Volume 17 Number 12 1989 Nucleic Acids Research

Coronavirus genome: prediction of putative functional domains in the non-structural polyproteinby comparative amino acid sequence analysis

Alexander E.Gorbalenya*, Eugene V.Koonin, Alexei P.Donchenko and Vladimir M.Blinov

Institute of Poliomyelitis and Viral Encephalitides, USSR Academy of Medical Sciences, 142782Moscow region, USSR

Received January 6, 1989; Revised and Accepted May 22, 1989

ABSTRACTAmino acid sequencee of 2 giant non-structural

polyproteins (Fl and F2) of infectious bronchitis virus (IBV),a aeiber of Coronaviridae, were conpared, by computer-aaaiatedmethods, to sequences of a number of other positive strand RNAviral and cellular proteins. By this approach, juxtaposedputative RNA-dependent RNA polymerase, nucleic acid binding<"finger"-like) and RNA helicase domains were identified in F2.Together, these domains might constitute the core of theprotein complex involved in the primer-dependent transcription,replication and recombination of coronaviruses. In Fl, twocysteine protease-like domains and a growth factor-like onewere revealed. One of the putative proteases of IBV is similarto 3C proteases of picornoviruaea and related enzymes of co»o-,nepo- and potyviruses. Search of IBV Fl and F2 sequences forsites similar to those cleaved by the latter proteases andlntercomparison of the surrounding sequence stretches revealed13 dipeptides O/S(G> which are probably cleaved by thecoronavirus 3C-like protease. Based on these observations, apartial tentative schene for the functional organization andexpression strategy of the non-structural polyproteins of IBVwas proposed. It implies that, despite the general similarityto other positive strand RNA viruses, and particularly topotyviruaes, coronaviruses possess a number of uniquestructural and functional features.

INTRODUCTIONCoronaviruses are enveloped positive strand RNA viruses

having by far the largest genome in this virus class (1-3).Recently, the genome sequence of the type member ofCoronaviridee, avian infectious bronchitis virus (IBV), hasbeen completed <4). The total length of IBV genome is 27 6O8nucleotides, excluding 3'-terminal poly(A). Of these, about8 OOO nucleotides at the 3'-end are dedicated to coding virionand some snail non-structural proteins, expressed as a nestedset of 3'co-terminal mRNAs, with only the 5'-terminal "unique"part probably translated in each (2). The 5'-terminal part ofgenonic RNA (approx. 2O OOO nucleotides) contains two largeORFs, potentially encoding two non-structural polypeptides <F1and F2> of 441 and 3OO kD, respectively. As no aubgenomic mRNAcorresponding to the F2 polypeptide has been detected, it was

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suggested that the two ORFs are expressed as a single giantpolyprotein, via riboeone frame-shifting (4). Subsequently,experimental evidence has been obtained corroborating thishypothesis (5).

Functional organization of the F1-F2 polyprotein of IBVrenamed, until very recently, completely obscure. Only a shortregion of F2 has been shown to possess a considerablesimilarity to non-structural proteins of alphaviruses andcertain plant viruses (4). We demonstrated that this segment infact comprised a part of a domain containing an NTP-bindingsequence notif and belonging to a vast auperfamily of positivestrand RNA viral proteins in which this motif is the mostconserved sequence (6). Moreover, it has been shown that one ofthe three protein families constituting this superfamily, theIBV domain included, possessed highly significant sequencesimilarity to DNA helicases (7-9). We suggested that proteinsof this family could be RNA helicasea involved in duplexunwinding during viral RNA replication <7,8). Encouraged bythese observations, we performed a systematic search of thesequences of the large non-structural polypeptidee of IBV forsequence stretches similar to highly conserved proteins ofpositive strand RNA viruses and to certain cellular proteins.Here we report the results of this study and discussimplications for functional organization and expressionstrategy of IBV genome.

METHODSftmlno acid sequence comparisons

Amino acid sequences were from current literature; forabbreviations and references see legends to figures.Comparisons were done by programs MULDI (MULtiple DIagon) andOPTAL <OPTimal ALignment). Program MULDI is a modification ofstandard DIAGON <1O> designed to reveal highly conservedsegments in amino acid sequences. Groups of aligned ammo acidsequences are compared in a diagonal plot, utilizing the MDM78amino acid residue comparison matrix <1O). What results, may beconsidered a superposition of several pairwise local similaritymaps in which only streaks corresponding to highly conservedsegments are filtered out. MULDI la principally similar to theprogram recently described by Argos <11). Program OPTAL (6,12), based on the original algorithm of Sankoff (13>, performsetepwiae optimal alignment of multiple amino acid sequences andits statistical assessment by a Monte Carlo procedure. Adjustedalignment score is calculated in standard deviation (SD) units:AS = So-Sr/Q" where S o is the score obtainedfor a given comparison utilizing MDM78 scoring matrix, Sris the mean score obtained upon intercompariaon of 25 randomlyjumbled sequences (or sequence sets) identical to the real onesin amino acid composition, and (̂ is the standard deviation. Theprograms were written in FORTRAH77 and run on a ES-1O6O computer.The statistical significance of manual alignments was assessedby program SCORE. Average per residue score was computedfor a query sequence versus a group of aligned sequences and ASwas calculated by the above equation using 3OO randomlyscrambled versions of the query sequence CE.V.K. et al.in preparation). The probabilltiy of chance similarity between

