Composite origin of major histocompatibility complex genes

Jan Klein and Colm O’huigin

University of Miami School of Medicine, Miami, USA and Max-Planck lnstitut fiir Biologie, Tiibingen, Germany

Major histocompatibility complex (MI-ICI genes have now been cloned from representatives of all vertebrate classes except Agnatha. The recent accumulation of sequence data has given great insight into the course of evolution of these genes. Although the primary structure of the M/-/C genes varies greatly from class to class and also within the individual classes, the general features of the tertiary and quaternary structure have been conserved remarkably well during more than 400 million years. of evolution. The ancestral M/-K genes may have been assembled from at least three structural elements derived from different gene families. Class II MHC genes appear to

have been assembled first, and then to have given rise to class I genes.

Current Opinion in Genetics and Development 1993, 3:923-930

Introduction

Some of the finest cathedrals in Europe were built over such a long time that they have become hybrids of different architectural styles; the foundations are Ro- manesque, the main body Gothic, and the towers, or at least their spires, baroque. Complex proteins, such as the major histocompatibility complex (MHC) molecules, seem to have a similar history, having grad- ually been put together over aeons from elements de- signed in different styles. The MHC molecule consists of three such elements, here referred to as modules: the peptide-binding module (PBM), the immunoglobulin- like module, and the membrane-anchoring module (Fig. 1). Each module is made up of domains de- rived from the two chains, a and j3, which consti- tute the MHC heterodimer, and is distinguished by a characteristic three-dimensional structure [I].

The peptide-binding domain (PBD) is characterized by an MHC fold-a half-sheet of four antiparallel p- strands connected by loops, and an a-helix that runs across the strands on one side of the half-sheet [2]. The two domains of the PBM form a full sheet-a floor of eight p-strands over which the two a-helices rise on both sides, almost parallel to each other. A large groove, which is capable of capturing and retain- ing peptides derived from other proteins, thus ensues. Amino acid residues that are important for the inter- action with peptides form the peptide-binding region

(PBR). In the class I MHC molecules, the two PBDs (al and a21 are provided by the same polypeptide chain (a>. In the class II molecules, on the other hand, the two PBDs (al and Bl> are provided by different chains (a and p>.

The immunoglobulin-like domain (ILD) has a very dif- ferent structure, namely that of an immunoglobulin fold-seven loop-connected, antiparallel p-strands ar- ranged into two sheets, which are sandwiched against each other and packed into a p-barrel [3,41. The two sheets, one consisting of four and the other of three p-strands, are held together by a single disulfide bond. In the class I MHC molecules, one ILD is part of the a-chain (the a3 domain), while the other is non-co- valently attached to it and also exists in a free form in body fluids as pz-microglobulin @2m), which is en- coded by a gene (B2m) not linked to the main MHC In the class II MHC molecules, each chain contains one ILD (the a2 and 82 domains).

The membrane-anchoring domain (MAD) consists of a connecting peptide, a transmembrane region, and a cytoplasmic tail. The configuration of the connect- ing peptide and the cytoplasmic tail is not known; the transmembrane region is believed to be coiled into an a-helix, with hydrophobic side chains facing the plasma membrane milieu 151. The class I MHC molecules are anchored to the membrane by a sin- gle MAD, which is part of the a-chain; in the class II molecules each of the two chains has a separate MAD.

Abbreviations f32m (B2m)-f3z-microglobulin (gene); Ig-immunoglobulin; ND-immunoglobulin-like domain;

IL-B-interleukin-8; MAD-membrane-anchoring domain; MHC-major histocompatibility complex; PBD-peptide-binding domain; PBM-peptide-binding module; PBR-peptide-binding region.

0 Current Biology Ltd ISSN 0959-437X 923

924 Genomes and evolution

Tral

Class I Peptide-binding

Peptide-binding module

Connecting oeotide

region 1

Cvtoplasmic 0

lmmunoglobulin- like module

Membrane- anchoring

module

Class II

Peptide-binding

>Connecting peptides

regions

tail tails Q 1993 Current Opinion in Genetics and Developmenl

Fig. 1. Structural elements of class I and class II MHC molecules. The three modules, the peptide-binding module, the immunoglobulin-like module, and the membrane-anchoring module, are derived from the a- and g-chains, which constitute the MHC heterodimer. In class I MHC molecules, the peptide-binding module is made up of two protein-binding domains from the a-chain, and the immunoglobulin-like module is made up of two immunoglobulin-like domains, one from the a-chain and the other being &-microglobulin t&m). Class I molecules are anchored to the plasma membrane by a single membrane-anchoring domain which is part of the a-chain. In class II MHC molecules, the peptide-binding module is made up of two peptide-binding domains, each from a different chain (one from the a-chain, the other from the g-chain), and the two immunoglobulin-like domains are from different chains (one from a, one from g). The class II molecules are anchored to the plasma membrane by two membrane-anchoring domains tone from a, one from g).

