1
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Crane YM, Crane CF, Schemerhorn BJ. Differential gene expression between viruliferous and non-viruliferous Schizaphis graminum (Rondani). PLoS One 2023; 18:e0294013. [PMID: 37939050 PMCID: PMC10631655 DOI: 10.1371/journal.pone.0294013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 10/16/2023] [Indexed: 11/10/2023] Open
Abstract
An experiment was performed to measure the effect of Cereal Yellow-Dwarf Virus (CYDV), strain CYDV-RPV, on gene expression in its insect vector, greenbug aphid (Schizaphis graminum (Rondani)). RNA was sampled in three replicates from four treatments (biotypes B and H with or without carried CYDV), at 0, 1, 2, 3, 5, 10, 15 and 20 days from the introduction of carrier and virus-free greenbugs to uninfected wheat cv. 'Newton'. Illumina paired-end sequencing produced 1,840,820,000,000 raw reads that yielded 1,089,950,000 clean reads, which were aligned to two greenbug, Trinity transcriptome assemblies with bowtie2. Read counts to contigs were analyzed with principal components and with DESeq2 after removing contaminating contigs of wheat or microbial origin. Likelihood ratio tests with one transcriptome showed that CYDV influenced gene expression about seven-fold less than time or biotype, which were approximately equal. With the other transcriptome, virus, time, and biotype were about equally important. Pairwise comparisons of virus to no virus for each timepoint yielded estimates of fold-change that comprised expression profiles for each contig when ordered by timepoint. Hierarchical clustering separated expression profiles into 20 groups of contigs that were significantly differentially expressed for at least one timepoint. Contigs were also sorted by timepoint of maximally differential expression between virus and no virus. All contigs that were significantly differentially expressed at FDR = 0.05 were annotated by blast searches against NCBI nr and nt databases. Interesting examples of up-regulation with virus included a lysosomal-trafficking regulator, peptidylprolylisomerase, RNA helicase, and two secreted effector proteins. However, carried virus did not consistently change aphid gene expression overall. Instead there was complex interaction of time, biotype, host response, and virus.
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Affiliation(s)
- Yan M. Crane
- Crop Production and Pest Control Research Unit, Agricultural Research Service, United States Department of Agriculture, West Lafayette, Indiana, United States of America
- Department of Entomology, Purdue University, West Lafayette, Indiana, United States of America
| | - Charles F. Crane
- Crop Production and Pest Control Research Unit, Agricultural Research Service, United States Department of Agriculture, West Lafayette, Indiana, United States of America
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, United States of America
| | - Brandon J. Schemerhorn
- Crop Production and Pest Control Research Unit, Agricultural Research Service, United States Department of Agriculture, West Lafayette, Indiana, United States of America
- Department of Entomology, Purdue University, West Lafayette, Indiana, United States of America
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2
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Chen AYS, Zhou JS, Liu JX, Ng JCK. Nuances of Whitefly Vector-Crinivirus Interactions Revealed in the Foregut Retention and Transmission of Lettuce Chlorosis Virus by Two Bemisia tabaci Cryptic Species. Viruses 2021; 13:v13081578. [PMID: 34452445 PMCID: PMC8402701 DOI: 10.3390/v13081578] [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: 05/14/2021] [Revised: 07/28/2021] [Accepted: 08/03/2021] [Indexed: 11/16/2022] Open
Abstract
Lettuce infectious yellows virus is the first crinivirus for which the retention of purified virions ingested into the whitefly (Bemisia tabaci New World (NW)) vector's foregut, has been demonstrated to be a requisite for successful virus transmission. This key finding supports the hypothesis that the determinant of foregut retention and transmission is present on the virion itself. However, whether this is also true for other criniviruses has not been established. Here, we provide evidence that lettuce chlorosis virus (LCV) acquired from plants is retained in the foreguts of both the B. tabaci NW and Middle East-Asia Minor 1 (MEAM1) vector species and transmitted upon inoculation feeding. An association between foregut retention and transmission by NW vectors is also observed following the acquisition and inoculation feeding of LCV virions purified using a standard procedure involving 2% or 4% (v/v) Triton™ X-100 (TX-100). However, while virions purified with 2% or 4% TX-100 are also retained in the foreguts of MEAM1 vectors, transmission is observed with the 4% TX-100-purified virions or when more vectors are used for acquisition and inoculation feeding. These results suggest that an intrinsic difference exists between NW and MEAM1 vectors in their interactions with, and transmission of, LCV virions.
