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Bromfield ESP, Cloutier S. Bradyrhizobium ontarionense sp. nov., a novel bacterial symbiont isolated from Aeschynomene indica (Indian jointvetch), harbours photosynthesis, nitrogen fixation and nitrous oxide (N 2O) reductase genes. Antonie Van Leeuwenhoek 2024; 117:69. [PMID: 38647727 PMCID: PMC11035471 DOI: 10.1007/s10482-024-01940-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/02/2024] [Indexed: 04/25/2024]
Abstract
A novel bacterial symbiont, strain A19T, was previously isolated from a root-nodule of Aeschynomene indica and assigned to a new lineage in the photosynthetic clade of the genus Bradyrhizobium. Here data are presented for the detailed genomic and taxonomic analyses of novel strain A19T. Emphasis is placed on the analysis of genes of practical or ecological significance (photosynthesis, nitrous oxide reductase and nitrogen fixation genes). Phylogenomic analysis of whole genome sequences as well as 50 single-copy core gene sequences placed A19T in a highly supported lineage distinct from described Bradyrhizobium species with B. oligotrophicum as the closest relative. The digital DNA-DNA hybridization and average nucleotide identity values for A19T in pair-wise comparisons with close relatives were far lower than the respective threshold values of 70% and ~ 96% for definition of species boundaries. The complete genome of A19T consists of a single 8.44 Mbp chromosome and contains a photosynthesis gene cluster, nitrogen-fixation genes and genes encoding a complete denitrifying enzyme system including nitrous oxide reductase implicated in the reduction of N2O, a potent greenhouse gas, to inert dinitrogen. Nodulation and type III secretion system genes, needed for nodulation by most rhizobia, were not detected. Data for multiple phenotypic tests complemented the sequence-based analyses. Strain A19T elicits nitrogen-fixing nodules on stems and roots of A. indica plants but not on soybeans or Macroptilium atropurpureum. Based on the data presented, a new species named Bradyrhizobium ontarionense sp. nov. is proposed with strain A19T (= LMG 32638T = HAMBI 3761T) as the type strain.
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Affiliation(s)
- Eden S P Bromfield
- Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, K1A 0C6, Canada.
| | - Sylvie Cloutier
- Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, K1A 0C6, Canada
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Sharma JS, Che M, Fetch T, McCallum BD, Xu SS, Hiebert CW. Identification of Sr67, a new gene for stem rust resistance in KU168-2 located close to the Sr13 locus in wheat. Theor Appl Genet 2024; 137:30. [PMID: 38265482 PMCID: PMC10808535 DOI: 10.1007/s00122-023-04530-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/14/2023] [Indexed: 01/25/2024]
Abstract
KEY MESSAGE Sr67 is a new stem rust resistance gene that represents a new resource for breeding stem rust resistant wheat cultivars Re-appearance of stem rust disease, caused by the fungal pathogen Puccinia graminis f. sp. tritici (Pgt), in different parts of Europe emphasized the need to develop wheat varieties with effective resistance to local Pgt populations and exotic threats. A Kyoto University wheat (Triticum aestivum L.) accession KU168-2 was reported to carry good resistance to leaf and stem rust. To identify the genomic region associated with the KU168-2 stem rust resistance, a genetic study was conducted using a doubled haploid (DH) population from the cross RL6071 × KU168-2. The DH population was phenotyped with three Pgt races (TTKSK, TPMKC, and QTHSF) and genotyped using the Illumina 90 K wheat SNP array. Linkage mapping showed the resistance to all three Pgt races was conferred by a single stem rust resistance (Sr) gene on chromosome arm 6AL, associated with Sr13. Presently, four Sr13 resistance alleles have been reported. Sr13 allele-specific KASP and STARP markers, and sequencing markers all showed null alleles in KU168-2. KU168-2 showed a unique combination of seedling infection types for five Pgt races (TTKSK, QTHSF, RCRSF, TMRTF, and TPMKC) compared to Sr13 alleles. The phenotypic uniqueness of the stem rust resistance gene in KU168-2 and null alleles for Sr13 allele-specific markers showed the resistance was conferred by a new gene, designated Sr67. Since Sr13 is less effective in hexaploid background, Sr67 will be a good source of stem rust resistance in bread wheat breeding programs.
