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Macedo MA, Melgarejo TA, Vasquez-Mayorga M, Cespedes M, Rojas MR, Turini TA, Batuman O, Wintermantel WM, Gilbertson RL. Squash vein yellowing virus from California emerged in the Middle East via intragenic and intergeneric recombination events in the hypervariable potyvirus P1 and ipomovirus P1a genes. J Gen Virol 2024; 105. [PMID: 39418084 DOI: 10.1099/jgv.0.002033] [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: 10/19/2024] Open
Abstract
We present the complete sequence of the genomic RNA of an isolate of squash vein yellowing virus (Ipomovirus cucurbitavenaflavi) from California (SqVYV-CA) and show it is a recombinant virus with a highly divergent 5' UTR and proximal P1a gene. The evolution of SqVYV-CA involved an intrageneric event between unknown potyviruses, related to isolates of papaya ringspot virus (Potyvirus papayanuli) from the Old World, and an intergeneric event between this recombinant potyvirus (minor parent) and an isolate of SqVYV from Israel (SqVYV-IL) (major parent). These events occurred in mixed infections and in the potyvirus P1 and ipomovirus P1a recombination hotspots and resulted in SqVYV-CA having a potyvirus 5' UTR and chimeric P1-P1a gene/protein and the remainder of the genome from SqVYV-IL. The SqVYV-CA chimeric P1-P1a gene is under positive selection, and the protein is intrinsically disordered and may localize to the nucleus via nuclear localization signals in the P1 part. The C-terminal SqVYV-IL P1a part also diverged but retained the conserved serine protease motif. Furthermore, substantial divergence in SqVYV isolates from the Middle East was associated with genetic drift and a long evolutionary history in this region. The finding that the host range and symptomatology in cucurbits of SqVYV-CA is similar to those of SqVYV from Florida and SqVYV-IL, indicated that the recombinant part of the genome had no obvious effect on the virus-host interaction. A divergent part of the P1 sequence of the SqVYV-CA P1-P1a gene was used to develop a primer pair and RT-PCR test for specific detection of SqVYV-CA. This test was used to detect spread of SqVYV-CA to a new production area of California in 2021 and 2022. Together, these results demonstrate (i) a high level of genetic diversity exists among isolates of SqVYV and involved intra- and intergeneric recombination and genetic drift (mutation), (ii) evidence that SqVYV originated in the Middle East and that there were independent introductions into the New World and (iii) the remarkable genetic flexibility of the 5' proximal genes of these viruses.
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Affiliation(s)
- M A Macedo
- Federal Institution of Brasília, Brasília, Federal District, Brazil
| | - T A Melgarejo
- Department of Plant Pathology, University of California, Davis, CA, USA
| | - M Vasquez-Mayorga
- Department of Plant Pathology, University of California, Davis, CA, USA
| | - M Cespedes
- Department of Plant Pathology, University of California, Davis, CA, USA
| | - M R Rojas
- Department of Plant Pathology, University of California, Davis, CA, USA
| | - T A Turini
- University of California Agriculture and Natural Resources, Fresno, CA, USA
| | - O Batuman
- Department of Plant Pathology, Southwest Florida Research and Education Center, University of Florida, Immokalee, Florida, USA
| | - W M Wintermantel
- United States Department of Agriculture, Agricultural Research Service, Salinas, CA, USA
| | - R L Gilbertson
- Department of Plant Pathology, University of California, Davis, CA, USA
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Saha D, Pramanik A, Freville A, Siddiqui AA, Pal U, Banerjee C, Nag S, Debsharma S, Pramanik S, Mazumder S, Maiti NC, Datta S, van Ooij C, Bandyopadhyay U. Structure-function analysis of nucleotide housekeeping protein HAM1 from human malaria parasite Plasmodium falciparum. FEBS J 2024; 291:4349-4371. [PMID: 39003571 DOI: 10.1111/febs.17216] [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: 01/20/2024] [Revised: 03/29/2024] [Accepted: 06/20/2024] [Indexed: 07/15/2024]
Abstract
Non-canonical nucleotides, generated as oxidative metabolic by-products, significantly threaten the genome integrity of Plasmodium falciparum and thereby, their survival, owing to their mutagenic effects. PfHAM1, an evolutionarily conserved inosine/xanthosine triphosphate pyrophosphohydrolase, maintains nucleotide homeostasis in the malaria parasite by removing non-canonical nucleotides, although structure-function intricacies are hitherto poorly reported. Here, we report the X-ray crystal structure of PfHAM1, which revealed a homodimeric structure, additionally validated by size-exclusion chromatography-multi-angle light scattering analysis. The two monomeric units in the dimer were aligned in a parallel fashion, and critical residues associated with substrate and metal binding were identified, wherein a notable structural difference was observed in the β-sheet main frame compared to human inosine triphosphate pyrophosphatase. PfHAM1 exhibited Mg++-dependent pyrophosphohydrolase activity and the highest binding affinity to dITP compared to other non-canonical nucleotides as measured by isothermal titration calorimetry. Modifying the pfham1 genomic locus followed by live-cell imaging of expressed mNeonGreen-tagged PfHAM1 demonstrated its ubiquitous presence in the cytoplasm across erythrocytic stages with greater expression in trophozoites and schizonts. Interestingly, CRISPR-Cas9/DiCre recombinase-guided pfham1-null P. falciparum survived in culture under standard growth conditions, indicating its assistive role in non-canonical nucleotide clearance during intra-erythrocytic stages. This is the first comprehensive structural and functional report of PfHAM1, an atypical nucleotide-cleansing enzyme in P. falciparum.
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Affiliation(s)
- Debanjan Saha
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Atanu Pramanik
- Division of Structural Biology & Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Aline Freville
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, UK
| | - Asim Azhar Siddiqui
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Uttam Pal
- Division of Structural Biology & Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Chinmoy Banerjee
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Shiladitya Nag
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Subhashis Debsharma
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Saikat Pramanik
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Somnath Mazumder
- Department of Zoology, Raja Peary Mohan College, Uttarpara, India
| | - Nakul C Maiti
- Division of Structural Biology & Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Saumen Datta
- Division of Structural Biology & Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Christiaan van Ooij
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, UK
| | - Uday Bandyopadhyay
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Department of Biological Sciences, Bose Institute, Kolkata, India
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Wosula EN, Shirima RR, Amour M, Woyengo VW, Otunga BM, Legg JP. Occurrence and Distribution of Major Cassava Pests and Diseases in Cultivated Cassava Varieties in Western Kenya. Viruses 2024; 16:1469. [PMID: 39339946 PMCID: PMC11437512 DOI: 10.3390/v16091469] [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: 08/21/2024] [Revised: 09/07/2024] [Accepted: 09/11/2024] [Indexed: 09/30/2024] Open
Abstract
Cassava is an important food crop in western Kenya, yet its production is challenged by pests and diseases that require routine monitoring to guide development and deployment of control strategies. Field surveys were conducted in 2022 and 2023 to determine the prevalence, incidence and severity of cassava mosaic disease (CMD) and cassava brown streak disease (CBSD), whitefly numbers and incidence of cassava green mite (CGM) in six counties of western Kenya. Details of the encountered cassava varieties were carefully recorded to determine the adoption of improved varieties. A total of 29 varieties were recorded, out of which 13 were improved, although the improved varieties were predominant in 60% of fields and the most widely grown variety was MM96/4271. The CMD incidence was higher in 2022 (26.4%) compared to 2023 (10.1%), although the proportion of CMD attributable to whitefly infection was greater (50.6%) in 2023 than in 2022 (18.0%). The CBSD incidence in 2022 was 6.4%, while in 2023 it was 4.1%. The CMD incidence was significantly lower (5.9%) for the improved varieties than it was for the local varieties (35.9%), although the CBSD incidence did not differ significantly between the improved (2.3%) and local varieties (9.7%). Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV) were both detected. Most infections were single CBSV infections (82.9%), followed by single UCBSV (34.3%) and coinfection with both viruses (16.7%). Whiteflies were more abundant in 2023, in which 28% of the fields had super-abundant populations of >100/plant, compared to 5% in 2022. KASP SNP genotyping designated 92.8% of the specimens as SSA-ECA for 2022, while it was 94.4% for 2023. The cassava green mite incidence was 65.4% in 2022 compared to 79.9% in 2023. This study demonstrates that cassava viruses, whiteflies and cassava green mites continue to be important constraints to cassava production in western Kenya, although the widespread cultivation of improved varieties is reducing the impact of cassava viruses. The more widespread application of high-quality seed delivery mechanisms could further enhance the management of these pests/diseases, coupled with wider application of IPM measures for whiteflies and mites.
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Affiliation(s)
- Everlyne N Wosula
- International Institute of Tropical Agriculture (IITA-Tanzania), Dar es Salaam P.O. BOX 34441, Tanzania
| | - Rudolph R Shirima
- International Institute of Tropical Agriculture (IITA-Tanzania), Dar es Salaam P.O. BOX 34441, Tanzania
| | - Massoud Amour
- International Institute of Tropical Agriculture (IITA-Tanzania), Dar es Salaam P.O. BOX 34441, Tanzania
| | - Vincent W Woyengo
- Kenya Agricultural Livestock Research Organization (KALRO), Kakamega P.O. Box 57811, Kenya
| | - Bonface M Otunga
- Kenya Agricultural Livestock Research Organization (KALRO), Kakamega P.O. Box 57811, Kenya
| | - James P Legg
- International Institute of Tropical Agriculture (IITA-Tanzania), Dar es Salaam P.O. BOX 34441, Tanzania
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Munguti FM, Kilalo DC, Yegon HK, Macharia I, Seal SE, Mwango'mbe AW, Nyaboga EN, Silva G. Real-time reverse transcription recombinase polymerase amplification (RT-RPA) assay for detection of cassava brown streak viruses. Sci Rep 2024; 14:12438. [PMID: 38816439 PMCID: PMC11139904 DOI: 10.1038/s41598-024-62249-y] [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: 02/10/2024] [Accepted: 05/15/2024] [Indexed: 06/01/2024] Open
Abstract
Cassava brown streak disease (CBSD) caused by Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV) is the most economically important viral disease of cassava. As cassava is a vegetatively propagated crop, the development of rapid and sensitive diagnostics would aid in the identification of virus-free planting material and development of effective management strategies. In this study, a rapid, specific and sensitive real-time reverse transcription recombinase polymerase amplification (RT-RPA) assay was developed for real-time detection of CBSV and UCBSV. The RT-RPA was able to detect as little as 2 pg/µl of purified RNA obtained from infected cassava leaves, a sensitivity equivalent to that obtained by quantitative real-time reverse transcription PCR (qRT-PCR), within 20 min at 37 °C. Further, the RT-RPA detected each target virus directly from crude leaf and stem extracts, avoiding the tedious and costly isolation of high-quality RNA. The developed RT-RPA assay provides a valuable diagnostic tool that can be adopted by cassava seed certification and virus resistance breeding programs to ensure distribution of virus-free cassava planting materials to farmers. This is the first report on the development and validation of crude sap-based RT-RPA assay for the detection of cassava brown streak viruses (UCBSV and CBSV) infection in cassava plants.
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Affiliation(s)
- Florence M Munguti
- Department of Plant Science and Crop Protection, University Nairobi, Nairobi, Kenya.
- Kenya Plant Health Inspectorate Service, Nairobi, Kenya.
| | - Dora C Kilalo
- Department of Plant Science and Crop Protection, University Nairobi, Nairobi, Kenya
| | | | | | - Susan E Seal
- Natural Resources Institute, Central Avenue, University of Greenwich, Chatham Maritime, ME4 4TB, UK
| | - Agnes W Mwango'mbe
- Department of Plant Science and Crop Protection, University Nairobi, Nairobi, Kenya
| | - Evans N Nyaboga
- Department of Biochemistry, University of Nairobi, Nairobi, Kenya
| | - Gonçalo Silva
- Natural Resources Institute, Central Avenue, University of Greenwich, Chatham Maritime, ME4 4TB, UK
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Mahillon M, Brodard J, Dubuis N, Gugerli P, Blouin AG, Schumpp O. Mixed infection of ITPase-encoding potyvirid and secovirid in Mercurialis perennis: evidences for a convergent euphorbia-specific viral counterstrike. Virol J 2024; 21:6. [PMID: 38178191 PMCID: PMC10768138 DOI: 10.1186/s12985-023-02257-y] [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] [Received: 09/26/2023] [Accepted: 12/04/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND In cellular organisms, inosine triphosphate pyrophosphatases (ITPases) prevent the incorporation of mutagenic deaminated purines into nucleic acids. These enzymes have also been detected in the genomes of several plant RNA viruses infecting two euphorbia species. In particular, two ipomoviruses produce replicase-associated ITPases to cope with high concentration of non-canonical nucleotides found in cassava tissues. METHOD Using high-throughput RNA sequencing on the wild euphorbia species Mercurialis perennis, two new members of the families Potyviridae and Secoviridae were identified. Both viruses encode for a putative ITPase, and were found in mixed infection with a new partitivirid. Following biological and genomic characterization of these viruses, the origin and function of the phytoviral ITPases were investigated. RESULTS While the potyvirid was shown to be pathogenic, the secovirid and partitivirid could not be transmitted. The secovirid was found belonging to a proposed new Comovirinae genus tentatively named "Mercomovirus", which also accommodates other viruses identified through transcriptome mining, and for which an asymptomatic pollen-associated lifestyle is suspected. Homology and phylogenetic analyses inferred that the ITPases encoded by the potyvirid and secovirid were likely acquired through independent horizontal gene transfer events, forming lineages distinct from the enzymes found in cassava ipomoviruses. Possible origins from cellular organisms are discussed for these proteins. In parallel, the endogenous ITPase of M. perennis was predicted to encode for a C-terminal nuclear localization signal, which appears to be conserved among the ITPases of euphorbias but absent in other plant families. This subcellular localization is in line with the idea that nucleic acids remain protected in the nucleus, while deaminated nucleotides accumulate in the cytoplasm where they act as antiviral molecules. CONCLUSION Three new RNA viruses infecting M. perennis are described, two of which encoding for ITPases. These enzymes have distinct origins, and are likely required by viruses to circumvent high level of cytoplasmic non-canonical nucleotides. This putative plant defense mechanism has emerged early in the evolution of euphorbias, and seems to specifically target certain groups of RNA viruses infecting perennial hosts.
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Affiliation(s)
- Mathieu Mahillon
- Research Group Virology, Bacteriology and Phytoplasmology, Plant Protection Department, Agroscope, Nyon, Switzerland
| | - Justine Brodard
- Research Group Virology, Bacteriology and Phytoplasmology, Plant Protection Department, Agroscope, Nyon, Switzerland
| | - Nathalie Dubuis
- Research Group Virology, Bacteriology and Phytoplasmology, Plant Protection Department, Agroscope, Nyon, Switzerland
| | - Paul Gugerli
- Research Group Virology, Bacteriology and Phytoplasmology, Plant Protection Department, Agroscope, Nyon, Switzerland
| | - Arnaud G Blouin
- Research Group Virology, Bacteriology and Phytoplasmology, Plant Protection Department, Agroscope, Nyon, Switzerland
| | - Olivier Schumpp
- Research Group Virology, Bacteriology and Phytoplasmology, Plant Protection Department, Agroscope, Nyon, Switzerland.
