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J. Biol. Chem., Vol. 276, Issue 23, 20039-20047, June 8, 2001

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Determination of the Complete Amino Acid Sequence for the Coat Protein of Brome Mosaic Virus by Time-of-Flight Mass Spectrometry
EVIDENCE FOR MUTATIONS ASSOCIATED WITH CHANGE OF PROPAGATION HOST^*

Yi-Min She, Steve Haber^§, Dallas L. Seifers^¶, Alexander Loboda, Igor Chernushevich, Hélène Perreault^**, Werner Ens, and Kenneth G. Standing

From the  Department of Physics & Astronomy, University of Manitoba, Winnipeg, MB R3T 2N2, Canada, the ^§ Cereal Research Centre, Agriculture & Agrifood Canada, Winnipeg, MB R3T 2M9, Canada, the ^¶ Agricultural Research Center, Kansas State University, Hays, Kansas 67601-9228,  MDS Sciex, Concord, ON L4K 4V8, Canada, and the ^** Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada

Time-of-flight mass spectrometry (TOFMS) has been applied to determine the complete coat protein amino acid sequences of a number of distinct brome mosaic virus (BMV) isolates. Ionization was carried out by both electrospray ionization and matrix-assisted laser desorption/ionization (MALDI). After determining overall coat protein masses, the proteins were digested with trypsin or Lys-C proteinases, and the digestion products were analyzed in a MALDI QqTOF mass spectrometer. The N terminus of the coat protein was found to be acetylated in each BMV isolate analyzed. In one isolate (BMV-Valverde), the amino acid sequence was identical to that predicted from the cDNA sequence of the "type" isolate, but deviations from the predicted amino acid sequence were observed for all the other isolates analyzed. When isolates were propagated in different host taxa, modified coat protein sequences were observed in some cases, along with the original sequence. Sequencing by TOFMS may therefore provide a basis for monitoring the effects of host passaging on a virus at the molecular level. Such TOFMS-based analyses assess the complete profiles of coat protein sequences actually present in infected tissues. They are therefore not subject to the selection biases inherent in deducing such sequences from reverse-transcribed viral RNA and cloning the resulting cDNA.

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