Two tools for applying chromatographic retention data to the mass-based identification of peptides during hydrogen/deuterium exchange experiments by nano-liquid chromatography/matrix-assisted laser desorption/ionization mass spectrometry.

Two tools are described for integrating LC elution position with mass-based data in hydrogen-deuterium exchange (HDX) experiments by nano-liquid chromatography/matrix-assisted laser desorption/ionization mass spectrometry (nanoLC/MALDI-MS, a novel approach to HDX-MS). The first of these, 'TOF2H-Z Comparator', highlights peptides in HDX experiments that are potentially misidentified on the basis of mass alone. The program first calculates normalized values for the organic solvent concentration responsible for the elution of ions in nanoLC/MALDI HDX experiments. It then allows the solvent gradients for the multiple experiments contributing to an MS/MS-confirmed peptic peptide library to be brought into mutual alignment by iteratively re-modeling variables among LC parameters such as gradient shape, solvent species, fraction duration and LC dead time. Finally, using the program, high-probability chromatographic outliers can be flagged within HDX experimental data. The role of the second tool, 'TOF2H-XIC Comparator', is to normalize the LC chromatograms corresponding to all deuteration timepoints of all HDX experiments of a project, to a common reference. Accurate normalization facilitates the verification of chromatographic consistency between all ions whose spectral segments contribute to particular deuterium uptake plots. Gradient normalization in this manner revealed chromatographic inconsistencies between ions whose masses were either indistinguishable or separated by precise isotopic increments.

pKa of the mRNA cap-specific 2'-O-methyltransferase catalytic lysine by HSQC NMR detection of a two-carbon probe.

We have characterized the side chain pKa for a single lysine analogue within a 316-residue protein containing 21 lysines and 1678 carbon atoms at natural isotope abundance. To do this, the single reactive cysteine of a K175C mutant of VP39 (the mRNA cap-specific 2'-O-methyltransferase from vaccinia virus) was modified to S-(beta-aminoethyl)cysteine (gamma-thialysine) using freshly prepared (13C)aziridine at room temperature. Modification was accompanied by the rescue of catalytic function at high specific activity. After the fastidious removal of the noncovalently protein-bound aziridine self-polymer using a novel chelating dialysis procedure, signals were monitored by HSQC NMR. Appropriately pH-shifting HSQC NMR peaks were identified in the (13C)aziridine-modified enzyme, corresponding to detection of the two covalently attached (13C)thioethylamino atoms. The identification was strengthened by comparison with the positions and pH shifts of spectral peaks for tripeptide controls, a small molecule aziridine self-polymer mimetic, and a cysteine-minus control enzyme. pH titration of the modified protein indicated an apparent pKa of 8.5, consistent with a perturbed pKa for the catalytic lysine and a model in which the surrounding charged groups direct the lysine epsilon-amino pKa via both local electrostatic environment and orbital directionality.

Structural basis for sequence-nonspecific recognition of 5'-capped mRNA by a cap-modifying enzyme.

Sequence-nonspecific binding of RNA, recognition of a 7-methylguanosine 5' mRNA cap, and methylation of a nucleic acid backbone are three crucial and ubiquitous events in eukaryotic nucleic acid processing and function. These three events occur concurrently in the modification of vaccinia transcripts by the methyltransferase VP39. We report the crystal structure of a ternary complex comprising VP39, coenzyme product S-adenosylhomocysteine, and a 5' m7 G-capped, single-stranded RNA hexamer. This structure reveals a novel and general mechanism for sequence-non-specific recognition of the mRNA transcript in which the protein interacts solely with the sugar-phosphate backbone of a short, single-stranded RNA helix. This report represents the first direct and detailed view of a protein complexed with single-stranded RNA or 5'-capped mRNA.

Recognition of capped RNA substrates by VP39, the vaccinia virus-encoded mRNA cap-specific 2'-O-methyltransferase.