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Affiliation(s)
- Jyoti Saini Sharma
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, 101 Route 100, Morden, MB, R6M 1Y5, Canada
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Mingzhe Che
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Thomas Fetch
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, 101 Route 100, Morden, MB, R6M 1Y5, Canada
| | - Brent D McCallum
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, 101 Route 100, Morden, MB, R6M 1Y5, Canada
| | - Steven S Xu
- Crop Improvement and Genetics Research Unit, Western Regional Research Center, USDA-ARS, 800 Buchanan Street, Albany, CA, 94710, USA
| | - Colin W Hiebert
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, 101 Route 100, Morden, MB, R6M 1Y5, Canada.
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Cloutier S, Edwards T, Zheng C, Booker HM, Islam T, Nabetani K, Kutcher HR, Molina O, You FM. Fine-mapping of a major locus for Fusarium wilt resistance in flax (Linum usitatissimum L.). Theor Appl Genet 2024; 137:27. [PMID: 38245903 PMCID: PMC10800302 DOI: 10.1007/s00122-023-04528-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 12/11/2023] [Indexed: 01/23/2024]
Abstract
KEY MESSAGE Fine-mapping of a locus on chromosome 1 of flax identified an S-lectin receptor-like kinase (SRLK) as the most likely candidate for a major Fusarium wilt resistance gene. Fusarium wilt, caused by the soil-borne fungal pathogen Fusarium oxysporum f. sp. lini, is a devastating disease in flax. Genetic resistance can counteract this disease and limit its spread. To map major genes for Fusarium wilt resistance, a recombinant inbred line population of more than 700 individuals derived from a cross between resistant cultivar 'Bison' and susceptible cultivar 'Novelty' was phenotyped in Fusarium wilt nurseries at two sites for two and three years, respectively. The population was genotyped with 4487 single nucleotide polymorphism (SNP) markers. Twenty-four QTLs were identified with IciMapping, 18 quantitative trait nucleotides with 3VmrMLM and 108 linkage disequilibrium blocks with RTM-GWAS. All models identified a major QTL on chromosome 1 that explained 20-48% of the genetic variance for Fusarium wilt resistance. The locus was estimated to span ~ 867 Kb but included a ~ 400 Kb unresolved region. Whole-genome sequencing of 'CDC Bethune', 'Bison' and 'Novelty' produced ~ 450 Kb continuous sequences of the locus. Annotation revealed 110 genes, of which six were considered candidate genes. Fine-mapping with 12 SNPs and 15 Kompetitive allele-specific PCR (KASP) markers narrowed down the interval to ~ 69 Kb, which comprised the candidate genes Lus10025882 and Lus10025891. The latter, a G-type S-lectin receptor-like kinase (SRLK) is the most likely resistance gene because it is the only polymorphic one. In addition, Fusarium wilt resistance genes previously isolated in tomato and Arabidopsis belonged to the SRLK class. The robust KASP markers can be used in marker-assisted breeding to select for this major Fusarium wilt resistance locus.
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Affiliation(s)
- S Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada.
| | - T Edwards
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - C Zheng
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - H M Booker
- Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
- Department of Plant Agriculture, Ontario Agricultural College, University of Guelph, 50 Stone Road E, Guelph, ON, N1G 2W1, Canada
| | - T Islam
- Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - K Nabetani
- Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - H R Kutcher
- Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - O Molina
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB, R6M 1Y5, Canada
| | - F M You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada.