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two sequences aligned without gape ('double Hatchingprobability') was calculated using the algorithm of HcLachlan

RESULTS AND DISCUSSIONApproach

As the first step to identification of functional domainsin coronavirus polyproteins, it was natural to try to findcoronaviral counterparts of the most highly conserved proteinsof positive strand RNA viruses. Such proteins are, in the orderof decreasing conservation: i) RNA-dependent RNA polyneraeespresent in all viruses of this class and always having aeinllar central segment (15,16); ii> NTP-bindingmotif-containing proteins involved in RNA replication some ofwhich are similar to helicaaes; proteins of this type wereidentified in all eukaryotic positive strand RNA viruses whosegenome lengths exceed 6.3 kb [(6-9) and manuscript inpreparation]; iii) 3C proteases of picornaviruses and similarenzymes revealed in coao-, nepo- and potyviruses (17-23).Clearly, at least for the first and the second groups ofenzymes, the case for existence of coronaviral honologs seemedquite strong.

Alignments of conserved fragments of these three groups ofviral proteins were used as probes to screen sequences of F\and F2 polypeptides of IBV by program MULDI. Segments of theseproteins best matching the probes were fitted into respectivealignments by program OPTAL (or visually) and the significanceof the observed similarity was correspondingly assessed.Additional search by the same procedure was made for segmentsof coronaviral proteins similar to different classes ofcellular proteases and to certain other sequence motifsconserved in cellular proteins. Identification of the putativehelicase was described previously (see Introduction); otherresults are presented below.RNA-dependent RNA polvmerase

In F2 polypeptide two segments similar to the two mostconserved sequence blocks of (putative) positive strand RNAviral RNA polymerases were detected. Inspection of theneighboring regions of F2 revealed also putative counterpartsof other conserved stretches of polymerases. As can be seen inthe resulting alignment (Fig.l), this part of F2 contained allthe anino acid residues invariant in other viral polyraerases,except one, as well as many partially conserved residues. Anotable exception is the substitution of S for G in the socalled GDD site considered to be the most characteristicsequence of positive strand RNA viral RNA polymerases (15,16,22). Presumably, it was this substitution that prevented otherinvestigators from identification of the IBV polyneraae.Evaluation of the alignment of the 4 p'icked segments of F2 withthe conserved segments of 4O (putative) polymerases of positivestrand RNA viruses by program SCORE showed significance at the9.2 SD level. Lengths of variable spacers separating conservedfragments in the putative polymerase of IBV are generallywithin the Units set by other polymeraaes although thecoronavirus one appears to be among the longest. Unexpectedly,a 19 amino acid residue segment of F2 has been shown to possess

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HS2 : 231 6 id lndqs iNQrLaQqgsvdg- -sLa t iD lssasd« I«DrLvwsfPV : 212 Gcdp-dHWsklpvlMeEk Lfa<DYtgyDaiLspa«<eAlHAV : 2 2 0 6 idp-drqWDELfKtMI r fgD—VgLdlDFsafDa iLspfMi reACPMV i 252 GinpysmeWsrLaarHkEkgN--dVLccDY*i*DgLLtkqV«dviYFV i 410 G i g l q y l G Y v i r d U A H D S g - — g f y a d D t a g w D t r l t E a d l d d eSNBV 1349 HdasaedFDa I IaEhFkqgD- -pVLt tD ia i fO IUqdDtMaLtgTMV i 239 rkTp-aqieDfFgdldshvpe--dVLtlDi«KyDKsqnEfhcAv«BMV i 438 fivpigkiesleLKNVrlnnr--yfLeaDUKfDK»qgELhltfqBSMV :50B h m T a - d e l n E t V a f l t p h k - y - - r a L e i D F B K f D K s k t g L h i k A vCarMV :201 GyTteevAqhiwBaHnqfqtp- -VaIGFD«sR<DqhVgvaalefsBBV i 562 Grnp- te iaDgVcefVsEcda- -eV Ie tDF«nlDgrV igwHqrn iPPV t222TEV 1222TVMV i222

