomyces xiamenensis 318, which has a naturally streamlined genome. In this strain, AdpA Sx negatively regulated cell growth and morphological differentiation by directly controlling genes associated with these functions. AdpA Sx also bidirectionally controlled the biosynthesis of xiamenmycin and PTMs by directly regulating their gene clusters rather than through other regulators. Our findings provide additional evidence for the versatility of AdpA in regulating morphological differentiation and secondary metabolism in Streptomyces.
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31
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Sarwar A, Latif Z, Zhang S, Hao J, Bechthold A. A Potential Biocontrol Agent Streptomyces violaceusniger AC12AB for Managing Potato Common Scab. Front Microbiol 2019; 10:202. [PMID: 30800116 PMCID: PMC6375851 DOI: 10.3389/fmicb.2019.00202] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 01/24/2019] [Indexed: 11/13/2022] Open
Abstract
Potato common scab (PCS) is an economically important disease worldwide. In this study we demonstrated the possible role of Streptomyces violaceusniger AC12AB in controlling PCS. Isolates of Streptomyces scabies were obtained from CS infected tubers collected from Maine United States, which were confirmed by morphological and molecular analysis including 16S rRNA sequencing and RFLP analysis of amplified 16S-23S ITS. Pathogenicity assays related genes including txtAB, nec1, and tomA were also identified in all S. scabies strains through PCR reaction. An antagonistic bacterial strain was isolated from soil in Punjab and identified as S. violaceusniger AC12AB based on 16S rRNA sequencing analysis. Methanolic extract of S. violaceusniger AC12AB contained azalomycin RS-22A which was confirmed by 1H and 13C-NMR, 1H/1H-COSY, HMBC and HMQC techniques. S. violaceusniger AC12AB exhibited plant growth promotion attributes including Indole-3-acetic acid production with 17 μgmL-1 titers, siderophores production, nitrogen fixation and phosphates solubilization potential. When tubers were inoculated with S. violaceusniger AC12AB, significant (P < 0.05) PCS disease reduction up to 90% was observed in greenhouse and field trials, respectively. Likewise, S. violaceusniger AC12AB significantly (P < 0.05) increased potato crop up to 26.8% in field trial. Therefore, plant growth promoting S. violaceusniger AC12AB could provide a dual benefit by decreasing PCS disease severity and increasing potato yield as an effective and inexpensive alternative strategy to manage this disease.
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Affiliation(s)
- Arslan Sarwar
- Department of Microbiology, Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan
| | - Zakia Latif
- Department of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Songya Zhang
- Department of Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, University of Freiburg, Freiburg im Breisgau, Germany
| | - Jianjun Hao
- School of Food and Agriculture, The University of Maine, Orono, ME, United States
| | - Andreas Bechthold
- Department of Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, University of Freiburg, Freiburg im Breisgau, Germany
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32
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Planckaert S, Jourdan S, Francis IM, Deflandre B, Rigali S, Devreese B. Proteomic Response to Thaxtomin Phytotoxin Elicitor Cellobiose and to Deletion of Cellulose Utilization Regulator CebR in Streptomyces scabies. J Proteome Res 2018; 17:3837-3852. [DOI: 10.1021/acs.jproteome.8b00528] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sören Planckaert
- Laboratory for Microbiology, Department of Biochemistry and Microbiology, Ghent University, B-9000 Ghent, Belgium
| | - Samuel Jourdan
- InBioS − Center for Protein Engineering, University of Liège, Institut de Chimie, B-4000 Liège, Belgium
| | - Isolde M. Francis
- Department of Biology, California State University Bakersfield, Bakersfield, California 93311-1022, United States
| | - Benoit Deflandre
- InBioS − Center for Protein Engineering, University of Liège, Institut de Chimie, B-4000 Liège, Belgium
| | - Sébastien Rigali
- InBioS − Center for Protein Engineering, University of Liège, Institut de Chimie, B-4000 Liège, Belgium
| | - Bart Devreese
- Laboratory for Microbiology, Department of Biochemistry and Microbiology, Ghent University, B-9000 Ghent, Belgium
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33
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Rigali S, Anderssen S, Naômé A, van Wezel GP. Cracking the regulatory code of biosynthetic gene clusters as a strategy for natural product discovery. Biochem Pharmacol 2018; 153:24-34. [DOI: 10.1016/j.bcp.2018.01.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 01/03/2018] [Indexed: 12/19/2022]
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34
