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. 2008 Nov 12;5:139. doi: 10.1186/1743-422X-5-139

Analysis of the nucleotide sequence of the guinea pig cytomegalovirus (GPCMV) genome

Mark R Schleiss 1,, Alistair McGregor 1, K Yeon Choi 1, Shailesh V Date 2, Xiaohong Cui 3, Michael A McVoy 3
PMCID: PMC2614972  PMID: 19014498

Abstract

In this report we describe the genomic sequence of guinea pig cytomegalovirus (GPCMV) assembled from a tissue culture-derived bacterial artificial chromosome clone, plasmid clones of viral restriction fragments, and direct PCR sequencing of viral DNA. The GPCMV genome is 232,678 bp, excluding the terminal repeats, and has a GC content of 55%. A total of 105 open reading frames (ORFs) of > 100 amino acids with sequence and/or positional homology to other CMV ORFs were annotated. Positional and sequence homologs of human cytomegalovirus open reading frames UL23 through UL122 were identified. Homology with other cytomegaloviruses was most prominent in the central ~60% of the genome, with divergence of sequence and lack of conserved homologs at the respective genomic termini. Of interest, the GPCMV genome was found in many cases to bear stronger phylogenetic similarity to primate CMVs than to rodent CMVs. The sequence of GPCMV should facilitate vaccine and pathogenesis studies in this model of congenital CMV infection.

Findings

Guinea pig cytomegalovirus (GPCMV) serves as a useful model of congenital infection, due to the ability of the virus to cross the placenta and infect the fetus in utero [1-3]. This model is well-suited to vaccine studies for prevention of congenital cytomegalovirus (CMV) infection, a major public health problem and a high-priority area for new vaccine development [4]. However, an impediment to studies in this model has been the lack of detailed DNA sequence data. Although a number of reports have identified specific gene products or clusters of genes [5-11], to date a full genomic sequence has not been available.

We recently reported the construction and preliminary sequence map of a GPCMV bacterial artificial chromosome (BAC) clone maintained in E. coli [12,13], and this clone was used as an initial template for sequence analysis of the full GPCMV genome. BAC DNA was purified using Clontech's NucleoBond® Plasmid Kits as described previously [14] and both strands were sequenced using an ABI PRISM® 377 DNA Sequencer, with primers synthesized, as needed, to 'primer-walk' the nucleotide sequence. In parallel, Hind III- and EcoR I-digested fragments were gel-purified and cloned into pUC and pBR322-based vectors as previously described [15]. Plasmid sequences were determined from overlapping Hind III and EcoR I fragments using the map coordinates originally described by Gao and Isom [16]. These sequences were compared to the BAC sequence to facilitate assembly of a full-length contiguous sequence. Since the cloning of the BAC in E. coli involved insertion of BAC origin sequences into the Hind III "N" region of the viral genome, sequence obtained from this specific restriction fragment cloned in pBR322 was utilized for assembly of the final contiguous sequence; analysis of this sequence confirmed that there were no adventitious deletions in the Hind III "N" region generated during the original BAC cloning process. Since a deletion in the Hind III "D" region occurred during cloning of the GPCMV BAC in E. coli [17], DNA sequence from a plasmid containing the full-length Hind III "D" fragment was similarly obtained, and used for assembly of the final contiguous sequence. The GPCMV genomic sequence has been deposited with GenBank (Accession Number FJ355434).

