DOI: 10.1128/jvi.78.20.11360-11370.2004. Genomic and Proteomic Analysis of Thirty-Nine Structural Proteins of Shrimp White Spot Syndrome Virus

Genomic and Proteomic Analysis of Thirty-Nine Structural Proteins of Shrimp White Spot Syndrome Virus

10.1128/jvi.78.20.11360-11370.2004

Crossref journal-article

American Society for Microbiology

Journal of Virology (235)

Abstract

ABSTRACT White spot syndrome virus (WSSV) virions were purified from the hemolymph of experimentally infected crayfish Procambarus clarkii , and their proteins were separated by 8 to 18% gradient sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) to give a protein profile. The visible bands were then excised from the gel, and following trypsin digestion of the reduced and alkylated WSSV proteins in the bands, the peptide sequence of each fragment was determined by liquid chromatography-nano-electrospray ionization tandem mass spectrometry (LC-nanoESI-MS/MS) using a quadrupole/time-of-flight mass spectrometer. Comparison of the resulting peptide sequence data against the nonredundant database at the National Center for Biotechnology Information identified 33 WSSV structural genes, 20 of which are reported here for the first time. Since there were six other known WSSV structural proteins that could not be identified from the SDS-PAGE bands, there must therefore be a total of at least 39 (33 + 6) WSSV structural protein genes. Only 61.5% of the WSSV structural genes have a polyadenylation signal, and preliminary analysis by 3′ rapid amplification of cDNA ends suggested that some structural protein genes produced mRNA without a poly(A) tail. Microarray analysis showed that gene expression started at 2, 6, 8, 12, 18, 24, and 36 hpi for 7, 1, 4, 12, 9, 5, and 1 of the genes, respectively. Based on similarities in their time course expression patterns, a clustering algorithm was used to group the WSSV structural genes into four clusters. Genes that putatively had common or similar roles in the viral infection cycle tended to appear in the same cluster.

Bibliography

Tsai, J.-M., Wang, H.-C., Leu, J.-H., Hsiao, H.-H., Wang, A. H.-J., Kou, G.-H., & Lo, C.-F. (2004). Genomic and Proteomic Analysis of Thirty-Nine Structural Proteins of Shrimp White Spot Syndrome Virus. Journal of Virology, 78(20), 11360â11370.

Authors 7

Jyh-Ming Tsai (first)
Han-Ching Wang (additional)
Jiann-Horng Leu (additional)
He-Hsuan Hsiao (additional)
Andrew H.-J. Wang (additional)
Guang-Hsiung Kou (additional)
Chu-Fang Lo (additional)