6mTKFrGGHDkLLRaLpEG«---IycdaDg*q<DnL»pyLinAvGnTKFYQGWNELHeaLpsfw---VycdaDgsqfDtfLtpfLinAvGoTKFYG6WNELLgkLpDS«---VycdaDg«qfDisLspyLinAv

IBV i597

18 vdGetirHel25 yknktYcvk627 lynccYhvCG30 ckntVNrvec37 AyedVifrrd29 pT6trFkfgi29 taSiktciwy28 hakvgasvsf29 nfGleaylly31 ngnlrYtKeG32 rfGfrYepgv33 pdGtlvkKU33 pdGtlikKhk34 pdGtlvkKfk

i : • iGtTKFYGGWDNHLRNLIQG^EdpILHGWDYpKcDRaMpNLLrlAA 33 ATGglYvKpG

• # *

MS2 i fSTn6NgfT{elESHHNaivkatQIHgPV i GepSGcsgTsifNSMiNnLiirTllLktyHAV i soipS6spcTAllNSIiNn!NlyyvfskUCPHV : gipSGfpmTvivNSIFNelliryhykklMYFV : qrgGGQvvTyalNTItNLkvqliroaeaeSNBV : orikSBmHTlFvNTVlNVViflSrvleeRlTMV : qrkSGDvTTfiGNTViiaaclaSalpmekBMV : qrrTGDAfTyFGNTLvtHaniayAedlsdBSMV : qqkSSNcdTygsNTKsaaLalldclpledCarMV: crnSGOnnTAlGNcLlacLitkhlakiRsBBV : 6vkSGssTTtphNTqYNgcve(TAlt<ehPPV t GnnSGQpSTvvdNTLnvILanTyslLklgTEV : GnnSGQpSTvvdNTLjivIIaBlytcekcgTVMV i GnnSGQpSTvvdNTLnvVLasyyAlsklg

: i : : i t : :IBV i GTSSGDATTAYANSVFNIIQATSANVaRL

ttt3 TIglygDDilcp8 kMUygDDvIAs11 rILcygDDvLIv16 glVtygDOnLU32 rHaVBgDOcVVr4 rMaVsgDDcVVr2 caaHgDDnllh2 caHsgDDsLIihfcVggDDsLLyrUnngODcVLiigpkcgDDGLfirryfVngDDlVLavyyVngDDlLIakHangDDHIaI M i :

SLMILBDDGVVC

20

11106

10

46

25 sgHrEsCgaHfyrg 16034 twenvtFlkrffrAd 7738 pvEeltFlkrsfnLV 8439 rleecDFlkrtfVqr 28133 D«envpFCShHfheL 18427 gerPpyFCggfiLqd 9725 kKqygyFCgryvIhh 9223 DpsvpyvCSkUVet 22025 OfkypaFCgkflLd 10331 EaekirFCqnapVfd 14624 peiglcFlSrvfVdp 15030 NKeelwFnShkgVLy 11630 DKtqlMFmShraLsr 11430 OKkeUFeShraLsk 114

I II I40 EKgPhEFCSqHtMLV 112

Fig.l. Alignment of a fragment of putative RNA-dependent RNApolynerase of IBV with evolutionary conserved fragments ofselected (putative) polynerasea of other positive strand RNAviruses.The sampling of the (putative) polymerases was couplJed so as torepresent the main groups of positive atrand RNA viruses and theentire range of sequence variability of this protein <cf.16).Abbreviations: MS2, MS2 bacteriophage; PV, poliovirus type 1,HAV, hepatitis A virus (picornavirusea); CPNV, cowpea mosaicvirus (a comovirus); YFV, yellow fever virus (a flavivirus);SNBV, Sindbis virus (an alphavirus) ;• TMV, tobacco noaaic virus(a tobamovirus); BMV, brote raosaiv virus (a tricornavirus);BSMV, barley stripe mosaic virus (a hordeivirus) ; CarMV,carnation mottle virus; BBV, black beetle virus (a nodavirus);PPV, plu» pox virus, TEV, tobacco etch virus, TVMV, tobacco vein•ottling virus (potyvirueee). The lengths of the terminalregions and of the variable spacers separating the conservedsegments are designated by numbers. For IBV, the boundaries ofthe polyaerase were predicted from analysis of the putative

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a very remarkable similarity to a segment of RNA polyneraees ofpotyviruees which is relatively variable among positive strandRNA viruses in general (Fig.l). For this segment, thesimilarity between IBV and the potyviruses is comparable tothat between potyviruses themselves, and unprecedented forpositive strand RNA viruses of different families. Takentogether, these observations strongly suggest that thepinpointed region of F2 is the core domain of IBV RNA-dependentRNA polymerase. As for the aforementioned substitution in the'GDD box', it is relatively conservative in nature and, moreimportantly, includes a residue which obviously plays astructural, rather than catalytic, role. It is perhaps relevantthat polymerasea of MS2 and related phages, for which theactivity had been firmly established, also bear a substitutionof an otherwise conserved residue, i.e. Glu for Asn i.d. Fig.l)-.

