scholarly journals Molecular cloning and characterization of Antheraea mylitta cytoplasmic polyhedrosis virus genome segment 9

2002 ◽  
Vol 83 (6) ◽  
pp. 1483-1491 ◽  
Author(s):  
Kaustubha R. Qanungo ◽  
Subhas C. Kundu ◽  
James I. Mullins ◽  
Ananta K. Ghosh
Keyword(s):  
Structure Prediction ◽  
Rna Binding ◽  
Secondary Structure Prediction ◽  
Virus Genome ◽  
Genome Segment ◽  
Viral Rna ◽  
Structural Protein ◽  
Antheraea Mylitta ◽  
Cytoplasmic Polyhedrosis Virus ◽  
Polyhedrosis Virus

Genome segment 9 of the 11-segment RNA genomes of three cytoplasmic polyhedrosis virus (CPV) isolates from Antheraea mylitta (AmCPV), Antheraea assamensis (AaCPV) and Antheraea proylei (ApCPV) were converted to cDNA, cloned and sequenced. In each case, this genome segment consists of 1473 nucleotides with one long ORF of 1035 bp and encodes a protein of 345 amino acids, termed NSP38, with a molecular mass of 38 kDa. Secondary structure prediction showed the presence of nine α-helices in the central and terminal domains with localized similarity to RNA-binding motifs of bluetongue virus and infectious bursal disease virus RNA polymerases. Nucleotide sequences were 99·6% identical between these three strains of CPVs, but no similarity was found to any other nucleotide or protein sequence in public databases. The ORF from AmCPV cDNA was expressed as a His-tagged fusion protein in E. coli and polyclonal antibody was raised against the purified protein. Immunoblot as well as immunofluorescence analysis with anti-NSP38 antibody showed that the protein was not present in polyhedra or uninfected cells but was present in AmCPV-infected host midgut cells. NSP38 was expressed in insect cells as soluble protein via a baculovirus expression vector and shown to possess the ability to bind poly(rI)–(rC) agarose, which was competitively removed by AmCPV viral RNA. These results indicate that NSP38 is expressed in virus-infected cells as a non-structural protein. By binding to viral RNA, it may play a role in the regulation of genomic RNA function and packaging.

scholarly journals Molecular characterization of genome segment 2 encoding RNA dependent RNA polymerase of Antheraea mylitta cytoplasmic polyhedrosis virus

Virology ◽  
2010 ◽  
Vol 404 (1) ◽  
pp. 21-31 ◽  
Author(s):  
Suvankar Ghorai ◽  
Mrinmay Chakrabarti ◽  
Sobhan Roy ◽  
Venkata Ramana Murthy Chavali ◽  
Abhisek Bagchi ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Molecular Characterization ◽  
Genome Segment ◽  
Rna Dependent Rna Polymerase ◽  
Antheraea Mylitta ◽  
Cytoplasmic Polyhedrosis Virus ◽  
Polyhedrosis Virus

scholarly journals Molecular Characterization of Bombyx mori Cytoplasmic Polyhedrosis Virus Genome Segment 4

2001 ◽  
Vol 75 (2) ◽  
pp. 988-995 ◽  
Author(s):  
Keiko Ikeda ◽  
Sumiharu Nagaoka ◽  
Stefan Winkler ◽  
Kumiko Kotani ◽  
Hiroaki Yagi ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Bombyx Mori ◽  
Fluorescent Protein ◽  
Chimeric Protein ◽  
Nilaparvata Lugens ◽  
Virus Genome ◽  
Genome Segment ◽  
Cytoplasmic Polyhedrosis Virus ◽  
Reading Frame ◽  
Polyhedrosis Virus

ABSTRACT The complete nucleotide sequence of the genome segment 4 (S4) ofBombyx mori cytoplasmic polyhedrosis virus (BmCPV) was determined. The 3,259-nucleotide sequence contains a single long open reading frame which spans nucleotides 14 to 3187 and which is predicted to encode a protein with a molecular mass of about 130 kDa. Western blot analysis showed that S4 encodes BmCPV protein VP3, which is one of the outer components of the BmCPV virion. Sequence analysis of the deduced amino acid sequence of BmCPV VP3 revealed possible sequence homology with proteins from rice ragged stunt virus (RRSV) S2,Nilaparvata lugens reovirus S4, and Fiji disease fijivirus S4. This may suggest that plant reoviruses originated from insect viruses and that RRSV emerged more recently than other plant reoviruses. A chimeric protein consisting of BmCPV VP3 and green fluorescent protein (GFP) was constructed and expressed with BmCPV polyhedrin using a baculovirus expression vector. The VP3-GFP chimera was incorporated into BmCPV polyhedra and released under alkaline conditions. The results indicate that specific interactions occur between BmCPV polyhedrin and VP3 which might facilitate BmCPV virion occlusion into the polyhedra.

