mRNA:guanine-N 7 cap methyltransferases: identification of novel members of the family, evolutionary analysis, homology modeling, and analysis of sequence-structure-function relationships
© Bujnicki et al, licensee BioMed Central Ltd. 2001
Received: 21 May 2001
Accepted: 22 June 2001
Published: 22 June 2001
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.
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.
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.
Transcripts produced by RNA polymerase II are modified at their 5' end by the addition of a methylated 5'-terminal cap structure m7G(5')ppp(5')N, which directs pre-mRNA to the processing and transport pathways in the cell nucleus and regulates both mRNA turnover and the initiation of translation [1,2]. Cap is formed by a series of three enzymatic reactions as follows: an RNA triphosphatase (TPase) removes the γ-phosphate at the 5' end of the transcript, a GTP:RNA guanylyltransferase (GTase) adds a GMP residue to the 5' diphosphate end in a 5'-to-5' orientation, and an RNA:guanine-N7 (m7G) methyltransferase (cap 0 MTase, for simplicity referred to hereafter as cap MTase) adds the methyl group to the guanine . Mutations in the TPase, GTase, or cap MTase of the yeast capping apparatus that inhibit any of these activities are lethal in vivo [4,5,6]. The capping apparatus differs significantly in fungi, metazoans, protozoa and viruses in respect to the evolutionary origin and structure of individual subunits and the subunit composition of the proteins that carry the three activities . Hence, the capping enzymes encoded by viral, fungal and protozoal pathogens are attractive targets for specific inhibitors that would exert limited effect on the host enzyme.
The mechanisms and structures of cellular and viral capping enzymes have been extensively studied. The crystal structures of the GTase from Chlorella virus PBVCV-1  and the TPase from yeast  have been solved and used to guide extensive site-directed mutagenesis experiments [9,10,11]. However, there are a few important gaps in our understanding of capping enzymes. For instance, there is a large body of mutagenesis data on cap MTase [5,12,13,14,15,16]; however, its structure remains unknown. Therefore, many important details of the cap binding and m7G methyltransfer reaction mechanism remain unexplained.
Cap MTase belongs to the AdoMet-dependent MTase superfamily , which contains numerous remotely related families of DNA, RNA, protein, and small molecule-modifying enzymes . To date, three-dimensional structures have been determined for more than a dozen MTases. The common fold of the catalytic domain, which bears the AdoMet binding site and the active site, has been identified (reviewed in ). Despite low sequence similarity, the catalytic domains of typical MTases display a common tertiary architecture, similar to the Rossmann-fold, but with a unique peripheral β-hairpin structure instead of a typical right-handed β-α turn . Another characteristic feature of many MTase families is the presence of an additional "variable" domain, which is primarily responsible for substrate recognition and binding. This domain has been initially characterized in DNA:cytosine-C5 (m5C) MTases and dubbed TRD (for target recognition domain). More recently, it was determined that the majority of TRDs of individual MTase families are unrelated. They occur in different locations in the primary structure of the protein and fold into different structures, suggesting that they have originated from independent gene fusions (. Nevertheless, it has been shown that the TRDs of m5C MTases are structurally similar, even though only several common residues could be delineated in their sequences that are critical for stability of the hydrophobic core and interactions of the TRD with the substrate. Moreover, based on the sequence-to-structure threading, it has been predicted that the TRDs of type I DNA MTases (a subclass of enzymes that modify adenine in DNA) share the common fold with the TRD of m5C MTases . This prediction has been later supported by mutagenesis studies . Therefore, aside from the structural and evolutionary diversity among TRDs, some MTase families may share conserved homology in the catalytic and substrate binding domains, even though their sequences seem dissimilar.
The prolonged unavailability of the atomic structure of cap MTase prompted us to predict its structure and construct a three-dimensional model, which is accompanied by an evolutionary study. The results form this report should aid in the interpretation and design of mutagenesis experiments and provide a framework for comparative sequence-structure-function analysis of members of the MTase family. Cap MTases exhibited limited similarities to other MTases in the common AdoMet-binding region, and the substrate-binding site could not be unambiguously identified, based on sequence analysis and mutagenesis results . Therefore, we resorted to the sequence-to-structure threading method to find a structural template for homology modeling. We report here that cap MTases are related in structure to the glycine N-MTase. In addition, we carried out extensive database searches to identify novel genes that exhibit homology to known cap MTases, which may encode yet unidentified RNA modification enzymes.
