Structural organization and unusual codon usage in the DNA polymerase gene from herpes simplex virus type 1

Molecular Dissection of Herpes Simplex Virus Type 1 to Elucidate Molecular Mechanisms Behind Latency and Comparison of Its Codon Usage Patterns with Genes Modulated During Alzheimer's Disease as a Part of Host-Pathogen Interaction

BACKGROUND

Herpes simplex virus type 1 (HSV-1) is associated with Alzheimer's disease, which goes into a cycle of latency and reactivation. The present study was envisaged to understand the reasons for latency and specific molecular patterns present in the HSV-1.

OBJECTIVE

The objective is the molecular dissection of Herpes simplex virus type 1 to elucidate molecular mechanisms behind latency and compare its codon usage patterns with genes modulated during Alzheimer's disease as a part of host-pathogen interaction.

METHODS

In the present study, we tried to investigate the potential reasons for the latency of HSV-1 virus bioinformatically by determining the CpG patterns. Also, we investigated the codon usage pattern, the presence of rare codons, codon context, and protein properties.

RESULTS

The top 222 codon pairs graded based on their frequency in the HSV-1 genome revealed that with only one exception (CUG-UUU), all other codon pairs have codons ending with G/C. Considering it an extension of host-pathogen interaction, we compared HSV-1 codon usage with that of codon usage of genes modulated during Alzheimer's disease, and we found that CGT and TTT are only two codons that exhibited similar codon usage patterns and other codons showed statistically highly significant different codon preferences. Dinucleotide CpG tends to mutate to TpG, suggesting the presence of mutational forces and the imperative role of CpG methylation in HSV-1 latency.

CONCLUSIONS

Upon comparison of codon usage between HSV-1 and Alzheimer's disease genes, no similarities in codon usage were found as a part of host-pathogen interaction. CpG methylation plays an imperative role in latency HSV-1.

Characterization of Synonymous Codon Usage in the Newly Identified Duck Plague Virus UL16 Gene

A comparative analysis of the codon usage bias in the newly identified UL16 gene(GenBank accession no.EU195095) of DPV and the UL16 gene of 22 reference herpesviruses was performed. In this study, the synonymous codon usage bias of UL16 gene in the 23 herpesviruses have been analyzed and the results showed obvious differences by the CAI, RSCU, ENC and GC_3s. The results revealed that the synonymous codons with A and T at the third codon positon have widely usage in the codon of UL16 gene of DPV. The ENC-GC_3s plot revealed that the genetic heterogeneity in UL16 gene of herpesviruses was constrained by G+C content at the third codon position. The phylogenetic analysis suggested that DPV was evolutionarily closer to herpesviruses which further clustered into Alphaherpesvirinae. Furthermore the ORF of DPV UL16 gene has sequential rare codons. There were 21 codons showing distinct usage differences between DPV with Escherichia coli, 19 codons showing distinct usage differences between DPV with yeast, and 20 between DPV and Human. Therefore the Escherichia coli, Yeast and Human expression system were suitable for the expression of DPV UL16 gene if some codons could be optimized.

Analysis of synonymous codon usage in the UL24 gene of duck enteritis virus

The analysis on codon usage bias of UL24 gene of duck enteritis virus (DEV) may improve our understanding of the evolution and pathogenesis of DEV and provide a basis for understanding the relevant mechanism for biased usage of synonymous codons and for selecting appropriate expression systems to improve the expression of target genes. The codon usage bias of UL24 genes of DEV and 27 reference herpesviruses were analyzed. The results showed that codon of UL24 gene of DEV was strong bias toward the synonymous codons with A and T at the third codon position. A high level of diversity in codon usage bias existed, and the effective number of codons used in a gene plot revealed that the genetic heterogeneity in UL24 gene of herpesviruses was constrained by the G + C content. The phylogentic analysis suggested that DEV was evolutionarily closer to Alphaherpesvirinae and that there was no significant deviation in codon usage in different virus strains. There were 20 codons showing distinct usage differences between DEV and Escherichia coli, 23 between DEV and Homo sapiens, but only 16 codons between DEV and yeast. Therefore the yeast expression system may be more suitable for the expression of DEV genes.

