1
|
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.
Collapse
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
| |
Collapse
|
2
|
Weisberg AJ, Pearce E, Kramer CG, Chang JH, Clarke CR. Diverse mobile genetic elements shaped the evolution of Streptomyces virulence. Microb Genom 2023; 9. [PMID: 37930748 DOI: 10.1099/mgen.0.001127] [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: 11/07/2023] Open
Abstract
Mobile genetic elements can innovate bacteria with new traits. In plant pathogenic Streptomyces, frequent and recent acquisition of integrative and conjugative or mobilizable genetic elements is predicted to lead to the emergence of new lineages that gained the capacity to synthesize Thaxtomin, a phytotoxin neccesary for induction of common scab disease on tuber and root crops. Here, we identified components of the Streptomyces-potato pathosystem implicated in virulence and investigated them as a nested and interacting system to reevaluate evolutionary models. We sequenced and analysed genomes of 166 strains isolated from over six decades of sampling primarily from field-grown potatoes. Virulence genes were associated to multiple subtypes of genetic elements differing in mechanisms of transmission and evolutionary histories. Evidence is consistent with few ancient acquisition events followed by recurrent loss or swaps of elements carrying Thaxtomin A-associated genes. Subtypes of another genetic element implicated in virulence are more distributed across Streptomyces. However, neither the subtype classification of genetic elements containing virulence genes nor taxonomic identity was predictive of pathogenicity on potato. Last, findings suggested that phytopathogenic strains are generally endemic to potato fields and some lineages were established by historical spread and further dispersed by few recent transmission events. Results from a hierarchical and system-wide characterization refine our understanding by revealing multiple mechanisms that gene and bacterial dispersion have had on shaping the evolution of a Gram-positive pathogen in agricultural settings.
Collapse
Affiliation(s)
- Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Emma Pearce
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Charles G Kramer
- USDA Agricultural Research Service, USDA Agricultural Research Service, Genetic Improvement for Fruits and Vegetables Lab, Beltsville, MD, USA
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Christopher R Clarke
- USDA Agricultural Research Service, USDA Agricultural Research Service, Genetic Improvement for Fruits and Vegetables Lab, Beltsville, MD, USA
| |
Collapse
|
3
|
Liu JL, Yao J, Zhou DL, Liu B, Liu H, Li M, Zhao C, Sunahara G, Duran R. Mining-related multi-resistance genes in sulfate-reducing bacteria treatment of typical karst nonferrous metal(loid) mine tailings in China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:104753-104766. [PMID: 37707732 DOI: 10.1007/s11356-023-29203-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 08/02/2023] [Indexed: 09/15/2023]
Abstract
Management of tailings at metal mine smelter sites can reduce the potential hazards associated with exposure to toxic metal(loid)s and residual organic flotation reagents. In addition, microbes in the tailings harboring multi-resistance genes (e.g., tolerance to multiple antimicrobial agents) can cause high rates of morbidity and global economic problems. The potential co-selection mechanisms of antibiotic resistance genes (ARGs) and metal(loid) resistance genes (MRGs) during tailings sulfate-reducing bacteria (SRB) treatment have been poorly investigated. Samples were collected from a nonferrous metal mine tailing site treated with an established SRB protocol and were analyzed for selected geochemical properties and high throughput sequencing of 16S rRNA gene barcoding. Based on the shotgun metagenomic analysis, the bacterial domain was dominant in nonferrous metal(loid)-rich tailings treated with SRB for 12 months. KEGGs related to ARGs and MRGs were detected. Thiobacillus and Sphingomonas were the main genera carrying the bacA and mexEF resistance operons, along with Sulfuricella which were also found as the main genera carrying MRGs. The SRB treatment may mediate the distribution of numerous resistance genes. KOs based on the metagenomic database indicated that ARGs (mexNW, merD, sul, and bla) and MRGs (czcABCR and copRS genes) were found on the same contig. The SRB strains (Desulfosporosinus and Desulfotomaculum), and the acidophilic strain Acidiphilium significantly contributed to the distribution of sul genes. The functional metabolic pathways related to siderophores metabolism were largely from anaerobic genera of Streptomyces and Microbacterium. The presence of arsenate reductase, metal efflux pump, and Fe transport genes indicated that SRB treatment plays a key role in the metal(loid)s transformation. Overall, our findings show that bio-treatment is an effective tool for managing ARGs/MRGs and metals in tailings that contain numerous metal(loid) contaminants.