Two types of RNA-synthesizing complexes greatly differingwith respect to enzymatic properties and products synthesizedwere isolated from coronavirus-infected cells (24). Also,coronaviruses are known to have a unique mechanism ofsubgenomlc RNA synthesis quite distinct from that of genomereplication (3). Thus, it is not unlikely that IBV could havemore than one RNA polymerase. However, our search did notreveal any segments of Fl or F2 significantly similar toviral polymerases except that shown in Fig.l; though somesequences of marginal similarity could be detected inC-terminal parts of both polyproteins. Thus, if IBV genomeencodes a 2nd RNA polymerase, its sequence should be verydifferent fro* those of other positive strand viral polymerases.3C-llke protease

In Fl polypepto.de, sequence stretches similar to all threeconserved segments of 3C-like proteases C19) were detected.Alignment of a 188 residue piece of Fl with 14 viral proteasesproved to be significant at the 5.7 SD level. Notably, His,Asp(Glu) and Cys residues conserved in 3C-like proteases andthought to constitute their catalytic triad (19) wereidentified also in the coronavirus sequence (Fig.2). Theputative coronavirus protease contains one replacement of aresidue invariant in other 3C-like proteases. This is thesubstitution of Tyr for Gly in the sequence GXH in the vicinityof the proposed catalytic Cya residue (Fig.2). It ia notablethat, just like the replacement in the~putative polyneraee

Fig.l legend contcleavage sites (see text and Fig.6); the sequence shown isresidues 549 to 780 of the F2 polypeptide (4). The PPV sequenceis from (39), and the BSMV one from (4O). For sources of theother sequences see (16). Capitals: residues identical orsimilar to respective residues'of IBV; colons: positions whereresidues identical or similar to those of IBV are observed inmore than a half of included sequences. Residues belonging toone of the following groups were regarded similar: L,I,V,H,; A,G; S,T; D,E,N,Q; K,R; F,Y,W. Asterisks: consensus residues ofpositive strand RNA viral polymerases CIS,16,22). Boxed: regionof high local similarity betwtin putative polymerasea of IBV andpotyvirusea.

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Rei. • * •PV (41): 24 ftMlGV-hdMvailPtH-29-lElTiit lkrnE-62-AGqCGg-vitct-6—-kvigMH-Vgg 19HRV (42): 24 ftglGV-ydrfVvvPtH-29-lEITvlkldrnE-62-s6yCGg-vlyki-G—-QvlglH-Vgg 19EMCV (43): 32 Q t d 1 V-rGrTLvvnRH-32-tDVSf i r USgp-65-k6wCGSal 1 adl-6gskki lglH-sag 25FMDV (44): 32 ccatGV-fGtaylvPRH-36-sDaal«wlMrgN-65-AGyCGgavlakD-GadtfivgtH-sag 29HftV (45): 32 nNalGV-kdDwLlvPsH-38-qDVvlnkvpTIp-74-p6mCG6alvssNqsIqnailglH-Vag 23CPMV (46): 24 191 vnV-pGrrf lacKH-34-sELvlyssipSLE-71-pedCGSlviahi-Ggkhki vgVH-Vag 217BRV (21): 22 vsamqy-knkSVrmtRH-36-sEIvTwlApSLp-73-nddC6mIi lcqi-kgknrvvgl i l -Vag 19TEV (331:217 ts lyGIgf GpHi tnKH-34-rDMi i irnpkd--5i-dGqCGSpl vs t rdG- - - f i vglHsasn 71

: : ; ; : : : : : : : : : : : : :18V (4) : 24 NNLnGLwLGDTIycPRH-21 HEVTTqhGVTLN-65-AGaCGSVgf niEkGVv-NffyMHhLel 142

Fig.2. Alignment o£ a fragment of putative 3C-like protease ofIBV with conserved fragnenta of selected cyateine proteases ofother positive strand RNA viruses.The representative sampling of (putative) proteases wasgenerated as indicated in the legend to Fig . l . Additionalabbreviations: HRV, human rhinovirua type 2; EMCV,encephalomyocarditis virus, FMDV, foot-and-mouth disease virus(picornaviruaea); TBRV, tomato black ring virus (a nepovirus).The boundaries of the putative protease of IBV were predicted asindicated in the legend to Fig. l ; the sequence shown i s residues28O4 to 2945 of the Fl polypeptide (4) . Source references forthe other sequences are given in parentheses before eachsequence. Asterisks: putative catalytic residues; otherdesignations as in F ig . l .