Results and Discussion
The sequences of viral, cellular cap MTases and the newly identified subfamily of putative MTases from higher plants exhibited relatively high similarity in their N-terminus. However, after different substitution matrices, gap opening and extension penalties were used in both PSI-BLAST and CLUSTALX, their C-termini were found to align poorly, and we observed substantial variation in the multiple sequence alignment in this region. Therefore, even the construction of a global alignment, including known viral and cellular cap MTases, presented considerable challenges. Since the sequences within the subfamilies showed high similarity and could be aligned over their entire length, we resorted to profile-to-profile alignment using FFAS, which was proven superior to pairwise or sequence-to-profile alignments . The results revealed that all three subfamilies shared homology not only at the N-terminus, but also at several moderately conserved regions at the C-terminus, separated by regions of high variability. Remarkably, the pattern of the secondary structures predicted for individual subfamilies using JPRED agreed very well with the alignment reported by FFAS. For example, not only were the number and order of predicted helices and strands the same, but also aligned well, showing strong correlation with the aforementioned blocks of moderately conserved sequence (the final alignment is shown in Figure 1).
To improve the multiple sequence alignment and to provide a structural framework for the interpretation of experimental studies and phylogenetic analysis, we attempted to predict the tertiary structure of cap MTase using sequence-to-structure threading and homology modeling. The rationale behind this approach is that most of the alignment errors that are undetectable at the level of primary and secondary structure would manifest themselves in the model. They could be identified and corrected by computer software for the evaluation of tertiary structures, followed by the analysis of graphic representations with a trained eye. We submitted sequences of several members of each subfamily, as well as artificial "consensus" sequences that represented the individual subfamilies or the entire family to the MetaServer (http://bioinfo.pl/meta), which combines several programs for prediction of secondary structure, solvent accessibility and fold recognition (i.e. detection of the known structure) that are most compatible with the query sequence (see Materials and Methods). A similar strategy based on only one fold recognition algorithm was recently applied for analysis of heterotrimeric PCNA family members .
Sequence conservation and evolutionary relationships in the cap MTase family
Another peculiarity emerging from the alignment is the mosaic character of similarity of the new plant MTase family to viral and "orthodox" cellular enzymes. For instance, the "ENYM" patch (corresponding to aa 306-309 in ScABD1) is conserved in viral MTases and in the newly identified proteins, but absent from "orthodox" cellular enzymes, and the "PLFGXKY" patch (corresponding to aa 328-334 in ScABD1) is common to all cellular enzymes, but absent from viral MTases (Figure 1). It should be noted however that viral and "orthodox" cellular enzymes are mutually similar in many regions that are otherwise considerably diverged in the plant MTases, which suggest that the latter are more ancient. We could not predict with confidence a potential function for the subfamily of plant MTases. It is possible that they represent genuine cap MTases from the yet unidentified plant viruses or small nuclear RNA capping enzymes. Their function remains to be determined experimentally.
General features of the three-dimensional model of S. cerevisiae cap MTase
The N-terminal 139 residues and the C-terminal 12 residues of ScABD1 were not included in the model. The present C-terminus maps to the "back" of the cap MTase, while the N-terminus protrudes outside its AdoMet-binding/catalytic face. Shuman and coworkers carried out deletion mutagenesis of ScABD1 and reported that mutants lacking the 130 N-terminal residues or the 10 C-terminal residues were fully active, whereas the activity of a mutant lacking 143 N-terminal residues was reduced to ∼ 5% of that of the wild type ScABD1 . The GNMT template lacks the counterpart of the C-terminal 12 residues of ScABD1 . This region is not conserved among other AdoMet-dependent MTases , suggesting it is dispensable for the stability of the MTase core. A C-terminal deletion of 55 amino acids (residues 381-436) was lethal . According to our model this region encompasses the antiparallel β-strand that takes part in formation of the hydrophobic core and its loss would destabilize the MTase structure.
