1
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Harper CP, Day A, Tsingos M, Ding E, Zeng E, Stumpf SD, Qi Y, Robinson A, Greif J, Blodgett JAV. Critical analysis of polycyclic tetramate macrolactam biosynthetic gene cluster phylogeny and functional diversity. Appl Environ Microbiol 2024; 90:e0060024. [PMID: 38771054 PMCID: PMC11218653 DOI: 10.1128/aem.00600-24] [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: 04/06/2024] [Accepted: 04/25/2024] [Indexed: 05/22/2024] Open
Abstract
Polycyclic tetramate macrolactams (PTMs) are bioactive natural products commonly associated with certain actinobacterial and proteobacterial lineages. These molecules have been the subject of numerous structure-activity investigations since the 1970s. New members continue to be pursued in wild and engineered bacterial strains, and advances in PTM biosynthesis suggest their outwardly simplistic biosynthetic gene clusters (BGCs) belie unexpected product complexity. To address the origins of this complexity and understand its influence on PTM discovery, we engaged in a combination of bioinformatics to systematically classify PTM BGCs and PTM-targeted metabolomics to compare the products of select BGC types. By comparing groups of producers and BGC mutants, we exposed knowledge gaps that complicate bioinformatics-driven product predictions. In sum, we provide new insights into the evolution of PTM BGCs while systematically accounting for the PTMs discovered thus far. The combined computational and metabologenomic findings presented here should prove useful for guiding future discovery.IMPORTANCEPolycyclic tetramate macrolactam (PTM) pathways are frequently found within the genomes of biotechnologically important bacteria, including Streptomyces and Lysobacter spp. Their molecular products are typically bioactive, having substantial agricultural and therapeutic interest. Leveraging bacterial genomics for the discovery of new related molecules is thus desirable, but drawing accurate structural predictions from bioinformatics alone remains challenging. This difficulty stems from a combination of previously underappreciated biosynthetic complexity and remaining knowledge gaps, compounded by a stream of yet-uncharacterized PTM biosynthetic loci gleaned from recently sequenced bacterial genomes. We engaged in the following study to create a useful framework for cataloging historic PTM clusters, identifying new cluster variations, and tracing evolutionary paths for these molecules. Our data suggest new PTM chemistry remains discoverable in nature. However, our metabolomic and mutational analyses emphasize the practical limitations of genomics-based discovery by exposing hidden complexity.
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Affiliation(s)
| | - Anna Day
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Maya Tsingos
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Edward Ding
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Elizabeth Zeng
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Spencer D. Stumpf
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Yunci Qi
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Adam Robinson
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Jennifer Greif
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
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2
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Shelley BA, Pandey B, Sarwar A, Douches D, Collins P, Qu X, Pasche J, Clarke CR. The Role of Soil Abundance of TxtAB in Potato Common Scab Disease Severity. PHYTOPATHOLOGY 2024; 114:1176-1185. [PMID: 38079373 DOI: 10.1094/phyto-09-23-0347-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: 03/12/2024]
Abstract
Common scab is an economically costly soilborne disease of potato endemic in many potato-growing regions. The disease is caused by species of Streptomyces bacteria that produce the phytotoxin thaxtomin A. The primary disease management tool available to growers is planting resistant cultivars, but no cultivar is fully resistant to common scab, and partially resistant cultivars are often not the preferred choice of growers because of agronomic or market considerations. Therefore, growers would benefit from knowledge of the presence and severity of common scab infestations in field soils to make informed planting decisions. We implemented a quantitative PCR diagnostic assay to enable field detection and quantification of all strains of Streptomyces that cause common scab in the United States through amplification of thaxtomin A biosynthetic genes. Greenhouse trials confirmed that pathogen abundance was highly correlated with disease severity for five distinct phytopathogenic Streptomyces species, although the degree of disease severity was dependent on the pathogen species. Correlations between the abundance of the thaxtomin biosynthetic genes from field soil with disease on tubers at field sites across four U.S. states and across 2 years were not as strong as correlations observed in greenhouse assays. We also developed an effective droplet digital PCR diagnostic assay that also has potential for field quantification of thaxtomin biosynthetic genes. Further improvement of the PCR assays and added modeling of other environmental factors that impact disease outcome, such as soil composition, can aid growers in making informed planting decisions.