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Affiliation(s)
- Angel Y. S. Chen
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA; (A.Y.S.C.); (J.S.Z.)
| | - Jaclyn S. Zhou
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA; (A.Y.S.C.); (J.S.Z.)
| | - Jin-Xiang Liu
- Citrus Research Institute, Southwest University, Beibei, Chongqing 400712, China;
- Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South St., Beijing 100080, China
| | - James C. K. Ng
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA; (A.Y.S.C.); (J.S.Z.)
- Center for Infectious Diseases and Vector Research, University of California, Riverside, CA 92521, USA
- Correspondence: ; Tel.: +1-(951)-827-4239
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3
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Rajarapu SP, Ullman DE, Uzest M, Rotenberg D, Ordaz NA, Whitfield AE. Plant–Virus–Vector Interactions. Virology 2021. [DOI: 10.1002/9781119818526.ch7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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4
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Kliot A, Johnson RS, MacCoss MJ, Kontsedalov S, Lebedev G, Czosnek H, Heck M, Ghanim M. A proteomic approach reveals possible molecular mechanisms and roles for endosymbiotic bacteria in begomovirus transmission by whiteflies. Gigascience 2020; 9:giaa124. [PMID: 33185242 PMCID: PMC7662926 DOI: 10.1093/gigascience/giaa124] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 07/21/2020] [Accepted: 10/08/2020] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Many plant viruses are vector-borne and depend on arthropods for transmission between host plants. Begomoviruses, the largest, most damaging and emerging group of plant viruses, infect hundreds of plant species, and new virus species of the group are discovered each year. Begomoviruses are transmitted by members of the whitefly Bemisia tabaci species complex in a persistent-circulative manner. Tomato yellow leaf curl virus (TYLCV) is one of the most devastating begomoviruses worldwide and causes major losses in tomato crops, as well as in many agriculturally important plant species. Different B. tabaci populations vary in their virus transmission abilities; however, the causes for these variations are attributed among others to genetic differences among vector populations, as well as to differences in the bacterial symbionts housed within B. tabaci. RESULTS Here, we performed discovery proteomic analyses in 9 whitefly populations from both Middle East Asia Minor I (MEAM1, formerly known as B biotype) and Mediterranean (MED, formerly known as Q biotype) species. We analysed our proteomic results on the basis of the different TYLCV transmission abilities of the various populations included in the study. The results provide the first comprehensive list of candidate insect and bacterial symbiont (mainly Rickettsia) proteins associated with virus transmission. CONCLUSIONS Our data demonstrate that the proteomic signatures of better vector populations differ considerably when compared with less efficient vector populations in the 2 whitefly species tested in this study. While MEAM1 efficient vector populations have a more lenient immune system, the Q efficient vector populations have higher abundance of proteins possibly implicated in virus passage through cells. Both species show a strong link of the facultative symbiont Rickettsia to virus transmission.
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Affiliation(s)
- Adi Kliot
- Department of Entomology, The Volcani Center, HaMacabim Rd., Rishon LeZion, 50250, Israel
- Institute of Plant Sciences and Genetics in Agriculture, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
- Genomic Pipelines, Earlham Institute, Colney lane, Norwich, NR7 4UH, UK
| | - Richard S Johnson
- Department of Genome Sciences, University of Washington, Foege Building, 98195-5065 Seattle, USA
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Foege Building, 98195-5065 Seattle, USA
| | - Svetlana Kontsedalov
- Department of Entomology, The Volcani Center, HaMacabim Rd., Rishon LeZion, 50250, Israel
| | - Galina Lebedev
- Department of Entomology, The Volcani Center, HaMacabim Rd., Rishon LeZion, 50250, Israel
| | - Henryk Czosnek
- Institute of Plant Sciences and Genetics in Agriculture, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Michelle Heck
- USDA-Agricultural Research Service, Boyce Thompson Institute for Plant Research, Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY, USA