Collapse
Affiliation(s)
- Jian-Li Liu
- School of Water Resources and Environment and Research Center of Environmental Science and Engineering, Sino-Hungarian Joint Laboratory of Environmental Science and Health, Beijing Key Laboratory of Water Resources & Environmental Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing, 100083, China.
| | - Jun Yao
- School of Water Resources and Environment and Research Center of Environmental Science and Engineering, Sino-Hungarian Joint Laboratory of Environmental Science and Health, Beijing Key Laboratory of Water Resources & Environmental Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - De-Liang Zhou
- Beijing Zhongdianyida Technology Co., Ltd, Beijing, 100190, China
| | - Bang Liu
- School of Water Resources and Environment and Research Center of Environmental Science and Engineering, Sino-Hungarian Joint Laboratory of Environmental Science and Health, Beijing Key Laboratory of Water Resources & Environmental Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Houquan Liu
- School of Water Resources and Environment and Research Center of Environmental Science and Engineering, Sino-Hungarian Joint Laboratory of Environmental Science and Health, Beijing Key Laboratory of Water Resources & Environmental Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Miaomiao Li
- School of Water Resources and Environment and Research Center of Environmental Science and Engineering, Sino-Hungarian Joint Laboratory of Environmental Science and Health, Beijing Key Laboratory of Water Resources & Environmental Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Chenchen Zhao
- School of Water Resources and Environment and Research Center of Environmental Science and Engineering, Sino-Hungarian Joint Laboratory of Environmental Science and Health, Beijing Key Laboratory of Water Resources & Environmental Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Geoffrey Sunahara
- School of Water Resources and Environment and Research Center of Environmental Science and Engineering, Sino-Hungarian Joint Laboratory of Environmental Science and Health, Beijing Key Laboratory of Water Resources & Environmental Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing, 100083, China
- Department of Natural Resource Sciences, McGill University, Montreal, Quebec, H9X3V9, Canada
| | - Robert Duran
- School of Water Resources and Environment and Research Center of Environmental Science and Engineering, Sino-Hungarian Joint Laboratory of Environmental Science and Health, Beijing Key Laboratory of Water Resources & Environmental Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing, 100083, China
- Université de Pau et des Pays de l'Adour/E2S UPPA, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Cui L, Yang C, Jin M, Wei L, Yang L, Zhou J. Identification and biological characterization of a new pathogen that causes potato scab in Gansu Province, China. Microb Pathog 2021; 161:105276. [PMID: 34728371 DOI: 10.1016/j.micpath.2021.105276] [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: 07/15/2021] [Revised: 10/28/2021] [Accepted: 10/29/2021] [Indexed: 10/19/2022]
Abstract
Potato scab caused by pathogenic Streptomyces is a serious soil-borne disease on potato. In this study, a new Streptomyces strain 5A-1 was isolated from potato samples in China. Based on morphological characteristics, 16S rDNA gene sequence analyses, it was identified as Streptomyces griseoplanus (Streptacidiphilus griseoplanus), pathogenicity of which was measured by the methods of small potato chips, radish slices and potato pot trial inoculation. Moreover, the pathogenic genes txtAB and tomA from the Streptomyces pathogenicity island (PAI) were detected. Determination of biological characteristics showed that the optimal temperature for the growth of S. griseoplanus strain 5A-1 was 25 °C, the optimal light condition was darkness, the optimal pH value was 8.5 and the most preferred carbon source and nitrogen source is glucose and aspartate, respectively. To our knowledge, it is the first report for S. griseoplanus, as a new pathogen, to cause potato scab.