We have investigated the interaction of VP39, the vaccinia-encoded mRNA cap-specific 2'-O-methyltransferase, with its capped RNA substrate. Two sites on the protein surface, responsible for binding the terminal cap nucleotide (m7G) and cap-proximal RNA, were characterized, and a third (downstream RNA binding) site was identified. Regarding the crystallographically defined m7G binding pocket, VP39 showed significant activity with adenine-capped RNA. Although VP39 mutants lacking specific m7G-contact side chains within the pocket showed reduced catalytic activity, none was transformed into a cap-independent RNA methyltransferase. Moreover, each retained a preference for m7G and A over unmethylated G as the terminal cap nucleotide, indicating a redundancy of m7G-contact residues able to confer cap-type specificity. Despite containing the 2'-O-methylation site, m7GpppG (cap dinucleotide) could not be methylated by VP39, but m7GpppGUbiotinp could. This indicated the minimum-length 2'-O-methyltransferase substrate to be either m7GpppGp, m7GpppGpN, or m7GpppGpNp. RNA-protein contacts immediately downstream of the m7GpppG moiety were found to be pH-sensitive. This was detectable only in the context of a weakened interaction of near-minimum-length substrates with VP39's m7G binding pocket (through the use of either adenine-capped substrate or a VP39 pocket mutant), as a dramatic elevation of KM at pH values above 7.5. KM values for substrates with RNA chain lengths of 2-6 nt were between 160 and 230 nM, but dropped to 9-15 nM upon increasing chain lengths to 20-50 nt. This suggested the binding of regions of the RNA substrate >6 nt from the 5' terminus to a previously unknown site on the VP39 surface.

Cap ribose methylation of c-mos mRNA stimulates translation and oocyte maturation in Xenopus laevis.

In Xenopus oocytes, progesterone stimulates the cytoplasmic polyadenylation and resulting translational activation of c-mos mRNA, which is necessary for the induction of oocyte maturation. Although details of the biochemistry of polyadenylation are beginning to emerge, the mechanism by which 3' poly(A) addition stimulates translation initiation is enigmatic. A previous report showed that polyadenylation induced cap-specific 2'-O-methylation, and suggested that this 5' end modification was important for translational activation. Here, we demonstrate that injected c-mos RNA undergoes polyadenylation and cap ribose methylation. Inhibition of this methylation by S-isobutylthioadenosine (SIBA), a methyltransferase inhibitor, has little effect on progesterone-induced c-mos mRNA polyadenylation or general protein synthesis, but prevents the synthesis of Mos protein as well as oocyte maturation. Maturation can be rescued, however, by the injection of factors that act downstream of Mos, such as cyclin A and B mRNAs. Most importantly, we show that the translational efficiency of injected mRNAs containing cap-specific 2'-O-methylation (cap I) is significantly enhanced compared to RNAs that do not contain the methylated ribose (cap 0). These results suggest that cap ribose methylation of c-mos mRNA is important for translational recruitment and for the progression of oocytes through meiosis.

The 1.85 A structure of vaccinia protein VP39: a bifunctional enzyme that participates in the modification of both mRNA ends.

VP39 is a bifunctional vaccinia virus protein that acts as both an mRNA cap-specific RNA 2'-O-methyltransferase and a poly(A) polymerase processivity factor. Here, we report the 1.85 A crystal structure of a VP39 variant complexed with its AdoMet cofactor. VP39 comprises a single core domain with structural similarity to the catalytic domains of other methyltransferases. Surface features and mutagenesis data suggest two possible RNA-binding sites with novel underlying architecture, one of which forms a cleft spanning the region adjacent to the methyltransferase active site. This report provides a prototypic structure for an RNA methyltransferase, a protein that interacts with the mRNA 5' cap, and an intact poxvirus protein.

Sequence analysis of HindIII Q2 fragment of capripoxvirus reveals a putative gene encoding a G-protein-coupled chemokine receptor homologue.

