Molecularcloning and physical mapping of varicella-zoster ...

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Proc. NatL Acad. Sci. USA Vol. 79, pp. 993-997, February 1982 Biochemistry Molecular cloning and physical mapping of varicella-zoster virus DNA* (restriction map) STEPHEN E. STRAUSt, JOHN OWENSt, WILLIAM T. RUYECHANt, HOWARD E. TAKIFFt, THOMAS A. CASEY§, GEORGE F. VANDE WOUDEO, AND JOHN HAY§ tLaboratory of Clinical Investigation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20205; tDepartment of Biochemistry, and §Department of Microbiology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20014; and TLaboratory of Molecular Virology, National Cancer Institute, National Institutes of Health, Bethesda, Marvland 20205 Communicated by Richard M. Krause, October 16, 1981 ABSTRACT Varicella-zoster virus (VZV) DNA was cleaved with restriction endonuclease EcoRI, and most of the resulting fragments were successfully cloned in the phage vector AgtWES-AB. Double digestions of cloned fragments with EcoRI and BamHI and hybridizations to blot-transferred BamHI digests of VZV DNA were used to construct a physical map of the genome. The molec- ular termini of the DNA were identified by restriction enzyme analysis after exonuclease HI digestion. The data indicate that VZV DNA exists in two isomeric forms that differ by inversion of one short terminal genome segment. Electron microscopic studies revealed that the short genome segment consists of a terminal se- quence of about 3.4 x 106 daltons that is separated from an in- ternal inverted repeat of itself by a 5.8 x 106-dalton unique DNA segment. Varicella-zoster virus (VZV) is a human herpesvirus which causes varicella (chicken pox) and, after a highly variable latency period, may reactivate to produce zoster (shingles) (1). The poor growth of VZV in cell culture and the inherent difficulty in ob- taining and purifying sufficient quantities of viral DNA have significantly impeded the detailed molecular characterization of the genome. Although early studies suggested that VZV DNA is a double-stranded molecule of 92-110 megadaltons (MDal) (2, 3), more recent estimates indicate that the genome is only about 80 MDal (4, 5). Initial restriction endonuclease-generated cleavage profiles of VZV DNA revealed the presence of sub- molar genome fragments, suggesting that this genome, like those of other herpesviruses, may exist in multiple conforma- tions (2, 6-8). Recently, we have shown by quantitative den- sitometry of gel profiles that endonuclease digestion can gen- erate up to four half-molar fragments, but no quarter-molar fragments. We postulated, therefore, that the genome may exist in either of two isomeric forms that differ by inversion of but one genome segment (5). In this report we describe the molecular cloning of VZV DNA restriction fragments in a phage A vector and present a physical restriction map of the VZV genome. This map plus electron microscopic analyses reported here demonstrate that VZV DNA exists in two isomeric forms. MATERIALS AND METHODS Cells and Viruses. VZV strain Ellen was obtained from the American Type Culture Collection (ATCC VR-586). Other VZV isolates used were recovered from vesicle fluid aspirates from patients with zoster infection. VZV was grown in human em- bryonic lung fibroblasts as described (5). Phage AgtWES-AB was grown and purified as described (9). Preparation, Labeling, and Analyses of DNAs. Previously described methods were utilized for extraction of VZV DNA from viral nucleocapsids (5) and for purification of phage A DNAs (10). DNAs were labeled in vitro with [32P]dCTP by the nick-translation methods of Maniatis et at (11) and Kelly et al (12). Restriction endonucleases were purchased from Bethesda Research Laboratories and New England BioLabs and were used according to the manufacturers' recommendations. Exo- nuclease III was purchased from Bethesda Research Labora- tories. Electrophoresis was carried out in slab gels of 0.5-1.2% agarose. DNA was stained with ethidium bromide and photo- graphed with UV transillumination. The DNA in agarose gels was transferred to nitrocellulose membranes by the method of Southern (13). Blot hybridizations were performed as described by Wahl et at (14). Autoradiography was performed with Kodak XR-5 film in cassettes containing intensification screens with exposures at -70°C for 2-240 hr. Cloning of VZV DNA. Purified VZV DNA was digested with EcoRI and ligated to purified AgtWES-AB vector arms as de- scribed (9, 10). The DNA was packaged into phage particles in vitro (15), and the virus was assayed by plaque formation and amplified in Escherichia coli LE 392 (9). This procedure rou- tinely yielded about 106 plaque-forming units/,ug of vector DNA. Recombinant A phage DNA was extracted and prepared as described (10). Electron Microscopy of VZV DNA. Viral DNAs (0.5-1.0 ,ug/ ml) were mixed with sufficient recrystallized formamide (16) to yield a final formamide concentration of 80% (vol/vol) and then denatured by heating at 60°C for 10 min. Sufficient 0.2 M Tris-HCV0.001 M EDTA, pH 8.5, were added to reduce the formamide concentration to 66%. The DNA was allowed to self- hybridize at room temperature for 2-3 hr. Then simian virus 40 form II and either 4X-174 or fd phage DNAs (all purchased from Bethesda Research Laboratories) were added as double- and single-strand-size markers, respectively. Finally, cyto- chrome c was added to a concentration of 0.3 mg/ml. The DNA was picked up from a buffered 10% (vol/vol) form- amide hypophase (17) by using Parlodian-coated 200-mesh cop- per grids. The grids were stained with uranyl acetate, air dried after an isopentane rinse, and rotary shadowed with gold/pal- ladium in an Edwards evaporator. The grids were examined in a Zeiss 10A electron microscope and photographed at a mag- nification of x 9800. Negatives were projected, and contour lengths of double- and single-strand regions were determined with a Keufel and Esser map measurer. Abbreviations: exoIII, exonuclease III; VZV, varicella-zoster virus; MDal, megadaltons. * Presented in part at the International Herpes Virus Workshop, Bo- logna, Italy, July, 1981. 993 The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertise- men?' in accordance with 18 U. S. C. §1734 solely to indicate this fact. Downloaded by guest on November 18, 2021

