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Phylogenetic prediction of cis-acting elements: a cre-like sequence in Norovirus genome?

Victoria M, Colina R, Miagostovich MP, Leite JP, Cristina J - BMC Res Notes (2009)

Bottom Line: These approaches have been successfully in predicting cis-acting signals in different members of the family Picornaviridae and Caliciviridae.A new predicted stem-loop has been identified near the 5' end of the RdRp of Human NoV genome.This is the same location recently reported for Hepatovirus cre stem-loop.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratório de Virologia Comparada e Ambiental, Instituto Oswaldo Cruz, FIOCRUZ, Av. Brasil 4365, Manguinhos, 21040-360 Rio deJaneiro, RJ, Brasil. matvicmon@yahoo.com

ABSTRACT

Background: Discrete RNA structures such as cis-acting replication elements (cre) in the coding region of RNA virus genomes create characteristic suppression of synonymous site variability (SSSV). Different phylogenetic methods have been developed to predict secondary structures in RNA viruses, for high-resolution thermodynamic scanning and for detecting SSSV. These approaches have been successfully in predicting cis-acting signals in different members of the family Picornaviridae and Caliciviridae. In order to gain insight into the identification of cis-acting signals in viruses whose mechanisms of replication are currently unknown, we performed a phylogenetic analysis of complete genome sequences from 49 Human Norovirus (NoV) strains.

Findings: The complete coding sequences of NoV ORF1 were obtained from the DDBJ database and aligned. Shannon entropy calculations and RNAalifold consensus RNA structure prediction identified a discrete, conserved, invariant sequence region with a characteristic AAACG cre motif at positions 240 through 291 of the RNA dependant RNA polymerase (RdRp) sequence (relative to strain [EMBL:EU794713]). This sequence region has a high probability to conform a stem-loop.

Conclusion: A new predicted stem-loop has been identified near the 5' end of the RdRp of Human NoV genome. This is the same location recently reported for Hepatovirus cre stem-loop.

No MeSH data available.


Related in: MedlinePlus

Shannon entrophy in ORF1 of Human NoV strains. The Shannon entropy at each position of the alignment is shown. Location of positions 3922 through 3973 of the alignment (which includes the AAACG motif) in a sequence region with zero entropy is shown by a red circle. A scheme showing the position of each gene in the NoV genome is shown below the graph. The location of the stem-loop is indicated sl.
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Figure 1: Shannon entrophy in ORF1 of Human NoV strains. The Shannon entropy at each position of the alignment is shown. Location of positions 3922 through 3973 of the alignment (which includes the AAACG motif) in a sequence region with zero entropy is shown by a red circle. A scheme showing the position of each gene in the NoV genome is shown below the graph. The location of the stem-loop is indicated sl.

Mentions: The complete codes of ORF1 of 49 Human NoV were obtained from the DDBJ database and aligned using the MUSCLE program [13] (for strain names and accession numbers see Additional File 1). Once aligned, the Shannon entropy at each position of the sequence dataset was calculated [14]. This permitted to measure the relative variation in each site of a sequence alignment. The results of these studies are shown in Fig. 1.


Phylogenetic prediction of cis-acting elements: a cre-like sequence in Norovirus genome?

Victoria M, Colina R, Miagostovich MP, Leite JP, Cristina J - BMC Res Notes (2009)

Shannon entrophy in ORF1 of Human NoV strains. The Shannon entropy at each position of the alignment is shown. Location of positions 3922 through 3973 of the alignment (which includes the AAACG motif) in a sequence region with zero entropy is shown by a red circle. A scheme showing the position of each gene in the NoV genome is shown below the graph. The location of the stem-loop is indicated sl.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2749865&req=5

Figure 1: Shannon entrophy in ORF1 of Human NoV strains. The Shannon entropy at each position of the alignment is shown. Location of positions 3922 through 3973 of the alignment (which includes the AAACG motif) in a sequence region with zero entropy is shown by a red circle. A scheme showing the position of each gene in the NoV genome is shown below the graph. The location of the stem-loop is indicated sl.
Mentions: The complete codes of ORF1 of 49 Human NoV were obtained from the DDBJ database and aligned using the MUSCLE program [13] (for strain names and accession numbers see Additional File 1). Once aligned, the Shannon entropy at each position of the sequence dataset was calculated [14]. This permitted to measure the relative variation in each site of a sequence alignment. The results of these studies are shown in Fig. 1.

Bottom Line: These approaches have been successfully in predicting cis-acting signals in different members of the family Picornaviridae and Caliciviridae.A new predicted stem-loop has been identified near the 5' end of the RdRp of Human NoV genome.This is the same location recently reported for Hepatovirus cre stem-loop.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratório de Virologia Comparada e Ambiental, Instituto Oswaldo Cruz, FIOCRUZ, Av. Brasil 4365, Manguinhos, 21040-360 Rio deJaneiro, RJ, Brasil. matvicmon@yahoo.com

ABSTRACT

Background: Discrete RNA structures such as cis-acting replication elements (cre) in the coding region of RNA virus genomes create characteristic suppression of synonymous site variability (SSSV). Different phylogenetic methods have been developed to predict secondary structures in RNA viruses, for high-resolution thermodynamic scanning and for detecting SSSV. These approaches have been successfully in predicting cis-acting signals in different members of the family Picornaviridae and Caliciviridae. In order to gain insight into the identification of cis-acting signals in viruses whose mechanisms of replication are currently unknown, we performed a phylogenetic analysis of complete genome sequences from 49 Human Norovirus (NoV) strains.

Findings: The complete coding sequences of NoV ORF1 were obtained from the DDBJ database and aligned. Shannon entropy calculations and RNAalifold consensus RNA structure prediction identified a discrete, conserved, invariant sequence region with a characteristic AAACG cre motif at positions 240 through 291 of the RNA dependant RNA polymerase (RdRp) sequence (relative to strain [EMBL:EU794713]). This sequence region has a high probability to conform a stem-loop.

Conclusion: A new predicted stem-loop has been identified near the 5' end of the RdRp of Human NoV genome. This is the same location recently reported for Hepatovirus cre stem-loop.

No MeSH data available.


Related in: MedlinePlus