The complete genome sequence of herpesvirus papio 2 (Cercopithecine herpesvirus 16) shows evidence of recombination events among various progenitor herpesviruses

We have sequenced the entire genome of herpesvirus papio 2 (HVP-2; Cercopithecine herpesvirus 16) strain X313, a baboon herpesvirus with close homology to other primate alphaherpesviruses, such as SA8, monkey B virus, and herpes simplex virus (HSV) type 1 and type 2. The genome of HVP-2 is 156,487 bp in length, with an overall GC content of 76.5%. The genome organization is identical to that of the other members of the genus Simplexvirus, with a long and a short unique region, each bordered by inverted repeats which end with an "a" sequence. All of the open reading frames detected in this genome were homologous and colinear with those of SA8 and B virus. The HSV gene RL1 (gamma(1)34.5; neurovirulence factor) is not present in HVP-2, as is the case for SA8 and B virus. The HVP-2 genome is 85% homologous to its closest relative, SA8. However, segment-by-segment bootstrap analysis of the genome revealed at least two regions that display closer homology to the corresponding sequences of B virus. The first region comprises the UL41 to UL44 genes, and the second region is located within the UL36 gene. We hypothesize that this localized and defined shift in homology is due to recombination events between an SA8-like progenitor of HVP-2 and a herpesvirus species more closely related to the B virus. Since some of the genes involved in these putative recombination events are determinants of virulence, a comparative analysis of their function may provide insight into the pathogenic mechanism of simplexviruses.

Complete genome sequence of cercopithecine herpesvirus 2 (SA8) and comparison with other simplexviruses

We have obtained the complete sequence of the herpesvirus simian agent 8 (SA8; cercopithecine herpesvirus 2) a baboon simplexvirus closely related to the monkey B virus and herpes simplex virus types 1 and 2. The genome of SA8 is 150,715 bp long, with an overall G/C content of 76%, the highest among the simplexviruses sequenced so far. The sequencing has confirmed that the genomic arrangement of SA8 is similar to that of other simplexviruses: unique long and unique short regions bordered by two sets of inverted repeats. All genes identified in SA8 are homologous and collinear with those of the monkey B virus, including the lack of the RL1 open reading frame, a gene responsible for neurovirulence in human herpes simplex viruses. This latter finding supports the hypothesis that a different pathogenetic mechanism may have developed in human simplexviruses, after their divergence from monkey simplexviruses.

Herpes simplex virus DNA replication

The Herpesviridae comprise a large class of animal viruses of considerable public health importance. Of the Herpesviridae, replication of herpes simplex virustype-1 (HSV-1) has been the most extensively studied. The linear 152-kbp HSV-1 genome contains three origins of DNA replication and approximately 75 open-reading frames. Of these frames, seven encode proteins that are required for originspecific DNA replication. These proteins include a processive heterodimeric DNA polymerase, a single-strand DNA-binding protein, a heterotrimeric primosome with 5'-3' DNA helicase and primase activities, and an origin-binding protein with 3'-5' DNA helicase activity. HSV-1 also encodes a set of enzymes involved in nucleotide metabolism that are not required for viral replication in cultured cells. These enzymes include a deoxyuridine triphosphatase, a ribonucleotide reductase, a thymidine kinase, an alkaline endo-exonuclease, and a uracil-DNA glycosylase. Host enzymes, notably DNA polymerase alpha-primase, DNA ligase I, and topoisomerase II, are probably also required. Following circularization of the linear viral genome, DNA replication very likely proceeds in two phases: an initial phase of theta replication, initiated at one or more of the origins, followed by a rolling-circle mode of replication. The latter generates concatemers that are cleaved and packaged into infectious viral particles. The rolling-circle phase of HSV-1 DNA replication has been reconstituted in vitro by a complex containing several of the HSV-1 encoded DNA replication enzymes. Reconstitution of the theta phase has thus far eluded workers in the field and remains a challenge for the future.

Differences in the capacity of two herpes simplex virus isolates to spread from eye to brain map to 1610 base pairs of DNA found in the gene for DNA polymerase

A intertypic recombinant, designated HSV-R(D1), had previously been generated from non-neuroinvasive HSV-2(186) and neuroinvasive HSV-1(17). Although the recombinant contained less than 2% of the HSV-1 genome, it retained the neuroinvasive phenotype. The nucleotide sequences responsible for the neuroinvasiveness of HSV-R(D1) were previously mapped to a 3.0 kb segment of DNA located within the DNA polymerase gene (mu 0.414 to 0.430) via marker rescue experiments. We have now sequenced this region and compared our results to the published nucleotide sequence of the HSV-1(17) and HSV-2(186) DNA polymerase genes. It was found that the 3.0 kb HSV-R(D1) DNA fragment consisted entirely of HSV-2(186) nucleotide sequences except for the presence of 1610 bp of HSV-1(17) DNA. The 1610 bp of HSV-1 DNA coded for a 536 amino acid (AA) region which were located between AA 254 and 790 of the DNA polymerase enzyme. Comparison of the 536 AA sequence of neuroinvasive HSV-1(17) with the homologous area of the non-neuroinvasive HSV-2(186) DNA polymerase indicated that the two polymerases differed at 56 AA positions. In addition, this area of the HSV-1(17) DNA polymerase was 5 AA acids shorter than the HSV-2(186) DNA polymerase. Specific amino acid changes that might account for the neuroinvasive phenotype of HSV-R(D1) are discussed.