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Affiliation(s)
- Brett A Shelley
- U.S. Department of Agriculture-Agricultural Research Service, Genetic Improvement for Fruits and Vegetables Lab, 10300 Baltimore Avenue, Beltsville, MD 20705
| | - Binod Pandey
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108
| | - Arslan Sarwar
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108
| | - David Douches
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824
| | - Paul Collins
- U.S. Department of Agriculture-Agricultural Research Service, Genetic Improvement for Fruits and Vegetables Lab, 10300 Baltimore Avenue, Beltsville, MD 20705
| | - Xinshun Qu
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802
| | - Julie Pasche
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108
| | - Christopher R Clarke
- U.S. Department of Agriculture-Agricultural Research Service, Genetic Improvement for Fruits and Vegetables Lab, 10300 Baltimore Avenue, Beltsville, MD 20705
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3
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Bello KE, Irekeola AA, Alshehri AA. Streptomyces isolate SOM013, a potential agent against microbial resistance and gastric ulcers. Saudi Pharm J 2024; 32:102101. [PMID: 38799000 PMCID: PMC11127256 DOI: 10.1016/j.jsps.2024.102101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 05/12/2024] [Indexed: 05/29/2024] Open
Abstract
The menace of microbial resistance and re-emerging disease is still a problem for healthcare givers globally, and the need for newer sources of potent antibiotics has become paramount. This study investigated the antimicrobial and antiulcer activities of Streptomyces isolate SOM013. Streptomyces isolates were cultivated and purified following standard microbiological protocols. Secondary metabolites were recovered and characterized from Streptomyces isolate SOM013 via broth fermentation and extraction. Varying concentrations (0.5 mg/mL, 0.025 mg/mL and 0.0125 mg/mL) of the SOM013 extract were used for antimicrobial screening against resistant bacteria and medically important fungi (methicillin-resistant Escherichia coli, Oxacillin resistant Helicobacter pylori, Shigella spp, extended broad-spectrum resistant Pseudomonas aeruginosa, Streptococcus spp, Campylobacter spp, Candida albicans, Aspergillus niger, and Aspergillus flavus). The antiulcer activity of the SOM013 was also examined in a methanol-induced gastric ulcer animal model. A total of 23 Streptomyces spp were recovered from the study. Methanolic extract of the SOM013 isolates was more potent across the clinical test microorganisms compared to water extract. The antimicrobial activity was dose dependent, with methanolic extract at 0.05 g/mL displaying the highest zone of inhibition (18.8 ± 0.3 mm) when tested against extended broad-spectrum resistant Pseudomonas aeruginosa. Further, the extract's ulcer index and protection efficacy were significant as the concentration increased (P < 0.01). SOM013 isolate has a moderate antimicrobial and high antiulcer activity worthy of pharmacological exploration.
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Affiliation(s)
- Kizito Eneye Bello
- Department of Microbiology, Faculty of Natural Science, Kogi State (Prince Abubakar Audu) University, Anyigba, PMB 1008, Anyigba, Kogi State, Nigeria
| | - Ahmad Adebayo Irekeola
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan 16150, Malaysia
- Microbiology Unit, Department of Biological Sciences, College of Natural and Applied Sciences, Summit University Offa, Offa PMB 4412, Kwara, Nigeria
| | - Ahmad A. Alshehri
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, P.O. Box 1988, Najran, Saudi Arabia
- Health research center, Najran University, P.O. Box 1988, Najran, Saudi Arabia
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4
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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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5
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Hudec C, Biessy A, Léger G, Albert D, Novinscak A, Filion M. Seasonal Dynamics of Various Scab-Causing Streptomyces Genotypes Among Potato Fields on Prince Edward Island. PHYTOPATHOLOGY 2024; 114:146-154. [PMID: 37366579 DOI: 10.1094/phyto-05-23-0149-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: 06/28/2023]
Abstract
Potato common scab is an important bacterial plant disease caused by numerous Streptomyces species and strains. A better understanding of the genetic diversity and population dynamics of these microorganisms in the field is crucial to develop effective control methods. Our research group previously studied the genetic diversity of scab-causing Streptomyces spp. in Prince Edward Island, one of Canada's most important potato-growing provinces. Fourteen distinct Streptomyces genotypes were identified and displayed contrasting aggressiveness toward potato tubers. To better understand the distribution and occurrence of these genotypes over time under field conditions, the population dynamics were studied in nine commercial potato fields throughout a growing season. A comparative genomic-driven approach was used to design genotype-specific primers and probes, allowing us to quantify, using quantitative polymerase chain reaction, the abundance of each of the 14 genotypes in field soil. Thirteen of the previously identified genotypes were detected in at least one soil sample, with various frequencies and population sizes across the different fields under study. Interestingly, weakly virulent genotypes dominated, independent of time or location. Among them, three genotypes accounted for more than 80% of the genotypes' combined population. Although the highly virulent genotypes were detected in lower relative abundance than the weakly virulent ones, an increase in the highly virulent genotypes' population size was observed over the growing season in most fields. The results will ultimately be useful for the development of targeted common scab control strategies.