Transcript of Molecularcloning and physical mapping of varicella-zoster ...

Page 1: Molecularcloning and physical mapping of varicella-zoster ...

Proc. NatL Acad. Sci. USAVol. 79, pp. 993-997, February 1982Biochemistry

Molecular cloning and physical mapping of varicella-zostervirus DNA*

(restriction map)

STEPHEN E. STRAUSt, JOHN OWENSt, WILLIAM T. RUYECHANt, HOWARD E. TAKIFFt, THOMAS A. CASEY§,GEORGE F. VANDE WOUDEO, AND JOHN HAY§tLaboratory of Clinical Investigation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20205; tDepartment ofBiochemistry, and §Department of Microbiology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20014; and TLaboratory of MolecularVirology, National Cancer Institute, National Institutes of Health, Bethesda, Marvland 20205

Communicated by Richard M. Krause, October 16, 1981

ABSTRACT Varicella-zoster virus (VZV) DNA was cleavedwith restriction endonuclease EcoRI, and most of the resultingfragments were successfully cloned in the phage vector AgtWES-AB.Double digestions ofcloned fragments with EcoRI and BamHI andhybridizations to blot-transferred BamHI digests of VZV DNAwere used to construct a physical map of the genome. The molec-ular termini of the DNA were identified by restriction enzymeanalysis after exonuclease HI digestion. The data indicate thatVZV DNA exists in two isomeric forms that differ by inversion ofone short terminal genome segment. Electron microscopic studiesrevealed that the short genome segment consists of a terminal se-quence of about 3.4 x 106 daltons that is separated from an in-ternal inverted repeat of itself by a 5.8 x 106-dalton unique DNAsegment.