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Zhang Y, Jiang G, Ding Y, Loria R. Genetic background affects pathogenicity island function and pathogen emergence in Streptomyces. MOLECULAR PLANT PATHOLOGY 2018; 19:1733-1741. [PMID: 29316196 PMCID: PMC6638181 DOI: 10.1111/mpp.12656] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/27/2017] [Accepted: 01/05/2018] [Indexed: 05/30/2023]
Abstract
With few exceptions, thaxtomin A (ThxA), a nitrated diketopiperazine, is the pathogenicity determinant for plant-pathogenic Streptomyces species. In Streptomyces scabiei (syn. S. scabies), the ThxA biosynthetic cluster is located within a 177-kb mobile pathogenicity island (PAI), called the toxicogenic region (TR). In S. turgidiscabies, the ThxA biosynthetic cluster is located within a 674-kb pathogenicity island (PAIst). The emergence of new plant pathogens occurs in this genus, but not frequently. This raises the question of whether the mobilization of these pathogenicity regions, through mating, is widespread and whether TR and PAIst can confer plant pathogenicity. We showed that ThxA biosynthetic clusters on TR and PAIst were transferred into strains from five non-pathogenic Streptomyces species through mating with S. scabiei and S. turgidiscabies. However, not all of the transconjugants produced ThxA and exhibited the virulence phenotype, indicating that the genetic background of the recipient strains affects the functionality of the ThxA biosynthetic cluster and therefore would be expected to affect the emergence of novel pathogenic Streptomyces species. Thxs have been patented as natural herbicides, but have yet to be commercialized. Our results also demonstrated the potential of the heterologous production of ThxA as a natural and biodegradable herbicide in non-pathogenic Streptomyces species.
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Affiliation(s)
- Yucheng Zhang
- Department of Plant PathologyUniversity of FloridaGainesvilleFL32611USA
| | - Guangde Jiang
- Department of Medicinal ChemistryUniversity of FloridaGainesvilleFL32610USA
| | - Yousong Ding
- Department of Medicinal ChemistryUniversity of FloridaGainesvilleFL32610USA
| | - Rosemary Loria
- Department of Plant PathologyUniversity of FloridaGainesvilleFL32611USA
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35
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Lin L, Xu X, Zheng Y, Zhang C. Effects of AttM lactonase on the pathogenicity of Streptomyces scabies. Lett Appl Microbiol 2018; 67:270-277. [PMID: 29897616 DOI: 10.1111/lam.13019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/21/2018] [Accepted: 06/04/2018] [Indexed: 11/30/2022]
Abstract
The biosynthesis of phytotoxin thaxtomin A (TXT) constitutes the major pathogenicity determinant in Streptomyces scabies, the most widely studied phytopathogen causing scab disease in potato and other root crops. It is recognized that S. scabies regulates its pathogenicity via γ-butyrolactone (GBL)-dependent quorum sensing (QS) signalling. AttM, from Agrobacterium tumefaciens C58 strain, has recently been proposed to have GBL-assimilative capacity. Here, we presented the introduction of A. tumefaciens-derived attM gene into S. scabies using the Escherichia coli-Streptomyces shuttle vector pIJ8600 via intergeneric conjugation, followed by the investigation of secondary metabolism (mycelium growth, TXT production and pathogenicity) in S. scabies attM exconjugants (S.s/attM) in comparison with their wild-type parent strain (S.s/WT). Among the resultant S.s/attM exconjugants, attM was found to be integrated into S. scabies chromosome as analysed by Southern blotting. Moreover, S.s/attM failed to evoke the disease symptoms in planta and displayed altered morphological differentiation in contrast to S.s/WT. The abolishment of TXT production in S.s/attM substantiated the loss of pathogenicity and also implied that attM, when constitutively expressed in S. scabies, could paralyse its GBL signalling pathway. Altogether, lactonase-coding gene attM would be useful in a quorum quenching strategy for plant protection via suppressing TXT production and pathogenicity of S. scabies. SIGNIFICANCE AND IMPACT OF THE STUDY This study provides an efficient means to introduce the lactonase gene attM from Agrobacterium tumefaciens into Streptomyces scabies for evaluating the role of γ-butyrolactone (GBL) in thaxtomin A production and pathogenicity, etc. Our results showed that pathogenicity was abrogated in attM-expressing S. scabies exconjugants. Although there are gene knockout approaches to inactivating GBL signalling and thus pathogenicity in S. scabies, they are not only time consuming due to refractory host but also possibly incomplete in view of gene redundancy. Our work is the first report for a kind of lactonase affecting pathogenicity and/or virulence of scab-causing Streptomyces species.