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Hu W, Dai Z, Liu P, Deng C, Shen W, Li Z, Cui H. The Single Distinct Leader Protease Encoded by Alpinia oxyphylla Mosaic Virus (Genus Macluravirus) Suppresses RNA Silencing Through Interfering with Double-Stranded RNA Synthesis. PHYTOPATHOLOGY 2023; 113:1103-1114. [PMID: 36576401 DOI: 10.1094/phyto-10-22-0371-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: 06/17/2023]
Abstract
The genomic 5'-terminal regions of viruses in the family Potyviridae (potyvirids) encode two types of leader proteases: serine-protease (P1) and cysteine-protease (HCPro), which differ greatly in the arrangement and sequence composition among inter-genus viruses. Most potyvirids have the same tandemly arranged P1 and HCPro, whereas viruses in the genus Macluravirus encode a single distinct leader protease, a truncated version of HCPro with yet-unknown functions. We investigated the RNA silencing suppression (RSS) activity and its underpinning mechanism of the distinct HCPro from alpinia oxyphylla mosaic macluravirus (aHCPro). Sequence analysis revealed that macluraviral HCPros have obvious truncations in the N-terminal and middle regions when aligned to their counterparts in potyviruses (well-characterized viral suppressors of RNA silencing). Nearly all defined elements essential for the RSS activity of potyviral counterparts are not distinguished in macluraviral HCPros. Here, we demonstrated that aHCPro exhibits a similar anti-silencing activity with the potyviral counterpart. However, aHCPro fails to block both the local and systemic spreading of RNA silencing. In line, aHCPro interferes with the dsRNA synthesis, an upstream step in the RNA silencing pathway. Affinity-purification and NanoLC-MS/MS analysis revealed that aHCPro has no association with core components or their potential interactors involving in dsRNA synthesis from the protein layer. Instead, the ectopic expression of aHCPro significantly reduces the transcript abundance of RDR2, RDR6, SGS3, and SDE5. This study represents the first report on the anti-silencing function of Macluravirus-encoded HCPro and the underlying molecular mechanism.
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Affiliation(s)
- Weiyao Hu
- Sanya Nanfan Research Institute, Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Ministry of Education) and College of Plant Protection, Hainan University, Haikou, Hainan, 570228, China
| | - Zhaoji Dai
- Sanya Nanfan Research Institute, Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Ministry of Education) and College of Plant Protection, Hainan University, Haikou, Hainan, 570228, China
| | - Peilan Liu
- Sanya Nanfan Research Institute, Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Ministry of Education) and College of Plant Protection, Hainan University, Haikou, Hainan, 570228, China
| | - Changhui Deng
- Sanya Nanfan Research Institute, Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Ministry of Education) and College of Plant Protection, Hainan University, Haikou, Hainan, 570228, China
| | - Wentao Shen
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, China
| | - Zengping Li
- Sanya Nanfan Research Institute, Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Ministry of Education) and College of Plant Protection, Hainan University, Haikou, Hainan, 570228, China
| | - Hongguang Cui
- Sanya Nanfan Research Institute, Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Ministry of Education) and College of Plant Protection, Hainan University, Haikou, Hainan, 570228, China
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Nanyiti S, Kabaalu R, Alicai T, Abidrabo P, Seal SE, Bouvaine S, Bailey AM, Foster GD. Detection of cassava brown streak ipomoviruses in aphids collected from cassava plants. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2023. [DOI: 10.3389/fsufs.2023.1027842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
Abstract
Cassava is an important staple food in Africa and a major source of carbohydrates for 800 million people globally. However, cassava suffers severe yield losses caused by many factors including pests and diseases. A devastating disease of cassava is cassava brown streak disease (CBSD) caused by the cassava brown streak ipomoviruses (CBSIs) (family Potyviridae), Cassava brown streak virus (CBSV), and Ugandan cassava brown streak virus (UCBSV). Spread of CBSD is mainly through planting infected stem cuttings used for propagation. Transmission of CBSIs by the insect vector (Bemisia tabaci) has been reported. However, experimental transmission efficiencies of CBSIs are usually low. Recent research has showed the occurrence of a DAG motif associated with aphid transmission in other potyviruses, within the coat protein gene of CBSV. Consequently this study aimed to explore the possibility that besides whiteflies, aphids may transmit CBSIs. Cassava plants were assessed during a survey for occurrence of CBSD and aphids as potential alternative CBSIs vectors. We collected aphids from CBSD-symptomatic and symptomless cassava plants within farmers' fields in Uganda during April–July 2020. The aphids were analyzed for the presence of CBSIs by reverse transcriptase-polymerase chain reaction (RT-PCR) and to determine aphid species using mitochondrial cytochrome oxidase (mtCOI) barcoding. Unusual aphid infestation of cassava plants was observed at 35 locations in nine districts across Uganda and on 11 other plant species within or adjacent to cassava fields. This is the first report of aphids infesting cassava in Uganda. Molecular analysis of the aphid confirmed presence of three different aphid species in the surveyed cassava fields, namely, Aphis solanella, Aphis fabae mordvilkoi, and Rhopalosiphum sp. mtCOI nucleotide sequences for the aphids in which CBSIs were detected are deposited with Genbank under accession numbers OP223337-40. Both UCBSV and CBSV were detected by RT-PCR in aphids collected from cassava fields with CBSD-affected plants. The CBSIs were detected in 14 aphid samples collected from 19 CBSD-symptomatic cassava plants. These results suggest the ability of aphids to acquire CBSIs, but transmission experiments are required on their vector potential.
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Carvajal-Yepes M, Jimenez J, Belalcazar J, Cuasquer JB, Lozano I, Olaya CA, Cuellar WJ. Genome Analysis and Pathobiology of Cassava-Infecting Torradoviruses Containing a Putative Maf/HAM1 Pyrophosphatase Domain. PLANT DISEASE 2022; 106:2808-2816. [PMID: 35471077 DOI: 10.1094/pdis-11-21-2520-re] [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: 06/14/2023]
Abstract
Next generation sequencing has been used to identify and characterize the full genome sequence of a cassava-infecting torradovirus, revealing the presence of a Maf/HAM1 domain downstream of the RNA-dependent RNA-polymerase (RdRp) domain in RNA1 in all isolates sequenced. A similar domain is also found in unrelated potyvirids infecting Euphorbiaceae hosts in the Americas and cassava in Africa. Even though cassava torrado-like virus (CsTLV) could not be mechanically transmitted to a series of herbaceous hosts, it can be efficiently transmitted by bud graft-inoculation to different cassava landraces. Our bioassays show that CsTLV has a narrow host range. Crystal-like structures of isometric virus-like particles were observed in cells of plants with single infection by CsTLV, and consistently induced chlorotic leaf spots and affected root yields significantly. Moreover, CsTLV infection induces changes in the accumulation of total sugars in storage roots. Field surveys indicated the presence of CsTLV in the main cassava growing regions of Colombia, and the occurrence of two different cassava-infecting torradovirus species. Profiles of small RNAs of 21 to 24 nucleotides in length, derived from CsTLV RNAs targeted by cassava RNA silencing defense mechanisms, are also reported.
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Affiliation(s)
| | - Jenyfer Jimenez
- International Center for Tropical Agriculture (CIAT), AA 6713, Cali, Colombia
- Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia (UNAL), Palmira, Colombia
| | - John Belalcazar
- International Center for Tropical Agriculture (CIAT), AA 6713, Cali, Colombia
| | - Juan B Cuasquer
- International Center for Tropical Agriculture (CIAT), AA 6713, Cali, Colombia
| | - Ivan Lozano
- International Center for Tropical Agriculture (CIAT), AA 6713, Cali, Colombia
| | - Cristian A Olaya
- International Center for Tropical Agriculture (CIAT), AA 6713, Cali, Colombia
| | - Wilmer J Cuellar
- International Center for Tropical Agriculture (CIAT), AA 6713, Cali, Colombia
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Shirima RR, Wosula EN, Hamza AA, Mohammed NA, Mouigni H, Nouhou S, Mchinda NM, Ceasar G, Amour M, Njukwe E, Legg JP. Epidemiological Analysis of Cassava Mosaic and Brown Streak Diseases, and Bemisia tabaci in the Comoros Islands. Viruses 2022; 14:v14102165. [PMID: 36298720 PMCID: PMC9608219 DOI: 10.3390/v14102165] [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] [Received: 08/02/2022] [Revised: 09/15/2022] [Accepted: 09/28/2022] [Indexed: 01/20/2023] Open
Abstract
A comprehensive assessment of cassava brown streak disease (CBSD) and cassava mosaic disease (CMD) was carried out in Comoros where cassava yield (5.7 t/ha) is significantly below the African average (8.6 t/ha) largely due to virus diseases. Observations from 66 sites across the Comoros Islands of Mwali, Ngazidja, and Ndzwani revealed that 83.3% of cassava fields had foliar symptoms of CBSD compared with 95.5% for CMD. Molecular diagnostics confirmed the presence of both cassava brown streak ipomoviruses (CBSIs) and cassava mosaic begomoviruses (CMBs). Although real-time RT-PCR only detected the presence of one CBSI species (Cassava brown streak virus, CBSV) the second species (Ugandan cassava brown streak virus, UCBSV) was identified using next-generation high-throughput sequencing. Both PCR and HTS detected the presence of East African cassava mosaic virus (EACMV). African cassava mosaic virus was not detected in any of the samples. Four whitefly species were identified from a sample of 131 specimens: Bemisia tabaci, B. afer, Aleurodicus dispersus, and Paraleyrodes bondari. Cassava B. tabaci comprised two mitotypes: SSA1-SG2 (89%) and SSA1-SG3 (11%). KASP SNP genotyping categorized 82% of cassava B. tabaci as haplogroup SSA-ESA. This knowledge will provide an important base for developing and deploying effective management strategies for cassava viruses and their vectors.
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Affiliation(s)
- Rudolph Rufini Shirima
- International Institute of Tropical Agriculture (IITA-Tanzania), P.O. Box 34441, Dar es Salaam 14112, Tanzania
- Correspondence: ; Tel.: +25-52-2270-0092
| | - Everlyne Nafula Wosula
- International Institute of Tropical Agriculture (IITA-Tanzania), P.O. Box 34441, Dar es Salaam 14112, Tanzania
| | - Abdou Azali Hamza
- Institut National de Recherche pour L’Agriculture, La Pêche et L’Environnement (INRAPE), Moroni BP 1406, Comoros
| | - Nobataine Ali Mohammed
- Institut National de Recherche pour L’Agriculture, La Pêche et L’Environnement (INRAPE), Moroni BP 1406, Comoros
| | - Hadji Mouigni
- Institut National de Recherche pour L’Agriculture, La Pêche et L’Environnement (INRAPE), Moroni BP 1406, Comoros
| | - Salima Nouhou
- Institut National de Recherche pour L’Agriculture, La Pêche et L’Environnement (INRAPE), Moroni BP 1406, Comoros
| | - Naima Mmadi Mchinda
- Institut National de Recherche pour L’Agriculture, La Pêche et L’Environnement (INRAPE), Moroni BP 1406, Comoros
| | - Gloria Ceasar
- International Institute of Tropical Agriculture (IITA-Tanzania), P.O. Box 34441, Dar es Salaam 14112, Tanzania
| | - Massoud Amour
- International Institute of Tropical Agriculture (IITA-Tanzania), P.O. Box 34441, Dar es Salaam 14112, Tanzania
| | - Emmanuel Njukwe
- West and Central African Council for Agricultural Research and Development (CORAF), Dakar CP 18523, Senegal
| | - James Peter Legg
- International Institute of Tropical Agriculture (IITA-Tanzania), P.O. Box 34441, Dar es Salaam 14112, Tanzania
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Casinga CM, Wosula EN, Sikirou M, Shirima RR, Munyerenkana CM, Nabahungu LN, Bashizi BK, Ugentho H, Monde G, Legg JP. Diversity and Distribution of Whiteflies Colonizing Cassava in Eastern Democratic Republic of Congo. INSECTS 2022; 13:849. [PMID: 36135550 PMCID: PMC9504715 DOI: 10.3390/insects13090849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 08/31/2022] [Indexed: 06/16/2023]
Abstract
The present study characterizes Bemisia tabaci and Bemisia afer from cassava in eastern Democratic Republic of Congo (DRC). The Mitochondrial COI sequencing revealed the occurrence of six cassava B. tabaci mitotypes, which were designated into four haplogroups (SSA-ECA, SSA-CA, SSA2, and SSA-ESA) using KASP SNP genotyping. SSA-ECA (72%) was the most prevalent and occurred in the northern part of the surveyed area, in the Ituri and Nord/Sud-Kivu provinces, whilst SSA-CA (21%) was present in the south, primarily in Haut-Katanga. SSA-ECA was predominant in the areas of north-eastern DRC most severely affected by cassava brown streak disease and was also reported in the new outbreak area in Pweto territory, Haut-Katanga, in the south. Bemisia afer comprised two major clusters with 85.5% of samples in cluster one, while the rest were in cluster two, which has no reference sequence in GenBank. This study provides important information on the genetic diversity of B. tabaci and B. afer in eastern DRC. This knowledge will be used as a basis for further studies to understand and to identify the role of whitefly haplogroups, their population densities and consequences for virus epidemics and spread as well as leading to improved vector and virus management strategies.