Structure-based analysis of site-directed mutagenesis results
Alanine scanning mutagenesis of the cofactor-binding region in S. cerevisiae and human cap MTases revealed that of all residues of the sequence patch 168-VLELGCGKGGDLRKY-182 (motif I) only E170, G174, and D178 are essential . The data for C. albicans suggest that the counterparts of L169 and L179 in ScABD1 (L204 and L214 in CaABD1) are also indispensable for both in vitro and in vivo activity of the enzyme. In ScABD1, L179 packs against the side chain of E170, while in CaABD1 L214 packs against the shorter side chain of D205, suggesting that the L214A substitution creates a larger cavity in the hydrophobic core of CaABD1 that may perturb the overall architecture of the AdoMet-binding site. The E170D mutant of ScABD1 was viable , suggesting that a carboxylate is essential at this position. Indeed, an acidic residue is present at this position in most AdoMet-dependent MTases . In the recently solved high-resolution structure of rRNA:2'-O-ribose MTase RrmJ, a D57 residue present at this position coordinates the nitrogen atom of AdoMet via an ordered water molecule . However, this carboxylate is replaced by Ala or Ser in cap MTases from all viruses except for ASFV (Figure 1). Notably, all viral MTases (again, except for ASFV) possess an Asp residue in the position corresponding to G172 in ScABD1. Modeling suggests that in viral MTases and in the ScABD1 double mutants E170A G172D, the carboxylate would make an equivalent, direct contact to the AdoMet moiety (data not shown), which suggests a textbook case of correlated mutations. This important difference between cellular and viral cap MTases may be utilized in rational drug design.
Alanine substitution of the other two residues in the AdoMet-binding region, i.e. D194 (in motif II) and R206 (in motif III) abrogates the enzyme's activity; however, conservative substitutions at these positions that allow retention of the charged functional groups are tolerated . According to our model, the carboxylate D194 directly coordinates the ribose oxygens while the role of R206 is less clear. It might participate in the binding of phosphate groups of the nascent RNA chain, for it forms part of a large basic patch at the protein surface (Figure 5). However, this hypothesis remains to be tested experimentally. Other polar residues that may be a part of this predicted binding patch include R147, N150, N151, K154, and Y155. All of these residues have been individually mutated to Ala without an observed loss of activity in vivo . It is conceivable that non-specific binding of mRNA depends on electrostatic interactions that are not dependent on the presence of the individual functional groups in the protein. It would be interesting to test if such simultaneous mutagenesis of the above residues can significantly lower the affinity of the protein to the mRNA substrate. Another group of non-essential residues includes E202, Y207, R208, Y215, and D223. They are not universally conserved in the cap MTase family and are localized in the variable edge region of the Rossmann-fold-like AdoMet-binding subdomain. In our model, only D223 is predicted to form a contact with the adenine ring of the AdoMet moiety. It would be interesting to test if the in vitro AdoMet-binding activity of cap MTase is influenced by the D223A mutation.
Alanine scanning mutagenesis identified only three residues in the central and C-terminal part of ScABD1 that are essential for catalysis [5,16]. In our model Y254 is buried in a hydrophobic core and F256 stacks with the adenine ring of AdoMet in a manner similar to W117 in the GNMT structure , which explains why hydrophobic residues at these positions are required for the cap MTase activity. According to our model, Y330 is located in the lid subdomain where it forms the external wall of the "molecular basket". A bulky hydrophobic residue is present at this position in all cap MTases (Figure 1).
Among the residues from the central and C-terminal part of ScABD1 that were found to be nonessential [5,13,16], D244, G276, G277, E287, E361, Y362, G363, L366, V367, and K423 are not located at the protein surface near any of the predicted binding sites, and their substitution should not influence the structure or function of cap MTase. Residues T282, P284, W305, and Y416 form a cluster at the surface of the catalytic domain near the entrance to the "molecular basket" where the substrate might bind. However, it is not apparent from the modeled structure alone if they can take part in catalysis or binding; therefore, their localization in the model is not inconsistent with the experimental data. W383, E385, E408, and E410 map to the loop between the C-terminal β-strands, which has not been included in the present model because its structure could not be predicted with confidence. On the other hand, F279, F419, and F421 are in the hydrophobic core of the catalytic domain. Y348, V349, and V350 form part of an interface between the "lid" subdomain and the catalytic domain, and F314 is located in the lid subdomain on the inside of the "molecular basket". No straightforward explanation is offered by the current model to rationalize why substitutions of conserved residues at these important locations do not have any influence on ScABD1 activity in vivo. It is possible that introducing cavities at these positions in the protein core may slightly destabilize the structure but not disrupt the overall fold, which allows cap MTase to retain its activity. We suggest that introducing polar or charged side chains at these positions (for instance Arg) should disrupt the protein core and render the enzyme inactive.