| | - Murad Ghanim
- Department of Entomology, The Volcani Center, HaMacabim Rd., Rishon LeZion, 50250, Israel
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5
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Badr KR, Parente‐Rocha JA, Baeza LC, Ficcadori FS, Souza M, Soares CM, Guissoni ACP, Almeida TN, Cardoso DD. Quantitative proteomic analysis of A549 cells infected with human adenovirus type 2. J Med Virol 2019; 91:1239-1249. [DOI: 10.1002/jmv.25439] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 01/30/2019] [Accepted: 02/19/2019] [Indexed: 12/31/2022]
Affiliation(s)
- Kareem R. Badr
- Department of Microbiology, Human Virology LaboratoryInstitute of Tropical Pathology and Public Health, Federal University of GoiásGoiânia Goiás Brazil
| | - Juliana A. Parente‐Rocha
- Department of Microbiology, Molecular Biology LaboratoryInstitute of Biological Sciences, Federal University of GoiásGoiânia Goiás Brazil
| | - Lilian C. Baeza
- Department of Microbiology, Molecular Biology LaboratoryInstitute of Biological Sciences, Federal University of GoiásGoiânia Goiás Brazil
| | - Fabiola S. Ficcadori
- Department of Microbiology, Human Virology LaboratoryInstitute of Tropical Pathology and Public Health, Federal University of GoiásGoiânia Goiás Brazil
| | - Menira Souza
- Department of Microbiology, Human Virology LaboratoryInstitute of Tropical Pathology and Public Health, Federal University of GoiásGoiânia Goiás Brazil
| | - Célia M. Soares
- Department of Microbiology, Molecular Biology LaboratoryInstitute of Biological Sciences, Federal University of GoiásGoiânia Goiás Brazil
| | - Ana Carla P. Guissoni
- Department of Microbiology, Human Virology LaboratoryInstitute of Tropical Pathology and Public Health, Federal University of GoiásGoiânia Goiás Brazil
| | - Tâmera N. Almeida
- Department of Microbiology, Human Virology LaboratoryInstitute of Tropical Pathology and Public Health, Federal University of GoiásGoiânia Goiás Brazil
| | - Divina D. Cardoso
- Department of Microbiology, Human Virology LaboratoryInstitute of Tropical Pathology and Public Health, Federal University of GoiásGoiânia Goiás Brazil
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6
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Targeted disruption of aphid transmission: a vision for the management of crop diseases caused by Luteoviridae members. Curr Opin Virol 2018; 33:24-32. [DOI: 10.1016/j.coviro.2018.07.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 07/05/2018] [Indexed: 12/18/2022]
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7
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Pinheiro PV, Ghanim M, Alexander M, Rebelo AR, Santos RS, Orsburn BC, Gray S, Cilia M. Host Plants Indirectly Influence Plant Virus Transmission by Altering Gut Cysteine Protease Activity of Aphid Vectors. Mol Cell Proteomics 2016; 16:S230-S243. [PMID: 27932519 DOI: 10.1074/mcp.m116.063495] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 11/29/2016] [Indexed: 11/06/2022] Open
Abstract
The green peach aphid, Myzus persicae, is a vector of the Potato leafroll virus (PLRV, Luteoviridae), transmitted exclusively by aphids in a circulative manner. PLRV transmission efficiency was significantly reduced when a clonal lineage of M. persicae was reared on turnip as compared with the weed physalis, and this was a transient effect caused by a host-switch response. A trend of higher PLRV titer in physalis-reared aphids as compared with turnip-reared aphids was observed at 24 h and 72 h after virus acquisition. The major difference in the proteomes of these aphids was the up-regulation of predicted lysosomal enzymes, in particular the cysteine protease cathepsin B (cathB), in aphids reared on turnip. The aphid midgut is the site of PLRV acquisition, and cathB and PLRV localization were starkly different in midguts of the aphids reared on the two host plants. In viruliferous aphids that were reared on turnip, there was near complete colocalization of cathB and PLRV at the cell membranes, which was not observed in physalis-reared aphids. Chemical inhibition of cathB restored the ability of aphids reared on turnip to transmit PLRV in a dose-dependent manner, showing that the increased activity of cathB and other cysteine proteases at the cell membrane indirectly decreased virus transmission by aphids. Understanding how the host plant influences virus transmission by aphids is critical for growers to manage the spread of virus among field crops.
