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mRNA:guanine-N7 cap methyltransferases: identification of novel members of the family, evolutionary analysis, homology modeling, and analysis of sequence-structure-function relationships.

Bujnicki JM, Feder M, Radlinska M, Rychlewski L - BMC Bioinformatics (2001)

Bottom Line: There is a large body of experimental data on viral and cellular methyltransferases (MTases) that carry out guanine-N7 (cap 0) methylation, including results of extensive mutagenesis.Computational methods were used to infer the evolutionary relationships and predict the structure of Eukaryotic cap MTase.Identification of novel cap MTase homologs suggests candidates for cloning and biochemical characterization, while the structural model will be useful in designing new experiments to better understand the molecular function of cap MTases.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bioinformatics Laboratory, International Institute of Cell and Molecular Biology, ul, ks, Trojdena 4, 02-109 Warsaw, Poland. iamb@bioinfo.pl

ABSTRACT

Background: The 5'-terminal cap structure plays an important role in many aspects of mRNA metabolism. Capping enzymes encoded by viruses and pathogenic fungi are attractive targets for specific inhibitors. There is a large body of experimental data on viral and cellular methyltransferases (MTases) that carry out guanine-N7 (cap 0) methylation, including results of extensive mutagenesis. However, a crystal structure is not available and cap 0 MTases are too diverged from other MTases of known structure to allow straightforward homology-based interpretation of these data.

Results: We report a 3D model of cap 0 MTase, developed using sequence-to-structure threading and comparative modeling based on coordinates of the glycine N-methyltransferase. Analysis of the predicted structural features in the phylogenetic context of the cap 0 MTase family allows us to rationalize most of the experimental data available and to propose potential binding sites. We identified a case of correlated mutations in the cofactor-binding site of viral MTases that may be important for the rational drug design. Furthermore, database searches and phylogenetic analysis revealed a novel subfamily of hypothetical MTases from plants, distinct from "orthodox" cap 0 MTases.

Conclusions: Computational methods were used to infer the evolutionary relationships and predict the structure of Eukaryotic cap MTase. Identification of novel cap MTase homologs suggests candidates for cloning and biochemical characterization, while the structural model will be useful in designing new experiments to better understand the molecular function of cap MTases.

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The phylogenetic tree of the cap MTase family. The numbers at the nodes indicate the statistical support of the branching order by the bootstrap criterion. The nodes with bootstrap support < 50% are shown as unresolved. The bar at the bottom of the phylogram indicates the evolutionary distance, to which the branch lengths are scaled based on the estimated divergence.
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Figure 3: The phylogenetic tree of the cap MTase family. The numbers at the nodes indicate the statistical support of the branching order by the bootstrap criterion. The nodes with bootstrap support < 50% are shown as unresolved. The bar at the bottom of the phylogram indicates the evolutionary distance, to which the branch lengths are scaled based on the estimated divergence.

Mentions: Analysis of the multiple sequence alignment revealed amino acid residues that are conserved among all or most of the individual family members as well as some differences between the three subfamilies (Figure 1). Together with the unrooted phylogenetic tree, which was calculated from this alignment (Figure 3), these results demonstrate that viral and cellular cap MTases and the newly identified proteins from green plants originate from three phylogenetically distinct lineages. It should be noted that sequences obtained from preliminary data and cDNA clones may contain errors that can influence the outcome of the comparative analysis. The fact that several sequences are truncated could have affected the calculated phylogenetic distances (i.e. the length of the branches). For instance, an elongated C-terminus of putative MTase from Giardia intestinalis (low-pass HTG sequence MJ2197) may be an artifact, for it shows little similarity to yeast MTases and could not be unambiguously threaded onto the GNMT structure. However, we believe that the predicted topology of the branching pattern is correct because it remained unchanged after the incomplete or preliminary sequences were removed. The topology is also strongly supported by bootstrap analysis, and the phylogenetic groups correlate well with the presence of sequence signatures that can be regarded as synapomorphies (shared features derived from a common ancestor). For instance, the MTases from yeast possess a unique insertion close to the C-terminus.


mRNA:guanine-N7 cap methyltransferases: identification of novel members of the family, evolutionary analysis, homology modeling, and analysis of sequence-structure-function relationships.