Sequence analysis of GPCMV revealed a genome length of 232,678 bp with a GC content of 55%. This value is in agreement with the value of 54.1% determined previously by CsCl buoyant density centrifugation [18]. A total of 326 open reading frames (ORFs) were identified that were capable of encoding proteins of ≥ 100 amino acids (aa). For ORFs predicted by the sequence analysis that had substantial overlap with other adjacent or complementary GPCMV ORFs that appeared to encode gene products that were highly conserved in other cytomegaloviruses, only those sequences with < 60% overlap with these highly conserved ORFs were further analyzed. ORFs homologous to those encoded by other CMVs with an e-value of < 0.1 and ≥ 100 aa were identified, based on comparisons analyzed using NCBI Blast (blastall version program 2.2.16). Of the ORFs so identified, 104 had sequence and/or positional homology to one or more ORFs encoded by human (HCMV), murine (MCMV), rat (RCMV), rhesus (RhCMV), chimpanzee (CCMV), or tupaia herpesvirus (THV) cytomegaloviruses (Table 1). Of note, homologs of HCMV ORFs UL23 through UL122 were identified [19]. For ease of nomenclature, we have designated these ORFs using upper case font (GP23 through GP122). ORFs with homologs in other CMVs that do not correspond to HCMV UL23 through UL122 have been designated with a lower case "gp" prefix. Homologs of HCMV UL41a (69 aa; gp38.2), UL51 (99 aa; GP51), and UL91 (87 aa; GP91) were annotated in these initial analyses, based primarily on positional, and not sequence, homology to the respective HCMV ORFs. Three ORFs, homologs of MHC class I genes known to be encoded by multiple other CMVs (gp 147–149, Table 1) were also identified. One ORF, gp1 (homolog of CC chemokines), did not have a positional or sequence homolog when compared to other CMVs, but was included in the annotation because of its previous molecular characterization [9]. Including ORFs with mapped exons, the total number of ORFs annotated in this preliminary analysis was 105 [Table 1].

Table 1.

GPCMV Open Reading Frames (ORFs)

ORF Strand Position Size (aa) Protein Characteristics and Cytomegalovirus Homologs

From To
gp1 C 12701 13006 101 GPCMV MIP 1-alpha; homology to multiple CC chemokines

gp2 15098 15949 283 Homology to MCMV M69a

gp3 C 17461 19827 788 Homology to THV T5b; US22 superfamily

gp4 C 21093 21416 107 Homology to RCMV r136d

gp5 C 26985 28097 370 Homology to MCMV m32a

gp6 30089 30454 121 Homology to MCMV glycoprotein family m02a

gp7 C 32003 32308 101 Homology to RhCMV rh42c

GP23 C 33561 34763 400 UL23 homolog; US22 gene superfamily

GP24 C 35000 36217 405 UL24 homolog; US22 superfamily

gp24.1 36802 37224 140 Homology to MCMV M34 proteina

GP25 37187 38455 422 UL25 homolog; tegument protein

GP26 C 38621 39058 145 UL26 homolog

GP27 C 39508 41472 654 UL27 homolog

GP28 C 41572 42639 355 UL28 homolog; US22 superfamily

GP28.1 C 43344 44546 400 UL28 homolog; US22 superfamily

GP28.2 C 44912 46099 395 UL28 homolog; US22 superfamily

GP29 C 46211 46882 223 UL29 homolog; US22 superfamily

gp29.1 C 47579 48034 151 Homology to RCMV R36 proteind; potential homolog of viral cell death suppressor