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Affiliation(s)
- Patricia V Pinheiro
- From the ‡Department of Entomology, Cornell University, Ithaca, New York 14853.,§Boyce Thompson Institute for Plant Research, Ithaca, New York 14853.,¶Embrapa Rice and Beans, Santo Antônio de Goiás 171, Brazil
| | - Murad Ghanim
- ‖Department of Entomology, Volcani Center, Bet Dagan 5025001, Israel
| | - Mariko Alexander
- **Plant Pathology and Plant Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York
| | - Ana Rita Rebelo
- §Boyce Thompson Institute for Plant Research, Ithaca, New York 14853
| | - Rogerio S Santos
- §Boyce Thompson Institute for Plant Research, Ithaca, New York 14853
| | | | - Stewart Gray
- **Plant Pathology and Plant Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York.,§§USDA Agricultural Research Service, Emerging Pests and Pathogens Research Unit, Robert W. Holley Center for Agriculture and Health, Ithaca, New York
| | - Michelle Cilia
- From the ‡Department of Entomology, Cornell University, Ithaca, New York 14853; .,**Plant Pathology and Plant Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York.,§§USDA Agricultural Research Service, Emerging Pests and Pathogens Research Unit, Robert W. Holley Center for Agriculture and Health, Ithaca, New York
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8
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DeBlasio SL, Johnson RS, MacCoss MJ, Gray SM, Cilia M. Model System-Guided Protein Interaction Mapping for Virus Isolated from Phloem Tissue. J Proteome Res 2016; 15:4601-4611. [DOI: 10.1021/acs.jproteome.6b00715] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Stacy L. DeBlasio
- Agricultural
Research Service, USDA, Ithaca, New York 14853, United States
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853, United States
| | - Richard S. Johnson
- Department
of Genome Sciences, University of Washington, Seattle Washington 98109, United States
| | - Michael J. MacCoss
- Department
of Genome Sciences, University of Washington, Seattle Washington 98109, United States
| | - Stewart M. Gray
- Agricultural
Research Service, USDA, Ithaca, New York 14853, United States
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York 14853, United States
| | - Michelle Cilia
- Agricultural
Research Service, USDA, Ithaca, New York 14853, United States
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853, United States
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York 14853, United States
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9
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Dietzgen RG, Mann KS, Johnson KN. Plant Virus-Insect Vector Interactions: Current and Potential Future Research Directions. Viruses 2016; 8:E303. [PMID: 27834855 PMCID: PMC5127017 DOI: 10.3390/v8110303] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 10/31/2016] [Accepted: 10/31/2016] [Indexed: 12/13/2022] Open
Abstract
Acquisition and transmission by an insect vector is central to the infection cycle of the majority of plant pathogenic viruses. Plant viruses can interact with their insect host in a variety of ways including both non-persistent and circulative transmission; in some cases, the latter involves virus replication in cells of the insect host. Replicating viruses can also elicit both innate and specific defense responses in the insect host. A consistent feature is that the interaction of the virus with its insect host/vector requires specific molecular interactions between virus and host, commonly via proteins. Understanding the interactions between plant viruses and their insect host can underpin approaches to protect plants from infection by interfering with virus uptake and transmission. Here, we provide a perspective focused on identifying novel approaches and research directions to facilitate control of plant viruses by better understanding and targeting virus-insect molecular interactions. We also draw parallels with molecular interactions in insect vectors of animal viruses, and consider technical advances for their control that may be more broadly applicable to plant virus vectors.
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Affiliation(s)
- Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia QLD 4072, Australia.
| | - Krin S Mann
- Agriculture and Agri-Food Canada, Summerland Research and Development Centre, Summerland, BC V0H 1Z0, Canada.
| | - Karyn N Johnson
- School of Biological Sciences, The University of Queensland, St. Lucia QLD 4072, Australia.