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Affiliation(s)
- L Lin
- Department of Bioengineering, School of Medicine, Southeast University, Nanjing, China
| | - X Xu
- Department of Bioengineering, School of Medicine, Southeast University, Nanjing, China
| | - Y Zheng
- Department of Bioengineering, School of Medicine, Southeast University, Nanjing, China
| | - C Zhang
- Division of Electronic Microscopy, School of Medicine, Southeast University, Nanjing, China
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Jourdan S, Francis IM, Deflandre B, Tenconi E, Riley J, Planckaert S, Tocquin P, Martinet L, Devreese B, Loria R, Rigali S. Contribution of the β-glucosidase BglC to the onset of the pathogenic lifestyle of Streptomyces scabies. MOLECULAR PLANT PATHOLOGY 2018; 19:1480-1490. [PMID: 29077242 PMCID: PMC6638027 DOI: 10.1111/mpp.12631] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 10/21/2017] [Accepted: 10/22/2017] [Indexed: 05/23/2023]
Abstract
Common scab disease on root and tuber plants is caused by Streptomyces scabies and related species which use the cellulose synthase inhibitor thaxtomin A as the main phytotoxin. Thaxtomin production is primarily triggered by the import of cello-oligosaccharides. Once inside the cell, the fate of the cello-oligosaccharides is dichotomized: (i) the fuelling of glycolysis with glucose for the saprophytic lifestyle through the action of β-glucosidase(s) (BGs); and (ii) elicitation of the pathogenic lifestyle by the inhibition of CebR-mediated transcriptional repression of thaxtomin biosynthetic genes. Here, we investigated the role of scab57721, encoding a putative BG (BglC), in the onset of the pathogenicity of S. scabies. Enzymatic assays showed that BglC was able to release glucose from cellobiose, cellotriose and all other cello-oligosaccharides tested. Its inactivation resulted in a phenotype opposite to that expected, as reduced production of thaxtomin was monitored when the mutant was cultivated on medium containing cello-oligosaccharides as unique carbon source. This unexpected phenotype could be attributed to the highly increased activity of alternative intracellular BGs, probably as a compensation for bglC inactivation, which then prevented cellobiose and cellotriose accumulation to reduce the activity of CebR. In contrast, when the bglC null mutant was cultivated on medium devoid of cello-oligosaccharides, it instead constitutively produced thaxtomin. This observed hypervirulent phenotype does not fit with the proposed model of the cello-oligosaccharide-mediated induction of thaxtomin production, and suggests that the role of BglC in the route to the pathogenic lifestyle of S. scabies is more complex than currently presented.
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Affiliation(s)
- Samuel Jourdan
- InBioS – Center for Protein EngineeringUniversity of Liège, Institut de ChimieLiège B‐4000Belgium
| | - Isolde M. Francis
- Department of Plant PathologyUniversity of FloridaGainesville 32611FLUSA
- Department of BiologyCalifornia State UniversityBakersfield 93311CAUSA
| | - Benoit Deflandre
- InBioS – Center for Protein EngineeringUniversity of Liège, Institut de ChimieLiège B‐4000Belgium
| | - Elodie Tenconi
- InBioS – Center for Protein EngineeringUniversity of Liège, Institut de ChimieLiège B‐4000Belgium
| | - Jennifer Riley
- Department of BiologyCalifornia State UniversityBakersfield 93311CAUSA
| | - Sören Planckaert
- Laboratory for Protein Biochemistry and Biomolecular Engineering, Department of Biochemistry and MicrobiologyGhent UniversityGhent B‐9000Belgium
| | - Pierre Tocquin
- InBioS – CARE PhytoSYSTEMS, University of Liège, Institut de BotaniqueLiège B‐4000Belgium
| | - Loïc Martinet
- InBioS – Center for Protein EngineeringUniversity of Liège, Institut de ChimieLiège B‐4000Belgium
| | - Bart Devreese
- Laboratory for Protein Biochemistry and Biomolecular Engineering, Department of Biochemistry and MicrobiologyGhent UniversityGhent B‐9000Belgium
| | - Rosemary Loria
- Department of Plant PathologyUniversity of FloridaGainesville 32611FLUSA
| | - Sébastien Rigali
- InBioS – Center for Protein EngineeringUniversity of Liège, Institut de ChimieLiège B‐4000Belgium
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High-Yield Production of Herbicidal Thaxtomins and Thaxtomin Analogs in a Nonpathogenic Streptomyces Strain. Appl Environ Microbiol 2018; 84:AEM.00164-18. [PMID: 29602787 DOI: 10.1128/aem.00164-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 03/27/2018] [Indexed: 12/13/2022] Open
Abstract