Varicella-zoster virus (VZV) is a human herpesvirus whichcauses varicella (chicken pox) and, after a highly variable latencyperiod, may reactivate to produce zoster (shingles) (1). The poorgrowth ofVZV in cell culture and the inherent difficulty in ob-taining and purifying sufficient quantities of viral DNA havesignificantly impeded the detailed molecular characterizationofthe genome. Although early studies suggested that VZV DNAis a double-stranded molecule of 92-110 megadaltons (MDal)(2, 3), more recent estimates indicate that the genome is onlyabout 80 MDal (4, 5). Initial restriction endonuclease-generatedcleavage profiles of VZV DNA revealed the presence of sub-molar genome fragments, suggesting that this genome, likethose of other herpesviruses, may exist in multiple conforma-tions (2, 6-8). Recently, we have shown by quantitative den-sitometry of gel profiles that endonuclease digestion can gen-erate up to four half-molar fragments, but no quarter-molarfragments. We postulated, therefore, that the genome may existin either of two isomeric forms that differ by inversion of butone genome segment (5).

In this report we describe the molecular cloning ofVZV DNArestriction fragments in a phage A vector and present a physicalrestriction map of the VZV genome. This map plus electronmicroscopic analyses reported here demonstrate that VZV DNAexists in two isomeric forms.

MATERIALS AND METHODSCells and Viruses. VZV strain Ellen was obtained from the

American Type Culture Collection (ATCC VR-586). Other VZVisolates used were recovered from vesicle fluid aspirates frompatients with zoster infection. VZV was grown in human em-bryonic lung fibroblasts as described (5). Phage AgtWES-AB wasgrown and purified as described (9).

Preparation, Labeling, and Analyses of DNAs. Previouslydescribed methods were utilized for extraction of VZV DNAfrom viral nucleocapsids (5) and for purification of phage ADNAs (10). DNAs were labeled in vitro with [32P]dCTP by thenick-translation methods of Maniatis et at (11) and Kelly et al(12). Restriction endonucleases were purchased from BethesdaResearch Laboratories and New England BioLabs and wereused according to the manufacturers' recommendations. Exo-nuclease III was purchased from Bethesda Research Labora-tories. Electrophoresis was carried out in slab gels of0.5-1.2%agarose. DNA was stained with ethidium bromide and photo-graphed with UV transillumination. The DNA in agarose gelswas transferred to nitrocellulose membranes by the method ofSouthern (13). Blot hybridizations were performed as describedby Wahl et at (14). Autoradiography was performed with KodakXR-5 film in cassettes containing intensification screens withexposures at -70°C for 2-240 hr.

Cloning ofVZV DNA. Purified VZV DNA was digested withEcoRI and ligated to purified AgtWES-AB vector arms as de-scribed (9, 10). The DNA was packaged into phage particles invitro (15), and the virus was assayed by plaque formation andamplified in Escherichia coli LE 392 (9). This procedure rou-tinely yielded about 106 plaque-forming units/,ug of vectorDNA. Recombinant A phage DNA was extracted and preparedas described (10).

Electron Microscopy ofVZV DNA. Viral DNAs (0.5-1.0 ,ug/ml) were mixed with sufficient recrystallized formamide (16) toyield a final formamide concentration of80% (vol/vol) and thendenatured by heating at 60°C for 10 min. Sufficient 0.2 MTris-HCV0.001 M EDTA, pH 8.5, were added to reduce theformamide concentration to 66%. The DNA was allowed to self-hybridize at room temperature for 2-3 hr. Then simian virus40 form II and either 4X-174 or fd phage DNAs (all purchasedfrom Bethesda Research Laboratories) were added as double-and single-strand-size markers, respectively. Finally, cyto-chrome c was added to a concentration of 0.3 mg/ml.The DNA was picked up from a buffered 10% (vol/vol) form-

amide hypophase (17) by using Parlodian-coated 200-mesh cop-per grids. The grids were stained with uranyl acetate, air driedafter an isopentane rinse, and rotary shadowed with gold/pal-ladium in an Edwards evaporator. The grids were examined ina Zeiss 10A electron microscope and photographed at a mag-nification of x 9800. Negatives were projected, and contourlengths of double- and single-strand regions were determinedwith a Keufel and Esser map measurer.

Abbreviations: exoIII, exonuclease III; VZV, varicella-zoster virus;MDal, megadaltons.* Presented in part at the International Herpes Virus Workshop, Bo-logna, Italy, July, 1981.