Translational regulation of herpes simplex virus DNA polymerase

Using as antigens fusion proteins expressed in bacteria, we have generated polyclonal antisera specific for the herpes simplex virus (HSV) type 1 DNA polymerase. A variety of immunologic, genetic, and biochemical assays were used to characterize these antisera and demonstrate their specificity for the HSV DNA polymerase. Using these antisera, measurements of the synthesis and accumulation of HSV DNA polymerase in infected Vero cells were made. Peak rates of polymerase synthesis were observed at 4 h postinfection, as much as 2 h before peak levels of polymerase mRNA accumulation. At all times examined, the HSV DNA polymerase polypeptide was found to be synthesized at a lower rate per mRNA than the viral thymidine kinase, with this difference being especially dramatic at later times. Infected-cell RNA isolated at 2 and 6 h postinfection directed the synthesis of similar amounts of polymerase polypeptide per polymerase transcript in rabbit reticulocyte lysates, indicating that polymerase transcripts are inherently as translatable at both times. An HSV mutant in which sequences including a short upstream open reading frame in the HSV DNA polymerase transcript were deleted specified polymerase mRNA whose translational efficiency was no more than marginally greater than that of the wild-type virus. These results demonstrate that polymerase expression is regulated by inefficient translation mediated by sequences other than the short upstream open reading frame and that this leads to an early shutoff of polymerase synthesis during HSV infection.

Isolation and characterization of herpes simplex virus mutants containing engineered mutations at the DNA polymerase locus

We have derived Vero cell lines containing the herpes simplex virus DNA polymerase (pol) gene that complement temperature-sensitive pol mutants. These cell lines were used to recover viruses containing new mutations at the pol locus. Two spontaneously arising host-range mutants, 6C4 and 7E4, were isolated. These mutants did not grow efficiently on Vero cells or synthesize late polypeptides but formed plaques on a cell line containing the pol gene (DP6 cells). Whereas mutant 6C4 specified a wild-type-size Pol protein, we detected no full-length Pol protein in 7E4-infected cell extracts. Complementation studies demonstrated that 6C4 and 7E4 contain different mutations and indicated that 6C4 is in a complementation group different from that of pol temperature-sensitive mutant tsC7 or tsD9. A mutant in which 2.2 kilobases of pol sequences were replaced with the Escherichia coli lacZ gene under the control of the herpes simplex virus thymidine kinase promoter was constructed. This mutant formed blue plaques on DP6 cells in the presence of 5-bromo-4-chloro-3-indolyl-beta-D-galactoside. Using this virus in marker rescue experiments, we engineered three mutants containing deletions in the pol coding region which grew efficiently on DP6 cells but not on Vero cells and which differed in their synthesis of Pol polypeptides. The lacZ insertion virus was also used to introduce a deletion in the region upstream of the pol long open reading frame, which removes a short open reading frame that could encode a 10-amino-acid peptide. This mutant grew to similar titers on Vero and DP6 cells, indicating that these sequences are not essential for growth of the virus in tissue culture.

Aphidicolin resistance in herpes simplex virus type I reveals features of the DNA polymerase dNTP binding site

We describe the mapping and sequencing of mutations within the DNA polymerase gene of herpes simplex virus type 1 which confer resistance to aphidicolin, a DNA polymerase inhibitor. The mutations occur near two regions which are highly conserved among DNA polymerases related to the herpes simplex enzyme. They also occur near other herpes simplex mutations which affect the interactions between the polymerase and deoxyribonucleoside triphosphate substrates. Consequently, we argue in favor of the idea that the aphidicolin binding site overlaps the substrate binding site and that the near-by conserved regions are functionally required for substrate binding. Our mutants also exhibit abnormal sensitivity to another DNA polymerase inhibitor, phosphonoacetic acid. This drug is thought to bind as an analogue of pyrophosphate. A second-site mutation which suppresses the hypersensitivity of one mutant to phosphonoacetic acid (but not its aphidicolin resistance) is described. This second mutation may represent a new class of mutations, which specifically affects pyrophosphate, but not substrate, binding.