Bujnicki JM, Feder M, Radlinska M, Rychlewski L - BMC Bioinformatics (2001)

The phylogenetic tree of the cap MTase family. The numbers at the nodes indicate the statistical support of the branching order by the bootstrap criterion. The nodes with bootstrap support < 50% are shown as unresolved. The bar at the bottom of the phylogram indicates the evolutionary distance, to which the branch lengths are scaled based on the estimated divergence.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC35267&req=5

Figure 3: The phylogenetic tree of the cap MTase family. The numbers at the nodes indicate the statistical support of the branching order by the bootstrap criterion. The nodes with bootstrap support < 50% are shown as unresolved. The bar at the bottom of the phylogram indicates the evolutionary distance, to which the branch lengths are scaled based on the estimated divergence.
Mentions: Analysis of the multiple sequence alignment revealed amino acid residues that are conserved among all or most of the individual family members as well as some differences between the three subfamilies (Figure 1). Together with the unrooted phylogenetic tree, which was calculated from this alignment (Figure 3), these results demonstrate that viral and cellular cap MTases and the newly identified proteins from green plants originate from three phylogenetically distinct lineages. It should be noted that sequences obtained from preliminary data and cDNA clones may contain errors that can influence the outcome of the comparative analysis. The fact that several sequences are truncated could have affected the calculated phylogenetic distances (i.e. the length of the branches). For instance, an elongated C-terminus of putative MTase from Giardia intestinalis (low-pass HTG sequence MJ2197) may be an artifact, for it shows little similarity to yeast MTases and could not be unambiguously threaded onto the GNMT structure. However, we believe that the predicted topology of the branching pattern is correct because it remained unchanged after the incomplete or preliminary sequences were removed. The topology is also strongly supported by bootstrap analysis, and the phylogenetic groups correlate well with the presence of sequence signatures that can be regarded as synapomorphies (shared features derived from a common ancestor). For instance, the MTases from yeast possess a unique insertion close to the C-terminus.

Bottom Line: There is a large body of experimental data on viral and cellular methyltransferases (MTases) that carry out guanine-N7 (cap 0) methylation, including results of extensive mutagenesis.Computational methods were used to infer the evolutionary relationships and predict the structure of Eukaryotic cap MTase.Identification of novel cap MTase homologs suggests candidates for cloning and biochemical characterization, while the structural model will be useful in designing new experiments to better understand the molecular function of cap MTases.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bioinformatics Laboratory, International Institute of Cell and Molecular Biology, ul, ks, Trojdena 4, 02-109 Warsaw, Poland. iamb@bioinfo.pl

ABSTRACT

Background: The 5'-terminal cap structure plays an important role in many aspects of mRNA metabolism. Capping enzymes encoded by viruses and pathogenic fungi are attractive targets for specific inhibitors. There is a large body of experimental data on viral and cellular methyltransferases (MTases) that carry out guanine-N7 (cap 0) methylation, including results of extensive mutagenesis. However, a crystal structure is not available and cap 0 MTases are too diverged from other MTases of known structure to allow straightforward homology-based interpretation of these data.

Results: We report a 3D model of cap 0 MTase, developed using sequence-to-structure threading and comparative modeling based on coordinates of the glycine N-methyltransferase. Analysis of the predicted structural features in the phylogenetic context of the cap 0 MTase family allows us to rationalize most of the experimental data available and to propose potential binding sites. We identified a case of correlated mutations in the cofactor-binding site of viral MTases that may be important for the rational drug design. Furthermore, database searches and phylogenetic analysis revealed a novel subfamily of hypothetical MTases from plants, distinct from "orthodox" cap 0 MTases.

Conclusions: Computational methods were used to infer the evolutionary relationships and predict the structure of Eukaryotic cap MTase. Identification of novel cap MTase homologs suggests candidates for cloning and biochemical characterization, while the structural model will be useful in designing new experiments to better understand the molecular function of cap MTases.

Show MeSH
Related in: MedlinePlus