References 60 Referenced 203

10.1016/S0022-2836(05)80360-2
Bairoch, A., and B. Boeckmann. 1994. The SWISS-PROT protein sequence data bank: current status. Nucleic Acids Res.1994:3578-3580. / Nucleic Acids Res. (1994)
10.1093/nar/30.1.276
10.3354/dao027131
10.1006/viro.2001.1273
10.1006/viro.2002.1536
10.1016/0965-1748(93)90085-7
10.1016/0092-8674(81)90521-3
10.1023/A:1018580301578
10.1093/nar/22.20.4342
10.1016/S0044-8486(97)00221-4
Hofmann, K., and W. Stoffel. 1993. Tmbase—a database of membrane spanning proteins segments. Biol. Chem. Hoppe-Seyler374:166. / Biol. Chem. Hoppe-Seyler (1993)
10.1099/0022-1317-83-10-2385
10.1074/mcp.M100035-MCP200
10.3147/jsfp.29.149
10.1128/jvi.70.11.7485-7497.1996
10.1128/JVI.77.18.10162-10167.2003
10.1083/jcb.108.2.229
10.1126/science.1081867
10.1007/s00705-003-0221-7
10.1006/viro.2002.1696
10.1006/viro.2001.1091
10.3354/dao025133
10.3354/dao027215
10.3354/dao030053
10.3147/jsfp.33.365
10.3354/dao035175
10.1099/vir.0.19018-0
10.1093/nar/22.2.208
10.3147/jsfp.29.141
10.1093/nar/gkg046
10.3354/dao033221
10.3354/dao033231
10.3147/jsfp.29.135
10.1093/protein/10.1.1
10.1073/pnas.94.1.15
10.1038/35015709
10.1074/jbc.R000003200
Seo, J., and B. Shneiderman. 2002. Understanding hierarchical clustering results by interactive exploration of dendrograms: a case study with genomic microarray data. IEEE Comput.35:80-86. / IEEE Comput. (2002)
10.1006/viro.2000.0596
10.1006/viro.2000.0597
10.1006/viro.2002.1480
10.1007/s00705-002-0822-6
van Hulten, M. C. W., M. F. Tsai, C. A. Schipper, C. F. Lo, G. H. Kou, and J. M. Vlak. 2000. Analysis of a genomic segment of white spot syndrome virus of shrimp containing ribonucleotide reductase genes and repeat regions. J. Gen. Virol.81:307-316. / J. Gen. Virol. (2000)
10.1006/viro.1999.0088
10.1006/viro.2001.0928
10.1006/viro.2001.1002
10.1099/0022-1317-83-1-257
10.3354/dao023239
10.1128/JVI.77.5.3131-3147.2003
Mar. Biotechnol.
10.1007/s007050050022
10.3354/dao021069
10.1006/viro.2001.1344
10.1016/S0969-2126(94)00126-X
10.1128/JVI.75.23.11811-11820.2001
10.1146/annurev.bi.60.070191.003353
10.1016/S0168-1702(01)00340-9
10.1099/0022-1317-83-2-471
10.1016/j.antiviral.2003.08.019

Dates

Type	When
Created	20 years, 11 months ago (Sept. 27, 2004, 1:28 p.m.)
Deposited	3 years, 5 months ago (March 5, 2022, 3:45 a.m.)
Indexed	1 week, 3 days ago (Aug. 21, 2025, 2:26 p.m.)
Issued	20 years, 10 months ago (Oct. 15, 2004)
Published	20 years, 10 months ago (Oct. 15, 2004)
Published Print	20 years, 10 months ago (Oct. 15, 2004)

Funders 0

None

BibTeX

@article{Tsai_2004, title={Genomic and Proteomic Analysis of Thirty-Nine Structural Proteins of Shrimp White Spot Syndrome Virus}, volume={78}, ISSN={1098-5514}, url={http://dx.doi.org/10.1128/jvi.78.20.11360-11370.2004}, DOI={10.1128/jvi.78.20.11360-11370.2004}, number={20}, journal={Journal of Virology}, publisher={American Society for Microbiology}, author={Tsai, Jyh-Ming and Wang, Han-Ching and Leu, Jiann-Horng and Hsiao, He-Hsuan and Wang, Andrew H.-J. and Kou, Guang-Hsiung and Lo, Chu-Fang}, year={2004}, month=oct, pages={11360–11370} }