GP30 C 49363 51060 565 UL30 homolog

GP31 51354 52832 492 UL31 homolog

GP32 C 53073 54626 518 UL32 homolog

GP33 54846 56129 427 UL33 homolog; 7-TMR GPCR superfamily

GP34 56482 58065 527 UL34 homolog

GP35 58269 59927 552 UL35 homolog

GP37 C 60047 60964 305 UL37 homolog

GP38 C 61321 62385 354 UL38 homolog

gp38.1 C 62960 63817 436 Positional homolog of HCMV UL40

gp38.2 C 63876 65186 69 Positional homolog of HCMV UL41a

gp38.3 C 65881 66735 284 Positional homolog of HCMV UL42

gp38.4 C 67254 67619 121 Homology to RCMV r42d

GP43 C 68208 69221 337 UL43 homolog

GP44 C 69209 70432 407 UL44 homolog

GP45 C 71144 73933 929 UL45 homolog

GP46 C 74036 74833 265 UL46 homolog

GP47 75441 77846 801 UL47 homolog

GP48 78051 84332 2093 UL48 homolog

GP49 C 84746 86386 546 UL49 homolog

GP50 C 86362 87426 354 UL50 homolog

GP51 C 87551 87850 99 UL51 homolog; terminase subunit

GP52 88170 89750 526 UL52 homolog

GP53 89743 90729 328 UL53 homolog

GP54 C 90821 94174 1117 UL54 homolog; DNA polymerase

GP55 C 94216 96921 901 UL55 homolog; glycoprotein B

GP56 C 96818 99085 755 UL56 homolog; terminase subunit

GP57 C 99236 102919 1227 UL57 homolog

gp57.1 C 104872 105258 128 Homology to RCMV r23.1d

gp57.2 107338 107712 124 Homology to RCMV R53d

GP69 C 108547 111678 1043 UL69 homolog

GP70 C 112387 115590 1067 UL70 homolog; helicase-primase

GP71 115589 116365 258 UL71 homolog

GP72 C 116528 117601 357 UL72 homolog; dUTPase

GP73 117683 118084 133 UL73 homolog; glycoprotein N

GP74 C 118031 119143 370 UL74 homolog; glycoprotein O

GP75 C 119595 121766 723 UL75 homolog; glycoprotein H

GP76 121931 122770 279 UL76 homolog

GP77 122484 124343 619 UL77 homolog

GP78 124725 125969 414 UL78 homolog; 7-TMR GPCR superfamily

GP79 C 126164 127111 315 UL79 homolog

GP80 126972 129281 769 UL80 homolog; CMV protease

GP82 C 129576 131141 521 UL82 homolog; pp71

GP83 C 131361 133058 565 UL83 homolog; pp65

GP84 C 133286 134737 483 UL84 homolog

gp84.1 134994 135476 160 Homolog of RhCMV rh116e

GP85 C 135035 135946 303 UL85 homolog

GP86 C 136227 140276 1349 UL86 homolog

GP87 140657 143578 973 UL87 homolog

GP88 143481 144752 423 UL88 homolog

GP89ex2 C 144798 145928 376 UL89 homolog; terminase subunit, exon 2

GP91 146356 146619 87 UL91 homolog

GP92 146616 147245 209 UL92 homolog

GP93 147456 148985 509 UL93 homolog

GP94 149118 149873 251 UL94 homolog

GP89ex1 C 150285 151166 291 UL89 homolog; terminase subunit, exon 1

GP95 151284 152489 401 UL95 homolog

GP96 152722 153084 120 UL96 homolog

GP97 153164 154981 605 UL97 homolog; protein kinase

GP98 155001 156788 595 UL98 homolog; alkaline nuclease

GP99 156701 157222 173 UL99 homolog; pp28

gp99.1 157406 158020 204 Homology to RCMV r4d

GP100 C 157529 158578 349 UL100 homolog; glycoprotein M

GP102 158908 161193 761 UL102 homolog

GP103 C 161307 162104 265 UL103 homolog

GP104 C 162067 164160 697 UL104 homolog; portal

GP105 164000 166783 927 UL105 homolog; helicase-primase

gp105.1 176502 176894 130 Homology to RhCMV rh55c

GP112ex1 177066 177839 258 UL112 homolog; replication accessory protein, exon 1

GP112ex2 178403 179257 284 UL112/UL113 homolog; replication accessory protein, exon 2

GP114 C 179168 180259 363 UL114 homolog; uracil glycosylase

GP115 C 180325 181101 258 UL115 homolog; glycoprotein L

GP116 C 181146 181994 282 Homology to THV t116b; possible functional homolog of UL119; Fc receptor/immunoglobulin binding domains