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Affiliation(s)
- Cindy Hudec
- Department of Biology, Université de Moncton, Moncton, NB E1A 3E9, Canada
| | - Adrien Biessy
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada
| | - Geneviève Léger
- Department of Biology, Université de Moncton, Moncton, NB E1A 3E9, Canada
| | - Daphné Albert
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada
| | - Amy Novinscak
- Agassiz Research and Development Centre, Agriculture and Agri-Food Canada, Agassiz, BC V0M 1A2, Canada
| | - Martin Filion
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada
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6
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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.
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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
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7
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Schuntermann DB, Fischer JT, Bile J, Gaier SA, Shelley BA, Awawdeh A, Jahn M, Hoffman KS, Westhof E, Söll D, Clarke CR, Vargas-Rodriguez O. Mistranslation of the genetic code by a new family of bacterial transfer RNAs. J Biol Chem 2023; 299:104852. [PMID: 37224963 PMCID: PMC10404621 DOI: 10.1016/j.jbc.2023.104852] [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: 04/05/2023] [Revised: 05/16/2023] [Accepted: 05/18/2023] [Indexed: 05/26/2023] Open
Abstract
The correct coupling of amino acids with transfer RNAs (tRNAs) is vital for translating genetic information into functional proteins. Errors during this process lead to mistranslation, where a codon is translated using the wrong amino acid. While unregulated and prolonged mistranslation is often toxic, growing evidence suggests that organisms, from bacteria to humans, can induce and use mistranslation as a mechanism to overcome unfavorable environmental conditions. Most known cases of mistranslation are caused by translation factors with poor substrate specificity or when substrate discrimination is sensitive to molecular changes such as mutations or posttranslational modifications. Here we report two novel families of tRNAs, encoded by bacteria from the Streptomyces and Kitasatospora genera, that adopted dual identities by integrating the anticodons AUU (for Asn) or AGU (for Thr) into the structure of a distinct proline tRNA. These tRNAs are typically encoded next to a full-length or truncated version of a distinct isoform of bacterial-type prolyl-tRNA synthetase. Using two protein reporters, we showed that these tRNAs translate asparagine and threonine codons with proline. Moreover, when expressed in Escherichia coli, the tRNAs cause varying growth defects due to global Asn-to-Pro and Thr-to-Pro mutations. Yet, proteome-wide substitutions of Asn with Pro induced by tRNA expression increased cell tolerance to the antibiotic carbenicillin, indicating that Pro mistranslation can be beneficial under certain conditions. Collectively, our results significantly expand the catalog of organisms known to possess dedicated mistranslation machinery and support the concept that mistranslation is a mechanism for cellular resiliency against environmental stress.
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Affiliation(s)
- Dominik B Schuntermann
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA; Department of Microbiology, Technical University of Braunschweig, Braunschweig, Germany
| | - Jonathan T Fischer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Jonmatthew Bile
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Sarah A Gaier
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Brett A Shelley
- Genetic Improvement for Fruits and Vegetables Lab, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland, USA
| | - Aya Awawdeh
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Martina Jahn
- Department of Microbiology, Technical University of Braunschweig, Braunschweig, Germany
| | | | - Eric Westhof
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, France
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA; Department of Chemistry, Yale University, New Haven, Connecticut, USA.
| | - Christopher R Clarke
- Genetic Improvement for Fruits and Vegetables Lab, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland, USA
| | - Oscar Vargas-Rodriguez
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA.