JSON

{
  "indexed": {
    "date-parts": [
      [
        2025,
        8,
        21
      ]
    ],
    "date-time": "2025-08-21T18:26:05Z",
    "timestamp": 1755800765469
  },
  "reference-count": 60,
  "publisher": "American Society for Microbiology",
  "issue": "20",
  "license": [
    {
      "start": {
        "date-parts": [
          [
            2004,
            10,
            15
          ]
        ],
        "date-time": "2004-10-15T00:00:00Z",
        "timestamp": 1097798400000
      },
      "content-version": "tdm",
      "delay-in-days": 0,
      "URL": "https://journals.asm.org/non-commercial-tdm-license"
    }
  ],
  "content-domain": {
    "domain": [
      "journals.asm.org"
    ],
    "crossmark-restriction": true
  },
  "published-print": {
    "date-parts": [
      [
        2004,
        10,
        15
      ]
    ]
  },
  "abstract": "<jats:title>ABSTRACT</jats:title>\n          <jats:p>\n            White spot syndrome virus (WSSV) virions were purified from the hemolymph of experimentally infected crayfish\n            <jats:italic>Procambarus clarkii</jats:italic>\n            , and their proteins were separated by 8 to 18% gradient sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) to give a protein profile. The visible bands were then excised from the gel, and following trypsin digestion of the reduced and alkylated WSSV proteins in the bands, the peptide sequence of each fragment was determined by liquid chromatography-nano-electrospray ionization tandem mass spectrometry (LC-nanoESI-MS/MS) using a quadrupole/time-of-flight mass spectrometer. Comparison of the resulting peptide sequence data against the nonredundant database at the National Center for Biotechnology Information identified 33 WSSV structural genes, 20 of which are reported here for the first time. Since there were six other known WSSV structural proteins that could not be identified from the SDS-PAGE bands, there must therefore be a total of at least 39 (33 + 6) WSSV structural protein genes. Only 61.5% of the WSSV structural genes have a polyadenylation signal, and preliminary analysis by 3\u2032 rapid amplification of cDNA ends suggested that some structural protein genes produced mRNA without a poly(A) tail. Microarray analysis showed that gene expression started at 2, 6, 8, 12, 18, 24, and 36 hpi for 7, 1, 4, 12, 9, 5, and 1 of the genes, respectively. Based on similarities in their time course expression patterns, a clustering algorithm was used to group the WSSV structural genes into four clusters. Genes that putatively had common or similar roles in the viral infection cycle tended to appear in the same cluster.\n          </jats:p>",
  "DOI": "10.1128/jvi.78.20.11360-11370.2004",
  "type": "journal-article",
  "created": {
    "date-parts": [
      [
        2004,
        9,
        27
      ]
    ],
    "date-time": "2004-09-27T17:28:05Z",
    "timestamp": 1096306085000
  },
  "page": "11360-11370",
  "update-policy": "http://dx.doi.org/10.1128/asmj-crossmark-policy-page",
  "source": "Crossref",
  "is-referenced-by-count": 203,
  "title": "Genomic and Proteomic Analysis of Thirty-Nine Structural Proteins of Shrimp White Spot Syndrome Virus",
  "prefix": "10.1128",
  "volume": "78",
  "author": [
    {
      "given": "Jyh-Ming",
      "family": "Tsai",
      "sequence": "first",
      "affiliation": [
        {
          "name": "Institute of Zoology, National Taiwan University"
        }
      ]
    },
    {
      "given": "Han-Ching",
      "family": "Wang",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "Institute of Zoology, National Taiwan University"
        }
      ]
    },
    {
      "given": "Jiann-Horng",
      "family": "Leu",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "Institute of Zoology, National Taiwan University"
        }
      ]
    },
    {
      "given": "He-Hsuan",
      "family": "Hsiao",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "Core Facilities for Proteomics Research"
        }
      ]
    },
    {
      "given": "Andrew H.-J.",
      "family": "Wang",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "Core Facilities for Proteomics Research"
        },
        {
          "name": "Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan"
        }
      ]
    },
    {
      "given": "Guang-Hsiung",
      "family": "Kou",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "Institute of Zoology, National Taiwan University"
        }
      ]
    },
    {
      "given": "Chu-Fang",
      "family": "Lo",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "Institute of Zoology, National Taiwan University"
        }
      ]
    }
  ],
  "member": "235",
  "reference": [
    {
      "key": "e_1_3_2_2_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0022-2836(05)80360-2"
    },
    {
      "key": "e_1_3_2_3_2",