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10
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DeBlasio SL, Chavez JD, Alexander MM, Ramsey J, Eng JK, Mahoney J, Gray SM, Bruce JE, Cilia M. Visualization of Host-Polerovirus Interaction Topologies Using Protein Interaction Reporter Technology. J Virol 2016; 90:1973-87. [PMID: 26656710 PMCID: PMC4733995 DOI: 10.1128/jvi.01706-15] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 11/30/2015] [Indexed: 01/08/2023] Open
Abstract
UNLABELLED Demonstrating direct interactions between host and virus proteins during infection is a major goal and challenge for the field of virology. Most protein interactions are not binary or easily amenable to structural determination. Using infectious preparations of a polerovirus (Potato leafroll virus [PLRV]) and protein interaction reporter (PIR), a revolutionary technology that couples a mass spectrometric-cleavable chemical cross-linker with high-resolution mass spectrometry, we provide the first report of a host-pathogen protein interaction network that includes data-derived, topological features for every cross-linked site that was identified. We show that PLRV virions have hot spots of protein interaction and multifunctional surface topologies, revealing how these plant viruses maximize their use of binding interfaces. Modeling data, guided by cross-linking constraints, suggest asymmetric packing of the major capsid protein in the virion, which supports previous epitope mapping studies. Protein interaction topologies are conserved with other species in the Luteoviridae and with unrelated viruses in the Herpesviridae and Adenoviridae. Functional analysis of three PLRV-interacting host proteins in planta using a reverse-genetics approach revealed a complex, molecular tug-of-war between host and virus. Structural mimicry and diversifying selection-hallmarks of host-pathogen interactions-were identified within host and viral binding interfaces predicted by our models. These results illuminate the functional diversity of the PLRV-host protein interaction network and demonstrate the usefulness of PIR technology for precision mapping of functional host-pathogen protein interaction topologies. IMPORTANCE The exterior shape of a plant virus and its interacting host and insect vector proteins determine whether a virus will be transmitted by an insect or infect a specific host. Gaining this information is difficult and requires years of experimentation. We used protein interaction reporter (PIR) technology to illustrate how viruses exploit host proteins during plant infection. PIR technology enabled our team to precisely describe the sites of functional virus-virus, virus-host, and host-host protein interactions using a mass spectrometry analysis that takes just a few hours. Applications of PIR technology in host-pathogen interactions will enable researchers studying recalcitrant pathogens, such as animal pathogens where host proteins are incorporated directly into the infectious agents, to investigate how proteins interact during infection and transmission as well as develop new tools for interdiction and therapy.
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Affiliation(s)
- Stacy L DeBlasio
- Boyce Thompson Institute for Plant Research, Ithaca, New York, USA USDA-Agricultural Research Service, Ithaca, New York, USA
| | - Juan D Chavez
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Mariko M Alexander
- Boyce Thompson Institute for Plant Research, Ithaca, New York, USA Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, USA
| | - John Ramsey
- Boyce Thompson Institute for Plant Research, Ithaca, New York, USA
| | - Jimmy K Eng
- University of Washington Proteomics Resources, Seattle, Washington, USA
| | - Jaclyn Mahoney
- Boyce Thompson Institute for Plant Research, Ithaca, New York, USA
| | - Stewart M Gray
- USDA-Agricultural Research Service, Ithaca, New York, USA Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, USA
| | - James E Bruce
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Michelle Cilia
- Boyce Thompson Institute for Plant Research, Ithaca, New York, USA USDA-Agricultural Research Service, Ithaca, New York, USA Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, USA
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11
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Lum KK, Cristea IM. Proteomic approaches to uncovering virus-host protein interactions during the progression of viral infection. Expert Rev Proteomics 2016; 13:325-40. [PMID: 26817613 PMCID: PMC4919574 DOI: 10.1586/14789450.2016.1147353] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 01/25/2016] [Indexed: 01/10/2023]
Abstract
The integration of proteomic methods to virology has facilitated a significant breadth of biological insight into mechanisms of virus replication, antiviral host responses and viral subversion of host defenses. Throughout the course of infection, these cellular mechanisms rely heavily on the formation of temporally and spatially regulated virus-host protein-protein interactions. Reviewed here are proteomic-based approaches that have been used to characterize this dynamic virus-host interplay. Specifically discussed are the contribution of integrative mass spectrometry, antibody-based affinity purification of protein complexes, cross-linking and protein array techniques for elucidating complex networks of virus-host protein associations during infection with a diverse range of RNA and DNA viruses. The benefits and limitations of applying proteomic methods to virology are explored, and the contribution of these approaches to important biological discoveries and to inspiring new tractable avenues for the design of antiviral therapeutics is highlighted.
