Structural protein reorganization and fold emergence investigated through amino acid sequence permutations

AbstractThe potential relationship between the establishment ofFoot-and-mouth disease virus(FMDV) persistent infection and gene variation was identified by investigating the variation ofVP1and3ABCgenes from yellow cattle persistent infection isolates. Five yellow cattle were inoculated on their tongue with 1.0×104ID50/ml of FMDV O/Akesu/58 strain. After displaying clinical or subclinical signs, they probably became asymptomatic carriers. Oesophageal–pharyngeal fluids were collected monthly from the carriers with a probang and inoculated into a baby hamster kidney cell line (BHK-21); 12 FMDV isolates were obtained. TheVP1and3ABCgenes of the 12 isolates were then amplified by reverse-transcriptase polymerase chain reaction (RT-PCR). Cloning and sequencing revealed that the homology of theVP1nucleotide and amino-acid sequence of all the isolates was above 98%, with no base deletion or insertion. When compared with the O/Akesu/58 FMDV strain, the homology of theVP1nucleotide sequence of the isolates was only 85%, and that of the deduced amino-acid sequence only 90%.There were several nucleotide mutations in theVP1gene of the isolates, including 16 consistent nucleotide mutations, with only two of them leading to a change in amino acid (I56→T, A210→E). Moreover, it was found that four nucleotide points and three amino-acid points had transversions among all isolates. The3ABCgene had only 13 nucleotide transversions and five amino-acid mutations. It was presumed that persistent FMDV infection might have little connection with variation in theVP1and3ABCgenes, and was probably related to other structural protein gene and key factors.

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Nucleotide and deduced amino acid sequence of the structural protein genes of Japanese encephalitis viruses from different geographical locations

Journal of General Virology ◽

10.1099/0022-1317-76-2-401 ◽

1995 ◽

Vol 76 (2) ◽

pp. 401-407 ◽

Cited By ~ 39

Author(s):

H. Ni ◽

A. D. T. Barrett

Keyword(s):

Amino Acid ◽

Amino Acid Sequence ◽

Japanese Encephalitis ◽

Structural Protein ◽

Geographical Locations

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Genetic and phenotypic variations of isolates of shrimp Taura syndrome virus found in Penaeus monodon and Metapenaeus ensis in Taiwan

Journal of General Virology ◽

10.1099/vir.0.80132-0 ◽

2004 ◽

Vol 85 (10) ◽

pp. 2963-2968 ◽

Cited By ~ 20

Author(s):

Yun-Shiang Chang ◽

Shao-En Peng ◽

Hon-Tsen Yu ◽

Feng-Chuan Liu ◽

Chung-Hsiung Wang ◽

...

Keyword(s):

Amino Acid ◽

Amino Acid Sequence ◽

Penaeus Monodon ◽

Clinical Signs ◽

Nucleotide Sequence Analysis ◽

Structural Protein ◽

Taura Syndrome Virus ◽

Metapenaeus Ensis ◽

Phenotypic Differences ◽

Close Relationship

Distinct Taura syndrome virus (TSV) isolates were found in Metapenaeus ensis (isolate Tw2KMeTSV), Penaeus monodon (isolate Tw2KPmTSV) and Litopenaeus vannamei (isolate Tw02LvTSV). Nucleotide sequence analysis of these three isolates revealed differences in the TSV structural protein (capsid protein precursor) gene orf2. TSV ORF2 amino acid sequence comparison and phylogenetic analysis suggested a comparatively close relationship between these three Taiwanese isolates and the Hawaiian isolate HI94TSV. In P. monodon specimens that were naturally and experimentally infected with the Tw2KPmTSV isolate, the virus was contained and shrimps showed no clinical signs of infection. However, when P. monodon was challenged with the Tw2KMeTSV isolate, the virus replicated freely. The ORF2 amino acid sequence of the Tw2KMeTSV isolate differed from that of isolate Tw2KPmTSV in four positions and these differences may account for their phenotypic differences, at least in terms of their ability to replicate in specific hosts.

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Nucleotide Sequence of the Simian Virus 40 Hind II + III Restriction Fragment J and the Total Amino Acid Sequence of the Major Structural Protein VP1

European Journal of Biochemistry ◽

10.1111/j.1432-1033.1978.tb12694.x ◽

1978 ◽

Vol 91 (2) ◽

pp. 415-430 ◽

Cited By ~ 5

Author(s):

Hugo HEUVERSWYN ◽

Andre VOORDE ◽

Walter FIERS

Keyword(s):

Amino Acid ◽

Nucleotide Sequence ◽

Amino Acid Sequence ◽

Restriction Fragment ◽

Simian Virus 40 ◽

Simian Virus ◽

Total Amino Acid ◽

Structural Protein ◽

Major Structural Protein

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Improving Proteolytic Cleavage at the 3A/3B Site of the Hepatitis A Virus Polyprotein Impairs Processing and Particle Formation, and the Impairment Can Be Complemented intrans by 3AB and 3ABC

Journal of Virology ◽

10.1128/jvi.73.12.9867-9878.1999 ◽

1999 ◽

Vol 73 (12) ◽

pp. 9867-9878 ◽

Cited By ~ 23

Author(s):

Yuri Kusov ◽

Verena Gauss-Müller

Keyword(s):

Amino Acid ◽

Amino Acid Sequence ◽

Cleavage Site ◽

Hepatitis A ◽

Hepatitis A Virus ◽

Particle Formation ◽

Proteolytic Processing ◽

Cleavage Sites ◽

Structural Protein ◽

Hydrophobic Domain

ABSTRACT The orchestrated liberation of viral proteins by 3Cpro-mediated proteolysis is pivotal for gene expression by picornaviruses. Proteolytic processing is regulated either by the amino acid sequence at the cleavage site of the substrate or by cofactors covalently or noncovalently linked to the viral proteinase. To determine the role of the amino acid sequence at cleavage sites 3A/3B and 3B/3C that are essential for the liberation of 3Cpro from its precursors and to assess the function of the stable processing intermediates 3AB and 3ABC, we studied the effect of cleavage site mutations on hepatitis A virus (HAV) polyprotein processing, particle formation, and replication. Using the recombinant vaccinia virus system, we showed that the normally retarded cleavage at the 3A/3B junction can be improved by altering the amino acid sequence at the scissile bond such that it matches the preferred HAV 3C cleavage sites. In contrast to the processing products of the wild-type polyprotein, 3ABC was no longer detectable in the mutant. VP0 and VP3 were generated less efficiently, implying that processing of the structural protein precursor P1-2A depends on the presence of stable 3ABC and/or 3AB. In addition, cleavage of 2BC was impaired in 3AB/3ABC-deficient mutants. Formation of HAV particles was not affected in mutants with blocked 3A/3B and/or 3B/3C cleavage sites. However, 3ABC-deficient mutants produced small numbers of HAV particles, which could be augmented by coexpressing 3AB or 3ABC. The hydrophobic domain of 3A that has been proposed to mediate membrane anchorage of the replication complex was crucial for restoration of defective particle formation. In vitro transcripts of the various cleavage site mutants were unable to initiate an infectious cycle, and no progeny viruses were obtained even after blind passages. Taken together, the data suggest that accumulation of uncleaved HAV 3AB and/or 3ABC is pivotal for both viral replication and efficient particle formation.

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