SP QPVVKSLLDSKGIHYNQGNPYNLL TPVIEKVKPGEQSFVGQAATGHCVATATAQIMKYHNYPDKGLKi • 1 1 i . i i n . i l l i i . . I I

IBV SNCPTCGANNTDEVIEASLPYLUFATDGPATVDCDEDAVGTVVFVGSTNSGHCYTQAAGOAFDNLAKDRKFGK

SP NYTYTLSSNPDYFDHPKNLFAAISTROYDNNNILPTYS 6RQSQNVKMAISELMADVG1SVDHDY6PSS6Si . . i . i : i . i

IBV KSPYITAHYTRFAFKNETSLPVAKgSKGKSKSVKEDVSNLATSSKASFDNLTDFEOWYDSNIYESLKVOESPDN

SP AG SSRVQRALKENFGYNQSVHQINRGDFSKQDHEABIDKELSQNQPVYY- E8V6K-V. . . . i . . i . i • 11 11 . i

IBV FDKYVSFTTKEDSKLPLTLKVR6IKSVVDFRSKDGFIYKLTPDTDENSKAPVYYPVLDAISUAIHVEGNANFV

tSP GGHA-FVIDD GA6RNFYHVDM6WGGVSDGFFRLDALNPSAL6T6GGAGSFN6YESAVVGIKP

I I . . > t . 1 1 1 . i..i .* 11 : i l lIBV VGHPNYYSKSLHIPTFHENAENFVKH6DKI6GVTnGLHRAEHLNKPNLERIFNIAKKAIVGSSVVTTBC

Fig.3. Alignment of the putative second cysteine proteasedomain of IBV with the protease of Streptococcus pneumoniae.The IBV sequence is residues 1385 to 1677 of the Fl polypeptide(4). The S. pneumonia* protease uquance was from C47) . Colons:identical residues; dots: similar residues; asterisks: putativecatalytic residues. The alignment generated by program OPTAL<••• Methods) was slightly corrected to improve localsimilarity around the catalytic His residue of the bacterialprotease and the corresponding residue of IBV.

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2 3 4 5factor VII spCqngggC kDql-qeYiCfCipfactor IX npCLnggaC kDdi-naYeCwCpf

II factor X spCqndgkC kDgl-geYtCtCleprC slCcghgtC iDgJ-gsFsCDCrSprZ qpCLnNgsC qDat-IGYACtCap

uPA --CLnggtCvSnkyfs-nihwCNCpktPA prCfnggtCqqqlyfs-dfv-CQCpe

I vaccinia 19K GYCLhgd-CiharDid-gmY-CrCchTGF qFC-fhgtC-rflvqe-dkpACvChSEGF GYCLnggVC-mhiEld-ssYtCNCvi

IBV Fl GFCLrNkVC-TVCQcw-IGYGCQCDS* • • • • • • •• • a • • • • •

III LDL R exon 7 —CLdNggCshVCNdlklGYeClCpdLDL R exon 8 —CqdpddCsqLCpdlegGYkCQCEe

2 3 1 4 5

Fig. 4. Alignment of a cystein«-rich segment of the Flpolypeptide of IBV with receptor-binding doialns.The IBV sequence waa from residue 3894 to 3917 (4).For eourcea of the other sequences see (25). Abbreviations:factors VTI-X, respective human coagulation factors; prC, humanplasma protein C; prZ, human plasma protein Z; uPA,urokinase-type plasminogen activator; tPA, tissue-typeplaaminogen activator; vaccinia 19K, growth factor-like proteinof vaccinia virus; TGF, transforming growth factor; EGF,epidermal growth factor; LDL R, low density lypoprotelnreceptor. The grouping of the EGF-like domains and thenumbering of Cys residues is according to (25). Disulflde bondsCya 1-3, Cys 2-4, Cys 5-6 are expected to form but Cya 6 havingno counterpart in the IBV aequence is not shown. Otherdesignations as in Fig.l.

discussed above, this one includes a Gly residue which cannotbe directly involved in catalysis. Another conserved Glyresidue is substituted by Glu in the CPHV protease, the activityof which was determined in unequivocal experiments (cf. 23).2nd cvateine protease