Thaxtomins are virulence factors of most plant-pathogenic Streptomyces strains. Due to their potent herbicidal activity, attractive environmental compatibility, and inherent biodegradability, thaxtomins are key active ingredients of bioherbicides approved by the U.S. Environmental Protection Agency. However, the low yield of thaxtomins in native Streptomyces producers limits their wide agricultural applications. Here, we describe the high-yield production of thaxtomins in a heterologous host. The thaxtomin gene cluster from S. scabiei 87.22 was cloned and expressed in S. albus J1074 after chromosomal integration. The production of thaxtomins and nitrotryptophan analogs was observed using liquid chromatography-mass spectrometry (LC-MS) analysis. When the engineered S. albus J1074 was cultured in the minimal medium Thx defined medium supplemented with 1% cellobiose (TDMc), the yield of the most abundant and herbicidal analog, thaxtomin A, was 10 times higher than that in S. scabiei 87.22, and optimization of the medium resulted in the highest yield of thaxtomin analogs at about 222 mg/liter. Further engineering of the thaxtomin biosynthetic gene cluster through gene deletion led to the production of multiple biosynthetic intermediates important to the chemical synthesis of new analogs. Additionally, the versatility of the thaxtomin biosynthetic system in S. albus J1074 was capitalized on to produce one unnatural fluorinated analog, 5-fluoro-thaxtomin A (5-F-thaxtomin A), whose structure was elucidated by a combination of MS and one-dimensional (1D) and 2D nuclear magnetic resonance (NMR) analyses. Natural and unnatural thaxtomins demonstrated potent herbicidal activity in radish seedling assays. These results indicated that S. albus J1074 has the potential to produce thaxtomins and analogs thereof with high yield, fostering their agricultural applications.IMPORTANCE Thaxtomins are agriculturally valuable herbicidal natural products, but the productivity of native producers is limiting. Heterologous expression of the thaxtomin gene cluster in S. albus J1074 resulted in the highest yield of thaxtomins ever reported, representing a significant leap forward in its wide agricultural use. Furthermore, current synthetic routes to thaxtomins and analogs are lengthy, and two thaxtomin biosynthetic intermediates produced at high yields in this work can provide precursors and building blocks to advanced synthetic routes. Importantly, the production of 5-F-thaxtomin A in engineered S. albus J1074 demonstrated a viable alternative to chemical methods in the synthesis of new thaxtomin analogs. Moreover, our work presents an attractive synthetic biology strategy to improve the supply of herbicidal thaxtomins, likely finding general applications in the discovery and production of many other bioactive natural products.
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Abstract
The acquisition of genetic material conferring the arsenal necessary for host virulence is a prerequisite on the path to becoming a plant pathogen. More subtle mutations are also required for the perception of cues signifying the presence of the target host and optimal conditions for colonization. The decision to activate the pathogenic lifestyle is not "taken lightly" and involves efficient systems monitoring environmental conditions. But how can a pathogen trigger the expression of virulence genes in a timely manner if the main signal inducing its pathogenic behavior originates from cellulose, the most abundant polysaccharide on earth? This situation is encountered by Streptomyces scabies, which is responsible for common scab disease on tuber and root crops. We propose here a series of hypotheses of how S. scabies could optimally distinguish whether cello-oligosaccharides originate from decomposing lignocellulose (nutrient sources, saprophyte) or, instead, emanate from living and expanding plant tissue (virulence signals, pathogen) and accordingly adapt its physiological response.
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Sun D, Zhu J, Chen Z, Li J, Wen Y. SAV742, a Novel AraC-Family Regulator from Streptomyces avermitilis, Controls Avermectin Biosynthesis, Cell Growth and Development. Sci Rep 2016; 6:36915. [PMID: 27841302 PMCID: PMC5107987 DOI: 10.1038/srep36915] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 10/20/2016] [Indexed: 11/09/2022] Open
Abstract
Avermectins are useful anthelmintic antibiotics produced by Streptomyces avermitilis. We demonstrated that a novel AraC-family transcriptional regulator in this species, SAV742, is a global regulator that negatively controls avermectin biosynthesis and cell growth, but positively controls morphological differentiation. Deletion of its gene, sav_742, increased avermectin production and dry cell weight, but caused delayed formation of aerial hyphae and spores. SAV742 directly inhibited avermectin production by repressing transcription of ave structural genes, and also directly regulated its own gene (sav_742) and adjacent gene sig8 (sav_741). The precise SAV742-binding site on its own promoter region was determined by DNase I footprinting assay coupled with site-directed DNA mutagenesis, and 5-nt inverted repeats (GCCGA-n10/n12-TCGGC) were found to be essential for SAV742 binding. Similar 5-nt inverted repeats separated by 3, 10 or 15 nt were found in the promoter regions of target ave genes and sig8. The SAV742 regulon was predicted based on bioinformatic analysis. Twenty-six new SAV742 targets were identified and experimentally confirmed, including genes involved in primary metabolism, secondary metabolism and development. Our findings indicate that SAV742 plays crucial roles in not only avermectin biosynthesis but also coordination of complex physiological processes in S. avermitilis.