GP117 C 182202 182777 191 UL117 homolog

GP119.1 C 185103 185591 162 UL119 homolog; homology to MCMV M119.1a

GP121 C 186635 187681 348 UL121 homolog; homology to THV t121.4b

GP122 C 188292 189260 322 UL122 homolog; HCMV IE2; immediate early transactivator

gp123 195838 196893 351 MCMV IE2 homologa; US22 superfamily

gp138 C 201275 202750 491 Homology to RCMV r138d

gp139 C 204624 206717 697 Homology to THV T5b; US22 superfamily

gp140 206446 206853 135 Homology to CCMV UL132g

gp141 C 206977 208584 535 Homology to HCMV US23h; US22 superfamily

gp142 C 208852 210546 564 Homology to HCMV US24h; US22 superfamily

gp143 C 210799 212532 577 Homology to THV T5b; US22 superfamily

gp144 C 213034 215328 764 Homology to US26h; US22 gene superfamily

gp145 C 215601 217499 632 Homology to HCMV IRS1/TRS1h; US22 superfamily

gp146 C 218106 219839 577 Homology to HCMV IRS1/TRS1h; US22 superfamily

gp147 C 223464 225026 520 MHC class I homolog

gp148 C 225938 227389 483 MHC class I homolog

gp149 C 228845 230728 627 MHC class I homolog

a Genbank NC_004065.1

b Genbank NC_004065.1

c Genbank NC_006150.1

d Genbank AF232689.2

e Genbank YP_068209.1

f Genbank AY486477.1

g Genbank NC_003521.1

h Genbank NC_001347

A map of the GPCMV genome illustrating the relative positions of these ORFs is shown in Fig. 1. ORFs that represent homologs of the individual exons of spliced HCMV genes, in particular UL89 (terminase) and UL112/UL113 (replication accessory protein) are annotated separately. The splice junction for the GP89 mRNA was predicted based on comparisons to other CMVs. For the UL112/113 region, further studies will be required to map the precise splicing patterns of the putative transcripts encoded by this region of the GPCMV genome. Similarly, the ORF encoding the sequence homolog of the HCMV IE transactivator, UL122, has been annotated without regard to the splicing events previously shown to take place in this region of the genome [20]; further analyses of cDNA from this and other GPCMV genome regions of IE transcription, including those encoded in the Hind III 'D' region of the genome, will likely result in annotation of multiple heretofore unidentified ORFs. A comprehensive table of all ORFs > 25 aa and their homology to other CMV genomes is provided in additional files 1 and 2. As RNA analyses are completed, the total number of annotated GPCMV ORFs will expand in number.

Figure 1.

Figure 1

Protein Coding Map of GPCMV Genome. Schematic representation of the GPCMV genome demonstrating ORFs described in the text. GPCMV ORFs with positional and/or sequence homology to HCMV ORFs are indicated in bold with upper case prefixes (GP23 through GP122). ORFs that lack sequence or positional homologs in HCMV but share homology with ORFs in other CMVs are indicated with lower case prefixes (see Table 1). Only the 5' terminal repeat (TR) is shown; however, in about 50% of genomes the TR is duplicated at the 3' end [18]. Color-coding indicates ORFs of interest for vaccine and pathogenesis studies: blue, envelope glycoprotein homologs; green, putative immune evasion/immune modulation gene homologs; red, US22 superfamily homologs.

The schematic representation of GPCMV ORFs demonstrated in Fig. 1 highlights several gene families of particular interest. Of particular interest and importance to vaccine studies in the guinea pig model are conserved homologs of the ORFs encoding major envelope glycoproteins gB, gH/gL/gO/, and gM/gN. These glycoproteins are important determinants of humoral immune responses in the setting of CMV infection, and serve as potential subunit vaccine candidates. Of these, the gB homolog has been demonstrated to confer protection against congenital GPCMV infection in subunit vaccine studies [21-23]. Homologs of putative HCMV immune modulation genes, including G-protein coupled receptors and major histocompatibility class I homologs, were also identified [24]. Also of interest was the presence of multiple US22 gene family homologs, heavily clustered near the rightward terminus of the GPCMV genome. These ORFs predict protein products that are analogous to the MCMV dsRNA-binding proteins, M142 and M143, that have been shown to inhibit dsRNA-activated antiviral pathways [25,26]. Members of this family have also been implicated in macrophage tropism in MCMV [27]. Our sequence analysis also confirmed the findings of Liu and Biegalke [8] that the GPCMV genome does not encode a positional homolog of the antiapoptotic HCMV UL36 gene [28]. However, an ORF with homology to R36, which encodes the presumed RCMV cell death suppressor, was identified (gp29.1, Table 1). Further studies will be required to determine whether this putative gene supplies a UL36-like function.