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Affiliation(s)
- Krystal K Lum
- Department of Molecular Biology, Princeton
University, Princeton, NJ, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton
University, Princeton, NJ, USA
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12
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DeBlasio SL, Johnson R, Sweeney MM, Karasev A, Gray SM, MacCoss MJ, Cilia M. Potato leafroll virus structural proteins manipulate overlapping, yet distinct protein interaction networks during infection. Proteomics 2015; 15:2098-112. [PMID: 25787689 DOI: 10.1002/pmic.201400594] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Revised: 02/08/2015] [Accepted: 03/16/2015] [Indexed: 01/20/2023]
Abstract
Potato leafroll virus (PLRV) produces a readthrough protein (RTP) via translational readthrough of the coat protein amber stop codon. The RTP functions as a structural component of the virion and as a nonincorporated protein in concert with numerous insect and plant proteins to regulate virus movement/transmission and tissue tropism. Affinity purification coupled to quantitative MS was used to generate protein interaction networks for a PLRV mutant that is unable to produce the read through domain (RTD) and compared to the known wild-type PLRV protein interaction network. By quantifying differences in the protein interaction networks, we identified four distinct classes of PLRV-plant interactions: those plant and nonstructural viral proteins interacting with assembled coat protein (category I); plant proteins in complex with both coat protein and RTD (category II); plant proteins in complex with the RTD (category III); and plant proteins that had higher affinity for virions lacking the RTD (category IV). Proteins identified as interacting with the RTD are potential candidates for regulating viral processes that are mediated by the RTP such as phloem retention and systemic movement and can potentially be useful targets for the development of strategies to prevent infection and/or viral transmission of Luteoviridae species that infect important crop species.
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Affiliation(s)
- Stacy L DeBlasio
- Boyce Thompson Institute for Plant Research, Ithaca, NY, USA.,USDA-Agricultural Research Service, Ithaca, NY, USA
| | - Richard Johnson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Alexander Karasev
- Department of Plant, Soil and Entomological Sciences, University of Idaho, Moscow, ID, USA
| | - Stewart M Gray
- USDA-Agricultural Research Service, Ithaca, NY, USA.,Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY, USA
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Michelle Cilia
- Boyce Thompson Institute for Plant Research, Ithaca, NY, USA.,USDA-Agricultural Research Service, Ithaca, NY, USA.,Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY, USA
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13
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DeBlasio SL, Johnson R, Mahoney J, Karasev A, Gray SM, MacCoss MJ, Cilia M. Insights into the polerovirus-plant interactome revealed by coimmunoprecipitation and mass spectrometry. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:467-81. [PMID: 25496593 DOI: 10.1094/mpmi-11-14-0363-r] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Identification of host proteins interacting with the aphidborne Potato leafroll virus (PLRV) from the genus Polerovirus, family Luteoviridae, is a critical step toward understanding how PLRV and related viruses infect plants. However, the tight spatial distribution of PLRV to phloem tissues poses challenges. A polyclonal antibody raised against purified PLRV virions was used to coimmunoprecipitate virus-host protein complexes from Nicotiana benthamiana tissue inoculated with an infectious PLRV cDNA clone using Agrobacterium tumefaciens. A. tumefaciens-mediated delivery of PLRV enabled infection and production of assembled, insect-transmissible virus in most leaf cells, overcoming the dynamic range constraint posed by a systemically infected host. Isolated protein complexes were characterized using high-resolution mass spectrometry and consisted of host proteins interacting directly or indirectly with virions, as well as the nonincorporated readthrough protein (RTP) and three phosphorylated positional isomers of the RTP. A bioinformatics analysis using ClueGO and STRING showed that plant proteins in the PLRV protein interaction network regulate key biochemical processes, including carbon fixation, amino acid biosynthesis, ion transport, protein folding, and trafficking.
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Affiliation(s)
- Stacy L DeBlasio
- 1 Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, U.S.A
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14
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Gray S, Cilia M, Ghanim M. Circulative, "nonpropagative" virus transmission: an orchestra of virus-, insect-, and plant-derived instruments. Adv Virus Res 2014; 89:141-99. [PMID: 24751196 DOI: 10.1016/b978-0-12-800172-1.00004-5] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Species of plant viruses within the Luteoviridae, Geminiviridae, and Nanoviridae are transmitted by phloem-feeding insects in a circulative, nonpropagative manner. The precise route of virus movement through the vector can differ across and within virus families, but these viruses all share many biological, biochemical, and ecological features. All share temporal and spatial constraints with respect to transmission efficiency. The viruses also induce physiological changes in their plant hosts resulting in behavioral changes in the insects that optimize the transmission of virus to new hosts. Virus proteins interact with insect, endosymbiont, and plant proteins to orchestrate, directly and indirectly, virus movement in insects and plants to facilitate transmission. Knowledge of these complex interactions allows for the development of new tools to reduce or prevent transmission, to quickly identify important vector populations, and to improve the management of these economically important viruses affecting agricultural and natural plant populations.
