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Development of Global Consensus Sequence and Analysis of Highly Conserved Domains of the HCV NS5B Prote in.

Waheed Y, Saeed U, Anjum S, Afzal MS, Ashraf M - Hepat Mon (2012)

Bottom Line: Nine different peptides from the highly conserved regions of HCV NS5B protein were drawn which can be used as a peptide vaccine.In spite of a high mutation rate in HCV, the residues which are present in the catalytic pocket, sugar selection and template/primer interaction are highly conserved.These are target sites for the development of antiviral agents or peptide vaccines.

View Article: PubMed Central - PubMed

Affiliation: Atta-ur-Rehman School of Applied BioSciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan.

ABSTRACT

Background: Hepatitis C virus (HCV) is a plus stranded RNA virus which encodes 10 different genes. The HCV NS5B gene encodes a polymerase, which is responsible for the replication of the virus and is a potential target for the development of antiviral agents. HCV has a high mutation rate and is classified into six major genotypes.

Objectives: The aim of this study was to draw a representing consensus sequence of each HCV genotype, align all six consensus sequences to draw a global consensus sequence and also study the highly conserved residues.

Materials and methods: 236 HCV NS5B sequences, belonging to all six genotypes, reported from all over the world were aligned then a representing phylogenetic tree wasdrawn.

Results: The active site residues D220, D225, D318 and D319, which bind the divalent cations, are highly conserved among all the HCV genotypes. The other catalytic pocket residues, R158, S367, R386, and T390 and R394, which interact with the triphosphate of NTPs, are also highly conserved while T390 is mutated to valine in the genotype 5. The motif B residues G283, T286, T287 and N291, which take part in sugar selection by RdRp, are also highly conserved except for T286 which is mutated to proline in the genotypes 3 and 6. The residues E18, Y191, C274, Y276 and H502, which take part in primer/template interaction, are also high conserved except for H502 which is mutated to serine in genotype 2. High variation in all the six consensus sequences was observed in a 12 amino acid beta hairpin loop, which interacts with the double stranded RNA. Nine different peptides from the highly conserved regions of HCV NS5B protein were drawn which can be used as a peptide vaccine. The HCV NS5B phylogenetic tree shows the clusters of different genotypes and their evolutionary association.

Conclusions: In spite of a high mutation rate in HCV, the residues which are present in the catalytic pocket, sugar selection and template/primer interaction are highly conserved. These are target sites for the development of antiviral agents or peptide vaccines. The phylogenetic analysis suggests that different HCV genotypes have been evolved from the genotype 1a.

No MeSH data available.


Related in: MedlinePlus

Multiple Sequence Alignment of Consensus Sequences of the Genotypes 1 to 6 of the HCV Ns5b Protein Are Shown
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fig353: Multiple Sequence Alignment of Consensus Sequences of the Genotypes 1 to 6 of the HCV Ns5b Protein Are Shown

Mentions: We have drawn the HCV NS5B consensus sequence of each HCV genotype. All the consensus sequences were aligned to study the residues which were highly conserved among all the genotypes. Figure 1 shows the alignment of the consensus sequence of all the six HCV genotypes; the global consensus sequence is shown at the base. Conserved residues are shown with their corresponding symbols while the highly variable amino acids are denoted by “x” symbol. The alignment of all the consensus sequences will help us to study the highly conserved residues in the HCV NS5B protein. Short peptides of 9 to 18 amino acids were designed from the highly conserved regions of the HCV NS5B consensus protein sequences; the sequence and position of these peptides are shown in Table 1. These are the positions which are highly conserved and are the targets to design peptide vaccines or site specific inhibitors. A phylogenetic tree of 236 HCV NS5B sequences belonging to the all six genotypes reported from all over the world was constructed using the UPGMA method in CLC work bench software as shown in Figure 2. A default value of 100 was used in bootstrap analysis and the values are present at each branch. Sequences from different genotypes are clustered together. The tree shows that the different HCV genotypes have been evolved from the genotype 1a.