It was also of interest to note the presence of ORFs that have apparent homology to the MCMV M129-133 region. This region has positional homologs in human and primate CMVs [29-31], but is absent in THV [32]. Recently, it was determined that passage of GPCMV in cultured fibroblasts promotes the deletion of a ~1.6-kb locus containing potential positional homologs of this gene cluster. The presence of this 1.6 kb locus was found by Inoue and colleagues to be associated with an enhanced pathogenesis of GPCMV in vivo [33]. We independently confirmed the presence of this locus and its sequence in our salivary gland-derived viral stocks, and have included this sequence in our GenBank annotation (Accession Number FJ355434). Further studies will be required to fully annotate the transcripts encoded by this region of the GPCMV genome. Interestingly, the original GPCMV BAC clone that we sequenced was derived using GPCMV viral DNA obtained after long-term tissue culture passage of ATCC 2122 viral stock, and not surprisingly this BAC was found to lack the 1.6 kb virulence locus [12]. Subsequently, PCR and preliminary sequencing of a more recently obtained GPCMV BAC clone with an excisable origin of replication [17] revealed that the 1.6-kb sequence was retained in this clone. The apparent modifications of this locus that occur following viral passage on fibroblast cells are reminiscent of the mutations and deletions that occurred during fibroblast-passage of HCMV [34] and rhesus CMV [35]. The congruence of these events suggests that the selective pressures that promote mutational inactivation of genes in this region may be similar across viral species. Additional analyses, including sequencing of a full-length GPCMV genome derived from replicating virus in vivo, will be required to determine what other deletions or mutations are present in genomes from tissue culture-passaged viruses. Since additional ORFs are likely to be identified by these analyses, we have annotated the first ORF identified in the BAC sequence to the right of this 1.6 kb region as gp138 (Fig. 1), to allow for ease of nomenclature as ORFs in this virulence locus are better characterized. Application of other genome sequence analysis methods, including identification of small or overlapping genes and further assessment of mRNA splicing or unconventional translation signals, will likely result in identification of other putative ORFs in future studies [36].

Comparisons of GPCMV ORFs with sequences from other CMV genomes yielded interesting results. ORF translations were compared with all proteins from the 6 sequenced CMV genomes (HCMV, MCMV, RCMV, RhCMV, THV, and CCMV), and hits with e-values less than 1e-5 were aligned individually for each protein, using both ClustalW (version 1.82; [37]) and Muscle (version 3.6; [38]). The alignments were then used to generate trees based on neighbor-joining using JalView. Clustal trees for glycoproteins B (GP55) and N (GP73) are shown in Fig. 2, with distance scores indicated. Overall, comparison of the various glycoproteins (gB, gM, gH, and gO) yielded similar phylogenies, with GPCMV glycoproteins generally appearing closer to primate CMVs than rodent CMVs [39], except for the gN homolog, which appears closer to rodents. ClustalW and Muscle comparisons of GPCMV ORFs with homologous ORFs from the other sequenced CMVs are provided in additional file 3.

Figure 2.

Figure 2

Comparison of GPCMV Glycoproteins with CMV Homologs. Sequences of GPCMV glycoproteins were aligned with glycoproteins from six other CMV genomes (HCMV, MCMV, RCMV, RhCMV, THV, and CCMV) using both ClustalW [37] and Muscle [38] using default parameters. Phylogenetic trees (neighbor joining) were generated from these alignments using Jalview. Numbers at each node indicate mismatch percentages. Interestingly, GPCMV sequences closely match THV sequences (see also, supplementary information), and generally appear closer to primate CMV glycoproteins in pair-wise comparisons than to rodent CMV glycoproteins, as previously observed for gB [39]. Clustal comparisons for conserved glycoproteins gB (GP55; Panel A) and gN (GP73; Panel B) are indicated.