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Affiliation(s)
- Clérisse M. Casinga
- International Institute of Tropical Agriculture, Bukavu-Kalambo, Bukavu, Democratic Republic of the Congo
- Department of Environmental Sciences, Université du Cinquantenaire de Lwiro, Kabare, Bukavu, Democratic Republic of the Congo
| | - Everlyne N. Wosula
- International Institute of Tropical Agriculture, Dar es Salaam, Tanzania
| | - Mouritala Sikirou
- International Institute of Tropical Agriculture, Kinshasa, Democratic Republic of the Congo
| | - Rudolph R. Shirima
- International Institute of Tropical Agriculture, Dar es Salaam, Tanzania
| | - Carine M. Munyerenkana
- International Institute of Tropical Agriculture, Bukavu-Kalambo, Bukavu, Democratic Republic of the Congo
| | - Leon N. Nabahungu
- International Institute of Tropical Agriculture, Bukavu-Kalambo, Bukavu, Democratic Republic of the Congo
| | - Benoit K. Bashizi
- International Institute of Tropical Agriculture, Bukavu-Kalambo, Bukavu, Democratic Republic of the Congo
| | - Henry Ugentho
- Programme National Manioc, Institut National d’Etude et de Recherche Agronomiques de Mulungu, Bukavu-Mulungu, Democratic Republic of the Congo
| | - Godefroid Monde
- Department of Plant Virology, Institut Facultaire des Sciences Agronomiques, Kisangani-Yangambi, Kisangani, Democratic Republic of the Congo
| | - James P. Legg
- International Institute of Tropical Agriculture, Dar es Salaam, Tanzania
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11
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Mero HR, Lyantagaye SL, Bongcam-Rudloff E. Cassava Brown Streak Viruses express second 6-kilodalton (6K2) protein with varied polarity and three dimensional (3D) structures: Basis for trait discrepancy between the virus species. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 98:105219. [PMID: 35066168 DOI: 10.1016/j.meegid.2022.105219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 12/15/2021] [Accepted: 01/17/2022] [Indexed: 10/19/2022]
Abstract
Cassava Brown Streak Virus (CBSV) and Ugandan Cassava Brown Streak Virus (UCBSV) are the two among six virus species speculated to cause the most catastrophic Brown Streak Disease of Cassava (CBSD) in Africa and Asia. Cassava Brown Streak Virus (CBSV) is hard to breed resistance for compared to Ugandan Cassava Brown Streak Virus (UCBSV) species. This is exemplified by incidences of CBSV species rather than UCBSV species in elite breeding line, KBH 2006/0026 at Bagamoyo, Tanzania. It is not yet understood as to why CBSV species could breakdown CBSD-resistance in the KBH 2006/0026 unlike the UCBSV species. This marks the first in silico study conducted to understand molecular basis for the trait discrepancy between CBSV and UCBSV species from structural biology view point. Following ab initio modelling and analysis of physical-chemical properties of second 6-kilodalton (6K2) protein encoded by CBSV and UCBSV species, using ROBETTA server and Protein Parameters tool, respectively we report that; three dimensional (3D) structures and polarity of the protein differs significantly between the two virus species. (95% and 5%) and (85% and 15%) strains of 20 CBSV and 20 UCBSV species respectively, expressed the protein in homo-trimeric and homo-tetrameric forms, correspondingly. 95% and 85% of studied strain population of the two virus species expressed hydrophilic and hydrophobic 6K2, respectively. Based on findings of the curent study, we hypothesize that; (i) The hydrophilic 6K2 expressed by the CBSV species, favour its faster systemic movement via vascular tissues of cassava host and hence result into higher tissue titres than the UCBSV species encoding hydrophobic form of the protein. t and (ii) The hydrophilic 6K2 expressed byCBSV species have additional interaction advantage with Nuclear Inclusion b protease domain (NIb) and Viral genome-linked protein (VPg), components of Virus Replication Complex (VRC) and hence contributing to faster replication of viral genome than the hydrophobic 6K2 expressed by the UCBSV species. Experimental studies are needed to resolve the 3D structures of the 6K2, VPg and NIb and comprehend complex molecular interactions between them. We suggest that, the 6K2 gene should be targeted for improvement of RNA interference (RNAi)-directed transgenesis of virus-resistant cassava as a more effective way to control the CBSD besides breeding.
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Affiliation(s)
- Herieth Rhodes Mero
- University of Dar es Salaam, Mkwawa University College of Education (MUCE), P. O. Box 2513, Iringa, Tanzania; Swedish University of Agricultural Sciences (SLU), SLU-Global Bioinformatics Centre, Department of Animal Breeding and Genetics, P. 0. BOX 7054, 750 07 Uppsala, Sweden.
| | | | - Erik Bongcam-Rudloff
- Swedish University of Agricultural Sciences (SLU), SLU-Global Bioinformatics Centre, Department of Animal Breeding and Genetics, P. 0. BOX 7054, 750 07 Uppsala, Sweden
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12
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Valli AA, García López R, Ribaya M, Martínez FJ, Gómez DG, García B, Gonzalo I, Gonzalez de Prádena A, Pasin F, Montanuy I, Rodríguez-Gonzalo E, García JA. Maf/ham1-like pyrophosphatases of non-canonical nucleotides are host-specific partners of viral RNA-dependent RNA polymerases. PLoS Pathog 2022; 18:e1010332. [PMID: 35180277 PMCID: PMC8893687 DOI: 10.1371/journal.ppat.1010332] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 03/03/2022] [Accepted: 02/02/2022] [Indexed: 11/18/2022] Open
Abstract
Cassava brown streak disease (CBSD), dubbed the “Ebola of plants”, is a serious threat to food security in Africa caused by two viruses of the family Potyviridae: cassava brown streak virus (CBSV) and Ugandan (U)CBSV. Intriguingly, U/CBSV, along with another member of this family and one secoviridae, are the only known RNA viruses encoding a protein of the Maf/ham1-like family, a group of widespread pyrophosphatase of non-canonical nucleotides (ITPase) expressed by all living organisms. Despite the socio-economic impact of CDSD, the relevance and role of this atypical viral factor has not been yet established. Here, using an infectious cDNA clone and reverse genetics, we demonstrate that UCBSV requires the ITPase activity for infectivity in cassava, but not in the model plant Nicotiana benthamiana. HPLC-MS/MS experiments showed that, quite likely, this host-specific constraint is due to an unexpected high concentration of non-canonical nucleotides in cassava. Finally, protein analyses and experimental evolution of mutant viruses indicated that keeping a fraction of the yielded UCBSV ITPase covalently bound to the viral RNA-dependent RNA polymerase (RdRP) optimizes viral fitness, and this seems to be a feature shared by the other members of the Potyviridae family expressing Maf/ham1-like proteins. All in all, our work (i) reveals that the over-accumulation of non-canonical nucleotides in the host might have a key role in antiviral defense, and (ii) provides the first example of an RdRP-ITPase partnership, reinforcing the idea that RNA viruses are incredibly versatile at adaptation to different host setups. Cassava is one the most important staple food around the world in term of caloric intake. The cassava brown streak disease, caused by cassava brown streak virus (CBSV) and Ugandan (U)CBSV–Ipomovirus genus, Potyviridae family-, produces massive losses in cassava production. Curiously, these two viruses, unlike the vast majority of members of the family, encode a Maf1/ham1-like pyrophosphatase (HAM1) of non-canonical nucleotides with unknown relevance and function in viruses. This study aims to fill this gap in our knowledge by using reverse genetics, biochemistry, metabolomics and directed virus evolution. Hence, we found that HAM1 is required for UCBSV to infect cassava, where its pyrophosphatase activity resulted critical, but not to propagate in the model plant Nicotiana benthamiana. In addition, we demonstrated that HAM1 works in partnership with the viral RdRP during infection. Unexpected high levels of ITP/XTP non-canonical nucleotides found in cassava, and the known flexibility of RNA viruses to incorporate additional factors when required, supports the idea that the high concentration of ITP/XTP worked as a selection pressure to promote the acquisition of HAM1 into the virus in order to promote a successful infection.
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Affiliation(s)
- Adrian A. Valli
- Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
- * E-mail:
| | | | - María Ribaya
- Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | | | - Diego García Gómez
- Departamento de Química Analítica, Nutrición y Bromatología, Universidad de Salamanca, Salamanca, Spain
| | - Beatriz García
- Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Irene Gonzalo
- Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | | | - Fabio Pasin
- Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Inmaculada Montanuy
- Facultad de Ciencias Experimentales, Universidad Francisco de Vitoria, Madrid, Spain
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13
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Leiva AM, Jimenez J, Sandoval H, Perez S, Cuellar WJ. Complete genome sequence of a novel secovirid infecting cassava in the Americas. Arch Virol 2022; 167:665-668. [PMID: 34977988 PMCID: PMC8844172 DOI: 10.1007/s00705-021-05325-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 10/24/2021] [Indexed: 11/25/2022]
Abstract
We report the complete genome sequence of a field isolate of a novel bipartite secovirid infecting cassava in Colombia, provisionally named "cassava torrado-like virus" (CsTLV). The genome sequence was obtained using Oxford Nanopore Technology, and the 5’ ends were confirmed by RACE. The RNA1 is 7252 nucleotides (nt) long, encoding a polyprotein of 2336 amino acids (aa) containing the typical “replication block”, conserved torradovirus motifs, and a Maf/Ham1 domain, which is not commonly found in viral genomes. The RNA2 is 4469 nt long and contains two overlapping ORFs encoding proteins of 226 and 1179 aa, showing the characteristic genome arrangement of members of the genus Torradovirus.
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Affiliation(s)
- Ana M Leiva
- Virology Laboratory, Cassava Program, Crops for Nutrition and Health, International Center for Tropical Agriculture, Palmira, Colombia
| | - Jenyfer Jimenez
- Virology Laboratory, Cassava Program, Crops for Nutrition and Health, International Center for Tropical Agriculture, Palmira, Colombia
| | - Hector Sandoval
- AGROSAVIA, Centro de Investigacion La Libertad, Sede Yopal, Colombia
| | - Shirley Perez
- AGROSAVIA, Centro de Investigacion La Libertad, Sede Yopal, Colombia
| | - Wilmer J Cuellar
- Virology Laboratory, Cassava Program, Crops for Nutrition and Health, International Center for Tropical Agriculture, Palmira, Colombia.
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14
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Pasin F, Daròs JA, Tzanetakis IE. OUP accepted manuscript. FEMS Microbiol Rev 2022; 46:6534904. [PMID: 35195244 PMCID: PMC9249622 DOI: 10.1093/femsre/fuac011] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 02/02/2022] [Accepted: 02/08/2022] [Indexed: 11/17/2022] Open
Abstract
Potyviridae, the largest family of known RNA viruses (realm Riboviria), belongs to the picorna-like supergroup and has important agricultural and ecological impacts. Potyvirid genomes are translated into polyproteins, which are in turn hydrolyzed to release mature products. Recent sequencing efforts revealed an unprecedented number of potyvirids with a rich variability in gene content and genomic layouts. Here, we review the heterogeneity of non-core modules that expand the structural and functional diversity of the potyvirid proteomes. We provide a family-wide classification of P1 proteinases into the functional Types A and B, and discuss pretty interesting sweet potato potyviral ORF (PISPO), putative zinc fingers, and alkylation B (AlkB)—non-core modules found within P1 cistrons. The atypical inosine triphosphate pyrophosphatase (ITPase/HAM1), as well as the pseudo tobacco mosaic virus-like coat protein (TMV-like CP) are discussed alongside homologs of unrelated virus taxa. Family-wide abundance of the multitasking helper component proteinase (HC-pro) is revised. Functional connections between non-core modules are highlighted to support host niche adaptation and immune evasion as main drivers of the Potyviridae evolutionary radiation. Potential biotechnological and synthetic biology applications of potyvirid leader proteinases and non-core modules are finally explored.
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Affiliation(s)
- Fabio Pasin
- Corresponding author: Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València (CSIC-UPV), UPV Building 8E, Ingeniero Fausto Elio, 46011 Valencia, Spain. E-mail:
| | - José-Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València (CSIC-UPV), 46011 Valencia, Spain
| | - Ioannis E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, 72701 Fayetteville, AR, USA
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15
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García B, Bedoya L, García JA, Rodamilans B. An Importin-β-like Protein from Nicotiana benthamiana Interacts with the RNA Silencing Suppressor P1b of the Cucumber Vein Yellowing Virus, Modulating Its Activity. Viruses 2021; 13:2406. [PMID: 34960675 PMCID: PMC8706682 DOI: 10.3390/v13122406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 11/26/2022] Open
Abstract
During a plant viral infection, host-pathogen interactions are critical for successful replication and propagation of the virus through the plant. RNA silencing suppressors (RSSs) are key players of this interplay, and they often interact with different host proteins, developing multiple functions. In the Potyviridae family, viruses produce two main RSSs, HCPro and type B P1 proteins. We focused our efforts on the less known P1b of cucumber vein yellowing virus (CVYV), a type B P1 protein, to try to identify possible factors that could play a relevant role during viral infection. We used a chimeric expression system based on plum pox virus (PPV) encoding a tagged CVYV P1b in place of the canonical HCPro. We used that tag to purify P1b in Nicotiana-benthamiana-infected plants and identified by mass spectrometry an importin-β-like protein similar to importin 7 of Arabidopsis thaliana. We further confirmed the interaction by bimolecular fluorescence complementation assays and defined its nuclear localization in the cell. Further analyses showed a possible role of this N. benthamiana homolog of Importin 7 as a modulator of the RNA silencing suppression activity of P1b.
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Affiliation(s)
| | | | | | - Bernardo Rodamilans
- Centro Nacional de Biotecnología CNB, Consejo Superior de Investigaciones Científicas CSIC, 28049 Madrid, Spain; (B.G.); (L.B.); (J.A.G.)
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16
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Tussipkan D, Manabayeva SA. Employing CRISPR/Cas Technology for the Improvement of Potato and Other Tuber Crops. FRONTIERS IN PLANT SCIENCE 2021; 12:747476. [PMID: 34764969 PMCID: PMC8576567 DOI: 10.3389/fpls.2021.747476] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/04/2021] [Indexed: 05/07/2023]
Abstract
New breeding technologies have not only revolutionized biological science, but have also been employed to generate transgene-free products. Genome editing is a powerful technology that has been used to modify genomes of several important crops. This review describes the basic mechanisms, advantages and disadvantages of genome editing systems, such as ZFNs, TALENs, and CRISPR/Cas. Secondly, we summarize in detail all studies of the CRISPR/Cas system applied to potato and other tuber crops, such as sweet potato, cassava, yam, and carrot. Genes associated with self-incompatibility, abiotic-biotic resistance, nutrient-antinutrient content, and post-harvest factors targeted utilizing the CRISPR/Cas system are analyzed in this review. We hope that this review provides fundamental information that will be useful for future breeding of tuber crops to develop novel cultivars.
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Affiliation(s)
| | - Shuga A. Manabayeva
- Plant Genetic Engineering Laboratory, National Center for Biotechnology, Nur-Sultan, Kazakhstan
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17
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Mero HR, Lyantagaye SL, Bongcam-Rudloff E. Why has permanent control of cassava brown streak disease in Sub-Saharan Africa remained a dream since the 1930s? INFECTION GENETICS AND EVOLUTION 2021; 94:105001. [PMID: 34271188 DOI: 10.1016/j.meegid.2021.105001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/07/2021] [Accepted: 07/11/2021] [Indexed: 10/20/2022]
Abstract
Effective control of ipomoviruses that cause cassava brown streak disease (CBSD) in Africa has remained problematic despite eight remarkable decades (1930-2021) of research efforts. Molecular mechanisms underlying resistance breakdown in genetically improved cassava are still unknown. The vast genetic diversity of cassava brown streak viruses, which is crucial for the improvement of routine reverse transcription polymerase chain reaction (RT-qPCR) assays in CBSD-endemic regions of Africa, is controversial and underrepresented. From a molecular epidemiology viewpoint, this review discusses the reasons for why permanent control of CBSD is difficult in the modern era, even with the presence of diverse in silico and omics tools, recombinant DNA, and high throughput next-generation sequencing technologies. Following an extensive nucleotide data search in the National Centre for Biotechnology Information (NCBI) database and a literature review in PubMed and Scopus, we report that genomic data of 87.62% (474/541) strains of cassava brown streak virus are missing due to poor sequencing capacity in Africa. The evolution dynamics of viral virulence and pathogenicity has not yet been fully explored from the available 67 (12.38%) genomic sequences, owing to poor bioinformatics capacity. Tanzania and Zambia have the highest and lowest disease inoculum pressure, correspondingly. Knowledge gaps in molecular biology and the overall molecular pathogenesis of CBSD viruses impede effective disease control in Africa. Recommendations for possible solutions to the research questions, controversies, and hypotheses raised in this study serve as a roadmap for the invention of more effective CBSD control methods.