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Affiliation(s)
- Di Sun
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jianya Zhu
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Zhi Chen
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jilun Li
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Ying Wen
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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Jourdan S, Francis IM, Kim MJ, Salazar JJC, Planckaert S, Frère JM, Matagne A, Kerff F, Devreese B, Loria R, Rigali S. The CebE/MsiK Transporter is a Doorway to the Cello-oligosaccharide-mediated Induction of Streptomyces scabies Pathogenicity. Sci Rep 2016; 6:27144. [PMID: 27250236 PMCID: PMC4890002 DOI: 10.1038/srep27144] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 05/16/2016] [Indexed: 11/15/2022] Open
Abstract
Streptomyces scabies is an economically important plant pathogen well-known for damaging root and tuber crops by causing scab lesions. Thaxtomin A is the main causative agent responsible for the pathogenicity of S. scabies and cello-oligosaccharides are environmental triggers that induce the production of this phytotoxin. How cello-oligosaccharides are sensed or transported in order to induce the virulent behavior of S. scabies? Here we report that the cellobiose and cellotriose binding protein CebE, and MsiK, the ATPase providing energy for carbohydrates transport, are the protagonists of the cello-oligosaccharide mediated induction of thaxtomin production in S. scabies. Our work provides the first example where the transport and not the sensing of major constituents of the plant host is the central mechanism associated with virulence of the pathogen. Our results allow to draw a complete pathway from signal transport to phytotoxin production where each step of the cascade is controlled by CebR, the cellulose utilization regulator. We propose the high affinity of CebE to cellotriose as possible adaptation of S. scabies to colonize expanding plant tissue. Our work further highlights how genes associated with primary metabolism in nonpathogenic Streptomyces species have been recruited as basic elements of virulence in plant pathogenic species.
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Affiliation(s)
- Samuel Jourdan
- Centre for Protein Engineering, Integrative Biological Sciences (InBioS) Research Unit, University of Liège, Institut de Chimie B6a, B-4000, Liège, Belgium
| | - Isolde Maria Francis
- Department of Biology, California State University Bakersfield, Bakersfield, CA 93311-1022, USA
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611-0180, USA
| | - Min Jung Kim
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611-0180, USA
| | - Joren Jeico C. Salazar
- Department of Biology, California State University Bakersfield, Bakersfield, CA 93311-1022, USA
| | - Sören Planckaert
- Laboratory for Protein Biochemistry and Biomolecular Engineering, Department of Biochemistry and Microbiology, Ghent University, B-9000, Ghent, Belgium
| | - Jean-Marie Frère
- Centre for Protein Engineering, Integrative Biological Sciences (InBioS) Research Unit, University of Liège, Institut de Chimie B6a, B-4000, Liège, Belgium
| | - André Matagne
- Centre for Protein Engineering, Integrative Biological Sciences (InBioS) Research Unit, University of Liège, Institut de Chimie B6a, B-4000, Liège, Belgium
| | - Frédéric Kerff
- Centre for Protein Engineering, Integrative Biological Sciences (InBioS) Research Unit, University of Liège, Institut de Chimie B6a, B-4000, Liège, Belgium
| | - Bart Devreese
- Laboratory for Protein Biochemistry and Biomolecular Engineering, Department of Biochemistry and Microbiology, Ghent University, B-9000, Ghent, Belgium
| | - Rosemary Loria
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611-0180, USA
| | - Sébastien Rigali
- Centre for Protein Engineering, Integrative Biological Sciences (InBioS) Research Unit, University of Liège, Institut de Chimie B6a, B-4000, Liège, Belgium
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Fyans JK, Bown L, Bignell DRD. Isolation and Characterization of Plant-Pathogenic Streptomyces Species Associated with Common Scab-Infected Potato Tubers in Newfoundland. PHYTOPATHOLOGY 2016; 106:123-131. [PMID: 26524546 DOI: 10.1094/phyto-05-15-0125-r] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Potato common scab (CS) is an economically important crop disease that is caused by several members of the genus Streptomyces. In this study, we characterized the plant-pathogenic Streptomyces spp. associated with CS-infected potato tubers harvested in Newfoundland, Canada. A total of 17 pathogenic Streptomyces isolates were recovered from potato scab lesions, of which eight were determined to be most similar to the known CS pathogen S. europaeiscabiei. All eight S. europaeiscabiei isolates were found to produce the thaxtomin A phytotoxin and to harbor the nec1 virulence gene, and most also carry the putative virulence gene tomA. The remaining isolates appear to be novel pathogenic species that do not produce thaxtomin A, and only two of these isolates were determined to harbor the nec1 or tomA genes. Of the non-thaxtomin-producing isolates, strain 11-1-2 was shown to exhibit a severe pathogenic phenotype against different plant hosts and to produce a novel, secreted phytotoxic substance. This is the first report documenting the plant-pathogenic Streptomyces spp. associated with CS disease in Newfoundland. Furthermore, our findings provide further evidence that phytotoxins other than thaxtomin A may also contribute to the development of CS by Streptomyces spp.