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The publication costs ofthis article were defrayed in part by page chargepayment. This article must therefore be hereby marked "advertise-men?' in accordance with 18 U. S. C. §1734 solely to indicate this fact.

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A mB

RESULTSStructure of the Invertible Genome Segment. We have

shown (5) that EcoRI cleavage ofVZV Ellen DNA generates fourfragments (A, E, F, and J) with mole ratios of 0.5 with respectto the remaining 13 fragments. The sum ofthe molecular massesof fragments A and J (:--15.9 MDal) is very nearly equal to thesum of the molecular masses of fragments E and F (- 15.7MDa1). Similar observations were made with four half-molarfragments of VZV DNA that result from cleavage with Bgl II.These data led us to postulate that each of the pairs ofhalf-molarrestriction fragments encompasses the inverted repeat se-quences of two isomeric forms of the VZV genome.

In order to define more precisely the structure of the invert-ible genome segment, electron microscopic studies were un-dertaken. The DNAs of VZV Ellen and two low-passage clinicalisolates (K. M. and Scott) were examined in the presence ofbothsingle-stranded [fd phage, 2.11 MDal (18); or 4OX174 phage,1.78 MDal (19)] and double-stranded [simian virus 40 form II,3.4 MDal (20)] marker DNAs. Thirty-three molecules, includ-ing several of the length expected for a complete VZV genome,were measured. All molecules showed intramolecular rehy-bridization at only one end (Fig. 1). By comparison to thelengths of the appropriate internal size markers, it was calcu-lated that a terminal segment of 3.4 ± 0.3 MDal rehybridizedto an internal sequence separated by a unique region of 5.8± 0.9 MDal (mean ± SEM). Within experimental error, nodifferences were noted in preparations with the three differentVZV DNAs. This indicated that the invertible genome segmentis about 12.6 MDal.

Assignment of Terminal Fragments. A comparison of themolecular masses of the four half-molar fragments with the sizeof the invertible genome segment obtained from electron mi-croscopic observations suggests that the EcoRI fragments A+ J or E + F encompass the entire segmentando that no ad-ditional EcoRI fragments are likely to be derived from this re-gion. Fragment A (=10.8 MDal) is too large to be the terminalfragment, so in the isomeric form containing fragment A, frag-menti must be terminal. Neither the endonuclease analysesnor the electron microscopic studies permitted us to determinewhether fragment E or F is terminal. In addition, the data pro-

J FIG. 1. Electron microscopy ofthe short, invertible segment of theVZV genome. (A) Electron photo-micrograph of a self-hybridizedVZV DNA molecule. (B) A tracingof the observed structures. In bothA and B, the arrows delineate thedouble-stranded region corre-sponding to the inverted repeat;double-stranded regions are shownby the heavier lines, andthe insertsdepict simian virus 40 (double-stranded) and fd phage (single-stranded) DNA size markers.

vided no clues as to the identity of the fragment that terminatesthe long, unique, noninvertible genome segment. In an effortto answer these questions, VZV DNAs (strains Ellen and Scott)were digested with exonuclease III, labeled in vitro by nicktranslation, and examined by electrophoresis in agarose gels.The autoradiograms showed quite clearly that the intensities ofthe bands in the positions ofEcoRI fragments C, F, and J weresignificantly diminished by the exonuclease III treatment (Fig.2). This indicates that fragment C occupies a terminal positionin the long, noninvertible genome segment. EcoRI J is the ter-minal fragment of the invertible segment in one isomeric form

FiG. 2. Exonuclease III diges-* tion of VZV DNA. VZV Scott DNA

(100 ng) was digested with 30 unitsof exonuclease III in 50 mM Hepes,pH 7.9/1 mM 2-mercaptoethanol/

w 1 mM MgCl2 at 37TC for 10 min.The reaction was terminated byheating for 20 min at 70TC. EcoRIand salts conducive to its actionwere added. After DNA cleavage,the reaction products were labeledin vitro with [32P]dCTP and ana-lyzed by agarose gel electrophore-sis (Left). VZV DNA not digestedwith exonuclease Ill. (Right) VZVDNAdigested with exonuclease III.The arrows point to fragments C,F, and J, in which the bands are ofreduced intensity after exonu-clease III digestion.