Upon comparison of the sequences of Fl and F2 with thoseof cellular proteases, a segment of Fl has been revealedremarkably similar to a fragment of the catalytic center ofStreptococcus pneumonioe cysteine protease. Alignment of therespective portion of Fl with this protease (Fig.3).issignificant at approx. 5 SD level. The two Host prominentregions of similarity <N- and C-terminal) include segments ofthe bacterial protease around the catalytic Cys and Hisresidues. Corresponding residues could be identified in IBV ,emphasizing the possibility that this segment of Fl could be anauthentic protease.Cvsteine-rlch segments

An interesting feature of Fl and F2 polypeptides is thepresence of several segments with anomalously high content ofCys residues. One of these segments resides in the C-terminal

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Fig.5. A model of possible organization of the putativemetal-binding ("finger") domain of the F2 polypeptide of IBV.Amino acid residue numbering is indicated. Alternativeconfigurations involving other pairs of Cys and His residuesare alto possible. M, metal (probably En2*) cation.Highlighted: similar sequence stretches adjacent to putativemetal-binding residues; aromatic residues conserved inTFIIIA-like fingers.

part of Fl. It was shown to be significantly similar to thereceptor-binding site of »urine epidermal growth factor(probability of fortuitous similarity approx. 1O~1O>.Recently EGF-like domains have been divided into three groupsdiffering in cystein residues arrangement and the lengths ofspacer segments (25). While bearing the most significantsimilarity to group 1 domains (EGF, uPA etc.), the IBV domaincontains counterparts to only 4 of 6 Cys residues (residues 2-5in Fig.4> which are highly conserved within this group and arethought to form three disulfide bonds. On the other hand, oneof the additional Cys residues present in the IBV sequencecould be aligned with Cys 1 of the group 3 domains (LDL R andsome other) to which the IBV domain is also considerablysimilar (Fig.4). Cys 6, however, is absent from this domain. Itmay be speculated that disulfide bonding night occur betweenCys 5 and some more distant Cys residue; several such residuesare available in Fl to the N-side of the EGF-like domain. Thus,IBV appears to possess a novel type of EGF-like domain.

Another cysteine-rich segnent lies in F2, between theputative RNA polymerase and the RHA hellcase. This 3O residuestretch contains 9 Cys and 4 His residues, conforming to theformula of the so called "finger" Zn2*-binding motif(C-X2-4-C-X2-15~a- X2-4~a where a is C or H,and X is any amino acid residue) characteristic of numerousDNA- and RNA-binding proteins (26-28). It is potentiallycapable of forming three "fingers" supported by Cys and Hisresidues which might tetrshedrally coordinate Zn2*cations (Fig.S), suggesting classification as a class I (i.e.multi-finger) domain (28). No general consensus for fingerdomains beyond the (putative) metal-binding Cys and His

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No

34

1011

1256•7/

89

1213

PUTATIVE CLEAVAGE

-7-6-5-4-3-2-1*1'

IIRD

aats

8

QKt

GGAS

dmAT

nPSc

VGPE

VVfN

Vkfy

sVTT

LIkI

V

ssp

RRTS

RKc1

V

Sa<J

LLLL

ffVI

LVLL

Q/SQ/SQ/SQ/G

Q/SQ/GQ/GQ/GQ/SQ/SQ/SQ/SQ/S

• 2<

GS

cT

AV

Ci

kV

iA

SITES

• 3<

FFGG

rFYG

GAdW

KVVL

VKMg

hgnt

• 5 '

KRCF

iand

eaiC

1-6-

LKVK

ay8

R

tsag

•7<

VAVI

eAfV

edyy

•a

sTCC

dTn1wnefnn

• 9

PSNN

V

TTP

X

VDmm

NC

71O81O56866

Coordinates

FlFlF2F2

FlFlFlFlFlFlFlF2F2

(Q>

27793O868911492

4402583321433653462378439282O12235O

PROTEINFUNCTION

MP13CLPOLHEL

MP2

GFL

Fig.6. Putative cleavage sitea in Fl and F2 polyproteina of IBV.The eitea are numbered beginning from the N-terainus of Fl. The4 aitea which were identified firat <3, 4, 10 and 11) andconstituted the reference aet for identification of the otherputative aitea are ahown in the upper 4 rowa. In the othersequences capitals highlight residues having identical orhomologous counterparts in at least one of the sequences of thereference set. NC: number of residues having counterparts inthe reference aequencea. MP1, MP2, putative Membrane proteins;POL, putative RNA-dependent RNA polymerase; HEL, putative RNAhelicaae; 3CL, putative 3C-llke protease; GFL, growthfactor-like domain. In the 'protein function' column proteinsare indicated whose C-terminus may be flanked by the given aite.