The DNA sequence of the HindIII Q2 fragment near the left terminus of the capripoxvirus (KS-1 strain) genome was determined. The sequence contains two complete open reading frames (ORFs) and a part of a third. Analysis of the deduced amino acid sequence of one of these ORFs, Q2/3L, revealed that this gene has the capacity to encode a protein which is related to members of the G-protein coupled chemokine receptor subfamily, the swinepoxvirus K2R and the human cytomegalovirus US28 ORFs. It has the key structural characteristics of the G-protein-coupled receptor superfamily, e.g., seven hydrophobic regions, predicted to span the cell membrane, and the cysteine residues in the first and second extracellular loops that are implicated in formation of a disulfide bond. Southern blot analysis showed that all three species of the Capripoxvirus genus, i.e., sheep pox, goat pox, and lumpy skin disease of cattle, contain copies of this putative G-protein-coupled chemokine receptor homologue.

Mutational analysis of a multifunctional protein, with mRNA 5' cap-specific (nucleoside-2'-O-)-methyltransferase and 3'-adenylyltransferase stimulatory activities, encoded by vaccinia virus.

The vaccinia virus-encoded protein VP39 is a poly(A) polymerase subunit that stimulates the formation of long poly(A) tails as well as a cap-specific mRNA (nucleoside-2'-O-)-methyltransferase. We have carried out mutagenesis studies aimed at locating regions of VP39 which are important for these activities. The open reading frame encoding VP39 was expressed in Escherichia coli as a glutathione S-transferase fusion protein. The affinity-purified protein had both mRNA modification activities, before and after removal of the glutathione S-transferase domain. Truncation, charge cluster-->Ala scanning, and Cys-->Ser substitution mutations of VP39 were made, and the proteins were synthesized, purified, and analyzed. Deletion of the RNA binding domain, experimentally localized within the carboxyl-terminal 112 amino acids, resulted in the loss of both mRNA modification activities. Eleven of the 21 charge cluster-->Ala mutated proteins had low to nondetectable methyltransferase activity. Four of those 11 also lacked adenylyl-transferase stimulatory function, whereas the remainder had amino acid substitutions that selectively affected methyltransferase activity. However, no mutated proteins lacking adenylyltransferase stimulatory function but possessing methyltransferase activity were isolated by the procedures used. Neither of the 2 cysteine residues in VP39 was necessary for either mRNA modification activity.

RNA polymerase-associated protein Rap94 confers promoter specificity for initiating transcription of vaccinia virus early stage genes.

The association of a 94,000-Da viral polypeptide, called Rap94, with 30-40% of the multisubunit DNA-dependent RNA polymerase molecules purified from infectious vaccinia virus particles was established by immunoaffinity chromatography. The submolar amount of Rap94, relative to RNA polymerase, was confirmed by quantitative immunoblotting of total virion extracts. Only the RNA polymerase molecules containing Rap94 could functionally interact with VETF, the vaccinia virus early transcription factor, to transcribe a double-stranded DNA template regulated by a viral early stage promoter. Rap94 was required for the synthesis of short oligoribonucleotides and for the formation of stable ternary transcription complexes. With a nonspecific single-stranded DNA template, however, the Rap94-deficient polymerase had greater catalytic activity than the Rap94-containing polymerase. These data support a model in which Rap94 confers specificity to the RNA polymerase for promoters of early stage genes.

Single capripoxvirus recombinant vaccine for the protection of cattle against rinderpest and lumpy skin disease.

A recombinant capripoxvirus has been constructed containing a full-length cDNA of the fusion protein gene of rinderpest virus. The gene was inserted in the thymidine kinase gene of the capripox genome under the control of the vaccinia virus major late promoter p11 together with the Escherichia coli gpt gene in the opposite orientation under the control of the vaccinia early/late promoter p7.5. A vaccine prepared from this recombinant virus protected cattle against clinical rinderpest after a lethal challenge with a virulent virus isolate. In addition, the vaccine protected the cattle against lumpy skin disease.

Transition from rapid processive to slow nonprocessive polyadenylation by vaccinia virus poly(A) polymerase catalytic subunit is regulated by the net length of the poly(A) tail.