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VZ 14 1 1 F 39 40 29 12 5 VZ VZ 14 11F 39 40 29 12 5 VZ

ABEi

G

KL

N-0 -.

---,_

4k

Q

FIG. 3. Identification of VZV DNA clones. The DNAs of seven clones were cleaved with EcoRI and analyzed together with EcoRI-cleaved VZVnucleocapsid DNA by electrophoresis in horizontal slab gels of 0.5% agarose. The DNAs were blot-transferred to sheets of nitrocellulose and hy-bridized to in vitro 32P-labeled VZV nucleocapsid DNA. (Left) The photograph of the UV transilluminated gel. (Right) The corresponding autora-diogram of the nitrocellulose sheet. Lanes contain EcoRI digests of the following DNAs: 1 and 9, VZV nucleocapsid DNA; 2, clone 14 containingEcoRI C; 3, clone 11F containing a fragment that fortuitously comigrates with EcoRI J but represents a portion of EcoRI B or G. or both; 4, clone39 containingEcoRI K; 5, clone 40 containingEcoRI M; 6, clone 29 containingEcoRI N; 7, clone 12 containingEcoRI 0; 8, clone 5 containing tandemlylinked EcoRI fragments H, P, and Q. Omitted from this figure are the data from similar experiments performed with recombinants bearing EcoRIB, D, E, G, H, I, and L.

of the genome, whereas fragment F occupies that position inthe second isomeric form.

Molecular Cloning of VZV DNA Fragments. To derive acomplete physical map of the genome, VZV fragments weremolecularly cloned in a phage A vector. A total of 89 individualplaques were picked, reassayed by plaque formation, and am-plified in 1-liter broth cultures. The phage was purified fromeach culture, and the phage DNA was extracted and then sub-jected to restriction endonuclease cleavage and agarose gel elec-trophoresis. Approximately 40% (36/89) of all clones containedVZV EcoRI H, whereas 20% (18/89) contained more than oneVZV DNA fragment. Nearly all clones contained EcoRI frag-ments that comigrated precisely with corresponding VZV DNAfragments. However, several recombinants possessed aber-rantly migrating VZV DNA fragments derived from the genomeregion in which EcoRI B and G map (see below).

Blot-hybridization experiments were undertaken to dem-onstrate that VZV DNA fragments had been successfullycloned. The DNAs of 14 clones believed to contain 15 VZVEcoRI fragments were cleaved with EcoRI, subjected to elec-trophoresis, transferred to nitrocellulose, and hybridized to invitro 32P-labeled VZV DNA. All inserted fragments hybridizedto the VZV probe (data for seven clones are shown in Fig. 3).Later studies showed that the VZV DNA sequence in clone llFrepresents a portion of EcoRI B or G rather than J with whichit fortuitously comigrates.

Mapping of VZV DNA Fragments. Mapping of the VZVEcoRI fragments was facilitated by a series ofblot-hybridizationexperiments. The DNAs of each of the 13 clones were individ-ually labeled in vitro and hybridized to strips of nitrocellulosepaper bearing blot-transferred lanes of endonuclease-cleavedVZV DNA.

Our model of the invertible short segment of the genomepredicted that the 0.5 M EcoRI fragments A, E, F, and J should

share sequences derived from the inverted repeat regions. Totest this, the DNA of clone llG, containing VZV EcoRI E, waslabeled in vitro and hybridized to a nitrocellulose membranebearing a blot-transferred VZV DNA EcoRI digest. This frag-ment annealed to VZV EcoRI fragments A, E, F, and J, as pre-dicted (Fig. 4A). A very small amount ofhybridization to EcoRIN was observed, suggesting that part of the EcoRI E DNA maybe repeated in, or may be very similar to, a portion of VZVEcoRI N. Hybridization ofthe other in vitro labeled VZV EcoRIrecombinants to nitrocellulose strips bearing VZV BamHI di-gests indicated those BamHI fragments that are homologous tothe EcoRI fragments (Fig. 4B; Table 1). Except for the invertedrepeat sequences, only neighboring EcoRI fragments shouldexhibit homology to the same BamHI fragment.The preliminary map prepared from the above data was ver-