The herpes simplex virus DNA polymerase: analysis of the functional domains

The structural and functional organization of the herpes simplex virus type I (HSV-1) DNA polymerase enzyme of strain ANG was studied by a combination of sequence and immunobiochemical analyses. Comparison of the HSV-1 ANG DNA polymerase sequence with those of pro- and eukaryotic DNA polymerases resulted in the allocation of eleven conserved regions within the HSV-1 DNA polymerase. From the analysis of all currently identified mutations of temperature-sensitive and drug-resistant HSV-1 DNA polymerase mutants as well as from the degree of conservancy observed, it could be deduced that the amino-acid residues 597-961, comprising the homologous sequence regions IV-IX, constitute the major structural components of the catalytic domain of the enzyme which should accommodate the sites for polymerizing and 3'-to-5' exonucleolytic functions. Further insight into the structural organization was gained by the use of polyclonal antibodies responding specifically to the N-terminal, central and C-terminal polypeptide domains of the ANG polymerase. Each of the antisera was able to immunostain as well as to immunoprecipitate a viral polypeptide of 132 +/- 5 kDa that corresponded well to the molecular mass of 136 kDa predicted from the coding sequences. Enzyme-binding and neutralization studies confirmed that both functions, polymerase and 3'-to-5' exonuclease, are intimately related to each other, and revealed that, in addition to the sequences of the proposed catalytic domain, the very C-terminal sequences, except for amino-acid residues 1072-1146, are important for the catalytic functions of the enzyme, most likely effecting the binding to DNA.

Expression of herpes simplex virus type 1 DNA polymerase gene by in vitro translation and effects of gene deletions on activity

A cloned herpes simplex virus type 1 DNA polymerase gene which is biologically functional was inserted into SP6 and T7 promoter-containing vectors for in vitro transcription-translation. pol-specific RNA synthesized in vitro will direct the synthesis of a 140-kilodalton polypeptide in rabbit reticulocyte lysates. RNAs prepared from pol templates linearized at internal restriction sites specified deleted polypeptides with sizes consistent with colinearity of the pol gene and the 140-kilodalton primary translation product. The in vitro translated pol gene product was enzymatically active, with salt resistance and sensitivity to acyclovir triphosphate, similar to the enzyme activity in crude extracts of herpes simplex virus type 1-infected Vero cells. An in-frame deletion of 78 residues (amino acids residues 881 to 959) was introduced into the expression vectors to investigate the function of a region of the polypeptide (amino acids residues 881 to 895) which is conserved in nine other DNA polymerases. In a complementation assay, this mutation abolished biological activity as well as the enzymatic activity of the in vitro translated product. A BAL31 mutation deleting the upstream open reading frame of pol had no effect on biological activity in a complementation assay but was found to increase the efficiency of in vitro translation of pol RNA. Two amino-terminal deletions of 27 and 67 residues were found to greatly enhance the enzymatic activity of the in vitro translated product, while all carboxy-terminal deletions examined (the smallest being 164 residues) abolished in vitro enzymatic activity. Expression of the 67-residue amino-terminal deleted pol gene in Escherichia coli, using a bacteriophage T7-based system, resulted in accumulation of large amounts of an insoluble fusion protein. An antiserum prepared against this fusion protein precipitated the 140-kilodalton DNA polymerase from herpes simplex virus type 1-infected cell lysates.

Analysis of the transcript of the herpes simplex virus DNA polymerase gene provides evidence that polymerase expression is inefficient at the level of translation

We have mapped the termini and determined the relative abundance and ribosome density of the major cytoplasmic transcript of the DNA polymerase (pol) gene of herpes simplex virus type 1. Nuclease protection and primer extension analyses located the 5' end of the major pol transcript at two closely spaced sites 51 and 57 nucleotides to the left of a BamHI site at map position 0.413. S1-sensitive sites corresponding to additional minor transcripts were found to map further upstream within a palindromic sequence that contains a viral replication origin. The major 3' end was found to map 90 nucleotides upstream of a KpnI site at map position 0.439. Quantitative S1 nuclease assays revealed that pol transcripts were nearly as abundant as transcripts encoded by the viral thymidine kinase gene. However, relatively few pol transcripts were found on large polysomes at 5.5 h after infection, when pol transcripts were most abundant. This was in marked contrast to the polyribosome distribution of transcripts from the thymidine kinase gene and the major DNA-binding protein gene. These results and sequence features of the pol transcript suggest that pol expression is regulated, in part, at the level of translation.