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Affiliation(s)
- Joanna K Fyans
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, A1B 3X9, Canada
| | - Luke Bown
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, A1B 3X9, Canada
| | - Dawn R D Bignell
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, A1B 3X9, Canada
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Padilla-Reynaud R, Simao-Beaunoir AM, Lerat S, Bernards MA, Beaulieu C. Suberin Regulates the Production of Cellulolytic Enzymes in Streptomyces scabiei, the Causal Agent of Potato Common Scab. Microbes Environ 2015; 30:245-53. [PMID: 26330095 PMCID: PMC4567563 DOI: 10.1264/jsme2.me15034] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 06/28/2015] [Indexed: 12/21/2022] Open
Abstract
Suberin, a major constituent of the potato periderm, is known to promote the production of thaxtomins, the key virulence factors of the common scab-causing agent Streptomyces scabiei. In the present study, we speculated that suberin affected the production of glycosyl hydrolases, such as cellulases, by S. scabiei, and demonstrated that suberin promoted glycosyl hydrolase activity when added to cellulose-, xylan-, or lichenin-containing media. Furthermore, secretome analyses revealed that the addition of suberin to a cellulose-containing medium increased the production of glycosyl hydrolases. For example, the production of 13 out of the 14 cellulases produced by S. scabiei in cellulose-containing medium was stimulated by the presence of suberin. In most cases, the transcription of the corresponding cellulase-encoding genes was also markedly increased when the bacterium was grown in the presence of suberin and cellulose. The level of a subtilase-like protease inhibitor was markedly decreased by the presence of suberin. We proposed a model for the onset of S. scabiei virulence mechanisms by both cellulose and suberin, the main degradation product of cellulose that acts as an inducer of thaxtomin biosynthetic genes, and suberin promoting the biosynthesis of secondary metabolites including thaxtomins.
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Affiliation(s)
- Rebeca Padilla-Reynaud
- Centre SÈVE, Département de Biologie, Université de Sherbrooke,
Sherbrooke (QC), J1K 2R1,
Canada
| | | | - Sylvain Lerat
- Centre SÈVE, Département de Biologie, Université de Sherbrooke,
Sherbrooke (QC), J1K 2R1,
Canada
| | - Mark A. Bernards
- Department of Biology, University of Western Ontario,
London (ON), N6A 5B7,
Canada
| | - Carole Beaulieu
- Centre SÈVE, Département de Biologie, Université de Sherbrooke,
Sherbrooke (QC), J1K 2R1,
Canada
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Romero-Rodríguez A, Robledo-Casados I, Sánchez S. An overview on transcriptional regulators in Streptomyces. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:1017-39. [PMID: 26093238 DOI: 10.1016/j.bbagrm.2015.06.007] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 06/09/2015] [Accepted: 06/12/2015] [Indexed: 12/19/2022]
Abstract
Streptomyces are Gram-positive microorganisms able to adapt and respond to different environmental conditions. It is the largest genus of Actinobacteria comprising over 900 species. During their lifetime, these microorganisms are able to differentiate, produce aerial mycelia and secondary metabolites. All of these processes are controlled by subtle and precise regulatory systems. Regulation at the transcriptional initiation level is probably the most common for metabolic adaptation in bacteria. In this mechanism, the major players are proteins named transcription factors (TFs), capable of binding DNA in order to repress or activate the transcription of specific genes. Some of the TFs exert their action just like activators or repressors, whereas others can function in both manners, depending on the target promoter. Generally, TFs achieve their effects by using one- or two-component systems, linking a specific type of environmental stimulus to a transcriptional response. After DNA sequencing, many streptomycetes have been found to have chromosomes ranging between 6 and 12Mb in size, with high GC content (around 70%). They encode for approximately 7000 to 10,000 genes, 50 to 100 pseudogenes and a large set (around 12% of the total chromosome) of regulatory genes, organized in networks, controlling gene expression in these bacteria. Among the sequenced streptomycetes reported up to now, the number of transcription factors ranges from 471 to 1101. Among these, 315 to 691 correspond to transcriptional regulators and 31 to 76 are sigma factors. The aim of this work is to give a state of the art overview on transcription factors in the genus Streptomyces.