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Affiliation(s)
- Herieth Rhodes Mero
- University of Dar es Salaam, Mkwawa University College of Education (MUCE), Department of Biological Sciences, P. O. BOX 2513, Iringa, Tanzania.; Swedish University of Agricultural Sciences (SLU), SLU-Global Bioinformatics Centre, Department of Animal Breeding and Genetics, PO Box 7054 750 07, Uppsala, Sweden.
| | | | - Erik Bongcam-Rudloff
- Swedish University of Agricultural Sciences (SLU), SLU-Global Bioinformatics Centre, Department of Animal Breeding and Genetics, PO Box 7054 750 07, Uppsala, Sweden
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18
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P1 of Sweet Potato Feathery Mottle Virus Shows Strong Adaptation Capacity, Replacing P1-HCPro in a Chimeric Plum Pox Virus. J Virol 2021; 95:e0015021. [PMID: 33952634 DOI: 10.1128/jvi.00150-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Potyviridae is the largest family of plant RNA viruses. Their genomes are expressed through long polyproteins that are usually headed by the leader endopeptidase P1. This protein can be classified as type A or type B based on host proteolytic requirements and RNA silencing suppression (RSS) capacity. The main Potyviridae genus is Potyvirus, and a group of potyviruses infecting sweet potato presents an enlarged P1 protein with a polymerase slippage motif that produces an extra product termed P1N-PISPO. These two proteins display some RSS activity and are expressed followed by HCPro, which appears to be the main RNA silencing suppressor in these viruses. Here, we studied the behavior of the P1 protein of Sweet potato feathery mottle virus (SPFMV) using a viral system based on a canonical potyvirus, Plum pox virus (PPV), and discovered that this protein is able to replace both PPV P1 and HCPro. We also found that P1N-PISPO, produced after polymerase slippage, provides extra RNA silencing suppression capacity to SPFMV P1 in this viral context. In addition, the results showed that presence of two type A P1 proteins was detrimental for viral viability. The ample recombination spectrum that we found in the recovered viruses supports the strong adaptation capacity of P1 proteins and signals the N-terminal part of SPFMV P1 as essential for RSS activity. Further analyses provided data to add extra layers to the evolutionary history of sweet potato-infecting potyvirids. IMPORTANCE Plant viruses represent a major challenge for agriculture worldwide and Potyviridae, being the largest family of plant RNA viruses, is one of the primary players. P1, the leader endopeptidase, is a multifunctional protein that contributes to the successful spread of these viruses over a wide host range. Understanding how P1 proteins work, their dynamic interplay during viral infection, and their evolutionary path is critical for the development of strategic tools to fight the multiple diseases these viruses cause. We focused our efforts on the P1 protein of Sweet potato feathery mottle virus, which is coresponsible for the most devastating disease in sweet potato. The significance of our research is in understanding the capacity of this protein to perform several independent functions, using this knowledge to learn more about P1 proteins in general and the potyvirids infecting this host.
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19
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James AM, Seal SE, Bailey AM, Foster GD. Viral inosine triphosphatase: A mysterious enzyme with typical activity, but an atypical function. MOLECULAR PLANT PATHOLOGY 2021; 22:382-389. [PMID: 33471956 PMCID: PMC7865087 DOI: 10.1111/mpp.13021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/22/2020] [Accepted: 10/23/2020] [Indexed: 05/03/2023]
Abstract
Plant viruses typically have highly condensed genomes, yet the plant-pathogenic viruses Cassava brown streak virus, Ugandan cassava brown streak virus, and Euphorbia ringspot virus are unusual in encoding an enzyme not yet found in any other virus, the "house-cleaning" enzyme inosine triphosphatase. Inosine triphosphatases (ITPases) are highly conserved enzymes that occur in all kingdoms of life and perform a house-cleaning function by hydrolysing the noncanonical nucleotide inosine triphosphate to inosine monophosphate. The ITPases encoded by cassava brown streak virus and Ugandan cassava brown streak virus have been characterized biochemically and are shown to have typical ITPase activity. However, their biological role in virus infection has yet to be elucidated. Here we review what is known of viral-encoded ITPases and speculate on potential roles in infection with the aim of generating a greater understanding of cassava brown streak viruses, a group of the world's most devastating viruses.
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Affiliation(s)
- Amy M. James
- School of Biological SciencesLife Sciences BuildingUniversity of BristolBristolUK
| | - Susan E. Seal
- Natural Resources Institute, Chatham MaritimeGillinghamUK
| | - Andy M. Bailey
- School of Biological SciencesLife Sciences BuildingUniversity of BristolBristolUK
| | - Gary D. Foster
- School of Biological SciencesLife Sciences BuildingUniversity of BristolBristolUK
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20
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Screening for Resistance in Farmer-Preferred Cassava Cultivars from Ghana to a Mixed Infection of CBSV and UCBSV. PLANTS 2020; 9:plants9081026. [PMID: 32823622 PMCID: PMC7465500 DOI: 10.3390/plants9081026] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/06/2020] [Accepted: 08/10/2020] [Indexed: 12/02/2022]
Abstract
Cassava brown streak disease (CBSD) caused by the Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV) is a threat to cassava production in Africa. The potential spread of CBSD into West Africa is a cause for concern, therefore screening for resistance in farmer-preferred genotypes is crucial for effective control and management. We multiplied a selection of eleven cassava cultivars grown by farmers in Ghana to test their response to a mixed infection of CBSV (TAZ-DES-01) and UCBSV (TAZ-DES-02) isolates using a stringent top-cleft graft inoculation method. Virus titers were quantified in the inoculated scions and cuttings propagated from the inoculated scions to assess virus accumulation and recovery. All cultivars were susceptible to the mixed infection although their response and symptom development varied. In the propagated infected scions, CBSV accumulated at higher titers in leaves of eight of the eleven cultivars. Visual scoring of storage roots from six-month-old virus-inoculated plants revealed the absence of CBSD-associated necrosis symptoms and detectable titers of CBSVs in the cultivar, IFAD. Although all eleven cultivars supported the replication of CBSV and UCBSV in their leaves, the absence of virus replication and CBSD-associated symptoms in the roots of some cultivars could be used as criteria to rapidly advance durable CBSD tolerance using breeding and genetic engineering approaches.
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21
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Abstract
Potyviridae is the largest family of plant-infecting RNA viruses, encompassing over 30% of known plant viruses. The family is closely related to animal picornaviruses such as enteroviruses and belongs to the picorna-like supergroup. Like all other picorna-like viruses, potyvirids employ polyprotein processing as a gene expression strategy and have single-stranded, positive-sense RNA genomes, most of which are monopartite with a long open reading frame. The potyvirid polyproteins are highly conserved in the central and carboxy-terminal regions. In contrast, the N-terminal region is hypervariable and contains position-specific mutations resulting from transcriptional slippage during viral replication, leading to translational frameshift to produce additional viral proteins essential for viral infection. Some potyvirids even lack one of the N-terminal proteins P1 or helper component-protease and have a genus-specific or species-specific protein instead. This review summarizes current knowledge about the conserved and divergent features of potyvirid genomes and biological relevance and discusses future research directions.
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Affiliation(s)
- Hongguang Cui
- College of Plant Protection, Hainan University, Haikou, Hainan 570228, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Haikou, Hainan 570228, China
| | - Aiming Wang
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario N5V 4T3, Canada
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22
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Utilization of infectious clones to visualize Cassava brown streak virus replication in planta and gain insights into symptom development. Virus Genes 2019; 55:825-833. [PMID: 31388891 PMCID: PMC6831539 DOI: 10.1007/s11262-019-01697-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 07/29/2019] [Indexed: 10/26/2022]
Abstract
Cassava brown streak disease (CBSD) is a leading cause of cassava yield losses across eastern and central Africa and is having a severe impact on food security across the region. Despite its importance, relatively little is known about the mechanisms behind CBSD viral infections. We have recently reported the construction of Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV) infectious clones (IC), which can be used to gain insights into the functions of viral proteins and sequences associated with symptom development. In this study, we perform the first reporter gene tagging of a CBSV IC, with the insertion of green fluorescent protein (GFP) sequence at two different genome positions. Nicotiana benthamiana infections with the CBSV_GFP ICs revealed active CBSV replication in inoculated leaves at 2-5 days post inoculation (dpi) and systemic leaves at 10-14 dpi. We also constructed the chimera CBSV_UCP IC, consisting of the CBSV genome with a UCBSV coat protein (CP) sequence replacement. N. benthamiana infections with CBSV_UCP revealed that the CBSV CP may be associated with high levels of viral accumulation and necrosis development during early infection. These initial manipulations pave the way for U/CBSV ICs to be used to understand U/CBSV biology that will inform vital CBSD control strategies.
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Tomlinson KR, Pablo‐Rodriguez JL, Bunawan H, Nanyiti S, Green P, Miller J, Alicai T, Seal SE, Bailey AM, Foster GD. Cassava brown streak virus Ham1 protein hydrolyses mutagenic nucleotides and is a necrosis determinant. MOLECULAR PLANT PATHOLOGY 2019; 20:1080-1092. [PMID: 31154674 PMCID: PMC6640186 DOI: 10.1111/mpp.12813] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Cassava brown streak disease (CBSD) is a leading cause of cassava losses in East and Central Africa, and is currently having a severe impact on food security. The disease is caused by two viruses within the Potyviridae family: Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV), which both encode atypical Ham1 proteins with highly conserved inosine triphosphate (ITP) pyrophosphohydrolase (ITPase) domains. ITPase proteins are widely encoded by plant, animal, and archaea. They selectively hydrolyse mutagenic nucleotide triphosphates to prevent their incorporation into nucleic acid and thereby function to reduce mutation rates. It has previously been hypothesized that U/CBSVs encode Ham1 proteins with ITPase activity to reduce viral mutation rates during infection. In this study, we investigate the potential roles of U/CBSV Ham1 proteins. We show that both CBSV and UCBSV Ham1 proteins have ITPase activities through in vitro enzyme assays. Deep-sequencing experiments found no evidence of the U/CBSV Ham1 proteins providing mutagenic protection during infections of Nicotiana hosts. Manipulations of the CBSV_Tanza infectious clone were performed, including a Ham1 deletion, ITPase point mutations, and UCBSV Ham1 chimera. Unlike severely necrotic wild-type CBSV_Tanza infections, infections of Nicotiana benthamiana with the manipulated CBSV infectious clones do not develop necrosis, indicating that that the CBSV Ham1 is a necrosis determinant. We propose that the presence of U/CBSV Ham1 proteins with highly conserved ITPase motifs indicates that they serve highly selectable functions during infections of cassava and may represent a euphorbia host adaptation that could be targeted in antiviral strategies.
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Affiliation(s)
- Katie R. Tomlinson
- School of Biological SciencesUniversity of BristolLife Sciences Building, 24 Tyndall Avenue BristolBS8 1TQUK
| | - José Luis Pablo‐Rodriguez
- School of Biological SciencesUniversity of BristolLife Sciences Building, 24 Tyndall Avenue BristolBS8 1TQUK
- CINVESTAVCampus IrapuatoMexico
| | - Hamidun Bunawan
- School of Biological SciencesUniversity of BristolLife Sciences Building, 24 Tyndall Avenue BristolBS8 1TQUK
- Institute of Systems Biology (INBIOSIS)Universiti Kebangsaan Malaysia, UKMBangi43600Selangor Darul EhsanMalaysia
| | - Sarah Nanyiti
- School of Biological SciencesUniversity of BristolLife Sciences Building, 24 Tyndall Avenue BristolBS8 1TQUK
- National Crops Resources Research Institute (NaCRRI)P.O. Box 7084KampalaUganda
| | - Patrick Green
- School of Biological SciencesUniversity of BristolLife Sciences Building, 24 Tyndall Avenue BristolBS8 1TQUK
| | - Josie Miller
- School of Biological SciencesUniversity of BristolLife Sciences Building, 24 Tyndall Avenue BristolBS8 1TQUK
| | - Titus Alicai
- National Crops Resources Research Institute (NaCRRI)P.O. Box 7084KampalaUganda
| | - Susan E. Seal
- Natural Resources InstituteChatham Maritime, KentME4 4TBUK
| | - Andy M. Bailey
- School of Biological SciencesUniversity of BristolLife Sciences Building, 24 Tyndall Avenue BristolBS8 1TQUK
| | - Gary D. Foster
- School of Biological SciencesUniversity of BristolLife Sciences Building, 24 Tyndall Avenue BristolBS8 1TQUK
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Amisse JJG, Ndunguru J, Tairo F, Ateka E, Boykin LM, Kehoe MA, Cossa N, Rey C, Sseruwagi P. Analyses of seven new whole genome sequences of cassava brown streak viruses in Mozambique reveals two distinct clades: evidence for new species. PLANT PATHOLOGY 2019; 68:1007-1018. [PMID: 31217639 PMCID: PMC6563196 DOI: 10.1111/ppa.13001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Cassava brown streak disease (CBSD) caused by Cassava brown streak virus (CBSV) and Uganda cassava brown streak virus (UCBSV) is a major constraint to cassava production in Mozambique. Full genome sequences of CBSD-associated virus isolates contribute to the understanding of genetic diversity and the development of new diagnostic primers that can be used for early detection of the viruses for sustainable disease management. This study determined seven new whole CBSV genomes from total RNA isolated from cassava leaves with CBSD symptoms collected from Nampula and Zambezia in Mozambique. Phylogenetic analyses of the new genomes with published CBSV and UCBSV sequences in GenBank grouped the CBSV isolates from Mozambique into two distinct clades together with CBSV isolates from Tanzania. Clade 1 and 2 isolates shared low nucleotide (79.1-80.4%) and amino acid (86.5-88.2%) sequence identity. Further, comparisons within the seven new CBSV isolates, and between them and the single published complete CBSV sequence (CBSV_MO_83_FN434436) from Mozambique, revealed nucleotide sequence identities of 79.3-100% and 79.3-98%, respectively, and amino acid identities of 86.7-100% and 86.7-98.8%. In addition, using RDP4, a recombination analysis comprising all CBSV and UCBSV genome sequences from GenBank detect 11 recombination events. Using several comprehensive evolutionary models and statistical programs, it was confirmed that CBSV and UCBSV are distinct virus species, with an additional probable new species (clade 2).