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Karim MM, Yu F. Identification of QTLs for resistance to 10 pathotypes of Plasmodiophora brassicae in Brassica oleracea cultivar ECD11 through genotyping-by-sequencing. Theor Appl Genet 2023; 136:249. [PMID: 37982891 PMCID: PMC10661809 DOI: 10.1007/s00122-023-04483-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 10/09/2023] [Indexed: 11/21/2023]
Abstract
KEY MESSAGE Two major quantitative trait loci (QTLs) and five minor QTLs for 10 pathotypes were identified on chromosomes C01, C03, C04 and C08 through genotyping-by-sequencing from Brassica oleracea. Clubroot caused by Plasmodiophora brassicae is an important disease in brassica crops. Managing clubroot disease of canola on the Canadian prairie is challenging due to the continuous emergence of new pathotypes. Brassica oleracea is considered a major source of quantitative resistance to clubroot. Genotyping-by-sequencing (GBS) was performed in the parental lines; T010000DH3 (susceptible), ECD11 (resistant) and 124 BC1 plants. A total of 4769 high-quality polymorphic SNP loci were obtained and distributed on 9 chromosomes of B. oleracea. Evaluation of 124 BC1S1 lines for resistance to 10 pathotypes: 3A, 2B, 5C, 3D, 5G, 3H, 8J, 5K, 5L and 3O of P. brassicae, was carried out. Seven QTLs, 5 originating from ECD11 and 2 from T010000DH3, were detected. One major QTL designated as Rcr_C03-1 on C03 contributed 16.0-65.6% of phenotypic variation explained (PVE) for 8 pathotypes: 2B, 5C, 5G, 3H, 8J, 5K, 5L and 3O. Another major QTL designated as Rcr_C08-1 on C08 contributed 8.3 and 23.5% PVE for resistance to 8J and 5K, respectively. Five minor QTLs designated as Rcr_C01-1, Rcr_C03-2, Rcr_C03-3, Rcr_C04-1 and Rcr_C08-2 were detected on chromosomes C01, C03, C04 and C08 that contributed 8.3-23.5% PVE for 5 pathotypes each of 3A, 2B, 3D, 8J and 5K. There were 1, 10 and 4 genes encoding TIR-NBS-LRR/CC-NBS-LRR class disease resistance proteins in the Rcr_C01-1, Rcr_C03-1 and Rcr_C08-1 flanking regions. The syntenic regions of the two major QTLs Rcr_C03-1 and Rcr_C08-1 in the B. rapa genome 'Chiifu' were searched.
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Affiliation(s)
- Md Masud Karim
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Fengqun Yu
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada.
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Kalbe C, Metzger K, Gariépy C, Palin MF. Effect of muscle fibre types and carnosine levels on the expression of carnosine-related genes in pig skeletal muscle. Histochem Cell Biol 2023; 160:63-77. [PMID: 37171629 PMCID: PMC10313551 DOI: 10.1007/s00418-023-02193-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2023] [Indexed: 05/13/2023]
Abstract
It is generally accepted that carnosine (β-alanyl-L-histidine) content is higher in glycolytic than in oxidative muscle fibres, but the underlying mechanisms responsible for this difference remain to be elucidated. A first study to better understand potential mechanisms involved was undertaken (1) to determine whether differences in the expression of carnosine-related enzymes (CARNS1, CNDP2) and transporters (SLC6A6, SLC15A3, SLC15A4, SLC36A1) exist between oxidative and glycolytic myofibres and (2) to study the effect of carnosine on myoblast proliferative growth and on carnosine-related gene expression in cultured myoblasts isolated from glycolytic and oxidative muscles. Immunohistochemistry analyses were conducted to determine the cellular localization of carnosine-related proteins. Laser-capture microdissection and qPCR analyses were performed to measure the expression of carnosine-related genes in different myofibres isolated from the longissimus dorsi muscle of ten crossbred pigs. Myogenic cells originating from glycolytic and oxidative muscles were cultured to assess the effect of carnosine (0, 10, 25 and 50 mM) on their proliferative growth and on carnosine-related gene expression. The mRNA abundance of CNDP2 and of the studied carnosine transporters was higher in oxidative than in glycolytic myofibres. Since carnosine synthase (CARNS1) mRNA abundance was not affected by either the fibre type or the addition of carnosine to myoblasts, its transcriptional regulation would not be the main process by which carnosine content differences are determined in oxidative and glycolytic muscles. The addition of carnosine to myoblasts leading to a dose-dependent increase in SLC15A3 transcripts, however, suggests a role for this transporter in carnosine uptake and/or efflux to maintain cellular homeostasis.
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Affiliation(s)
- Claudia Kalbe
- Research Institute for Farm Animal Biology, Institute of Muscle Biology and Growth, Dummerstorf, Germany
| | - Katharina Metzger
- Research Institute for Farm Animal Biology, Institute of Behavioural Physiology, Dummerstorf, Germany
| | - Claude Gariépy
- Agriculture and Agri-Food Canada, St-Hyacinthe Research and Development Centre, St-Hyacinthe, QC, Canada
| | - Marie-France Palin
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada.