Development of Global Consensus Sequence and Analysis of Highly Conserved Domains of the HCV NS5B Prote in.

Waheed Y, Saeed U, Anjum S, Afzal MS, Ashraf M - Hepat Mon (2012)

Multiple Sequence Alignment of Consensus Sequences of the Genotypes 1 to 6 of the HCV Ns5b Protein Are Shown
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3475062&req=5

fig353: Multiple Sequence Alignment of Consensus Sequences of the Genotypes 1 to 6 of the HCV Ns5b Protein Are Shown
Mentions: We have drawn the HCV NS5B consensus sequence of each HCV genotype. All the consensus sequences were aligned to study the residues which were highly conserved among all the genotypes. Figure 1 shows the alignment of the consensus sequence of all the six HCV genotypes; the global consensus sequence is shown at the base. Conserved residues are shown with their corresponding symbols while the highly variable amino acids are denoted by “x” symbol. The alignment of all the consensus sequences will help us to study the highly conserved residues in the HCV NS5B protein. Short peptides of 9 to 18 amino acids were designed from the highly conserved regions of the HCV NS5B consensus protein sequences; the sequence and position of these peptides are shown in Table 1. These are the positions which are highly conserved and are the targets to design peptide vaccines or site specific inhibitors. A phylogenetic tree of 236 HCV NS5B sequences belonging to the all six genotypes reported from all over the world was constructed using the UPGMA method in CLC work bench software as shown in Figure 2. A default value of 100 was used in bootstrap analysis and the values are present at each branch. Sequences from different genotypes are clustered together. The tree shows that the different HCV genotypes have been evolved from the genotype 1a.

Bottom Line: Nine different peptides from the highly conserved regions of HCV NS5B protein were drawn which can be used as a peptide vaccine.In spite of a high mutation rate in HCV, the residues which are present in the catalytic pocket, sugar selection and template/primer interaction are highly conserved.These are target sites for the development of antiviral agents or peptide vaccines.

View Article: PubMed Central - PubMed

Affiliation: Atta-ur-Rehman School of Applied BioSciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan.

ABSTRACT

Background: Hepatitis C virus (HCV) is a plus stranded RNA virus which encodes 10 different genes. The HCV NS5B gene encodes a polymerase, which is responsible for the replication of the virus and is a potential target for the development of antiviral agents. HCV has a high mutation rate and is classified into six major genotypes.

Objectives: The aim of this study was to draw a representing consensus sequence of each HCV genotype, align all six consensus sequences to draw a global consensus sequence and also study the highly conserved residues.

Materials and methods: 236 HCV NS5B sequences, belonging to all six genotypes, reported from all over the world were aligned then a representing phylogenetic tree wasdrawn.

Results: The active site residues D220, D225, D318 and D319, which bind the divalent cations, are highly conserved among all the HCV genotypes. The other catalytic pocket residues, R158, S367, R386, and T390 and R394, which interact with the triphosphate of NTPs, are also highly conserved while T390 is mutated to valine in the genotype 5. The motif B residues G283, T286, T287 and N291, which take part in sugar selection by RdRp, are also highly conserved except for T286 which is mutated to proline in the genotypes 3 and 6. The residues E18, Y191, C274, Y276 and H502, which take part in primer/template interaction, are also high conserved except for H502 which is mutated to serine in genotype 2. High variation in all the six consensus sequences was observed in a 12 amino acid beta hairpin loop, which interacts with the double stranded RNA. Nine different peptides from the highly conserved regions of HCV NS5B protein were drawn which can be used as a peptide vaccine. The HCV NS5B phylogenetic tree shows the clusters of different genotypes and their evolutionary association.

Conclusions: In spite of a high mutation rate in HCV, the residues which are present in the catalytic pocket, sugar selection and template/primer interaction are highly conserved. These are target sites for the development of antiviral agents or peptide vaccines. The phylogenetic analysis suggests that different HCV genotypes have been evolved from the genotype 1a.

No MeSH data available.


Related in: MedlinePlus