Collapse
Affiliation(s)
- Lingxiao Cui
- Laboratory of Biocontrol Engineering of Crop Pests and Diseases in Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou, 730070, China
| | - Chengde Yang
- Laboratory of Biocontrol Engineering of Crop Pests and Diseases in Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Mengjun Jin
- Laboratory of Biocontrol Engineering of Crop Pests and Diseases in Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou, 730070, China
| | - Lijuan Wei
- Laboratory of Biocontrol Engineering of Crop Pests and Diseases in Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou, 730070, China
| | - Liping Yang
- Laboratory of Biocontrol Engineering of Crop Pests and Diseases in Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou, 730070, China
| | - Jingjiang Zhou
- Laboratory of Biocontrol Engineering of Crop Pests and Diseases in Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou, 730070, China; State Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxin District, Guiyang, 550025, China
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Lapaz MI, López A, Huguet-Tapia JC, Pérez-Baldassari MF, Iglesias C, Loria R, Moyna G, Pianzzola MJ. Isolation and structural characterization of a non-diketopiperazine phytotoxin from a potato pathogenic Streptomyces strain. Nat Prod Res 2018; 33:2951-2957. [PMID: 30304960 DOI: 10.1080/14786419.2018.1511554] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Two Streptomyces spp. strains responsible for potato common scab infections in Uruguay which do not produce diketopiperazines were identified through whole-genome sequencing, and the virulence factor produced by one of them was isolated and characterized. Phylogenetic analysis showed that both pathogenic strains can be identified as S. niveiscabiei, and the structure of the phytotoxin was elucidated as that of the polyketide desmethylmensacarcin using MS and NMR methods. The metabolite is produced in yields of ∼200 mg/L of culture media, induces deep necrotic lesions on potato tubers, stuns root and shoot growth in radish seedlings, and is comparatively more aggressive than thaxtomin A. This is the first time that desmethylmensacarcin, a member of a class of compounds known for their antitumor and antibiotic activity, is associated with phytotoxicity. More importantly, it represents the discovery of a new virulence factor related to potato common scab, an economically-important disease affecting potato production worldwide.
Collapse
Affiliation(s)
- María Inés Lapaz
- a Área Microbiología, Departamento de Biociencias, Facultad de Química, UdelaR , Montevideo , Uruguay
| | - Andrés López
- b Laboratorio de Fisicoquímica Orgánica, Departamento de Química del Litoral, CENUR Litoral Norte, UdelaR , Paysandú , Uruguay
| | - José Carlos Huguet-Tapia
- c Plant Pathology Department, Institute of Food and Agricultural Sciences, University of Florida , Gainesville , FL , USA
| | | | - Cesar Iglesias
- a Área Microbiología, Departamento de Biociencias, Facultad de Química, UdelaR , Montevideo , Uruguay
| | - Rosemary Loria
- c Plant Pathology Department, Institute of Food and Agricultural Sciences, University of Florida , Gainesville , FL , USA
| | - Guillermo Moyna
- b Laboratorio de Fisicoquímica Orgánica, Departamento de Química del Litoral, CENUR Litoral Norte, UdelaR , Paysandú , Uruguay
| | - María Julia Pianzzola
- a Área Microbiología, Departamento de Biociencias, Facultad de Química, UdelaR , Montevideo , Uruguay
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Lapaz MI, Huguet-Tapia JC, Siri MI, Verdier E, Loria R, Pianzzola MJ. Genotypic and Phenotypic Characterization of Streptomyces Species Causing Potato Common Scab in Uruguay. PLANT DISEASE 2017; 101:1362-1372. [PMID: 30678602 DOI: 10.1094/pdis-09-16-1348-re] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Isolation and characterization of common scab (CS) pathogen Streptomyces spp. from Uruguayan potato tubers and soil samples were done in response to significant economic losses due to CS on potato in autumn 2010. Seventy of the 331 isolates were classified as pathogenic owing to their ability to induce necrosis on tuber disks and stunting of radish seedling. Streptomyces spp. causing CS on potato in Uruguay were found to represent a range of different species by virtue