ified and completed by electrophoretic analyses of the VZVDNA recombinants after digestions with EcoRI and BamHIalone or in combination (Table 1). These studies permittedidentification and in some cases precise localization of BamHIfragments that lie entirely within the EcoRI fragments or over-lap with adjacent EcoRI fragments. The combined data fromthese experiments, the blot hybridizations, the exonuclease IIIdigestions, and the electron microscopic analyses provided afirm basis for constructing a physical map of the VZV genome(Fig. 5).

DISCUSSIONOfthe five human herpesviruses, varicella-zoster virus has beenmost difficult to characterize molecularly because of the avail-ability of only limited quantities of DNA. Detailed investiga-tions have succeeded in defining the genomic structures, themajor classes of transcribed messenger RNAs, and the virallyencoded polypeptides of Epstein-Barr virus, cytomegalovirus,and herpes simplex viruses types 1 and 2. For these four viruses,

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B

Eco Bam Bam Eco B+H C

F

: ; I

Ii_....1 I

*:

D H I K VZV

.'.

_ 4

*

I

i

-

U=m

FIG. 4. Southern analyses of VZV DNA. (A) The phage A recombinant (llG) containing EcoRI E was labeled in vitro by nick translation andwas hybridized to a nitrocellulose strip bearing blot-transferred lanes of VZV DNA that had been cleaved with EcoRI or BamHI. (B) VZV nucleo-capsid DNA was cleaved with BamHI, run in multiple lanes in agarose gels, and blot-transferred to nitrocellulose. The membranes were cut intostrips and hybridized to individual in vitro labeled cloned DNAs. Lanes are identified by the EcoRI fragment(s) contained in the cloned DNAs. Thephotographs of the ethidium bromide-stained gels (A Left andB Right) are shown with the corresponding autoradiographs. Data have been omittedfor similar experiments performed with recombinant DNA probes containing EcoRI fragments G, L, M, N, 0, P, and Q.

molecular epidemiologic studies have been performed, and the

sites of viral latency in the human host have been established.Varicella-zoster virus proteins only recently have been char-acterized (21, 22), and essentially nothing is known of the viraltranscripts. VZV DNA is assumed to reside in a latent state in

Table 1. Identification of BamHI fragments that lie within oroverlap with each cloned EcoRI fragment of VZV DNA

EcoRI BamHI fragments*fragment Homologous Internal Overlapping

B A,H,T,Y,Z T,Y,Z A,HC E,Q,W,X,AA,BB E,Q,W,AA XD H,L,M,O,P MOP H,LE B,J,K,N,R,S,Ut J B,KG A,I None AIH C,F None C,FI B,D None B,DK D,G None D,GL G,L,V V G,LM F,X None F,XN C,I,N N CIO I None IP F None FQ F None F

* Homologies were determined by Southern-type experiments. Inter-nal fragments were mapped by double digestions of recombinantswith EcoRI/BamHI. Overlapping BamHI fragments demonstratedhomology to two or more EcoRI fragments.

tEcoRI demonstrated homology to fragments lying elsewhere in theinvertible genome region as expected.

dorsal root ganglia (1), but direct evidence for this has not beenobtained.