      "first-page": "3578",
      "volume": "1994",
      "year": "1994",
      "unstructured": "Bairoch, A., and B. Boeckmann. 1994. The SWISS-PROT protein sequence data bank: current status. Nucleic Acids Res.1994:3578-3580.",
      "journal-title": "Nucleic Acids Res."
    },
    {
      "key": "e_1_3_2_4_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1093/nar/30.1.276"
    },
    {
      "key": "e_1_3_2_5_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.3354/dao027131"
    },
    {
      "key": "e_1_3_2_6_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1006/viro.2001.1273"
    },
    {
      "key": "e_1_3_2_7_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1006/viro.2002.1536"
    },
    {
      "key": "e_1_3_2_8_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0965-1748(93)90085-7"
    },
    {
      "key": "e_1_3_2_9_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0092-8674(81)90521-3"
    },
    {
      "key": "e_1_3_2_10_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1023/A:1018580301578"
    },
    {
      "key": "e_1_3_2_11_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1093/nar/22.20.4342"
    },
    {
      "key": "e_1_3_2_12_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0044-8486(97)00221-4"
    },
    {
      "key": "e_1_3_2_13_2",
      "first-page": "166",
      "volume": "374",
      "year": "1993",
      "unstructured": "Hofmann, K., and W. Stoffel. 1993. Tmbase\u2014a database of membrane spanning proteins segments. Biol. Chem. Hoppe-Seyler374:166.",
      "journal-title": "Biol. Chem. Hoppe-Seyler"
    },
    {
      "key": "e_1_3_2_14_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1099/0022-1317-83-10-2385"
    },
    {
      "key": "e_1_3_2_15_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1074/mcp.M100035-MCP200"
    },
    {
      "key": "e_1_3_2_16_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.3147/jsfp.29.149"
    },
    {
      "key": "e_1_3_2_17_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1128/jvi.70.11.7485-7497.1996"
    },
    {
      "key": "e_1_3_2_18_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1128/JVI.77.18.10162-10167.2003"
    },
    {
      "key": "e_1_3_2_19_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1083/jcb.108.2.229"
    },
    {
      "key": "e_1_3_2_20_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1126/science.1081867"
    },
    {
      "key": "e_1_3_2_21_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1007/s00705-003-0221-7"
    },
    {
      "key": "e_1_3_2_22_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1006/viro.2002.1696"
    },
    {
      "key": "e_1_3_2_23_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1006/viro.2001.1091"
    },
    {
      "key": "e_1_3_2_24_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.3354/dao025133"
    },
    {
      "key": "e_1_3_2_25_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.3354/dao027215"
    },
    {
      "key": "e_1_3_2_26_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.3354/dao030053"
    },
    {
      "key": "e_1_3_2_27_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.3147/jsfp.33.365"
    },
    {
      "key": "e_1_3_2_28_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.3354/dao035175"
    },
    {
      "key": "e_1_3_2_29_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1099/vir.0.19018-0"
    },
    {
      "key": "e_1_3_2_30_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1093/nar/22.2.208"
    },
    {
      "key": "e_1_3_2_31_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.3147/jsfp.29.141"
    },
    {
      "key": "e_1_3_2_32_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1093/nar/gkg046"
    },
    {
      "key": "e_1_3_2_33_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.3354/dao033221"
    },
    {
      "key": "e_1_3_2_34_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.3354/dao033231"
    },
    {
      "key": "e_1_3_2_35_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.3147/jsfp.29.135"
    },
    {
      "key": "e_1_3_2_36_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1093/protein/10.1.1"
    },
    {
      "key": "e_1_3_2_37_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.94.1.15"
    },
    {
      "key": "e_1_3_2_38_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/35015709"
    },
    {
      "key": "e_1_3_2_39_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1074/jbc.R000003200"
    },
    {
      "key": "e_1_3_2_40_2",
      "first-page": "80",
      "volume": "35",
      "year": "2002",
      "unstructured": "Seo, J., and B. Shneiderman. 2002. Understanding hierarchical clustering results by interactive exploration of dendrograms: a case study with genomic microarray data. IEEE Comput.35:80-86.",
      "journal-title": "IEEE Comput."
    },
    {