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8
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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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9
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Nguyen HP, Shelley BA, Mowery J, Clarke CR. Description of Streptomyces griseiscabiei sp. nov. and reassignment of Streptomyces sp. strain NRRL B-16521 to Streptomyces acidiscabies. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Streptomyces
strain NRRL B-2795T (DSM 112329T=NRRL B-2795T) is described as the type strain of Streptomyces griseiscabiei sp. nov. using whole-genome average nucleotide identity and multilocus sequence analyses in addition to phenotypic characterization of carbon source utilization, spore chain morphology, melanin production, salt tolerance, pH tolerance, plant pathogenicity and antibiotic resistance. This strain was previously classified as
Streptomyces scabiei
but suggested as a potential novel species. A second
Streptomyces
strain, NRRL B-16521, previously named
Streptomyces scabiei
, and also previously suggested as a potential novel species, is assigned to
Streptomyces acidiscabies
based on whole-genome average nucleotide identity. Morphological and biochemical characterizations also support this designation for NRRL B-16521. Both
Streptomyces
sp. strain NRRL B-2795T and NRRL B-16521 cause common scab on multiple cultivars of potato.
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Affiliation(s)
- Hien P. Nguyen
- Genetic Improvement for Fruits and Vegetables Lab, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Brett A. Shelley
- Genetic Improvement for Fruits and Vegetables Lab, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Joseph Mowery
- Electron and Confocal Microscopy Unit, Beltsville Agricultural Research Center, Agricultural Research Service, USDA , Beltsville, MD 20705, USA
| | - Christopher R. Clarke
- Genetic Improvement for Fruits and Vegetables Lab, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
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10
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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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11
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Nguyen HP, Weisberg AJ, Chang JH, Clarke CR. Streptomyces caniscabiei sp. nov., which causes potato common scab and is distributed across the world. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005225] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fourteen strains of
Streptomyces
isolated from scab lesions on potato are described as members of a novel species based on genetic distance, morphological observation and biochemical analyses. Morphological and biochemical characteristics of these strains are distinct from other described phytopathogenic species. Strain NE06-02DT has white aerial mycelium and grey, cylindrical, smooth spores on rectus-flexibilis spore chains. Members of this species group can utilize most of the International
Streptomyces
Project sugars, utilize melibiose and trehalose, produce melanin, grow on 6–7 % NaCl and pH 5–5.5 media, and are susceptible to oleandomycin (100 µg ml−1), streptomycin (20 µg ml−1) and penicillin G (30 µg ml−1). Though the 16S rRNA gene sequences from several members of this novel species are identical to the
Streptomyces bottropensis
16S rRNA gene sequence, whole-genome average nucleotide identity and multi-locus sequence analysis confirm that the strains are members of a novel species. Strains belonging to this novel species have been isolated from the United States, Egypt and China with the earliest known members being isolated in 1961 from common scab lesions of potato in both California, USA, and Maine, USA. The name Streptomyces caniscabiei sp. nov. is proposed for strain NE06-02DT (=DSM111602T=ATCC TSD-236T) and the other members of this novel species group.
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Affiliation(s)
- Hien P. Nguyen
- Genetic Improvement for Fruits and Vegetables Lab, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | | | - Jeff H. Chang
- Department of Botany and Plant Pathology, Oregon State University, OR 97331, USA
| | - Christopher R. Clarke
- Genetic Improvement for Fruits and Vegetables Lab, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
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12
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Bacterial translation machinery for deliberate mistranslation of the genetic code. Proc Natl Acad Sci U S A 2021; 118:2110797118. [PMID: 34413202 DOI: 10.1073/pnas.2110797118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Inaccurate expression of the genetic code, also known as mistranslation, is an emerging paradigm in microbial studies. Growing evidence suggests that many microbial pathogens can deliberately mistranslate their genetic code to help invade a host or evade host immune responses. However, discovering different capacities for deliberate mistranslation remains a challenge because each group of pathogens typically employs a unique mistranslation mechanism. In this study, we address this problem by studying duplicated genes of aminoacyl-transfer RNA (tRNA) synthetases. Using bacterial prolyl-tRNA synthetase (ProRS) genes as an example, we identify an anomalous ProRS isoform, ProRSx, and a corresponding tRNA, tRNAProA, that are predominately found in plant pathogens from Streptomyces species. We then show that tRNAProA has an unusual hybrid structure that allows this tRNA to mistranslate alanine codons as proline. Finally, we provide biochemical, genetic, and mass spectrometric evidence that cells which express ProRSx and tRNAProA can translate GCU alanine codons as both alanine and proline. This dual use of alanine codons creates a hidden proteome diversity due to stochastic Ala→Pro mutations in protein sequences. Thus, we show that important plant pathogens are equipped with a tool to alter the identity of their sense codons. This finding reveals the initial example of a natural tRNA synthetase/tRNA pair for dedicated mistranslation of sense codons.
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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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