of their diverse morphological and physiological traits as well as rep-PCR, rpoB phylogenetic analysis, and multi-locus sequences analysis. We identified isolates primarily as Streptomyces scabiei, S. acidiscabies, and S. europaeiscabiei. However, some of the pathogenic isolates still remain to be identified at the species level. This highlights the need for improved methods for discrimination among pathogenic Streptomyces species. The presence of Streptomyces pathogenicity island (PAI) genes was analyzed, including genes encoding for thaxtomin synthetase (txtA, txtB), tomatinase (tomA), and a necrosis protein (nec1). Among the isolates that were pathogenic, 50% contained the four pathogenicity genes, 33% had an atypical composition of PAI marker genes, and 17% did not contain any genes. The absence of the genes reported to be involved in thaxtomin biosynthesis (txtA, txtB) was confirmed by whole-genome sequencing of two representative strains of this group. This finding suggests the participation of other virulence factors in plant pathogenicity.
Collapse
Affiliation(s)
- M I Lapaz
- Cátedra de Microbiología, Departamento de Biociencias, Facultad de Química (FQ), Universidad de la República, 11800 Montevideo, Uruguay
| | - J C Huguet-Tapia
- Department of Plant Pathology, Institute of Food and Agricultural Sciences, University of Florida (UF-IFAS), Gainesville 32611 USA
| | - M I Siri
- Cátedra de Microbiología, Departamento de Biociencias, FQ, Universidad de la República, 11800 Montevideo, Uruguay
| | - E Verdier
- Dirección General de Servicios Agrícolas, Departamento Laboratorios Biológicos, Ministerio de Ganadería Agricultura y Pesca, 12900 Montevideo, Uruguay
| | - R Loria
- Department of Plant Pathology, UF-IFAS, Gainesville 32611 USA
| | - M J Pianzzola
- Cátedra de Microbiología, Departamento de Biociencias, FQ, Universidad de la República, 11800 Montevideo, Uruguay
| |
Collapse
|
12
|
Abstract
About 2,500 papers dated 2014–2016 were recovered by searching the PubMed database for
Streptomyces, which are the richest known source of antibiotics. This review integrates around 100 of these papers in sections dealing with evolution, ecology, pathogenicity, growth and development, stress responses and secondary metabolism, gene expression, and technical advances. Genomic approaches have greatly accelerated progress. For example, it has been definitively shown that interspecies recombination of conserved genes has occurred during evolution, in addition to exchanges of some of the tens of thousands of non-conserved accessory genes. The closeness of the association of
Streptomyces with plants, fungi, and insects has become clear and is reflected in the importance of regulators of cellulose and chitin utilisation in overall
Streptomyces biology. Interestingly, endogenous cellulose-like glycans are also proving important in hyphal growth and in the clumping that affects industrial fermentations. Nucleotide secondary messengers, including cyclic di-GMP, have been shown to provide key input into developmental processes such as germination and reproductive growth, while late morphological changes during sporulation involve control by phosphorylation. The discovery that nitric oxide is produced endogenously puts a new face on speculative models in which regulatory Wbl proteins (peculiar to actinobacteria) respond to nitric oxide produced in stressful physiological transitions. Some dramatic insights have come from a new model system for
Streptomyces developmental biology,
Streptomyces venezuelae, including molecular evidence of very close interplay in each of two pairs of regulatory proteins. An extra dimension has been added to the many complexities of the regulation of secondary metabolism by findings of regulatory crosstalk within and between pathways, and even between species, mediated by end products. Among many outcomes from the application of chromosome immunoprecipitation sequencing (ChIP-seq) analysis and other methods based on “next-generation sequencing” has been the finding that 21% of
Streptomyces mRNA species lack leader sequences and conventional ribosome binding sites. Further technical advances now emerging should lead to continued acceleration of knowledge, and more effective exploitation, of these astonishing and critically important organisms.