In summary, the complete DNA sequence of GPCMV was determined, using a combination of sequencing of BAC DNA, viral DNA, and cloned Hind III and EcoRI fragments. These analyses identified both conserved ORFs found in all mammalian CMVs, as well as the presence of novel genes apparently unique to the GPCMV. These similarities underscore the usefulness of the guinea pig model, with positive translational implications for development and testing of CMV intervention strategies in humans. Further characterization of the GPCMV genome should facilitate ongoing vaccine and pathogenesis studies in this uniquely useful small animal model of congenital CMV infection.

Competing interests

The authors declare that they have no competing interest. SVD is an employee of Genentech Corporation.

Authors' contributions

MRS cloned viral fragments, performed sequence analysis, analyzed the data and prepared the communication. AM and XC cloned the GPCMV BACs. AM cloned individual genes for sequence analysis. AM, XC and KYC, performed sequence analysis, participated in data analysis, and helped in preparation of the communication. MAM cloned viral DNA fragments, performed sequence analysis, participated in BAC cloning, and aided in preparation of the communication. SVD performed comparative genomic analyses and comparisons and aided in the preparation of the communication.

Supplementary Material

Additional file 1

ORFs of ≥ 25 aa (tab A). 50 aa (tab B), or 100 aa (tab C) with Blast analysis against other sequenced CMV genomes; e-value cutoff of 0.1.

Click here for file (671KB, xls)
Additional file 2

ORFs of ≥ 25 aa (tab A). 50 aa (tab B), or 100 aa (tab C) with Blast analysis against other sequenced CMV genomes; e-value cutoff of 1e-5.

Click here for file (458.5KB, xls)
Additional file 3

Phylogenetic trees for glycoproteins gB, gH, gO, gL, gM and gN, IRS 1–3 family, and GP116 (functional homolog of UL119; Fc receptor/immunoglobulin binding domains). Alignments generated using both ClustalW and Muscle, as described in the text.

Click here for file (149.4KB, pdf)

Acknowledgments

Acknowledgements

Grant support was provided from NIH HD044864-01 and HD38416-01 (to MRS) and R01AI46668 (to MAM). The authors acknowledge helpful discussions and input from Becket Feierbach (Genentech, Inc.). The authors also acknowledge the technical contributions of Yonggen Song and the gift of the Hind III "D" plasmid from HC Isom, Penn State University.

Contributor Information

Mark R Schleiss, Email: schleiss@umn.edu.

Alistair McGregor, Email: mcgre077@umn.edu.

K Yeon Choi, Email: choix207@umn.edu.

Shailesh V Date, Email: date.shailesh@gene.com.

Xiaohong Cui, Email: xcui@vcu.edu.

Michael A McVoy, Email: mmcvoy@vcu.edu.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Additional file 1

ORFs of ≥ 25 aa (tab A). 50 aa (tab B), or 100 aa (tab C) with Blast analysis against other sequenced CMV genomes; e-value cutoff of 0.1.

Click here for file (671KB, xls)
Additional file 2

ORFs of ≥ 25 aa (tab A). 50 aa (tab B), or 100 aa (tab C) with Blast analysis against other sequenced CMV genomes; e-value cutoff of 1e-5.

Click here for file (458.5KB, xls)
Additional file 3

Phylogenetic trees for glycoproteins gB, gH, gO, gL, gM and gN, IRS 1–3 family, and GP116 (functional homolog of UL119; Fc receptor/immunoglobulin binding domains). Alignments generated using both ClustalW and Muscle, as described in the text.

Click here for file (149.4KB, pdf)

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