Earlier restriction endonuclease analyses and electron mi-croscopic investigations succeeded in defining the size of theVZV genome and hinted at the presence of inverting and non-

inverting segments (2, 4-8). The present report sheds additionallight on the genomic organization. By a combination of meth-odologies, we have demonstrated that, similar to the DNAs ofother herpesviruses including pseudorabies virus and equineabortion virus (EHV-1) (8, 23, 24), VZV DNA may exist in eitherof two isomeric forms. The genome contains an invertible ter-minal segment of about 12.6 MDal that is linked to a nonin-vertible segment ofabout 66-68 MDal. The invertible segmentis comprised of a unique region ofabout 5.8 MDal that is brack-eted by inverted repeat sequences of approximately 3.4 MDaleach. Thus far, we have failed to uncover evidence for the in-vertibility of the longer genome segment. In addition, it is as

yet uncertain whether small terminal redundancies exist in VZVDNA as they do in other herpesviruses.The organization of the VZV genome defined by the present

studies agrees very well with that proposed by Dumas et al. (25)while this manuscript was being completed. Her group suc-

ceeded in developing VZV DNA cleavage maps for enzymes BglII, Pst I, and Xba I using a cross-blot-hybridization system.Their map places Bgl II fragments C, E, G, and J in the inver-tible genome segment. Our data suggest a similar arrangement,but with Bgl II D rather than the slightly smaller-sized fragmentE for strain Ellen DNA. The electron microscopic analyses ofthe invertible segment reported by Dumas et aL (25) are con-

sistent with the general structure we observe.

A

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10 20 30 40I 1 I

0.1 0.2 0.3

50 00 70 80I I I I

C MPQ H N O G

EcoR1 t fif f fB D L K I , A

f i flIE

UL

L

FIG. 5. The physical map of the two isomeric forms of VZV DNA cleaved by EcoRI. The drawing shows that the genome consists of a long (L)

segment of -67 MDal covalently linked to a short (S) segment of -12.6 MDal. We have no currentdata to suggest that the genome contains invertedterminal repetitions, so that all of the long segment represents unique sequences (UL). The short segment is composed of a 5.8-MDal unique sequence(Us) that is bracketed by 3.4-MDal inverted repeat sequences in terminal (TRs) and internal positions (1RE).

Completion of an endonuclease cleavage map for the VZVgenome helps to clarify a number of earlier observations. First,in some VZV DNA enzyme-digest profiles, there appeared tobe fragments present in mole ratios of 0.8-0.9-for example,EcoRI fragments B and G. The physical map of the genomeplaces these fragments in the center ofthe long unique segment.Corresponding fragments in other digests (BamHI and Bgl II;unpublished observations) seem to be similarly underrepre-sented. Sequence rearrangements and deletions appear to becommon in this region of the genome. Several recombinantswere shown to contain aberrant VZV DNA fragments homol-ogous to EcoRI B or G, or both.

Another observation that is now better explained with thephysical map of the genome is the variability of restriction pro-

files among different clinical isolates (5, 7). In preliminary stud-ies, we have examined the cleavage pattern of 10 different VZVisolates. Most of the differences in the cleavage patterns appearto derive from changes in the invertible segment and in themidportion of the long segment of the genome (unpublishedobservations).One perplexing observation that questioned aspects of the

physical map proposed here has been the cloning of terminalfragment EcoRI C. In general, the terminal fragments of alinear genome resist cloning because endonuclease cleavagedoes not produce the proper terminal overlapping base se-

quence required for successful ligation to the vector DNA. Webelieve that fragment C may be cloneable for either oftwo rea-sons. First, some portion of each pool ofVZV DNA moleculesis circular (5). Ifan EcoRI cleavage site exists in the circular formofthe genome in the neighborhood ofthe junction offragmentsC and J or F, all ofthe "terminal" fragments could be cloneable.Alternatively, because we have failed thus far to clone terminalfragments F and J, it is possible that EcoRI C lies internal toa very small, terminal fragment that we fail to observe in ourgels.The preparation of a library ofDNA recombinants that con-

tain sequences homologous to 94.7% of the VZV genome (4.2MDal of the unique short sequence has not yet been cloned)has now made it easier to map viral mutants and transcripts andto explore further the important question of viral latency inhuman tissues.

We thank Dr. H. S. Aulakh, H. A. Smith, and M. Oskarsson for helpin the early aspects of this work, K. Leighty for editorial assistance, andDr. Michael Bartkoski, Jr., for continued advice and support. Part ofthis work was supported by Uniformed Services University GrantsC07311 to J.H. and C07114 to W.T.R.

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