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Affiliation(s)
- Alba Romero-Rodríguez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México, D.F. 04510, Mexico
| | - Ivonne Robledo-Casados
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México, D.F. 04510, Mexico
| | - Sergio Sánchez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México, D.F. 04510, Mexico.
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Abstract
A relatively small number of species in the large genus Streptomyces are pathogenic; the best characterized of these is Streptomyces scabies. The pathogenicity of S. scabies strains is dependent on the production of the nitrated diketopiperazine thaxtomin A, which is a potent plant cellulose synthesis inhibitor. Much is known about the genetic loci associated with plant virulence; however, the molecular mechanisms by which S. scabies triggers expression of thaxtomin biosynthetic genes, beyond the pathway-specific activator TxtR, are not well understood. In this study, we demonstrate that binding sites for the cellulose utilization repressor CebR occur and function within the thaxtomin biosynthetic cluster. This was an unexpected result, as CebR is devoted to primary metabolism and nutritive functions in nonpathogenic streptomycetes. In S. scabies, cellobiose and cellotriose inhibit the DNA-binding ability of CebR, leading to an increased expression of the thaxtomin biosynthetic and regulatory genes txtA, txtB, and txtR. Deletion of cebR results in constitutive thaxtomin A production and hypervirulence of S. scabies. The pathogenicity of S. scabies is thus under dual direct positive and negative transcriptional control where CebR is the cellobiose-sensing key that locks the expression of txtR, the key necessary to unlock the production of the phytotoxin. Interestingly, CebR-binding sites also lie upstream of and within the thaxtomin biosynthetic clusters in Streptomyces turgidiscabies and Streptomyces acidiscabies, suggesting that CebR is most likely an important regulator of virulence in these plant-pathogenic species as well. What makes a microorganism pathogenic is not limited to the genes acquired for virulence. Using the main causative agent of scab lesions on root and tuber crops as an example, our work identified the subtle but essential genetic changes that generate the cis-acting elements necessary for proper timing of the expression of the cluster of genes responsible for the biosynthesis of thaxtomin A, the primary virulence factor in plant-pathogenic streptomycetes. These data illustrate a situation in which a regulator associated with primary metabolism in nonpathogens, CebR, has been coopted as a master regulator of virulence in pathogenic species. Furthermore, the manipulation of CebR-mediated control of thaxtomin production will facilitate overproduction of this natural and biodegradable herbicide for commercial purposes. Our work thus provides a concrete example of how a strictly theoretical and computational work was able to elucidate a regulatory mechanism associated with the virulence of a plant pathogen and to generate solutions to purely agro-industrial concerns.
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Bignell DRD, Francis IM, Fyans JK, Loria R. Thaxtomin A production and virulence are controlled by several bld gene global regulators in Streptomyces scabies. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:875-85. [PMID: 24678834 DOI: 10.1094/mpmi-02-14-0037-r] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Streptomyces scabies is the main causative agent of common scab disease, which leads to significant annual losses to potato growers worldwide. The main virulence factor produced by S. scabies is a phytotoxic secondary metabolite called thaxtomin A, which functions as a cellulose synthesis inhibitor. Thaxtomin A production is controlled by the cluster-situated regulator TxtR, which activates expression of the thaxtomin biosynthetic genes in response to cello-oligosaccharides. Here, we demonstrate that at least five additional regulatory genes are required for wild-type levels of thaxtomin A production and plant pathogenicity in S. scabies. These regulatory genes belong to the bld gene family of global regulators that control secondary metabolism or morphological differentiation in Streptomyces spp. Quantitative reverse-transcriptase polymerase chain reaction showed that expression of the thaxtomin biosynthetic genes was significantly downregulated in all five bld mutants and, in four of these mutants, this downregulation was attributed to the reduction in expression of txtR. Furthermore, all of the mutants displayed reduced expression of other known or predicted virulence genes, suggesting that the bld genes may function as global regulators of virulence gene expression in S. scabies.