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Affiliation(s)
- Stewart Gray
- Biological Integrated Pest Management Research Unit, USDA, ARS, Ithaca, New York, USA; Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, USA.
| | - Michelle Cilia
- Biological Integrated Pest Management Research Unit, USDA, ARS, Ithaca, New York, USA; Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, USA; Boyce Thompson Institute for Plant Research, Ithaca, New York, USA
| | - Murad Ghanim
- Department of Entomology, Volcani Center, Bet Dagan, Israel
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Cilia M, Johnson R, Sweeney M, DeBlasio SL, Bruce JE, MacCoss MJ, Gray SM. Evidence for lysine acetylation in the coat protein of a polerovirus. J Gen Virol 2014; 95:2321-2327. [PMID: 24939649 PMCID: PMC4165934 DOI: 10.1099/vir.0.066514-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 06/13/2014] [Indexed: 12/17/2022] Open
Abstract
Virions of the RPV strain of Cereal yellow dwarf virus-RPV were purified from infected oat tissue and analysed by MS. Two conserved residues, K147 and K181, in the virus coat protein, were confidently identified to contain epsilon-N-acetyl groups. While no functional data are available for K147, K181 lies within an interfacial region critical for virion assembly and stability. The signature immonium ion at m/z 126.0919 demonstrated the presence of N-acetyllysine, and the sequence fragment ions enabled an unambiguous assignment of the epsilon-N-acetyl modification on K181. We hypothesize that selection favours acetylation of K181 in a fraction of coat protein monomers to stabilize the capsid by promoting intermonomer salt bridge formation.
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Affiliation(s)
- Michelle Cilia
- USDA-Agricultural Research Service, Ithaca, NY 14853, USA
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA
| | - Richard Johnson
- Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA
| | - Michelle Sweeney
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA
| | - Stacy L. DeBlasio
- USDA-Agricultural Research Service, Ithaca, NY 14853, USA
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA
| | - James E. Bruce
- Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA
| | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA
| | - Stewart M. Gray
- USDA-Agricultural Research Service, Ithaca, NY 14853, USA
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
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Jones R. Trends in plant virus epidemiology: Opportunities from new or improved technologies. Virus Res 2014; 186:3-19. [DOI: 10.1016/j.virusres.2013.11.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Revised: 10/30/2013] [Accepted: 11/01/2013] [Indexed: 12/16/2022]
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Tamborindeguy C, Bereman MS, DeBlasio S, Igwe D, Smith DM, White F, MacCoss MJ, Gray SM, Cilia M. Genomic and proteomic analysis of Schizaphis graminum reveals cyclophilin proteins are involved in the transmission of cereal yellow dwarf virus. PLoS One 2013; 8:e71620. [PMID: 23951206 PMCID: PMC3739738 DOI: 10.1371/journal.pone.0071620] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 06/30/2013] [Indexed: 01/21/2023] Open
Abstract
Yellow dwarf viruses cause the most economically important virus diseases of cereal crops worldwide and are transmitted by aphid vectors. The identification of aphid genes and proteins mediating virus transmission is critical to develop agriculturally sustainable virus management practices and to understand viral strategies for circulative movement in all insect vectors. Two cyclophilin B proteins, S28 and S29, were identified previously in populations of Schizaphisgraminum that differed in their ability to transmit the RPV strain of Cereal yellow dwarf virus (CYDV-RPV). The presence of S29 was correlated with F2 genotypes that were efficient virus transmitters. The present study revealed the two proteins were isoforms, and a single amino acid change distinguished S28 and S29. The distribution of the two alleles was determined in 12 F2 genotypes segregating for CYDV-RPV transmission capacity and in 11 genetically independent, field-collected S. graminum biotypes. Transmission efficiency for CYDV-RPV was determined in all genotypes and biotypes. The S29 isoform was present in all genotypes or biotypes that efficiently transmit CYDV-RPV and more specifically in genotypes that efficiently transport virus across the hindgut. We confirmed a direct interaction between CYDV-RPV and both S28 and S29 using purified virus and bacterially expressed, his-tagged S28 and S29 proteins. Importantly, S29 failed to interact with a closely related virus that is transported across the aphid midgut. We tested for in vivo interactions using an aphid-virus co-immunoprecipitation strategy coupled with a bottom-up LC-MS/MS analysis using a Q Exactive mass spectrometer. This analysis enabled us to identify a third cyclophilin protein, cyclophilin A, interacting directly or in complex with purified CYDV-RPV. Taken together, these data provide evidence that both cyclophilin A and B interact with CYDV-RPV, and these interactions may be important but not sufficient to mediate virus transport from the hindgut lumen into the hemocoel.