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Affiliation(s)
- J. J. G. Amisse
- Mozambique Agricultural Research InstitutePosto Agronómico de Nampula, PO Box 622, Rua de corrane, km 7NampulaMozambique
- Jomo Kenyatta University of Agriculture and TechnologyPO Box 62000, City SquareNairobiThikaKenya
| | - J. Ndunguru
- Tanzania Agricultural Research Institute – MikocheniPO Box 6226Dar es SalaamTanzania
| | - F. Tairo
- Tanzania Agricultural Research Institute – MikocheniPO Box 6226Dar es SalaamTanzania
| | - E. Ateka
- Jomo Kenyatta University of Agriculture and TechnologyPO Box 62000, City SquareNairobiThikaKenya
| | - L. M. Boykin
- The University of Western AustraliaARC Centre of Excellence in Plant Energy Biology and School of Molecular SciencesCrawley6009Australia
| | - M. A. Kehoe
- Department of Primary Industries and Regional Development Diagnostic Laboratory ServiceLocked Bag 4Bentley Delivery CentreSouth Perth6983Australia
| | - N. Cossa
- Mozambique Agricultural Research InstitutePosto Agronómico de Nampula, PO Box 622, Rua de corrane, km 7NampulaMozambique
| | - C. Rey
- School of Molecular and Cell BiologyUniversity of the Witwatersrand1 Jan Smuts Ave, BraamfonteinJohannesburg2000South Africa
| | - P. Sseruwagi
- Tanzania Agricultural Research Institute – MikocheniPO Box 6226Dar es SalaamTanzania
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25
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Rose H, Döring I, Vetten HJ, Menzel W, Richert-Pöggeler KR, Maiss E. Complete genome sequence and construction of an infectious full-length cDNA clone of celery latent virus - an unusual member of a putative new genus within the Potyviridae. J Gen Virol 2019; 100:308-320. [PMID: 30667354 DOI: 10.1099/jgv.0.001207] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Celery latent virus (CeLV) is an incompletely described plant virus known to be sap and seed transmissible and to possess flexuous filamentous particles measuring about 900 nm in length, suggesting it as a possible member of the family Potyviridae. Here, an Italian isolate of CeLV was transmitted by sap to a number of host plants and shown to have a single-stranded and monopartite RNA genome being 11 519 nucleotides (nts) in size and possessing some unusual features. The RNA contains a large open reading frame (ORF) that is flanked by a short 5' untranslated region (UTR) of 13 nt and a 3' UTR consisting of 586 nt that is not polyadenylated. CeLV RNA shares nt sequence identity of only about 40 % with other members of the Potyviridae (potyvirids). The CeLV polyprotein is notable in that it starts with a signal peptide, has a putative P3N-PIPO ORF and shares low aa sequence identity (about 18 %) with other potyvirids. Although potential cleavage sites were not identified for the N-terminal two-thirds of the polyprotein, the latter possesses a number of sequence motifs, the identity and position of which are characteristic of other potyvirids. Attempts at constructing an infectious full-length cDNA clone of CeLV were successful following Rhizobium radiobacter infiltration of Nicotiana benthamiana and Apium graveolens. CeLV appears to have the largest genome of all known potyvirids and some unique genome features that may warrant the creation of a new genus, for which we propose the name 'celavirus'.
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Affiliation(s)
- Hanna Rose
- 1Department Phytomedicine, Leibniz University Hannover, Institute of Horticultural Production Systems, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Ines Döring
- 1Department Phytomedicine, Leibniz University Hannover, Institute of Horticultural Production Systems, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | | | - Wulf Menzel
- 3Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7 B, 38124 Braunschweig, Germany
| | - Katja R Richert-Pöggeler
- 4Julius Kühn Institut JKI, Federal Research Centre for Cultivated Plants, Institute of Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Edgar Maiss
- 1Department Phytomedicine, Leibniz University Hannover, Institute of Horticultural Production Systems, Herrenhäuser Str. 2, 30419, Hannover, Germany
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26
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Gomez MA, Lin ZD, Moll T, Chauhan RD, Hayden L, Renninger K, Beyene G, Taylor NJ, Carrington JC, Staskawicz BJ, Bart RS. Simultaneous CRISPR/Cas9-mediated editing of cassava eIF4E isoforms nCBP-1 and nCBP-2 reduces cassava brown streak disease symptom severity and incidence. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:421-434. [PMID: 30019807 PMCID: PMC6335076 DOI: 10.1111/pbi.12987] [Citation(s) in RCA: 145] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 06/27/2018] [Indexed: 05/02/2023]
Abstract
Cassava brown streak disease (CBSD) is a major constraint on cassava yields in East and Central Africa and threatens production in West Africa. CBSD is caused by two species of positive-sense RNA viruses belonging to the family Potyviridae, genus Ipomovirus: Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). Diseases caused by the family Potyviridae require the interaction of viral genome-linked protein (VPg) and host eukaryotic translation initiation factor 4E (eIF4E) isoforms. Cassava encodes five eIF4E proteins: eIF4E, eIF(iso)4E-1, eIF(iso)4E-2, novel cap-binding protein-1 (nCBP-1), and nCBP-2. Protein-protein interaction experiments consistently found that VPg proteins associate with cassava nCBPs. CRISPR/Cas9-mediated genome editing was employed to generate ncbp-1, ncbp-2, and ncbp-1/ncbp-2 mutants in cassava cultivar 60444. Challenge with CBSV showed that ncbp-1/ncbp-2 mutants displayed delayed and attenuated CBSD aerial symptoms, as well as reduced severity and incidence of storage root necrosis. Suppressed disease symptoms were correlated with reduced virus titre in storage roots relative to wild-type controls. Our results demonstrate the ability to modify multiple genes simultaneously in cassava to achieve tolerance to CBSD. Future studies will investigate the contribution of remaining eIF4E isoforms on CBSD and translate this knowledge into an optimized strategy for protecting cassava from disease.
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Affiliation(s)
- Michael A. Gomez
- Department of Plant and Microbial Biology and Innovative Genomics InstituteUniversity of CaliforniaBerkeleyCAUSA
| | | | | | | | - Luke Hayden
- Donald Danforth Plant Science CenterSt. LouisMOUSA
| | | | - Getu Beyene
- Donald Danforth Plant Science CenterSt. LouisMOUSA
| | | | | | - Brian J. Staskawicz
- Department of Plant and Microbial Biology and Innovative Genomics InstituteUniversity of CaliforniaBerkeleyCAUSA
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Maruthi M, Whitfield EC, Otti G, Tumwegamire S, Kanju E, Legg JP, Mkamilo G, Kawuki R, Benesi I, Zacarias A, Munga T, Mwatuni F, Mbugua E. A method for generating virus-free cassava plants to combat viral disease epidemics in Africa. PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY 2019; 105:77-87. [PMID: 31007376 PMCID: PMC6472600 DOI: 10.1016/j.pmpp.2018.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 07/25/2018] [Accepted: 09/13/2018] [Indexed: 06/09/2023]
Abstract
Here, we report a method to clean cassava plants from viral infections that cause cassava mosaic and brown streak diseases in Africa. Infected plants of resistant or tolerant varieties from Malawi, Mozambique, Kenya, Tanzania and Uganda were cleaned in the UK using a combination of tissue culture, chemotherapy and thermotherapy. In the first cycle of our virus-indexing procedure, we successfully cleaned 27 of the 31 varieties (87%), and after an additional three cleaning cycles, all plants were virus-free. Virus-free tissue-cultured plants were shipped back to Africa for distribution to farmers. This first cross-boundary effort provides important lessons for mitigating the two-major cassava viral diseases.
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Key Words
- ACMV, African cassava mosaic virus
- CBSD, Cassava brown streak disease
- CBSV, Cassava brown streak virus
- CMD, Cassava mosaic disease
- CTAB, Cetyl trimethylammonium bromide
- Cassava brown streak disease
- Cassava mosaic disease
- EACMV, East African cassava mosaic virus
- EACMV-Ug, East African cassava mosaic virus-Uganda
- LFC, Laminar flow cabinet
- MS, Murashige and Skoog
- Manihot esculenta
- PPM, Plant Preservation Mixture
- RH, Relative humidity
- SDW, Sterilised deionised water
- UCBSV, Ugandan cassava brown streak virus
- UIC, Unique identifying code
- Virus diagnosis
- Virus indexing
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Affiliation(s)
- M.N. Maruthi
- Natural Resources Institute (NRI), University of Greenwich, Chatham Maritime, Kent, United Kingdom
| | - E. Charles Whitfield
- Natural Resources Institute (NRI), University of Greenwich, Chatham Maritime, Kent, United Kingdom
| | - Gerald Otti
- Natural Resources Institute (NRI), University of Greenwich, Chatham Maritime, Kent, United Kingdom
| | - Silver Tumwegamire
- International Institute of Agriculture (IITA), P.O Box 34441, Dar es Salaam, Tanzania
| | - Edward Kanju
- International Institute of Agriculture (IITA), P.O Box 34441, Dar es Salaam, Tanzania
| | - James P. Legg
- International Institute of Agriculture (IITA), P.O Box 34441, Dar es Salaam, Tanzania
| | - Geoffrey Mkamilo
- Department of Agricultural Research and Development (DRD), P.O Box 2066, Dar es Salaam, Tanzania
| | - Robert Kawuki
- National Agricultural Research Organization (NARO), P.O Box 295, Entebbe, Uganda
| | - Ibrahim Benesi
- Department for Agricultural Research Services (DARS), Chitedze Research Station, P. O. Box 158, Lilongwe, Malawi
| | - Anabela Zacarias
- National Institute of Agricultural Research (IIAM), P.O Box 3658, Maputo, Mozambique
| | - Therezia Munga
- Kenya Agricultural and Livestock Research Organization (KALRO), Kenya
| | - Francis Mwatuni
- Kenya Plant Inspectorate Services (KEPHIS), Plant Quarantine and Biosecurity Station, Muguga, P.O. Box 49592 00100, Nairobi, Kenya
| | - Edward Mbugua
- Genetic Technologies International Limited (GTIL), P.O. Box 47430-00100, Nairobi, Kenya
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28
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Saggaf MH, Ndunguru J, Tairo F, Sseruwagi P, Ascencio-Ibáñez JT, Kilalo D, Miano DW. Immunohistochemical localization of Cassava brown streak virus and its morphological effect on cassava leaves. PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY 2019; 105:67-76. [PMID: 31007375 PMCID: PMC6472608 DOI: 10.1016/j.pmpp.2018.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 05/26/2018] [Accepted: 06/08/2018] [Indexed: 05/24/2023]
Abstract
The localization of Cassava brown streak virus (CBSV) in cassava (Manihot esculenta) leaf tissues was determined and cellular morphological changes in CBSV-infected tissues were evaluated. CBSV-symptomatic leaves were screened with CBSV-specific primers using reverse-transcriptase polymerase chain reaction. Immunohistochemical reactions showed precipitation in CBSV-infected but not CBSV-free tissues, demonstrating successful localization of CBSV. Microscopic inspection showed significantly larger (P < 0.001) midribs in CBSV-infected compared with control (uninfected) leaves. Viral accumulation occurred in middle and lower but rarely in young upper leaves. This immunohistochemical method for virus localization will be invaluable for efficient screening of CBSV and for breeding resistant cassava.
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Affiliation(s)
- Maliha H. Saggaf
- Mikocheni Agricultural Research Institute, P.O. Box, 6226, Dar-es-Salaam, Tanzania
| | - Joseph Ndunguru
- Mikocheni Agricultural Research Institute, P.O. Box, 6226, Dar-es-Salaam, Tanzania
| | - Fred Tairo
- Mikocheni Agricultural Research Institute, P.O. Box, 6226, Dar-es-Salaam, Tanzania
| | - Peter Sseruwagi
- Mikocheni Agricultural Research Institute, P.O. Box, 6226, Dar-es-Salaam, Tanzania
| | | | - Dora Kilalo
- University of Nairobi, P.O. Box 30197-00100, Nairobi, Kenya
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29
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Rodamilans B, Valli A, Mingot A, San León D, López-Moya JJ, García JA. An atypical RNA silencing suppression strategy provides a snapshot of the evolution of sweet potato-infecting potyviruses. Sci Rep 2018; 8:15937. [PMID: 30374036 PMCID: PMC6206096 DOI: 10.1038/s41598-018-34358-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 10/10/2018] [Indexed: 12/13/2022] Open
Abstract
Plant viruses usually encode proteins with RNA silencing suppression (RSS) activity to counteract plant defenses. In Potyvirus, the largest genus in the family Potyviridae, this role is taken over by the multifunctional HCPro, also involved in aphid transmission, polyprotein processing and virion formation. Recently, the large P1 of Sweet potato feathery mottle virus (SPFMV) was characterized finding an extra ORF produced after polymerase slippage, which originates the product P1N-PISPO. Transient expression assays showed that SPFMV P1 and P1N-PISPO presented RSS activity, while HCPro did not. In this work, we analyze possible differences between HCPro of SPFMV and other potyviruses, testing HCPro RSS activity in a transient expression assay, and using a Plum pox virus-based system to test the ability of SPFMV P1N-PISPO and HCPro to serve as RNA silencing suppressors in the context of a viral infection. Our results indicate that not only P1 and P1N-PISPO, but also HCPro display RSS activity when expressed in a suitable context, stressing the importance of the selected experimental system for testing anti-silencing capacity of proteins. The presence of multiple viral silencing suppressors in SPFMV adds complexity to an already intricate RSS system, and provides insight into the hypothetical evolution of sweet potato-infecting potyvirids.