The mRNA of vaccinia virus, like that of eukaryotes, possesses a poly(A) tail. VP55, the catalytic subunit of the heterodimeric vaccinia virus poly(A) polymerase, was overexpressed and purified to near homogeneity. VP55 polyadenylated a 30-mer primer representing the 3' end of a vaccinia virus mRNA bimodally: 30-35 adenylates were added in a rapid, processive, initial burst, after which polyadenylation decelerated dramatically and became nonprocessive. Polyadenylation of variants of the 30-mer primer, which contained preformed 3'-oligo(A) extensions, showed that the transition between the two modes of polyadenylation was regulated by the net length of the 3'-oligo(A) tail rather than the number of adenylate additions catalyzed by VP55. Primers comprising oligo(A) alone were polyadenylated only if they were greater than 34 nucleotides in length and, then, only in the slow nonprocessive mode. These data support a dynamic model whereby the mode of polyadenylation by VP55 is regulated by sequences within the 3' 30-35 nucleotides of the mRNA: Polyadenylation is rapid and processive until a net 3'-oligo(A) length of 30-35 nucleotides is achieved. Consistent with this, excess oligo(A) did not compete with the 30-mer primer for rapid processive polyadenylation. The primer specificity of VP55 may contribute to the selective polyadenylation of newly formed mRNA.

Cap-specific mRNA (nucleoside-O2'-)-methyltransferase and poly(A) polymerase stimulatory activities of vaccinia virus are mediated by a single protein.

The vaccinia virus gene for S-adenosyl-L-methionine:mRNA (nucleoside-O2'-)-methyltransferase, an enzyme required for the formation of the 5' cap structure of mRNA, was identified. Protein sequence analysis revealed that this cap-specific methyltransferase is derived from the same open reading frame as that previously shown to encode VP39, a Mr 39,000 dissociable subunit of poly(A) polymerase that stimulates the formation of long poly(A) tails. Consistent with this finding, methyltransferase activity was associated with the heterodimeric poly(A) polymerase, which is composed of VP55 and VP39 subunits, as well as with monomeric VP39 protein isolated from vaccinia virions. In addition, cap-specific nucleoside-O2'-methyltransferase activity is associated with recombinant VP39, which was purified to near homogeneity from mammalian cells. From these data, we concluded that the same protein functions as a methyltransferase and a poly(A) polymerase stimulatory factor to modify the 5' and 3' ends of mRNA, respectively.

Poly(A) polymerase and a dissociable polyadenylation stimulatory factor encoded by vaccinia virus.

mRNA made in eukaryotic cells typically has a 3' poly(A) tail that is added posttranscriptionally. To investigate mechanisms by which 3' poly(A) is formed, we identified the genes for the two vaccina virus-encoded polypeptides, VP55 and VP39. Primer-dependent polyadenylation activity was associated exclusively with purified VP55-VP39 heterodimer, which, although stable to column chromatography and glycerol gradient sedimentation, was readily dissociated by antibody to an N-terminal peptide of VP55. Poly(A) polymerase activity was associated with immunopurified VP55, but not with immunopurified or chromatographically purified VP39. VP39 was, however, required for the formation of long poly(A) molecules, in conjunction with either purified VP55 or low concentrations of the heterodimer, and was shown to bind free poly(A). Thus, a catalytic polypeptide and a dissociable poly(A)-binding stimulatory factor each contribute to poly(A) tail formation. No prokaryotic or eukaryotic homologs of either polypeptide were detected in sequence data bases, consistent with the absence of previously reported poly(A) polymerase genes from any source.

Identification of rpo30, a vaccinia virus RNA polymerase gene with structural similarity to a eucaryotic transcription elongation factor.