Structure-based prediction of guanine-binding residues
In GNMT, the additional "S" domain, composed of a three-stranded β-sheet, forms the wall of a large "molecular basket" structure, which may accommodate a variety of small molecules, including AdoMet, tetrahydrofolate and polycyclic aromatic hydrocarbon molecules, such as benzopyrene (reviewed in ). According to the secondary structure prediction and threading algorithms, cap MTases also possess a similar structure that is a good candidate for a target-binding site. Therefore, we looked for conserved residues that could correspond to the guanine-binding site at the inner walls of the "molecular basket" of the cap MTase model. To our knowledge, all structurally characterized MTases, which modify bases in nucleic acids and do not employ covalent bond formation with the target, use aromatic or aliphatic side chains to bind the base to be methylated via hydrophobic interactions with the heterocycle for stabilization in the active site. Examples of such MTases, for which the structure of the active site was determined experimentally or predicted from sequence analysis, include enzymes generating N6-methyladenine in DNA and RNA (reviewed in ), N4-methylcytosine in DNA , and N2-guanine in RNA . On the other hand, various polar residues could be implicated in specific contacts to the hydrophilic edge of the base as it has been proposed for DNA amino-MTases .
We have identified several conserved residues that localize to the inner surface of the "basket", which have not yet been tested whether they are important for the catalytic activity of ScABD1. They include the invariant Asn residue (N307 in ScABD1), which may hydrogen bond to the O6 atom, the N2 amino group of the target guanine and the aromatic residue (Y310 in ScABD1), which could be involved in stacking interactions with the aromatic heterocycle. The aromatic residue is present at this position only in proteins from entomopoxviruses and in "orthodox" cellular enzymes (Figure 1), except for the protein from C. elegans, which is substituted by a Cys residue that is quite big and hydrophobic and may be involved in van der Waals interactions with the target guanine. Interestingly, in all sequences from viruses (except for ASFV) and in putative proteins from higher plants, a Tyr residue is present at the position corresponding to S308 in ScABD1. Modeling of viral MTases and in silico mutagenesis of ScABD1 suggests that aromatic residues located in these two alternative positions could have their side chains oriented in a similar manner (data not shown), arguing for a similar case of correlated mutations as described previously for a carboxylate residue involved in AdoMet binding (see above).
We considered several candidates for the possible second aromatic residue localized in the vicinity of the conserved N307, and the methyl group of AdoMet. F250A, W305A, and Y416A mutants were shown to be functional in vivo . However, it would be interesting to test whether mutations at these positions influence binding of the substrate in vitro. F149 in ScABD1, which has not been analyzed by mutagenesis, is located further away from the predicted substrate-binding site (7.5 Å from N307) and is conserved only in cellular proteins. Nevertheless, the conformation of the N-terminus of the template GNMT structure changes between the closed and open forms of the protein . As we proposed (see above), the corresponding region may be mobile also in the ScABD1 structure, thus F149 could be relocated upon target binding. It cannot be ruled out that the mechanism of cap binding by cap 0 MTases is different from that of cap 1 MTase from vaccinia virus , or that target base binding by nucleic acid amino-MTases does not necessarily employ stacking of the guanine base between two aromatic sidechains. Another possibility remains that the side chains involved in guanine binding are poorly conserved between the subfamilies, or the corresponding alanine mutants retain their function in vivo  and a more sensitive approach is required to analyze the influence of mutations on the efficiency of catalysis.