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Affiliation(s)
| | - Adrián Valli
- Centro Nacional de Biotecnología CNB, CSIC, Madrid, Spain
| | - Ares Mingot
- Center for Research in Agricultural Genomics CRAG, CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, Cerdanyola del Vallès, Barcelona, Spain
| | - David San León
- Centro Nacional de Biotecnología CNB, CSIC, Madrid, Spain
| | - Juan José López-Moya
- Center for Research in Agricultural Genomics CRAG, CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, Cerdanyola del Vallès, Barcelona, Spain
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30
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Nyström K, Wanrooij PH, Waldenström J, Adamek L, Brunet S, Said J, Nilsson S, Wind-Rotolo M, Hellstrand K, Norder H, Tang KW, Lagging M. Inosine Triphosphate Pyrophosphatase Dephosphorylates Ribavirin Triphosphate and Reduced Enzymatic Activity Potentiates Mutagenesis in Hepatitis C Virus. J Virol 2018; 92:e01087-18. [PMID: 30045981 PMCID: PMC6146798 DOI: 10.1128/jvi.01087-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 07/17/2018] [Indexed: 12/19/2022] Open
Abstract
A third of humans carry genetic variants of the ITP pyrophosphatase (ITPase) gene (ITPA) that lead to reduced enzyme activity. Reduced ITPase activity was earlier reported to protect against ribavirin-induced hemolytic anemia and to diminish relapse following ribavirin and interferon therapy for hepatitis C virus (HCV) genotype 2 or 3 infections. While several hypotheses have been put forward to explain the antiviral actions of ribavirin, details regarding the mechanisms of interaction between reduced ITPase activity and ribavirin remain unclear. The in vitro effect of reduced ITPase activity was assessed by means of transfection of hepatocytes (Huh7.5 cells) with a small interfering RNA (siRNA) directed against ITPA or a negative-control siRNA in the presence or absence of ribavirin in an HCV culture system. Low ribavirin concentrations strikingly depleted intracellular GTP levels in HCV-infected hepatocytes whereas higher ribavirin concentrations induced G-to-A and C-to-U single nucleotide substitutions in the HCV genome, with an ensuing reduction of HCV RNA expression and HCV core antigen production. Ribavirin triphosphate (RTP) was dephosphorylated in vitro by recombinant ITPase to a similar extent as ITP, a naturally occurring substrate of ITPase, and reducing ITPA expression in Huh 7.5 cells by siRNA increased intracellular levels of RTP in addition to increasing HCV mutagenesis and reducing progeny virus production. Our results extend the understanding of the biological impact of reduced ITPase activity, demonstrate that RTP is a substrate of ITPase, and may point to personalized ribavirin dosage according to ITPA genotype in addition to novel antiviral strategies.IMPORTANCE This study highlights the multiple modes of action of ribavirin, including depletion of intracellular GTP and increased hepatitis C virus mutagenesis. In cell culture, reduced ITP pyrophosphatase (ITPase) enzyme activity affected the intracellular concentrations of ribavirin triphosphate (RTP) and augmented the impact of ribavirin on the mutation rate and virus production. Additionally, our results imply that RTP, similar to ITP, a naturally occurring substrate of ITPase, is dephosphorylated in vitro by ITPase.
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Affiliation(s)
- Kristina Nyström
- Department of Infectious Diseases/Virology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Paulina H Wanrooij
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Jesper Waldenström
- Department of Infectious Diseases/Virology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Ludmila Adamek
- Department of Infectious Diseases/Virology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Sofia Brunet
- Department of Infectious Diseases/Virology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Joanna Said
- Department of Infectious Diseases/Virology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Staffan Nilsson
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | | | - Kristoffer Hellstrand
- Department of Infectious Diseases/Virology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Helene Norder
- Department of Infectious Diseases/Virology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Ka-Wei Tang
- Department of Infectious Diseases/Virology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Martin Lagging
- Department of Infectious Diseases/Virology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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31
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Shan H, Pasin F, Tzanetakis IE, Simón‐Mateo C, García JA, Rodamilans B. Truncation of a P1 leader proteinase facilitates potyvirus replication in a non-permissive host. MOLECULAR PLANT PATHOLOGY 2018; 19:1504-1510. [PMID: 29115017 PMCID: PMC6638051 DOI: 10.1111/mpp.12640] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 10/25/2017] [Accepted: 11/03/2017] [Indexed: 05/08/2023]
Abstract
The Potyviridae family is a major group of plant viruses that includes c. 200 species, most of which have narrow host ranges. The potyvirid P1 leader proteinase self-cleaves from the remainder of the viral polyprotein and shows large sequence variability linked to host adaptation. P1 proteins can be classified as Type A or Type B on the basis, amongst other things, of their dependence or not on a host factor to develop their protease activity. In this work, we studied Type A proteases from the Potyviridae family, characterizing their host factor requirements. Our in vitro cleavage analyses of potyvirid P1 proteases showed that the N-terminal domain is relevant for host factor interaction and suggested that the C-terminal domain is also involved. In the absence of plant factors, the N-terminal end of Plum pox virus P1 antagonizes protease self-processing. We performed extended deletion mutagenesis analysis to define the N-terminal antagonistic domain of P1. In viral infections, removal of the P1 protease antagonistic domain led to a gain-of-function phenotype, strongly increasing local infection in a non-permissive host. Altogether, our results shed new insights into the adaptation and evolution of potyvirids.
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Affiliation(s)
- Hongying Shan
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB‐CSIC)Campus Universidad Autónoma de Madrid, Darwin 3Madrid 28049Spain
| | - Fabio Pasin
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB‐CSIC)Campus Universidad Autónoma de Madrid, Darwin 3Madrid 28049Spain
- Present address:
Agricultural Biotechnology Research CenterAcademia Sinica11529 TaipeiTaiwan
| | - Ioannis E. Tzanetakis
- Department of Plant Pathology, Division of AgricultureUniversity of Arkansas SystemFayettevilleAR 72701USA
| | - Carmen Simón‐Mateo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB‐CSIC)Campus Universidad Autónoma de Madrid, Darwin 3Madrid 28049Spain
| | - Juan Antonio García
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB‐CSIC)Campus Universidad Autónoma de Madrid, Darwin 3Madrid 28049Spain
| | - Bernardo Rodamilans
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB‐CSIC)Campus Universidad Autónoma de Madrid, Darwin 3Madrid 28049Spain
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Okul Valentor A, Ochwo-Ssemakula M, Kaweesi T, Ozimati A, Mrema E, Mwale E, Gibson P, Achola E, Edema R, Baguma Y, Kawuki R. Plot based heritability estimates and categorization of cassava genotype response to cassava brown streak disease. CROP PROTECTION (GUILDFORD, SURREY) 2018; 108:39-46. [PMID: 29861529 PMCID: PMC5890358 DOI: 10.1016/j.cropro.2018.02.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 01/23/2018] [Accepted: 02/07/2018] [Indexed: 05/21/2023]
Abstract
Cassava brown streak disease (CBSD) caused by Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV) is a threat to food security in sub-Saharan Africa, where the disease persistently reduces overall root quality and quantity resulting in up to 100% yield losses. Complexities in CBSD symptom expression and the damage caused on leaves, stems and roots throughout the 12 months of cassava growth require that appropriate ways of categorizing genotype response and optimal stages of evaluation be identified. This study aimed at: 1) determining plot based heritability of CBSD based on symptom expression and 2) categorizing genotype resistance to CBSD based on symptom expression. Herein, 41 genotypes were evaluated for two years at Namulonge with an additional evaluation conducted across three locations. Evaluations were done at three, six, nine and twelve months after planting. Genotype responses to CBSD varied significantly. High broad sense heritability estimates of up to 0.81 (incidence) and 0.71 (severity) were obtained. Average disease severity scores had higher broad sense heritability estimates (0.53 and 0.65) than maximum disease severity scores (0.33 and 0.61) for root and foliar severities respectively. These findings are important in choosing an appropriate evaluation method for CBSD. Genotypes displayed differing CBSD responses in type, locality and severity of symptoms. This suggested that genotypes had differences in mechanisms of resistance that can be exploited in CBSD resistance breeding.
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Affiliation(s)
- A. Okul Valentor
- Makerere University, Department of Agricultural Production, P.O. Box 7062, Kampala, Uganda
- Corresponding author.
| | - M. Ochwo-Ssemakula
- Makerere University, Department of Agricultural Production, P.O. Box 7062, Kampala, Uganda
| | - T. Kaweesi
- National Crops Resources Research Institute, Root Crops Program, P.O. Box 7084, Kampala, Uganda
| | - A. Ozimati
- National Crops Resources Research Institute, Root Crops Program, P.O. Box 7084, Kampala, Uganda
| | - E. Mrema
- Makerere University, Department of Agricultural Production, P.O. Box 7062, Kampala, Uganda
| | - E.S. Mwale
- Makerere University, Department of Agricultural Production, P.O. Box 7062, Kampala, Uganda
| | - P. Gibson
- Makerere University, Department of Agricultural Production, P.O. Box 7062, Kampala, Uganda
| | - E. Achola
- Makerere University, Department of Agricultural Production, P.O. Box 7062, Kampala, Uganda
| | - R. Edema
- Makerere University, Department of Agricultural Production, P.O. Box 7062, Kampala, Uganda
| | - Y. Baguma
- National Crops Resources Research Institute, Root Crops Program, P.O. Box 7084, Kampala, Uganda
| | - R. Kawuki
- National Crops Resources Research Institute, Root Crops Program, P.O. Box 7084, Kampala, Uganda
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Tomlinson KR, Bailey AM, Alicai T, Seal S, Foster GD. Cassava brown streak disease: historical timeline, current knowledge and future prospects. MOLECULAR PLANT PATHOLOGY 2018; 19:1282-1294. [PMID: 28887856 PMCID: PMC5947582 DOI: 10.1111/mpp.12613] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 09/07/2017] [Accepted: 09/07/2017] [Indexed: 05/09/2023]
Abstract
Cassava is the second most important staple food crop in terms of per capita calories consumed in Africa and holds potential for climate change adaptation. Unfortunately, productivity in East and Central Africa is severely constrained by two viral diseases: cassava mosaic disease (CMD) and cassava brown streak disease (CBSD). CBSD was first reported in 1936 from northeast Tanzania. For approximately 70 years, CBSD was restricted to coastal East Africa and so had a relatively low impact on food security compared with CMD. However, at the turn of the 21st century, CBSD re-emerged further inland, in areas around Lake Victoria, and it has since spread through many East and Central African countries, causing high yield losses and jeopardizing the food security of subsistence farmers. This recent re-emergence has attracted intense scientific interest, with studies shedding light on CBSD viral epidemiology, sequence diversity, host interactions and potential sources of resistance within the cassava genome. This review reflects on 80 years of CBSD research history (1936-2016) with a timeline of key events. We provide insights into current CBSD knowledge, management efforts and future prospects for improved understanding needed to underpin effective control and mitigation of impacts on food security.
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Affiliation(s)
| | - Andy M. Bailey
- School of Biological SciencesUniversity of BristolBristolBS8 1TQUK
| | - Titus Alicai
- National Crops Resources Research InstituteKampala 7084Uganda
| | - Sue Seal
- Natural Resources InstituteUniversity of GreenwichChatham MaritimeKent ME4 4TBUK
| | - Gary D. Foster
- School of Biological SciencesUniversity of BristolBristolBS8 1TQUK
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Valli AA, Gallo A, Rodamilans B, López‐Moya JJ, García JA. The HCPro from the Potyviridae family: an enviable multitasking Helper Component that every virus would like to have. MOLECULAR PLANT PATHOLOGY 2018; 19:744-763. [PMID: 28371183 PMCID: PMC6638112 DOI: 10.1111/mpp.12553] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 03/21/2017] [Accepted: 03/24/2017] [Indexed: 05/18/2023]
Abstract
RNA viruses have very compact genomes and so provide a unique opportunity to study how evolution works to optimize the use of very limited genomic information. A widespread viral strategy to solve this issue concerning the coding space relies on the expression of proteins with multiple functions. Members of the family Potyviridae, the most abundant group of RNA viruses in plants, offer several attractive examples of viral factors which play roles in diverse infection-related pathways. The Helper Component Proteinase (HCPro) is an essential and well-characterized multitasking protein for which at least three independent functions have been described: (i) viral plant-to-plant transmission; (ii) polyprotein maturation; and (iii) RNA silencing suppression. Moreover, multitudes of host factors have been found to interact with HCPro. Intriguingly, most of these partners have not been ascribed to any of the HCPro roles during the infectious cycle, supporting the idea that this protein might play even more roles than those already established. In this comprehensive review, we attempt to summarize our current knowledge about HCPro and its already attributed and putative novel roles, and to discuss the similarities and differences regarding this factor in members of this important viral family.
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Affiliation(s)
| | - Araiz Gallo
- Centro Nacional de Biotecnología (CNB‐CSIC)Madrid28049Spain
| | | | - Juan José López‐Moya
- Center for Research in Agricultural Genomics (CRAG‐CSIC‐IRTA‐UAB‐UB), Campus UABBellaterraBarcelona08193Spain
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Reyes MI, Flores‐Vergara MA, Guerra‐Peraza O, Rajabu C, Desai J, Hiromoto‐Ruiz YH, Ndunguru J, Hanley‐Bowdoin L, Kjemtrup S, Ascencio‐Ibáñez JT, Robertson D. A VIGS screen identifies immunity in the Arabidopsis Pla-1 accession to viruses in two different genera of the Geminiviridae. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:796-807. [PMID: 28901681 PMCID: PMC5725698 DOI: 10.1111/tpj.13716] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 09/01/2017] [Accepted: 09/06/2017] [Indexed: 05/21/2023]
Abstract
Geminiviruses are DNA viruses that cause severe crop losses in different parts of the world, and there is a need for genetic sources of resistance to help combat them. Arabidopsis has been used as a source for virus-resistant genes that derive from alterations in essential host factors. We used a virus-induced gene silencing (VIGS) vector derived from the geminivirus Cabbage leaf curl virus (CaLCuV) to assess natural variation in virus-host interactions in 190 Arabidopsis accessions. Silencing of CH-42, encoding a protein needed to make chlorophyll, was used as a visible marker to discriminate asymptomatic accessions from those showing resistance. There was a wide range in symptom severity and extent of silencing in different accessions, but two correlations could be made. Lines with severe symptoms uniformly lacked extensive VIGS, and lines that showed attenuated symptoms over time (recovery) showed a concomitant increase in the extent of VIGS. One accession, Pla-1, lacked both symptoms and silencing, and was immune to wild-type infectious clones corresponding to CaLCuV or Beet curly top virus (BCTV), which are classified in different genera in the Geminiviridae. It also showed resistance to the agronomically important Tomato yellow leaf curl virus (TYLCV). Quantitative trait locus mapping of a Pla-1 X Col-0 F2 population was used to detect a major peak on chromosome 1, which is designated gip-1 (geminivirus immunity Pla-1-1). The recessive nature of resistance to CaLCuV and the lack of obvious candidate genes near the gip-1 locus suggest that a novel resistance gene(s) confers immunity.