Eucaryotic transcription factors that stimulate RNA polymerase II by increasing the efficiency of elongation of specifically or randomly initiated RNA chains have been isolated and characterized. We have identified a 30-kilodalton (kDa) vaccinia virus-encoded protein with apparent homology to SII, a 34-kDa mammalian transcriptional elongation factor. In addition to amino acid sequence similarities, both proteins contain C-terminal putative zinc finger domains. Identification of the gene, rpo30, encoding the vaccinia virus protein was achieved by using antibody to the purified viral RNA polymerase for immunoprecipitation of the in vitro translation products of in vivo-synthesized early mRNA selected by hybridization to cloned DNA fragments of the viral genome. Western immunoblot analysis using antiserum made to the vaccinia rpo30 protein expressed in bacteria indicated that the 30-kDa protein remains associated with highly purified viral RNA polymerase. Thus, the vaccinia virus protein, unlike its eucaryotic homolog, is an integral RNA polymerase subunit rather than a readily separable transcription factor. Further studies showed that the expression of rpo30 is regulated by dual early and later promoters.

Early transcription factor subunits are encoded by vaccinia virus late genes.

The vaccinia virus early transcription factor (VETF) was shown to be a virus-encoded heterodimer. The gene for the 82-kDa subunit was identified as open reading frame (ORF) A8L, based on the N-terminal sequence of factor purified by using DNA-affinity magnetic beads. The 70-kDa subunit of VETF was refractory to N-terminal analysis, and so N-terminal sequences were obtained for three internal tryptic peptides. All three peptides matched sequences within ORF D6R. ORFs A8L and D6R are located within the central region of the vaccinia virus genome and are separated by about 13,600 base pairs. Proteins corresponding to the 3' ends of ORFs A8L and D6R were overexpressed in Escherichia coli and used to prepare antisera that bound to the larger and smaller subunits, respectively, of affinity-purified VETF. Immunoblot analysis of proteins from infected cells indicated that both subunits are expressed exclusively in the late phase of infection, just prior to their packaging in virus particles. The two subunits of VETF have no significant local or overall amino acid sequence homology to one another, to other entries in biological sequence data bases including bacterial sigma factors, or to recently determined sequences of some eukaryotic transcription factors. The 70-kDa subunit, however, has motifs in common with a super-family of established and putative DNA and RNA helicases.

A capripoxvirus pseudogene whose only intact homologs are in other poxvirus genomes.

Equivalent regions from within the inverted terminal repeats (ITRs) of the genomes of two capripoxviruses, KS-1 and InS-1, were sequenced. The sequence from KS-1 DNA covers the major part of three contiguous open reading frames (ORFs), which match three contiguous ORFs from within the genomic ITRs of the leporipoxvirus Shope Fibroma Virus (SFV). The sequenced region of InS-1 DNA contains only two of the three ORFs. The region homologous to the third ORF has no coding potential due to the presence of several stop codons, resulting from small frameshifting deletions and insertions. The significance of a degenerate poxvirus gene, intact homologs of which are only found in other poxvirus genomes, is discussed.

The nucleotide sequence around the capripoxvirus thymidine kinase gene reveals a gene shared specifically with leporipoxvirus.

We have extended previous comparisons of genetic organization between poxvirus genera by sequencing a 2.5K genomic fragment from isolate KS-1 (Kenya sheep-1) of the genus capripoxvirus. The fragment is located in the central region of the capripoxvirus genome and contains three complete and two incomplete open reading frames (ORFs). One of the complete ORFs is a gene for thymidine kinase (TK). This gene, with one of the other two complete ORFs and both the incomplete ORFs, are homologous to four contiguous ORFs from the central region of vaccinia virus (VV) DNA. They also match four ORFs of fowlpox virus (FPV) DNA, three of which are contiguous and the fourth, the FPV TK gene, is located elsewhere on the FPV genome. The third complete ORF of the capripoxvirus DNA fragment is located between the TK gene and the capripoxvirus homologue of the ORF immediately downstream of the VV TK gene. We show that a homologue to this third ORF is absent from VV and FPV DNAs, but is present downstream of the TK gene on Shope fibroma virus DNA. The sequence immediately upstream of the capripoxvirus homologue of a VV late gene contains a motif which is required for VV late gene expression. The motif required for VV early gene transcription termination is present in eight positions in the capripoxvirus sequence, and five of these positions are consistent with the motif having an equivalent function in capripoxvirus to that in VV.