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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

"Mountain plot" of a NoV ORF1 sequence region with an entrophy equals to zero. A mountain plot representing a secondary structure in a plot of height versus position is shown. Sequences from positions 3922 through 3973 of the alignment are shown at the bottom of the figure. Numbers at the top of the figure show site position in the alignment. Colors correspond to the Vienna RNA conservation coloring schema [16] (see also Fig. 3). Note that the AAACG motif (underlined in red) is predicted to be located in a loop of the secondary structure.
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Figure 2: "Mountain plot" of a NoV ORF1 sequence region with an entrophy equals to zero. A mountain plot representing a secondary structure in a plot of height versus position is shown. Sequences from positions 3922 through 3973 of the alignment are shown at the bottom of the figure. Numbers at the top of the figure show site position in the alignment. Colors correspond to the Vienna RNA conservation coloring schema [16] (see also Fig. 3). Note that the AAACG motif (underlined in red) is predicted to be located in a loop of the secondary structure.

Mentions: In order to observe if this cre motif is situated in a sequence region that has a high probability to conform a secondary structure [8,15], we used the RNAalifold Web Server [16]. First, we obtained a graphical representation of the secondary structure in a plot of height versus position, where the height m(k) is given by the number of base pairs enclosing the base at position k in the structure (i.e. loops correspond to plateaus, hairpin loops are peaks and helices to slopes). The results of these studies are shown in Fig. 2. The AAACG cre sequence motif is embedded in a sequence region with a very high probability to conform a stem-loop structure (see Fig. 2).


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)

"Mountain plot" of a NoV ORF1 sequence region with an entrophy equals to zero. A mountain plot representing a secondary structure in a plot of height versus position is shown. Sequences from positions 3922 through 3973 of the alignment are shown at the bottom of the figure. Numbers at the top of the figure show site position in the alignment. Colors correspond to the Vienna RNA conservation coloring schema [16] (see also Fig. 3). Note that the AAACG motif (underlined in red) is predicted to be located in a loop of the secondary structure.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: "Mountain plot" of a NoV ORF1 sequence region with an entrophy equals to zero. A mountain plot representing a secondary structure in a plot of height versus position is shown. Sequences from positions 3922 through 3973 of the alignment are shown at the bottom of the figure. Numbers at the top of the figure show site position in the alignment. Colors correspond to the Vienna RNA conservation coloring schema [16] (see also Fig. 3). Note that the AAACG motif (underlined in red) is predicted to be located in a loop of the secondary structure.
Mentions: In order to observe if this cre motif is situated in a sequence region that has a high probability to conform a secondary structure [8,15], we used the RNAalifold Web Server [16]. First, we obtained a graphical representation of the secondary structure in a plot of height versus position, where the height m(k) is given by the number of base pairs enclosing the base at position k in the structure (i.e. loops correspond to plateaus, hairpin loops are peaks and helices to slopes). The results of these studies are shown in Fig. 2. The AAACG cre sequence motif is embedded in a sequence region with a very high probability to conform a stem-loop structure (see Fig. 2).

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