residues can be derived (26-28}, and the putative finger domainof IBV does not appear to bear significant sequence similarityto any particular finger domain of other proteins.Specifically, it does not contain a more strict consensustypical of classical TFIIIA-like fingers <29), although two ofthe residues thought to be important for proper folding of thelatter are present (highlighted in Fig.5>. Nevertheless, theconservation of the typical "polarity" of finger domains, withthe N-terminal pair of consensus residues represented byCy&2, and the C-terminal pair by any possible combinationof Cys and His, in all the three coronavirus fingers isnotable. Also of interest is the similarity between shortsequence stretches adjacent to some of the candidatemetal-binding residues (Fig.5). Moreover, two of thesestretches flanking the Cy'e residues from the N-side strikinglyresembled respective sequences in the finger domains of yeasttranscription activator ADR1 (3O; data not shown). Thus,whereas the finger-like structures of IBV may not be closestructural analogs of TFIIIA-like fingers (cf.29>, it seemslikely that they constitute an authentic metal-binding andnucleic acid-binding domain.

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Putative cleavage BitesWe have tentatively identified two protease domains in Fl

polypeptide of IBV. Of these, the cleavage specificities of3C-like proteases have been studied in considerable detail (forreviews see Refe. 31,32). They primarily cleave at dipeptidesQ,E/G,S,A. Cleavage occurs selectively and, unfortunately, therequirements for a site to be utilized are not fullyunderstood, probably differing considerably in differentviruses. Nevertheless, in potyviruses a clear consensus (thoughunique for each virus) for the sequences flanking the cleavagesites has been derived (20,33). This encouraged comparison ofthe sequence stretches centering at Q/S,G dipeptidea in thepolyproteins of IBV. At the first step, we compared those siteswhich could flank the putative protease, polymerase andhelicase domains. We observed that the distances between highlyconserved sequence stretches and protein termini vary to arather limited extent in most enzymes of each class (Figs.1,2and data not shown). Thus, three Q/S and one Q/G site wereidentified in the respective regions of the IBV polyproteins,1. e. sites 3, 4, 10 and 11 in Fig.6. Sites 3 and 4 flank theputative protease, and sites 10 and 11 the putative helicase,site 10 being also the probable C-terminus of the polymerase;the site flanking the polymerase from the N-side was lesseasily determined (see below). Sequences around these 4 sitesbear considerable similarity to each other. Especiallypronounced is the similarity between consecutive sitesdelineating each domain. It could be calculated that theprobability of the similarity between sites 3 and 4 beingfortuitous wae about 1O~&» and for cites 10 and 11 about1O~S, it could be shown that the similarity within thesetwo pairs was most prominent among all sequence stretchessurrounding Q/G,S dipeptides in Fl and F2.

Based on these observations, we further compared sequencesflanking all the 0/S,G dipeptides contained in the Fl and F2polyproteins to those surrounding the 4 tentatively identifiedcleavage sites (Fig. 6). Thus, 9 additional putative cleavagesites bearing some resemblance to the first 4 were identified(Fig. 6). A notable feature of all the 13 detected sites is thepresence of a hydrophobic residue (mostly L) in position -1which is thought to be most important for cleavage by 3C-likeproteases <31). Also of interest are peculiarities of sites 3and 4 flanking the putative 3C-like protease (F in position • 3and a positively charged residue in position -3) shared by site2. It is tempting to speculate that these may be specificrequirements for intramolecular cleavage. Some of the sequencesshown in Fig. 6 bear additional similarities to each other (forexample, sites 12 and 13), emphasizing the case for theirauthenticity. Finally, a striking resemblance is observedbetween some of the putative cleavage sites of IBV (especiallysites 1, 2 and 4) and the consensus (VRFQ/S,G) derLvad for thepolyprotein cleavage sites of one of the potyviruses, TVMV <2O> .However, contrary to what is observed in potyviruses (34,35),the C-flanking sequences of the putative coronavirus cleavage•it«8 are also somewhat siailar to each other <Fig. 6) and, byimplication, might be important for processing.

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12 13

TfT? T

POL ZnD HEL

2400

Fig.7. A scheie depicting possible organization of functionaldomains in the non-structural polyprotein of IBV.Fl and F2 polypeptides are shown to scale. Filled circles:putative cleavage sites numbered as in Fig.6; empty circles:Q/G,S dlpeptides whose flanking sequences bear no significantresemblance to those of the reference set (Fig.6) and which arethought to be not utilized. SPL, putative protease similar tothe S. pneuioniae protease; ZnD, putative Zn2*-bindingdomain. Regions of significant sequence similarity torespective viral or cellular proteins are shown in black. Otherdesignations as in Fig.6.