In this report, we used computational methods to infer the evolutionary relationships and predict the structure of cap MTase. A tertiary model has been built for the Eukaryotic enzyme and used to interpret the available mutation data and guide the comparative sequence analysis. We propose that cap MTases share the catalytic domain and the "S" domain with glycine N-MTases, which raises the possibility that these two families of N-MTases are relatively closely related. Moreover, we have identified a novel family of putative MTases that are specific to green plants and share structure and mechanism with cap MTases. Therefore, the alignment presented in this work will be a good starting point for further analysis of other N-MTase subfamilies that may share the "molecular basket" structure. Our analysis of the AdoMet-binding site in cap MTases, combined with evolutionary considerations, highlighted a case of correlated mutation in viral enzymes, which may be important for design of specific antivirals. We also used the model to predict the guanine binding site and identify conserved residues that may serve catalytic or structural function, which can be tested by site-directed mutagenesis. A putative non-specific mRNA binding patch was also proposed. Prior to the experimental solution of the structure of cap MTase, our model will be useful in designing new experiments to better understand the molecular function of cap MTases, whereas the identification of a novel family of genes will aid in identifying candidates for cloning and biochemical characterization. We hope that the prediction of numerous structural and functional features presented in this paper will advance these studies.
Materials and Methods
PSI-BLAST  and FFAS  algorithms were used to search the non-redundant version of current sequence databases (nr) and the publicly available complete and incomplete genome sequences via the Gene Relational DataBase (GRDB) (http://grdb.bioinfo.pl). The EST (expressed sequence tag), STS (sequence-tagged site), HTG (high throughput genomic) and GSS (genome survey sequence) divisions of the GenBank database  were searched at NCBI (http://www.ncbi.nlm.nih.gov/) using TBLASTN . Fragments of sequences were assembled into partial ORFs using the sequences of genuine cap MTases as guides; the predicted splicing sites were verified in reciprocal BLAST searches against the database comprising sequences of cap MTase homologs. All sequences were subsequently realigned using the CLUSTALX program  to the degapped profiles obtained from the multiple sequence alignments reported by BLAST. Manual adjustments were introduced based on the BLAST pairwise comparison, secondary structure prediction, threading results, and finally, superposition of modeled structures (see below).
The number of amino acid replacements per sequence position in the alignment was estimated using the JTT  model. The sampling variance of the distance values was estimated from 1000 bootstrap resamplings of the alignment columns. The evolutionary inference was performed according to the neighbor-joining method of Saitou and Nei . Multiple runs were conducted with randomized sequence input order to avoid the tree being caught in a local statistical minimum.
In search for structurally characterized homologs of cap MTase we used the MetaServer available at http://bioinfo.pl/meta/ , which uses fold recognition methods such as FFAS , 3DPSSM , BIOINBGU , GenThreader , SAM-T99 , FUGUE (http://www-cryst.bioc.cam.ac.uk/~fugue/), and 123D+ . These methods "thread" the query sequence (the target) onto every fold in libraries of structures (templates) and return 10 alignments that scored best according to the criterion of compatibility, which is specific for a given algorithm. The results are collected by the MetaServer and submitted to the Pcons neural network (J.Lundstrom, L.Rychlewski, J.M.Bujnicki, and A.Eloffson, manuscript submitted), which compares the models and the associated scores and produces a ranking of potentially best predictions. Pcons differs from other "consensus" methods since it predicts the quality of a model and not simply if a correct fold is recognized or not. This is especially advantageous in cases where several alternative folds are reported or if the correct fold is reported by most servers, but the alignments differ, or if one needs to choose the best template from several similar structures. In addition to prediction of the three-dimensional fold, the MetaServer displays the independently predicted secondary structure according to PSIPRED , SAM -T99 , and JPRED , with the latter server reporting also the predicted solvent accessibility profile. These predictions were compared with secondary structures and solvent accessibility calculated directly from the threading-based models of cap MTases.
Homology modeling was carried out following a modified version of the "multiple models" approach . Using the SWISS-MODEL/PROMOD II server  and the GROMOS forcefield for energy minimization  we generated a set of preliminary models based on threading-derived pairwise target-template alignments obtained from the MetaServer. The preliminary models were then superimposed using SWISS-PDB VIEWER  and the best fragments were merged into the final structure. The choice of fragments was based on the evaluation of their stereochemical and energetic parameters by WHATCHECK  and PROSA II software embedded within PROMOD II , consensus between the individual methods, agreement with the independently predicted pattern of secondary structures and solvent accessibility (see above).
We would like to thank Frank King for critical reading of the manuscript. This work was supported by KBN (grant 8T11F01019 to J.M.B.) and BioInfoBank. Coordinates of the model have been deposited in the Protein Data Bank with entry code 1IC3.
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