Collapse
Affiliation(s)
- Keith F Chater
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| |
Collapse
|
13
|
Zhang Y, Bignell DRD, Zuo R, Fan Q, Huguet-Tapia JC, Ding Y, Loria R. Promiscuous Pathogenicity Islands and Phylogeny of Pathogenic Streptomyces spp. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2016; 29:640-50. [PMID: 27502745 DOI: 10.1094/mpmi-04-16-0068-r] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Approximately 10 Streptomyces species cause disease on underground plant structures. The most economically important of these is potato scab, and the most studied of these pathogens is Streptomyces scabiei (syn. S. scabies). The main pathogenicity determinant of scab-causing Streptomyces species is a nitrated diketopiperazine, known as thaxtomin A (ThxA). In the pathogenic species Streptomyces turgidiscabies, ThxA biosynthetic genes reside on a mobile pathogenicity island (PAI). However, the mobilization of PAIs in other Streptomyces species remains uncharacterized. Here, we investigated the mobilization of the PAI of S. scabiei 87-22. Based on whole genome sequences, we inferred the evolutionary relationships of pathogenic Streptomyces species and discovered that Streptomyces sp. strain 96-12, a novel pathogenic species isolated from potatoes in Egypt, was phylogenetically grouped with nonpathogenic species rather than with known pathogenic species. We also found that Streptomyces sp. strain 96-12 contains a PAI that is almost identical to the PAI in S. scabiei 87-22, despite significant differences in their genome sequences. This suggested direct or indirect in vivo mobilization of the PAI between S. scabiei and nonpathogenic Streptomyces species. To test whether the S. scabiei 87-22 PAI could, indeed, be mobilized, S. scabiei 87-22 deletion mutants containing antibiotic resistance markers in the PAI were mated with Streptomyces diastatochromogenes, a nonpathogenic species. The PAI of S. scabiei was site-specifically inserted into the aviX1 gene of S. diastatochromogenes and conferred pathogenicity in radish seedling assays. Our results demonstrated that S. scabiei, the earliest described Streptomyces pathogen, could be the source of a PAI responsible for the emergence of novel pathogenic species.
Collapse
Affiliation(s)
- Yucheng Zhang
- 1 Department of Plant Pathology, University of Florida, Gainesville, Florida, U.S.A
| | - Dawn R D Bignell
- 2 Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Ran Zuo
- 3 Department of Medicinal Chemistry, University of Florida, Gainesville, Florida, U.S.A.; and
| | - Qiurong Fan
- 4 College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Jose C Huguet-Tapia
- 1 Department of Plant Pathology, University of Florida, Gainesville, Florida, U.S.A
| | - Yousong Ding
- 3 Department of Medicinal Chemistry, University of Florida, Gainesville, Florida, U.S.A.; and
| | - Rosemary Loria
- 1 Department of Plant Pathology, University of Florida, Gainesville, Florida, U.S.A
| |
Collapse
|
14
|
Chapleau M, Guertin JF, Farrokhi A, Lerat S, Burrus V, Beaulieu C. Identification of genetic and environmental factors stimulating excision from Streptomyces scabiei chromosome of the toxicogenic region responsible for pathogenicity. MOLECULAR PLANT PATHOLOGY 2016; 17:501-9. [PMID: 26177341 PMCID: PMC6638466 DOI: 10.1111/mpp.12296] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The genes conferring pathogenicity in Streptomyces turgidiscabies, a pathogen causing common scab of potato, are grouped together on a pathogenicity island (PAI), which has been found to be mobile and appears to transfer and disseminate like an integrative and conjugative element (ICE). However, in Streptomyces scabiei, another common scab-inducing species, the pathogenicity genes are clustered in two regions: the toxicogenic region (TR) and the colonization region. The S. scabiei 87.22 genome was analysed to investigate the potential mobility of the TR. Attachment sites (att), short homologous sequences that delineate ICEs, were identified at both extremities of the TR. An internal att site was also found, suggesting that the TR has a composite structure (TR1 and TR2). Thaxtomin biosynthetic genes, essential for pathogenicity, were found in TR1, whereas candidate genes with known functions in recombination, replication and conjugal transfer were found in TR2. Excision of the TR1 or TR2 subregions alone, or of the entire TR region, was observed, although the excision frequency of TR was low. However, the excision frequency was considerably increased in the presence of either mitomycin C or Streptomyces coelicolor cells. A composite TR structure was not observed in all S. scabiei and Streptomyces acidiscabies strains tested. Of the ten strains analysed, seven lacked TR2 and no TR excision event could be detected in these strains, thus suggesting the implication of TR2 in the mobilization of S. scabiei TR.