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Sura S, Larney FJ, Charest J, McAllister TA, Headley JV, Cessna AJ. Veterinary antimicrobials in cattle feedlot environs and irrigation conveyances in a high-intensity agroecosystem in southern Alberta, Canada. Environ Sci Pollut Res Int 2023; 30:12235-12256. [PMID: 36107301 PMCID: PMC9898329 DOI: 10.1007/s11356-022-22889-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 09/01/2022] [Indexed: 06/15/2023]
Abstract
The South Saskatchewan River Basin (SSRB) is considered one of the most intensively farmed regions in Canada, with high densities of livestock and expansive areas of irrigated cropland. We measured concentrations of seven veterinary antimicrobials (VAs) in 114 surface water samples from feedlot environs and 219 samples from irrigation conveyances in the SSRB. Overall, detection frequencies in feedlot environs were 100% for chlortetracycline (CTC) and tetracycline (TC), 94% for monensin (MON), 84% for tylosin (TYL), 72% for lincomycin (LIN), 66% for erythromycin (ERY), and 23% for sulfamethazine (SMZ). For irrigation conveyances, detection frequencies for CTC and TC remained high (94-100%), but dropped to 18% for ERY, 15% for TYL, 10% for MON, and 4% for SMZ. Lincomycin was not detected in irrigation conveyance water. Maximum concentrations of VAs ranged from 1384 µg L-1 (TC) to 17 ng L-1 (SMZ) in feedlot environs while those in irrigation conveyances were 155 ng L-1 (TC) to 29 ng L-1 (ERY). High detection frequencies and median concentrations of VAs in both feedlot environs and irrigation conveyances were associated with high amounts of precipitation. However, an irrigation district (ID) with high livestock density (Lethbridge Northern) did not exhibit higher concentrations of VAs compared to IDs with less livestock, while levels of VAs in irrigation conveyances were less influenced by the degree of surface runoff. The ubiquity of CTC and TC in our study is likely a reflection of its widespread use in intensive livestock operations. Additional investigation is required to link environmental concentrations of VAs with livestock densities and increase our understanding of potential antimicrobial resistance in high-intensity agroecosystems.
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Affiliation(s)
- Srinivas Sura
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, 101 Route 100, Morden, MB, R6M 1Y5, Canada.
| | - Francis J Larney
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, 5403 1st Avenue S, Lethbridge, AB, T1J 4B1, Canada
| | - Jollin Charest
- Natural Resource Management Branch, Alberta Agriculture, Forestry, and Rural Economic Development, 5401 1st Avenue S, Lethbridge, AB, T1J 4V6, Canada
| | - Tim A McAllister
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, 5403 1st Avenue S, Lethbridge, AB, T1J 4B1, Canada
| | - John V Headley
- Environment and Climate Change Canada, National Hydrology Research Centre, 11 Innovation Blvd, Saskatoon, SK, S7N 3H5, Canada
| | - Allan J Cessna
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
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Hegedus D, Coutu C, Gjetvaj B, Hannoufa A, Harrington M, Martin S, Parkin IAP, Perera S, Wanasundara J. Genetic variation and structural diversity in major seed proteins among and within Camelina species. Planta 2022; 256:93. [PMID: 36201059 PMCID: PMC9537204 DOI: 10.1007/s00425-022-03998-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 09/12/2022] [Indexed: 06/16/2023]
Abstract
Genetic variation in seed protein composition, seed protein gene expression and predictions of seed protein physiochemical properties were documented in C. sativa and other Camelina species. Seed protein diversity was examined in six Camelina species (C. hispida, C. laxa, C. microcarpa, C. neglecta, C. rumelica and C. sativa). Differences were observed in seed protein electrophoretic profiles, total seed protein content and amino acid composition between the species. Genes encoding major seed proteins (cruciferins, napins, oleosins and vicilins) were catalogued for C. sativa and RNA-Seq analysis established the expression patterns of these and other genes in developing seed from anthesis through to maturation. Examination of 187 C. sativa accessions revealed limited variation in seed protein electrophoretic profiles, though sufficient to group the majority into classes based on high MW protein profiles corresponding to the cruciferin region. C. sativa possessed four distinct types of cruciferins, named CsCRA, CsCRB, CsCRC and CsCRD, which corresponded to orthologues in Arabidopsis thaliana with members of each type encoded by homeologous genes on the three C. sativa sub-genomes. Total protein content and amino acid composition varied only slightly; however, RNA-Seq analysis revealed that CsCRA and CsCRB genes contributed > 95% of the cruciferin transcripts in most lines, whereas CsCRC genes were the most highly expressed cruciferin genes in others, including the type cultivar DH55. This was confirmed by proteomics analyses. Cruciferin is the most abundant seed protein and contributes the most to functionality. Modelling of the C. sativa cruciferins indicated that each type possesses different physiochemical attributes that were predicted to impart unique functional properties. As such, opportunities exist to create C. sativa cultivars with seed protein profiles tailored to specific technical applications.