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Abstract
The most common prokaryotic signal transduction mechanisms are the one-component systems in which a single polypeptide contains both a sensory domain and a DNA-binding domain. Among the >20 classes of one-component systems, the TetR family of regulators (TFRs) are widely associated with antibiotic resistance and the regulation of genes encoding small-molecule exporters. However, TFRs play a much broader role, controlling genes involved in metabolism, antibiotic production, quorum sensing, and many other aspects of prokaryotic physiology. There are several well-established model systems for understanding these important proteins, and structural studies have begun to unveil the mechanisms by which they bind DNA and recognize small-molecule ligands. The sequences for more than 200,000 TFRs are available in the public databases, and genomics studies are identifying their target genes. Three-dimensional structures have been solved for close to 200 TFRs. Comparison of these structures reveals a common overall architecture of nine conserved α helices. The most important open question concerning TFR biology is the nature and diversity of their ligands and how these relate to the biochemical processes under their control.
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Structural insights into the mechanism for recognizing substrate of the cytochrome P450 enzyme TxtE. PLoS One 2013; 8:e81526. [PMID: 24282603 PMCID: PMC3840065 DOI: 10.1371/journal.pone.0081526] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Accepted: 10/14/2013] [Indexed: 11/19/2022] Open
Abstract
Thaxtomins, a family of phytotoxins produced by Streptomyces spp., can cause dramatic plant cell hypertrophy and seedling stunting. Thaxtomin A is the dominant form from Streptomyces scabies and has demonstrated herbicidal action. TxtE, a cytochrome P450 enzyme from Streptomyces scabies 87.22, catalyzes direct nitration of the indolyl moiety of L-tryptophan to L-4-nitrotryptophan using nitric oxide, dioxygen and NADPH. The crystal structure of TxtE was determined at 2.1 Å resolution and described in this work. A clearly defined substrate access channel is observed and can be classified as channel 2a, which is common in bacteria cytochrome P450 enzymes. A continuous hydrogen bond chain from the active site to the external solvent is observed. Compared with other cytochrome P450 enzymes, TxtE shows a unique proton transfer pathway which crosses the helix I distortion. Polar contacts of Arg59, Tyr89, Asn293, Thr296, and Glu394 with L-tryptophan are seen using molecular docking analysis, which are potentially important for substrate recognition and binding. After mutating Arg59, Asn293, Thr296 or Glu394 to leucine, the substrate binding ability of TxtE was lost or decreased significantly. Based on the docking and mutation results, a possible mechanism for substrate recognition and binding is proposed.
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Bignell D, Fyans J, Cheng Z. Phytotoxins produced by plant pathogenic Streptomyces
species. J Appl Microbiol 2013; 116:223-35. [DOI: 10.1111/jam.12369] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 10/11/2013] [Accepted: 10/12/2013] [Indexed: 01/18/2023]
Affiliation(s)
- D.R.D. Bignell
- Department of Biology; Memorial University of Newfoundland; St. John's NL Canada
| | - J.K. Fyans
- Department of Biology; Memorial University of Newfoundland; St. John's NL Canada
| | - Z. Cheng
- Department of Biology; Memorial University of Newfoundland; St. John's NL Canada
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Rebets Y, Brötz E, Tokovenko B, Luzhetskyy A. Actinomycetes biosynthetic potential: how to bridge in silico and in vivo? J Ind Microbiol Biotechnol 2013; 41:387-402. [PMID: 24127068 DOI: 10.1007/s10295-013-1352-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Accepted: 09/18/2013] [Indexed: 10/26/2022]
Abstract
Actinomycetes genome sequencing and bioinformatic analyses revealed a large number of "cryptic" gene clusters coding for secondary metabolism. These gene clusters have the potential to increase the chemical diversity of natural products. Indeed, reexamination of well-characterized actinomycetes strains revealed a variety of hidden treasures. Growing information about this metabolic diversity has promoted further development of strategies to discover novel biologically active compounds produced by actinomycetes. This new task for actinomycetes genetics requires the development and use of new approaches and tools. Application of synthetic biology approaches led to the development of a set of strategies and tools to satisfy these new requirements. In this review, we discuss strategies and methods to discover small molecules produced by these fascinating bacteria and also discuss a variety of genetic instruments and regulatory elements used to activate secondary metabolism cryptic genes for the overproduction of these metabolites.
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Affiliation(s)
- Yuriy Rebets
- Helmholtz-Institute for Pharmaceutical Research Saarland, Campus, Building C2.3, Saarbrücken, 66123, Germany
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Cai X, Teta R, Kohlhaas C, Crüsemann M, Ueoka R, Mangoni A, Freeman M, Piel J. Manipulation of Regulatory Genes Reveals Complexity and Fidelity in Hormaomycin Biosynthesis. ACTA ACUST UNITED AC 2013; 20:839-46. [DOI: 10.1016/j.chembiol.2013.04.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 04/19/2013] [Accepted: 04/26/2013] [Indexed: 12/28/2022]
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