      "key": "e_1_3_2_41_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1006/viro.2000.0596"
    },
    {
      "key": "e_1_3_2_42_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1006/viro.2000.0597"
    },
    {
      "key": "e_1_3_2_43_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1006/viro.2002.1480"
    },
    {
      "key": "e_1_3_2_44_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1007/s00705-002-0822-6"
    },
    {
      "key": "e_1_3_2_45_2",
      "first-page": "307",
      "volume": "81",
      "year": "2000",
      "unstructured": "van Hulten, M. C. W., M. F. Tsai, C. A. Schipper, C. F. Lo, G. H. Kou, and J. M. Vlak. 2000. Analysis of a genomic segment of white spot syndrome virus of shrimp containing ribonucleotide reductase genes and repeat regions. J. Gen. Virol.81:307-316.",
      "journal-title": "J. Gen. Virol."
    },
    {
      "key": "e_1_3_2_46_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1006/viro.1999.0088"
    },
    {
      "key": "e_1_3_2_47_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1006/viro.2001.0928"
    },
    {
      "key": "e_1_3_2_48_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1006/viro.2001.1002"
    },
    {
      "key": "e_1_3_2_49_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1099/0022-1317-83-1-257"
    },
    {
      "key": "e_1_3_2_50_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.3354/dao023239"
    },
    {
      "key": "e_1_3_2_51_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1128/JVI.77.5.3131-3147.2003"
    },
    {
      "key": "e_1_3_2_52_2",
      "unstructured": "Mar. Biotechnol."
    },
    {
      "key": "e_1_3_2_53_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1007/s007050050022"
    },
    {
      "key": "e_1_3_2_54_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.3354/dao021069"
    },
    {
      "key": "e_1_3_2_55_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1006/viro.2001.1344"
    },
    {
      "key": "e_1_3_2_56_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0969-2126(94)00126-X"
    },
    {
      "key": "e_1_3_2_57_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1128/JVI.75.23.11811-11820.2001"
    },
    {
      "key": "e_1_3_2_58_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1146/annurev.bi.60.070191.003353"
    },
    {
      "key": "e_1_3_2_59_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0168-1702(01)00340-9"
    },
    {
      "key": "e_1_3_2_60_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1099/0022-1317-83-2-471"
    },
    {
      "key": "e_1_3_2_61_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/j.antiviral.2003.08.019"
    }
  ],
  "container-title": "Journal of Virology",
  "original-title": [],
  "language": "en",
  "link": [
    {
      "URL": "https://journals.asm.org/doi/pdf/10.1128/JVI.78.20.11360-11370.2004",
      "content-type": "application/pdf",
      "content-version": "vor",
      "intended-application": "text-mining"
    },
    {
      "URL": "https://journals.asm.org/doi/pdf/10.1128/JVI.78.20.11360-11370.2004",
      "content-type": "unspecified",
      "content-version": "vor",
      "intended-application": "similarity-checking"
    }
  ],
  "deposited": {
    "date-parts": [
      [
        2022,
        3,
        5
      ]
    ],
    "date-time": "2022-03-05T08:45:16Z",
    "timestamp": 1646469916000
  },
  "score": 1,
  "resource": {
    "primary": {
      "URL": "https://journals.asm.org/doi/10.1128/JVI.78.20.11360-11370.2004"
    }
  },
  "subtitle": [],
  "short-title": [],
  "issued": {
    "date-parts": [
      [
        2004,
        10,
        15
      ]
    ]
  },
  "references-count": 60,
  "journal-issue": {
    "issue": "20",
    "published-print": {
      "date-parts": [
        [
          2004,
          10,
          15
        ]
      ]
    }
  },
  "alternative-id": [
    "10.1128/JVI.78.20.11360-11370.2004"
  ],
  "URL": "http://dx.doi.org/10.1128/JVI.78.20.11360-11370.2004",
  "relation": {},
  "ISSN": [
    "0022-538X",
    "1098-5514"
  ],
  "subject": [],
  "container-title-short": "J Virol",
  "published": {
    "date-parts": [
      [
        2004,
        10,
        15
      ]
    ]
  },
  "assertion": [
    {
      "value": "2004-02-12",
      "order": 0,
      "name": "received",
      "label": "Received",
      "group": {
        "name": "publication_history",
        "label": "Publication History"
      }
    },
    {
      "value": "2004-05-28",
      "order": 1,
      "name": "accepted",
      "label": "Accepted",
      "group": {
        "name": "publication_history",
        "label": "Publication History"
      }
    },
    {
      "value": "2004-10-15",
      "order": 2,
      "name": "published",
      "label": "Published",
      "group": {
        "name": "publication_history",
        "label": "Publication History"
      }
    }
  ]
}