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Affiliation(s)
- Cecilia Tamborindeguy
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
- * E-mail: (MC); (CT)
| | - Michael S. Bereman
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Stacy DeBlasio
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
| | - David Igwe
- Virology and Molecular Diagnostics Unit, International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Dawn M. Smith
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
| | - Frank White
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas, United States of America
| | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Stewart M. Gray
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
| | - Michelle Cilia
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
- * E-mail: (MC); (CT)
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Watanabe S, Greenwell AM, Bressan A. Localization, concentration, and transmission efficiency of Banana bunchy top virus in four asexual lineages of Pentalonia aphids. Viruses 2013; 5:758-76. [PMID: 23435241 PMCID: PMC3640525 DOI: 10.3390/v5020758] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 02/14/2013] [Accepted: 02/14/2013] [Indexed: 02/01/2023] Open
Abstract
Banana bunchy top virus (BBTV) is the most destructive pathogenic virus of banana plants worldwide. The virus is transmitted in a circulative non-propagative manner by the banana aphid, Pentalonia nigronervosa Coquerel. In this work, we examined the localization, accumulation, and transmission efficiency of BBTV in four laboratory-established lineages of Pentalonia aphids derived from four different host plants: taro (Colocasia esculenta), heliconia (Heliconia spp.), red ginger (Alpinia purpurata), and banana (Musa sp.). Mitochondrial sequencing identified three and one lineages as Pentalonia caladii van der Goot, a recently proposed species, and P. nigronervosa, respectively. Microsatellite analysis separated the aphid lineages into four distinct genotypes. The transmission of BBTV was tested using leaf disk and whole-plant assays, both of which showed that all four lineages are competent vectors of BBTV, although the P. caladii from heliconia transmitted BBTV to the leaf disks at a significantly lower rate than did P. nigronervosa. The concentration of BBTV in dissected guts, haemolymph, and salivary glands was quantified by real-time PCR. The BBTV titer reached similar concentrations in the guts, haemolymph, and salivary glands of aphids from all four lineages tested. Furthermore, immunofluorescence assays showed that BBTV antigens localized to the anterior midguts and the principal salivary glands, demonstrating a similar pattern of translocations across the four lineages. The results reported in this study showed for the first time that P. caladii is a competent vector of BBTV.
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Affiliation(s)
- Shizu Watanabe
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI 96822, USA
- Department of Molecular Bioscience and Bioengineering, University of Hawaii, Honolulu, HI 96822; USA; E-Mail: (S.W.)
| | - April M. Greenwell
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI 96822, USA
- NSF-Center for Integrated Pest Management, North Carolina State University, USDA APHIS PPQ office, Honolulu, HI 96850, USA; E-Mail: (A.M.G.)
| | - Alberto Bressan
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI 96822, USA
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Bragard C, Caciagli P, Lemaire O, Lopez-Moya JJ, MacFarlane S, Peters D, Susi P, Torrance L. Status and prospects of plant virus control through interference with vector transmission. ANNUAL REVIEW OF PHYTOPATHOLOGY 2013; 51:177-201. [PMID: 23663003 DOI: 10.1146/annurev-phyto-082712-102346] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Most plant viruses rely on vector organisms for their plant-to-plant spread. Although there are many different natural vectors, few plant virus-vector systems have been well studied. This review describes our current understanding of virus transmission by aphids, thrips, whiteflies, leafhoppers, planthoppers, treehoppers, mites, nematodes, and zoosporic endoparasites. Strategies for control of vectors by host resistance, chemicals, and integrated pest management are reviewed. Many gaps in the knowledge of the transmission mechanisms and a lack of available host resistance to vectors are evident. Advances in genome sequencing and molecular technologies will help to address these problems and will allow innovative control methods through interference with vector transmission. Improved knowledge of factors affecting pest and disease spread in different ecosystems for predictive modeling is also needed. Innovative control measures are urgently required because of the increased risks from vector-borne infections that arise from environmental change.
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Affiliation(s)
- C Bragard
- Earth & Life Institute, Université Catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium.
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