Collapse
Affiliation(s)
- Mélanie Chapleau
- Centre SÈVE, Département de biologie, Université de Sherbrooke, Sherbrooke, QC, Canada, J1K 2R1
| | - Julien F Guertin
- Centre SÈVE, Département de biologie, Université de Sherbrooke, Sherbrooke, QC, Canada, J1K 2R1
| | - Ali Farrokhi
- Centre SÈVE, Département de biologie, Université de Sherbrooke, Sherbrooke, QC, Canada, J1K 2R1
| | - Sylvain Lerat
- Centre SÈVE, Département de biologie, Université de Sherbrooke, Sherbrooke, QC, Canada, J1K 2R1
| | - Vincent Burrus
- Centre SÈVE, Département de biologie, Université de Sherbrooke, Sherbrooke, QC, Canada, J1K 2R1
| | - Carole Beaulieu
- Centre SÈVE, Département de biologie, Université de Sherbrooke, Sherbrooke, QC, Canada, J1K 2R1
| |
Collapse
|
15
|
Genome Content and Phylogenomics Reveal both Ancestral and Lateral Evolutionary Pathways in Plant-Pathogenic Streptomyces Species. Appl Environ Microbiol 2016; 82:2146-2155. [PMID: 26826232 DOI: 10.1128/aem.03504-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 01/25/2016] [Indexed: 11/20/2022] Open
Abstract
Streptomyces spp. are highly differentiated actinomycetes with large, linear chromosomes that encode an arsenal of biologically active molecules and catabolic enzymes. Members of this genus are well equipped for life in nutrient-limited environments and are common soil saprophytes. Out of the hundreds of species in the genus Streptomyces, a small group has evolved the ability to infect plants. The recent availability of Streptomyces genome sequences, including four genomes of pathogenic species, provided an opportunity to characterize the gene content specific to these pathogens and to study phylogenetic relationships among them. Genome sequencing, comparative genomics, and phylogenetic analysis enabled us to discriminate pathogenic from saprophytic Streptomyces strains; moreover, we calculated that the pathogen-specific genome contains 4,662 orthologs. Phylogenetic reconstruction suggested that Streptomyces scabies and S. ipomoeae share an ancestor but that their biosynthetic clusters encoding the required virulence factor thaxtomin have diverged. In contrast, S. turgidiscabies and S. acidiscabies, two relatively unrelated pathogens, possess highly similar thaxtomin biosynthesis clusters, which suggests that the acquisition of these genes was through lateral gene transfer.
Collapse
|
16
|
Correction: characterization of the integration and modular excision of the integrative conjugative element PAISt in Streptomyces turgidiscabies Car8. PLoS One 2015; 10:e0121152. [PMID: 25830767 PMCID: PMC4382285 DOI: 10.1371/journal.pone.0121152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
|