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Affiliation(s)
- Dwayne Hegedus
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada.
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK, Canada.
| | - Cathy Coutu
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Branimir Gjetvaj
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | | | - Myrtle Harrington
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Sara Martin
- Agriculture and Agri-Food Canada, London, ON, Canada
| | - Isobel A P Parkin
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Suneru Perera
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Janitha Wanasundara
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK, Canada
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Gagné MJ, Savard T, Brassard J. Interactions Between Infectious Foodborne Viruses and Bacterial Biofilms Formed on Different Food Contact Surfaces. Food Environ Virol 2022; 14:267-279. [PMID: 36030359 PMCID: PMC9458689 DOI: 10.1007/s12560-022-09534-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Bacterial biofilms contribute to contamination, spoilage, persistence, and hygiene failure in the food industry, but relatively little is known about the behavior of foodborne viruses evolving in the complex communities that make up biofilm. The aim of this study was to evaluate the association between enteric viruses and biofilms on food contact surfaces. Formed biofilms of mono- and multispecies cultures were prepared on glass, stainless steel, and polystyrene coupons and 105 pfu/ml of murine norovirus, rotavirus, and hepatitis A virus were added and incubated for 15 min, 90 min, and 24 h. The data obtained clearly demonstrate that the presence of biofilms generally influences the adhesion of enteric viruses to different surfaces. Many significant increases in attachment rates were observed, particularly with rotavirus whose rate of viral infectious particles increased 7000 times in the presence of Pseudomonas fluorescens on polystyrene after 24 h of incubation and with hepatitis A virus, which seems to have an affinity for the biofilms formed by lactic acid bacteria. Murine norovirus seems to be the least influenced by the presence of biofilms with few significant increases. However, the different factors surrounding this association are unknown and seem to vary according to the viruses, the environmental conditions, and the composition of the biofilm.
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Affiliation(s)
- Marie-Josée Gagné
- Agriculture and Agri-Food Canada, Saint-Hyacinthe Research and Development Centre, 3600 Casavant Boulevard West, Saint-Hyacinthe, QC, J2S 8E3, Canada
| | - Tony Savard
- Agriculture and Agri-Food Canada, Saint-Hyacinthe Research and Development Centre, 3600 Casavant Boulevard West, Saint-Hyacinthe, QC, J2S 8E3, Canada
| | - Julie Brassard
- Agriculture and Agri-Food Canada, Saint-Hyacinthe Research and Development Centre, 3600 Casavant Boulevard West, Saint-Hyacinthe, QC, J2S 8E3, Canada.
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Sanfaçon H. Re-examination of nepovirus polyprotein cleavage sites highlights the diverse specificities and evolutionary relationships of nepovirus 3C-like proteases. Arch Virol 2022; 167:2529-2543. [PMID: 36042138 PMCID: PMC9741568 DOI: 10.1007/s00705-022-05564-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 06/30/2022] [Indexed: 12/14/2022]
Abstract
Plant-infecting viruses of the genus Nepovirus (subfamily Comovirinae, family Secoviridae, order Picornavirales) are bipartite positive-strand RNA viruses with each genomic RNA encoding a single large polyprotein. The RNA1-encoded 3C-like protease cleaves the RNA1 polyprotein at five sites and the RNA2 polyprotein at two or three sites, depending on the nepovirus. The specificity of nepovirus 3C-like proteases is notoriously diverse, making the prediction of cleavage sites difficult. In this study, the position of nepovirus cleavage sites was systematically re-evaluated using alignments of the RNA1 and RNA2 polyproteins, phylogenetic relationships of the proteases, and sequence logos to examine specific preferences for the P6 to P1' positions of the cleavage sites. Based on these analyses, the positions of previously elusive cleavage sites, notably the 2a-MP cleavage sites of subgroup B nepoviruses, are now proposed. Distinct nepovirus protease clades were identified, each with different cleavage site specificities, mostly determined by the nature of the amino acid at the P1 and P1' positions of the cleavage sites, as well as the P2 and P4 positions. The results will assist the prediction of cleavage sites for new nepoviruses and help refine the taxonomy of nepoviruses. An improved understanding of the specificity of nepovirus 3C-like proteases can also be used to investigate the cleavage of plant proteins by nepovirus proteases and to understand their adaptation to a broad range of hosts.