scholarly journals Long-Range RNA-RNA Interactions Circularize the Dengue Virus Genome

2005 ◽  
Vol 79 (11) ◽  
pp. 6631-6643 ◽  
Author(s):  
Diego E. Alvarez ◽  
María F. Lodeiro ◽  
Silvio J. Ludueña ◽  
Lía I. Pietrasanta ◽  
Andrea V. Gamarnik
Keyword(s):  
Dengue Virus ◽  
Rna Binding ◽  
Rna Replication ◽  
Virus Genome ◽  
Viral Rna ◽  
Physical Interaction ◽  
Virus Rna ◽  
Rna Elements ◽  
Rna Interaction

ABSTRACT Secondary and tertiary RNA structures present in viral RNA genomes play essential regulatory roles during translation, RNA replication, and assembly of new viral particles. In the case of flaviviruses, RNA-RNA interactions between the 5′ and 3′ ends of the genome have been proposed to be required for RNA replication. We found that two RNA elements present at the ends of the dengue virus genome interact in vitro with high affinity. Visualization of individual molecules by atomic force microscopy reveled that physical interaction between these RNA elements results in cyclization of the viral RNA. Using RNA binding assays, we found that the putative cyclization sequences, known as 5′ and 3′ CS, present in all mosquito-borne flaviviruses, were necessary but not sufficient for RNA-RNA interaction. Additional sequences present at the 5′ and 3′ untranslated regions of the viral RNA were also required for RNA-RNA complex formation. We named these sequences 5′ and 3′ UAR (upstream AUG region). In order to investigate the functional role of 5′-3′ UAR complementarity, these sequences were mutated either separately, to destroy base pairing, or simultaneously, to restore complementarity in the context of full-length dengue virus RNA. Nonviable viruses were recovered after transfection of dengue virus RNA carrying mutations either at the 5′ or 3′ UAR, while the RNA containing the compensatory mutations was able to replicate. Since sequence complementarity between the ends of the genome is required for dengue virus viability, we propose that cyclization of the RNA is a required conformation for viral replication.

scholarly journals Molecular Characterization, Bioinformatic Analysis, and Expression Profile of Lin-28 Gene and Its Protein from Arabian Camel (Camelus dromedarius)

2019 ◽  
Vol 20 (9) ◽  
pp. 2291 ◽  
Author(s):  
Sultan N. Alharbi ◽  
Ibtehal S. Alduhaymi ◽  
Lama Alqahtani ◽  
Musaad A. Altammaami ◽  
Fahad M. Alhoshani ◽  
...  
Keyword(s):  
Structure Prediction ◽  
Rna Binding ◽  
Secondary Structure Prediction ◽  
Bos Taurus ◽  
Sequence Similarity ◽  
Zinc Fingers ◽  
3D Structure ◽  
Bioinformatic Analysis ◽  
Peptide Mass ◽  
Arabian Camel

Lin-28 is an RNA-binding protein that is known for its role in promoting the pluripotency of stem cells. In the present study, Arabian camel Lin-28 (cLin-28) cDNA was identified and analyzed. Full length cLin-28 mRNA was obtained using the reverse transcription polymerase chain reaction (RT-PCR). It was shown to be 715 bp in length, and the open reading frame (ORF) encoded 205 amino acids. The molecular weight and theoretical isoelectric point (pI) of the cLin-28 protein were predicted to be 22.389 kDa and 8.50, respectively. Results from the bioinformatics analysis revealed that cLin-28 has two main domains: an N-terminal cold-shock domain (CSD) and a C-terminal pair of retroviral-type Cysteine3Histidine (CCHC) zinc fingers. Sequence similarity and phylogenetic analysis showed that the cLin-28 protein is grouped together Camelus bactrianus and Bos taurus. Quantitative real-time PCR (qPCR) analysis showed that cLin-28 mRNA is highly expressed in the lung, heart, liver, and esophageal tissues. Peptide mass fingerprint-mass spectrometry (PMF-MS) analysis of the purified cLin-28 protein confirmed the identity of this protein. Comparing the modeled 3D structure of cLin-28 protein with the available protein 3D structure of the human Lin-28 protein confirmed the presence of CSD and retroviral-type CCHC zinc fingers, and high similarities were noted between the two structures by using super secondary structure prediction.

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