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Affiliation(s)
- Maria Ines Reyes
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNCUSA
| | - Miguel A. Flores‐Vergara
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNCUSA
- Paradigm GeneticsResearch Triangle ParkNCUSA
| | - Orlene Guerra‐Peraza
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNCUSA
- Present address:
Citrus Research and Education CenterUniversity of FloridaLake AlfredFL33850USA
| | - Cyprian Rajabu
- Mikocheni Agricultural Research InstituteDar es SalaamTanzania
| | - Jigar Desai
- Department of Molecular and Structural BiochemistryNorth Carolina State UniversityRaleighNCUSA
| | | | - Joseph Ndunguru
- Mikocheni Agricultural Research InstituteDar es SalaamTanzania
| | - Linda Hanley‐Bowdoin
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNCUSA
| | - Susanne Kjemtrup
- Paradigm GeneticsResearch Triangle ParkNCUSA
- Present address:
Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNCUSA
| | - Jose T. Ascencio‐Ibáñez
- Department of Molecular and Structural BiochemistryNorth Carolina State UniversityRaleighNCUSA
| | - Dominique Robertson
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNCUSA
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Maruthi MN, Jeremiah SC, Mohammed IU, Legg JP. The role of the whitefly, Bemisia tabaci (Gennadius), and farmer practices in the spread of cassava brown streak ipomoviruses. JOURNAL OF PHYTOPATHOLOGY (1986) 2017; 165:707-717. [PMID: 29213187 PMCID: PMC5703439 DOI: 10.1111/jph.12609] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 07/16/2017] [Indexed: 05/13/2023]
Abstract
Cassava brown streak disease (CBSD) is arguably the most dangerous current threat to cassava, which is Africa's most important food security crop. CBSD is caused by two RNA viruses: Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). The roles of the whitefly Bemisia tabaci (Gennadius) and farmer practices in the spread of CBSD were investigated in a set of field and laboratory experiments. The virus was acquired and transmitted by B. tabaci within a short time (5-10 min each for virus acquisition and inoculation), and was retained for up to 48 hr. Highest virus transmission (60%) was achieved using 20-25 suspected viruliferous whiteflies per plant that were given acquisition and inoculation periods of 24 and 48 hr, respectively. Experiments mimicking the agronomic practices of cassava leaf picking or the use of contaminated tools for making cassava stem cuttings did not show the transmission of CBSV or UCBSV. Screenhouse and field experiments in Tanzania showed that the spread of CBSD next to spreader rows was high, and that the rate of spread decreased with increasing distance from the source of inoculum. The disease spread in the field up to a maximum of 17 m in a cropping season. These results collectively confirm that CBSV and UCBSV are transmitted by B. tabaci semipersistently, but for only short distances in the field. This implies that spread over longer distances is due to movements of infected stem cuttings used for planting material. These findings have important implications for developing appropriate management strategies for CBSD.
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Affiliation(s)
| | - Simon C. Jeremiah
- Ministry of Agriculture, Livestock and Fisheries DevelopmentUkiriguru ResearchMwanzaTanzania
| | - Ibrahim U. Mohammed
- Natural Resources InstituteUniversity of GreenwichChatham MaritimeKentUK
- Present address:
Kebbi State University of Science and TechnologyAliero (KSUSTA)Nigeria
| | - James P. Legg
- International Institute of Tropical Agriculture (IITA)Dar es SalaamTanzania
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37
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Shi S, Zhang X, Mandel MA, Zhang P, Zhang Y, Ferguson M, Amuge T, Rounsley S, Liu Z, Xiong Z. Variations of five eIF4E genes across cassava accessions exhibiting tolerant and susceptible responses to cassava brown streak disease. PLoS One 2017; 12:e0181998. [PMID: 28771520 PMCID: PMC5542559 DOI: 10.1371/journal.pone.0181998] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 07/11/2017] [Indexed: 11/19/2022] Open
Abstract
Cassava (Manihot esculenta) is an important tropical subsistence crop that is severely affected by cassava brown streak disease (CBSD) in East Africa. The disease is caused by Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). Both have a (+)-sense single-stranded RNA genome with a 5' covalently-linked viral protein, which functionally resembles the cap structure of mRNA, binds to eukaryotic translation initiation factor 4E (eIF4E) or its analogues, and then enable the translation of viral genomic RNA in host cells. To characterize cassava eIF4Es and their potential role in CBSD tolerance and susceptibility, we cloned five eIF4E transcripts from cassava (accession TMS60444). Sequence analysis indicated that the cassava eIF4E family of proteins consisted of one eIF4E, two eIF(iso)4E, and two divergent copies of novel cap-binding proteins (nCBPs). Our data demonstrated experimentally the coding of these five genes as annotated in the published cassava genome and provided additional evidence for refined annotations. Illumina resequencing data of the five eIF4E genes were analyzed from 14 cassava lines tolerant or susceptible to CBSD. Abundant single nucleotide polymorphisms (SNP) and biallelic variations were observed in the eIF4E genes; however, most of the SNPs were located in the introns and non-coding regions of the exons. Association studies of non-synonymous SNPs revealed no significant association between any SNP of the five eIF4E genes and the tolerance or susceptibility to CBSD. However, two SNPs in two genes were weakly associated with the CBSD responses but had no direct causal-effect relationship. SNPs in an intergenic region upstream of eIF4E_me showed a surprising strong association with CBSD responses. Digital expression profile analysis showed differential expression of different eIF4E genes but no significant difference in gene expression was found between susceptible and tolerant cassava accessions despite the association of the intergenic SNPs with CBSD responses.
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Affiliation(s)
- Shanshan Shi
- Institute of Tropical biology and biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- School of Plant Sciences and BIO5 Institute, University of Arizona, Tucson, Arizona, United States of America
| | - Xiuchun Zhang
- Institute of Tropical biology and biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - M. Alejandra Mandel
- School of Plant Sciences and BIO5 Institute, University of Arizona, Tucson, Arizona, United States of America
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yuliang Zhang
- Institute of Tropical biology and biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Morag Ferguson
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
| | - Teddy Amuge
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
| | - Steve Rounsley
- Genus plc, DeForest, Wisconsin, United States of America
| | - Zhixin Liu
- Institute of Tropical biology and biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- * E-mail: (ZX); (ZL)
| | - Zhongguo Xiong
- School of Plant Sciences and BIO5 Institute, University of Arizona, Tucson, Arizona, United States of America
- * E-mail: (ZX); (ZL)
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38
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Abstract
Cassava is the fourth largest source of calories in the world but is subject to economically important yield losses due to viral diseases, including cassava brown streak disease and cassava mosaic disease. Cassava mosaic disease occurs in sub-Saharan Africa and the Asian subcontinent and is associated with nine begomovirus species, whereas cassava brown streak disease has to date been reported only in sub-Saharan Africa and is caused by two distinct ipomovirus species. We present an overview of key milestones and their significance in the understanding and characterization of these two major diseases as well as their associated viruses and whitefly vector. New biotechnologies offer a wide range of opportunities to reduce virus-associated yield losses in cassava for farmers and can additionally enable the exploitation of this valuable crop for industrial purposes. This review explores established and new technologies for genetic manipulation to achieve desired traits such as virus resistance.
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Affiliation(s)
- Chrissie Rey
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2000, South Africa;
| | - Hervé Vanderschuren
- AgroBioChem Department, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium;
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39
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Mbewe W, Tairo F, Sseruwagi P, Ndunguru J, Duffy S, Mukasa S, Benesi I, Sheat S, Koerbler M, Winter S. Variability in P1 gene redefines phylogenetic relationships among cassava brown streak viruses. Virol J 2017; 14:118. [PMID: 28637472 PMCID: PMC5480109 DOI: 10.1186/s12985-017-0790-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 06/16/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cassava brown streak disease is emerging as the most important viral disease of cassava in Africa, and is consequently a threat to food security. Two distinct species of the genus Ipomovirus (family Potyviridae) cause the disease: Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). To understand the evolutionary relationships among the viruses, 64 nucleotide sequences from the variable P1 gene from major cassava producing areas of east and central-southern Africa were determined. METHODS We sequenced an amplicon of the P1 region of 31 isolates from Malawi and Tanzania. In addition to these, 33 previously reported sequences of virus isolates from Uganda, Kenya, Tanzania, Malawi and Mozambique were added to the analysis. RESULTS Phylogenetic analyses revealed three major P1 clades of Cassava brown streak viruses (CBSVs): in addition to a clade of most CBSV and a clade containing all UCBSV, a novel, intermediate clade of CBSV isolates which has been tentatively called CBSV-Tanzania (CBSV-TZ). Virus isolates of the distinctive CBSV-TZ had nucleotide identities as low as 63.2 and 63.7% with other members of CBSV and UCBSV respectively. CONCLUSIONS Grouping of P1 gene sequences indicated for distinct sub-populations of CBSV, but not UCBSV. Representatives of all three clades were found in both Tanzania and Malawi.
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Affiliation(s)
- Willard Mbewe
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ 08901 USA
- School of Agriculture and Environmental Science, Department of Agricultural Production, Makerere University, P. O. Box, 7062 Kampala, Uganda
| | - Fred Tairo
- Mikocheni Agricultural Research Institute, P. O. Box 6226, Dar es Salaam, PO Tanzania
| | - Peter Sseruwagi
- Mikocheni Agricultural Research Institute, P. O. Box 6226, Dar es Salaam, PO Tanzania
| | - Joseph Ndunguru
- Mikocheni Agricultural Research Institute, P. O. Box 6226, Dar es Salaam, PO Tanzania
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ 08901 USA
| | - Ssetumba Mukasa
- School of Agriculture and Environmental Science, Department of Agricultural Production, Makerere University, P. O. Box, 7062 Kampala, Uganda
| | - Ibrahim Benesi
- Chitedze Agricultural Research Station, P. O. Box, 153 Lilongwe, Malawi
| | - Samar Sheat
- Leibniz Institute - DSMZ Plant Virus Department, Braunschweig, Germany
| | - Marianne Koerbler
- Leibniz Institute - DSMZ Plant Virus Department, Braunschweig, Germany
| | - Stephan Winter
- Leibniz Institute - DSMZ Plant Virus Department, Braunschweig, Germany
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40
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Burgis NE. A disease spectrum for ITPA variation: advances in biochemical and clinical research. J Biomed Sci 2016; 23:73. [PMID: 27770805 PMCID: PMC5075207 DOI: 10.1186/s12929-016-0291-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 10/19/2016] [Indexed: 12/15/2022] Open
Abstract
Human ITPase (encoded by the ITPA gene) is a protective enzyme which acts to exclude noncanonical (deoxy)nucleoside triphosphates ((d)NTPs) such as (deoxy)inosine 5′-triphosphate ((d)ITP), from (d)NTP pools. Until the last few years, the importance of ITPase in human health and disease has been enigmatic. In 2009, an article was published demonstrating that ITPase deficiency in mice is lethal. All homozygous null offspring died before weaning as a result of cardiomyopathy due to a defect in the maintenance of quality ATP pools. More recently, a whole exome sequencing project revealed that very rare, severe human ITPA mutation results in early infantile encephalopathy and death. It has been estimated that nearly one third of the human population has an ITPA status which is associated with decreased ITPase activity. ITPA status has been linked to altered outcomes for patients undergoing thiopurine or ribavirin therapy. Thiopurine therapy can be toxic for patients with ITPA polymorphism, however, ITPA polymorphism is associated with improved outcomes for patients undergoing ribavirin treatment. ITPA polymorphism has also been linked to early-onset tuberculosis susceptibility. These data suggest a spectrum of ITPA-related disease exists in human populations. Potentially, ITPA status may affect a large number of patient outcomes, suggesting that modulation of ITPase activity is an important emerging avenue for reducing the number of negative outcomes for ITPA-related disease. Recent biochemical studies have aimed to provide rationale for clinical observations, better understand substrate selectivity and provide a platform for modulation of ITPase activity.
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Affiliation(s)
- Nicholas E Burgis
- Department of Chemistry and Biochemistry, Eastern Washington University, 226 Science Building, Cheney, WA, 99004, USA.
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41
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Untiveros M, Olspert A, Artola K, Firth AE, Kreuze JF, Valkonen JPT. A novel sweet potato potyvirus open reading frame (ORF) is expressed via polymerase slippage and suppresses RNA silencing. MOLECULAR PLANT PATHOLOGY 2016; 17:1111-23. [PMID: 26757490 PMCID: PMC4979677 DOI: 10.1111/mpp.12366] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 12/10/2015] [Accepted: 12/17/2015] [Indexed: 05/20/2023]
Abstract
The single-stranded, positive-sense RNA genome of viruses in the genus Potyvirus encodes a large polyprotein that is cleaved to yield 10 mature proteins. The first three cleavage products are P1, HCpro and P3. An additional short open reading frame (ORF), called pipo, overlaps the P3 region of the polyprotein ORF. Four related potyviruses infecting sweet potato (Ipomoea batatas) are predicted to contain a third ORF, called pispo, which overlaps the 3' third of the P1 region. Recently, pipo has been shown to be expressed via polymerase slippage at a conserved GA6 sequence. Here, we show that pispo is also expressed via polymerase slippage at a GA6 sequence, with higher slippage efficiency (∼5%) than at the pipo site (∼1%). Transient expression of recombinant P1 or the 'transframe' product, P1N-PISPO, in Nicotiana benthamiana suppressed local RNA silencing (RNAi), but only P1N-PISPO inhibited short-distance movement of the silencing signal. These results reveal that polymerase slippage in potyviruses is not limited to pipo expression, but can be co-opted for the evolution and expression of further novel gene products.
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Affiliation(s)
- Milton Untiveros
- Department of Agricultural Sciences, University of Helsinki, FI-00014, Helsinki, Finland
| | - Allan Olspert
- Department of Pathology, Division of Virology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Katrin Artola
- Department of Agricultural Sciences, University of Helsinki, FI-00014, Helsinki, Finland
| | - Andrew E Firth
- Department of Pathology, Division of Virology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | | | - Jari P T Valkonen
- Department of Agricultural Sciences, University of Helsinki, FI-00014, Helsinki, Finland
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42
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Anjanappa RB, Mehta D, Maruthi MN, Kanju E, Gruissem W, Vanderschuren H. Characterization of Brown Streak Virus-Resistant Cassava. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2016; 29:527-34. [PMID: 27070326 DOI: 10.1094/mpmi-01-16-0027-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Cassava brown streak disease (CBSD) has become a major constraint to cassava production in East and Central Africa. The identification of new sources of CBSD resistance is essential to deploy CBSD mitigation strategies, as the disease is progressing westwards to new geographical areas. A stringent infection method based on top cleft-grafting combined with precise virus titer quantitation was utilized to screen 14 cassava cultivars and elite breeding lines. When inoculated with mixed infections of Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV), the scions of elite breeding lines KBH 2006/18 and KBH 2006/26 remained symptom-free during a 16-week period of virus graft inoculation, while susceptible varieties displayed typical CBSD infection symptoms at 4 weeks after grafting. The identified CBSD resistance was stable under the coinoculation of CBSV and UCBSV with cassava geminiviruses. Double-grafting experiments revealed that transmission of CBSV and UCBSV to CBSD-susceptible top scions was delayed when using intermediate scions of elite breeding lines KBH 2006/18 and KBH 2006/26. Nonetheless, comparison of virus systemic movement using scions from KBH2006/18 and a transgenic CBSD resistant 60444 line (60444-Hp9 line) showed that both CBSV and UCBSV move at undetectable levels through the stems. Further, protoplast-based assays of virus titers showed that the replication of CBSV is inhibited in the resistant line KBH2006/18, suggesting that the identified CBSD resistance is at least partially based on inhibition of virus replication. Our molecular characterization of CBSD resistance in cassava offers a robust virus-host system to further investigate the molecular determinants of CBSD resistance.