-Implications for coronavlrus polyprotein organization andexpression

Fig. 7 schematically summarizes what could be derived fromamino acid sequence of the coronavirus non-structuralpolyprotein(s) by computer-assisted comparisons. The approx.6600 amino residue polyprotein (provided Fl and F2 are actuallyjoined by translation frame-shift> may be provisionallyseparated into two vast regions, the N-temlnal one of about26OO residues, and the approx. 4OOO residue C-terminal one. TheC-terminal part encompasses the putative cleavage sites for the3C-like protease which are predicted to be cleaved (see above)and it is tempting to suggest that expression of this region ofthe polyprotein might be completely controlled by the 3C-likeprotease. In principle, cleavage at sites shown in Fig. 6might be sufficient for the generation of all the proteins ofIBV essential for genome replication and expression.Organization of the complex of these proteins (domains) isprincipally similar to that observed in other positive strandRNA viruses but certain interesting unique features are alsopresent. Specifically, the putative 3C-like protease may beflanked by two relatively small proteins having long N-terminalstretches of hydrophobic amino acid residues, presumablymembrane-spanning domains, which might influence theintracellular topology of the protease. Localization of the3C-like protease relative to the polymerase is also typical of

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other viruses having enzymes of this family, though a largedomain of unknown function is inserted between the twoconserved domains. This domain contains the EGF-like sequenceunique for IBV. The best guess concerning the function of thisdomain is that it might be involved in some special kind ofprotein-protein interaction. In fact, it is not clear what maybe the N-terminue of the polymerase, the size of this enzymevarying to a large extent among positive strand RNA viruses<cf. Flg.l and refs. 16,22). Still, site 9 separating theEGF-like sequence from the putative polymerase and bearing someresemblance to site 1O (Fig. 6> is the most plausible candidate.

What is unusual in the organization of the putativecomplex of replication proteins of IBV, is the mutualorientation of the polymeraae and helicase domains which isconversed as compared to that observed in other positive strandRNA viruses <6>. An interesting possibility is that this arraycould arise as a result of a recombinational event, highfrequency of recombination being a salient feature ofcoronavirus reproduction (1-3). Another unique feature ofcoronaviruees is the presence of the "finger" domain which,provided the cleavage sites are determined correctly, may bethe N-terminal part of the helicase (Fig. 7>. It has recentlybeen demonstrated that small finger proteins of retrovirusespossess RNA annealing activity and mediate positioning of thereplicative primer (a specific tRNA) on the viral genome (36).A similar role in the primer-dependent transcription andrecombination of the coronavirus genome (cf. 3) is plausiblefor the finger domain of IBV. These functions might beperformed in conjunction with the helicase domain. A putativesingle-finger domain has been identified also in the N-terminalportion of the polyprotein of another coronavirus, MHV (37). Noobvious similarity between this region and any IBV sequencecould be revealed. Evaluation of the significance of thisobservation awaits complete sequencing of the MHV genome.

In the N-terminal portion of the polyprotein, the onlydomain for which a function could be proposed is the putative2nd thiol protease. Possibly, it nay control processing of thisregion whose pathway as well as functions of the productsremain obscure. A possible exception is a 440 residue domain atthe very N-terninus of Fl flanked by one of the putativecleavage sites of the 3C-like protease (Fig. 7). Some sequencesimilarity has been detected between a portion of this regionand the replication initiation protein of the R6K plasmid (4,38). In the absence of any data about functional sites of thelatter, it is, however, difficult to assess the significance ofthis observation.

Generally, the identification, in IBV, of putative homologeof three conserved domains of positive strand RNA virusessuggests an evolutionary relationship between coronaviruses andother groups of this class. On the other hand, the uniquebiochemistry of coronaviruses seems to be reflected in theunusual arrangement of these domains, and in the presence ofadditional specific ones.

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CONCLUDING REMARKSThe findings reported here way prove inportant in several

dimensions. First, and most obvious, one may hope that thepredictions made night canalyze studies directed onexperimental dissection o£ coronavirus non-structuralpolyprotein(a). Second, the putative polynerase, helicase and3C-like protease of IBV, while related to the similar enzymesof other positive strand RNA viruses at a statisticallysignificant level, loosened the respective consensus patterns,thus providing a new groundwork for probing newly sequencedviral genomes. Finally, the general approach utilized also

' night be helpful in analysis of other genomes.

(,ACKNOWLEDGEMENTS

The authors are grateful to Professor V. I. Agol forencouragement and critical reading of the manuscript, to Dr. K.H. Chuaakov for help with programming, and to Dr. S. Yu.Morozov for helpful suggestions.

I,

"To whom correspondence should be addressed

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