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Affiliation(s)
- Hélène Sanfaçon
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, 4200 Highway 97, V0H1Z0, Summerland, BC, Canada.
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Grady EN, MacDonald J, Ho MT, Weselowski B, McDowell T, Solomon O, Renaud J, Yuan ZC. Characterization and complete genome analysis of the surfactin-producing, plant-protecting bacterium Bacillus velezensis 9D-6. BMC Microbiol 2019; 19:5. [PMID: 30621587 PMCID: PMC6325804 DOI: 10.1186/s12866-018-1380-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 12/25/2018] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Bacillus velezensis is an endospore-forming, free-living soil bacterium with potential as a biopesticide against a broad spectrum of microbial pathogens of plants. Its potential for commercial development is enhanced by rapid replication and resistance to adverse environmental conditions, typical of Bacillus species. However, the use of beneficial microbes against phytopathogens has not gained dominance due to limitations that may be overcome with new biopesticidal strains and/or new biological knowledge. RESULTS Here, we isolated B. velezensis strain 9D-6 and showed that it inhibits the in vitro growth of prokaryotic and eukaryotic pathogens, including the bacteria Bacillus cereus , Clavibacter michiganensis, Pantoea agglomerans, Ralstonia solanacearum, Xanthomonas campestris, and Xanthomonas euvesicatoria; and the fungi Alternaria solani, Cochliobolus carbonum, Fusarium oxysporum, Fusarium solani, Gibberella pulicaris, Gibberella zeae, Monilinia fructicola, Pyrenochaeta terrestris and Rhizoctonia solani. Antimicrobial compounds with activity against Clavibacter michiganensis were isolated from B. velezensis 9D-6 and characterized by high resolution LC-MS/MS, yielding formulae of C52H91N7O13 and C53H93N7O13, which correspond to [Leu7] surfactins C14 and C15 (also called surfactin B and surfactin C), respectively. We further sequenced the B. velezensis 9D-6 genome which consists of a single circular chromosome and revealed 13 gene clusters expected to participate in antimicrobial metabolite production, including surfactin and two metabolites that have not typically been found in this species - ladderane and lantipeptide. Despite being unable to inhibit the growth of Pseudomonas syringae DC3000 in an in vitro plate assay, B. velezensis 9D-6 significantly reduced root colonization by DC3000, suggesting that 9D-6 uses methods other than antimicrobials to control phytopathogens in the environment. Finally, using in silico DNA-DNA hybridization (isDDH), we confirm previous findings that many strains currently classified as B. amyloliquefaciens are actually B. velezensis. CONCLUSIONS The data presented here suggest B. velezensis 9D-6 as a candidate plant growth promoting bacterium (PGPB) and biopesticide, which uses a unique complement of antimicrobials, as well as other mechanisms, to protect plants against phytopathogens. Our results may contribute to future utilization of this strain, and will contribute to a knowledge base that will help to advance the field of microbial biocontrol.
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Affiliation(s)
- Elliot Nicholas Grady
- Department of Microbiology & Immunology, Schulich School of Medicine & Dentistry, Dental Science Building Rm. 3014, University of Western Ontario, London, ON N6A 5C1 Canada
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
| | - Jacqueline MacDonald
- Department of Microbiology & Immunology, Schulich School of Medicine & Dentistry, Dental Science Building Rm. 3014, University of Western Ontario, London, ON N6A 5C1 Canada
| | - Margaret T. Ho
- Department of Microbiology & Immunology, Schulich School of Medicine & Dentistry, Dental Science Building Rm. 3014, University of Western Ontario, London, ON N6A 5C1 Canada
| | - Brian Weselowski
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
| | - Tim McDowell
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
| | - Ori Solomon
- Department of Microbiology & Immunology, Schulich School of Medicine & Dentistry, Dental Science Building Rm. 3014, University of Western Ontario, London, ON N6A 5C1 Canada
| | - Justin Renaud
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
| | - Ze-Chun Yuan
- Department of Microbiology & Immunology, Schulich School of Medicine & Dentistry, Dental Science Building Rm. 3014, University of Western Ontario, London, ON N6A 5C1 Canada
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
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