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Affiliation(s)
- Ravi B Anjanappa
- 1 Department of Biology, Plant Biotechnology, ETH Zurich, Zurich, Switzerland
| | - Devang Mehta
- 1 Department of Biology, Plant Biotechnology, ETH Zurich, Zurich, Switzerland
| | - M N Maruthi
- 2 Natural Resources Institute (NRI), University of Greenwich, Chatham Maritime, Kent ME4 4TB, U.K
| | - Edward Kanju
- 3 International Institute of Tropical Agriculture, P.O Box 34441, Dar es Salaam, Tanzania; and
| | - Wilhelm Gruissem
- 1 Department of Biology, Plant Biotechnology, ETH Zurich, Zurich, Switzerland
| | - Hervé Vanderschuren
- 1 Department of Biology, Plant Biotechnology, ETH Zurich, Zurich, Switzerland
- 4 AgroBioChem Department, Gembloux Agro-Bio Tech, University of Liège, 4000 Liège, Belgium
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Wagaba H, Patil BL, Mukasa S, Alicai T, Fauquet CM, Taylor NJ. Artificial microRNA-derived resistance to Cassava brown streak disease. J Virol Methods 2016; 231:38-43. [PMID: 26912232 PMCID: PMC4819903 DOI: 10.1016/j.jviromet.2016.02.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 12/08/2015] [Accepted: 02/08/2016] [Indexed: 11/23/2022]
Abstract
Artificial miRNAs (amiRNA) were generated targeting conserved sequences within the genomes of the two causal agents of Cassava brown streak disease (CBSD): Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). Transient expression studies on ten amiRNAs targeting 21nt conserved sequences of P1(CBSV and UCBSV), P3(CBSV and UCBSV), CI(UCBSV), NIb(CBSV and UCBSV), CP(UCBSV) and the un-translated region (3'-UTR) were tested in Nicotiana benthamiana. Four out of the ten amiRNAs expressed the corresponding amiRNA at high levels. Transgenic N. benthamiana plants were developed for the four amiRNAs targeting the P1 and NIb genes of CBSV and the P1 and CP genes of UCBSV and shown to accumulate miRNA products. Transgenic plants challenged with CBSV and UCBSV isolates showed resistance levels that ranged between ∼20-60% against CBSV and UCBSV and correlated with expression levels of the transgenically derived miRNAs. MicroRNAs targeting P1 and NIb of CBSV showed protection against CBSV and UCBSV, while amiRNAs targeting the P1 and CP of UCBSV showed protection against UCBSV but were less efficient against CBSV. These results indicate a potential application of amiRNAs for engineering resistance to CBSD-causing viruses in cassava.
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Affiliation(s)
- Henry Wagaba
- National Crops Resources Research Institute, Namulonge, P.O. Box 7084, Kampala, Uganda; Makerere University, P.O. Box 7062, University Rd, Kampala, Uganda
| | - Basavaprabhu L Patil
- ICAR-National Research Center on Plant Biotechnology, IARI, Pusa Campus, New Delhi 110012, India
| | - Settumba Mukasa
- Makerere University, P.O. Box 7062, University Rd, Kampala, Uganda
| | - Titus Alicai
- National Crops Resources Research Institute, Namulonge, P.O. Box 7084, Kampala, Uganda
| | - Claude M Fauquet
- Centro Internacional de Agricultura Tropical, Cali, Apartado Aéreo 6713, Cali, Colombia
| | - Nigel J Taylor
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, USA.
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Ogwok E, Ilyas M, Alicai T, Rey MEC, Taylor NJ. Comparative analysis of virus-derived small RNAs within cassava (Manihot esculenta Crantz) infected with cassava brown streak viruses. Virus Res 2016; 215:1-11. [PMID: 26811902 PMCID: PMC4796025 DOI: 10.1016/j.virusres.2016.01.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 01/18/2016] [Accepted: 01/21/2016] [Indexed: 01/02/2023]
Abstract
The 21-nt virus-derived small RNAs were predominant, followed by the 22-nt class. Susceptible cassava genotypes accumulated higher CBSV- than UCBSV-derived small RNA. Tolerant cassava genotype accumulated high CBSV- and low UCBSV-derived small RNAs. AGO2, DCL2 and DCL4 were differentially regulated in CBSV/UCBSV-infected plants. CBSV and UCBSV interact differently in the same host genetic background
Infection of plant cells by viral pathogens triggers RNA silencing, an innate antiviral defense mechanism. In response to infection, small RNAs (sRNAs) are produced that associate with Argonaute (AGO)-containing silencing complexes which act to inactivate viral genomes by posttranscriptional gene silencing (PTGS). Deep sequencing was used to compare virus-derived small RNAs (vsRNAs) in cassava genotypes NASE 3, TME 204 and 60444 infected with the positive sense single-stranded RNA (+ssRNA) viruses cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV), the causal agents of cassava brown streak disease (CBSD). An abundance of 21–24 nt vsRNAs was detected and mapped, covering the entire CBSV and UCBSV genomes. The 21 nt vsRNAs were most predominant, followed by the 22 nt class with a slight bias toward sense compared to antisense polarity, and a bias for adenine and uracil bases present at the 5′-terminus. Distribution and frequency of vsRNAs differed between cassava genotypes and viral genomes. In susceptible genotypes TME 204 and 60444, CBSV-derived sRNAs were seen in greater abundance than UCBSV-derived sRNAs. NASE 3, known to be resistant to UCBSV, accumulated negligible UCBSV-derived sRNAs but high populations of CBSV-derived sRNAs. Transcript levels of cassava homologues of AGO2, DCL2 and DCL4, which are central to the gene-silencing complex, were found to be differentially regulated in CBSV- and UCBSV-infected plants across genotypes, suggesting these proteins play a role in antiviral defense. Irrespective of genotype or viral pathogen, maximum populations of vsRNAs mapped to the cytoplasmic inclusion, P1 and P3 protein-encoding regions. Our results indicate disparity between CBSV and UCBSV host-virus interaction mechanisms, and provide insight into the role of virus-induced gene silencing as a mechanism of resistance to CBSD.
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Affiliation(s)
- Emmanuel Ogwok
- National Crops Resources Research Institute, Namulonge, P.O Box 7084, Kampala, Uganda; Institute for International Crop Improvement, Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; School of Molecular and Cell Biology, University of the Witwatersrand, Private Bag 3, P.O Wits 2050, Johannesburg, South Africa
| | - Muhammad Ilyas
- Institute for International Crop Improvement, Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Titus Alicai
- National Crops Resources Research Institute, Namulonge, P.O Box 7084, Kampala, Uganda
| | - Marie E C Rey
- School of Molecular and Cell Biology, University of the Witwatersrand, Private Bag 3, P.O Wits 2050, Johannesburg, South Africa
| | - Nigel J Taylor
- Institute for International Crop Improvement, Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.
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Mingot A, Valli A, Rodamilans B, San León D, Baulcombe DC, García JA, López-Moya JJ. The P1N-PISPO trans-Frame Gene of Sweet Potato Feathery Mottle Potyvirus Is Produced during Virus Infection and Functions as an RNA Silencing Suppressor. J Virol 2016; 90:3543-57. [PMID: 26792740 PMCID: PMC4794657 DOI: 10.1128/jvi.02360-15] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 01/07/2016] [Indexed: 12/31/2022] Open
Abstract
UNLABELLED The positive-sense RNA genome of Sweet potato feathery mottle virus (SPFMV) (genus Potyvirus, family Potyviridae) contains a large open reading frame (ORF) of 3,494 codons translatable as a polyprotein and two embedded shorter ORFs in the -1 frame: PISPO, of 230 codons, and PIPO, of 66 codons, located in the P1 and P3 regions, respectively. PISPO is specific to some sweet potato-infecting potyviruses, while PIPO is present in all potyvirids. In SPFMV these two extra ORFs are preceded by conserved G2A6 motifs. We have shown recently that a polymerase slippage mechanism at these sites could produce transcripts bringing these ORFs in frame with the upstream polyprotein, thus leading to P1N-PISPO and P3N-PIPO products (B. Rodamilans, A. Valli, A. Mingot, D. San Leon, D. B. Baulcombe, J. J. Lopez-Moya, and J.A. Garcia, J Virol 89:6965-6967, 2015, doi:10.1128/JVI.00337-15). Here, we demonstrate by liquid chromatography coupled to mass spectrometry that both P1 and P1N-PISPO are produced during viral infection and coexist in SPFMV-infected Ipomoea batatas plants. Interestingly, transient expression of SPFMV gene products coagroinfiltrated with a reporter gene in Nicotiana benthamiana revealed that P1N-PISPO acts as an RNA silencing suppressor, a role normally associated with HCPro in other potyviruses. Moreover, mutation of WG/GW motifs present in P1N-PISPO abolished its silencing suppression activity, suggesting that the function might require interaction with Argonaute components of the silencing machinery, as was shown for other viral suppressors. Altogether, our results reveal a further layer of complexity of the RNA silencing suppression activity within the Potyviridae family. IMPORTANCE Gene products of potyviruses include P1, HCPro, P3, 6K1, CI, 6K2, VPg/NIaPro, NIb, and CP, all derived from the proteolytic processing of a large polyprotein, and an additional P3N-PIPO product, with the PIPO segment encoded in a different frame within the P3 cistron. In sweet potato feathery mottle virus (SPFMV), another out-of-frame element (PISPO) was predicted within the P1 region. We have shown recently that a polymerase slippage mechanism can generate the transcript variants with extra nucleotides that could be translated into P1N-PISPO and P3N-PIPO. Now, we demonstrate by mass spectrometry analysis that P1N-PISPO is indeed produced in SPFMV-infected plants, in addition to P1. Interestingly, while in other potyviruses the suppressor of RNA silencing is HCPro, we show here that P1N-PISPO exhibited this activity in SPFMV, revealing how the complexity of the gene content could contribute to supply this essential function in members of the Potyviridae family.
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Affiliation(s)
- Ares Mingot
- Center for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Cerdanyola del Vallès, Barcelona, Spain
| | - Adrián Valli
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | | | - David San León
- Centro Nacional de Biotecnología CNB, CSIC, Madrid, Spain
| | - David C Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | | | - Juan José López-Moya
- Center for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Cerdanyola del Vallès, Barcelona, Spain
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Gilbertson RL, Batuman O, Webster CG, Adkins S. Role of the Insect SupervectorsBemisia tabaciandFrankliniella occidentalisin the Emergence and Global Spread of Plant Viruses. Annu Rev Virol 2015; 2:67-93. [DOI: 10.1146/annurev-virology-031413-085410] [Citation(s) in RCA: 247] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Robert L. Gilbertson
- Department of Plant Pathology, University of California, Davis, California 95616; ,
| | - Ozgur Batuman
- Department of Plant Pathology, University of California, Davis, California 95616; ,
| | - Craig G. Webster
- US Horticultural Research Laboratory, Agricultural Research Service, US Department of Agriculture, Fort Pierce, Florida 34945; ,
| | - Scott Adkins
- US Horticultural Research Laboratory, Agricultural Research Service, US Department of Agriculture, Fort Pierce, Florida 34945; ,
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Patil BL, Legg JP, Kanju E, Fauquet CM. Cassava brown streak disease: a threat to food security in Africa. J Gen Virol 2015; 96:956-68. [PMID: 26015320 DOI: 10.1099/vir.0.000014] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Cassava brown streak disease (CBSD) has emerged as the most important viral disease of cassava (Manihot esculenta) in Africa and is a major threat to food security. CBSD is caused by two distinct species of ipomoviruses, Cassava brown streak virus and Ugandan cassava brown streak virus, belonging to the family Potyviridae. Previously, CBSD was reported only from the coastal lowlands of East Africa, but recently it has begun to spread as an epidemic throughout the Great Lakes region of East and Central Africa. This new spread represents a major threat to the cassava-growing regions of West Africa. CBSD-resistant cassava cultivars are being developed through breeding, and transgenic RNA interference-derived field resistance to CBSD has also been demonstrated. This review aims to provide a summary of the most important studies on the aetiology, epidemiology and control of CBSD and to highlight key research areas that need prioritization.
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Affiliation(s)
- Basavaprabhu L Patil
- National Research Centre on Plant Biotechnology, IARI, Pusa Campus, New Delhi 110012, India
| | - James P Legg
- International Institute of Tropical Agriculture, PO Box 34441, Dar-Es-Salaam, Tanzania
| | - Edward Kanju
- International Institute of Tropical Agriculture, PO Box 34441, Dar-Es-Salaam, Tanzania
| | - Claude M Fauquet
- Centro Internacional de Agricultura Tropical, Apartado Aéreo 6713, Cali, Colombia
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Patil BL, Legg JP, Kanju E, Fauquet CM. Cassava brown streak disease: a threat to food security in Africa. J Gen Virol 2015. [DOI: 10.1099/jgv.0.000014] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Affiliation(s)
- Basavaprabhu L. Patil
- National Research Centre on Plant Biotechnology, IARI, Pusa Campus, New Delhi 110012, India
| | - James P. Legg
- International Institute of Tropical Agriculture, PO Box 34441, Dar-Es-Salaam, Tanzania
| | - Edward Kanju
- International Institute of Tropical Agriculture, PO Box 34441, Dar-Es-Salaam, Tanzania
| | - Claude M. Fauquet
- Centro Internacional de Agricultura Tropical, Apartado Aéreo 6713, Cali, Colombia
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Anthony P, Yona B, Titus A, Robert K, Edward K, Anton B, Christopher AO, Paul G, David SO, Dennis M, Phinehas T. Stability of resistance to cassava brown streak disease in major agro-ecologies of Uganda. ACTA ACUST UNITED AC 2015. [DOI: 10.5897/jpbcs2013.0490] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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50
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Abstract
Potyvirus is the largest genus of plant viruses causing significant losses in a wide range of crops. Potyviruses are aphid transmitted in a nonpersistent manner and some of them are also seed transmitted. As important pathogens, potyviruses are much more studied than other plant viruses belonging to other genera and their study covers many aspects of plant virology, such as functional characterization of viral proteins, molecular interaction with hosts and vectors, structure, taxonomy, evolution, epidemiology, and diagnosis. Biotechnological applications of potyviruses are also being explored. During this last decade, substantial advances have been made in the understanding of the molecular biology of these viruses and the functions of their various proteins. After a general presentation on the family Potyviridae and the potyviral proteins, we present an update of the knowledge on potyvirus multiplication, movement, and transmission and on potyvirus/plant compatible interactions including pathogenicity and symptom determinants. We end the review providing information on biotechnological applications of potyviruses.
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