Origin of MHC domains

Structures similar to the PBD have recently been found in the interleukin-8 (IL-B) family of proteins. In addi- tion to IL-8 161, the family includes the platelet factor 4 (PF4) 171, monocyte chemoattractant factor (MCAF) 181, a growth-related protein 191, murine macrophage in- flammatory protein-2 (MIP) 1101, tLsrc inducible protein (9E3) 11 II, p-thromboglobulin 1121, and y-interferon-in- duced protein (W-10) 1131. The IL-8 molecule is a dimer of two identical polypeptide chains of 72 amino acid residues. Each monomer consists of three loop-con- nected antiparallel p-strands and an a-helix, so that the dimer forms a groove similar to that of the MHC-PBM. It differs from the MHC-PBM in that its floor is com- posed of six instead of eight p-strands, there is smaller separation between the helices (10A instead of 14A), and the angle at which the helices cross the B-sheet is 52’ instead of -45’ [61. No significant sequence similarity seems to exist between the PBD of the MHC and the IL-8 family of proteins.

Another potential relative of the MHC-I’BD may exist in the stock of the heat shock proteins. This stock consists of several families, distinguished (among other things)

by the molecular mass of their proteins 1141. Proteins with an M, of 70000 are known to facilitate folding and unfolding of intracellular proteins and their trans- port to specific organelles. They are either present in the cytoplasm under normal conditions (heat shock cognates, HSC70) or their expression is induced by heat shock or other forms of stress (heat shock pro- tein, HSP70). The HSC70 proteins form homodimers in which each monomer is comprised of two modules, an amino-terminal ATEase module and a carboxy-termi- nal peptide-binding module. The ATEase module has the same three-dimensional structure as actin [15,16]; the three-dimensional structure of the peptide-binding module has not yet been determined but its secondary structure has been predicted to be similar to that of the MHC-PBM 117,181. Interestingly, some of the h-p70 genes reside in the middle of the human MHC [19], and this association with the MHC is evolutionarily conserved (L Salter-Cid, M Kasahara, MF Flajnik, per- sonal communication). If it can be confirmed by X-ray crystallography that the three-dimensional structure of the HS1’70 peptide-binding module is indeed similar to the MHC-PBM, the postulated evolutionary tie between the two modules would be strengthened considerably.

Major hi&compatibility complex genes Klein and O’hUigin 925

The ILD is a member of a large immunoglobulin (Ig) superfamily that includes >30 different proteins 120,211. The superfamily is evolutionarily old, its roots reaching back at least as far as the divergence of the nematodes from the rest of the animal phyla 1221. All its members have at least one domain with the Ig-fold, but have otherwise acquired a variety of functions. Significant sequence similarity can be observed between the var- ious members of the superfamily, including the ILD of the MHC 1201.

Domains similar to the MAD of the MHC have been found in a variety of unrelated proteins 1231. The trans- membrane portion of the different proteins has a sim- ilar three-dimensional structure, which has apparently been acquired independently many times over by con- vergent evolution.

Originally, the PBD was thought to be derived from the ILD by exon duplication 124,251 and a number of arguments have been put forward to support this as- sumption. First, the PBD and ILD are of similar length, each being about 100 amino acid residues, and the main body of each domain is encoded in a single exon [Il. Second, the disulfide bond-forming cysteine residues of the ILD and of some PBDs are separated by approximately 60 residues ill. Third, weak sequence similarity exists between the ILDs of a carp class I molecule and the CD8 molecule, which is one of the members of the Ig-superfamily 1261. These arguments, however, are not convincing. First, there are other pro- tein superfamilies with domains that are also approx- imately 100 residues long but which are unrelated to the ILD, for example the cytokine receptor 1271 or the libronectin type II 1281 families. Second, there are pro- teins with domains in which the disulfide bond spans approximately 60 residues and which are not consid- ered to be members of the Ig-superfamily, for example superoxide dismutase 1291. Third, no MHC other than that of the carp shows significant sequence similarity of its PBDs with ILDs and the grouping of the carp PBD with ILD has a low bootstrap value 130**1 so that the similarity may be accidental.

We believe that the arguments suggesting that the PBD did not originate from the ILD are more convincing. First, the tertiary structure of the PBD is so different from that of the ILD that transformation of one into the other is difficult to imagine. Second, variants of the MHC fold exist in non-MHC proteins-in the IL-8 family of proteins 16,71 and possibly also in the heat shock protein family 117,181. The three-strand structure of the IL-8 half-sheet can easily be converted into the four-strand structure of the MHC-PBD half-sheet, or vice versa, by simple duplication, or deletion, of one strand-encoding segment in the corresponding exon. Although significant sequence similarity between IL-8 and MHC-PBDs could not be ascertained, and the re- ported similarity of HSP70 with MHC-PBDs 117,181 has been questioned 130**1, a lack of similarity in proteins that may have diverged more than 500 million years ago (see below) is not surprising. In general three- dimensional structure is more highly conserved than

primary structure [231, and hence the MHC-PBD could be derived from a protein of the IL-8 or HSP70 families, but the traces of its origin may have been obliterated at the level of the primary structure.

Model for the assembly of MHC molecules

On the basis of the foregoing arguments, we posit that during evolution, the MHC molecule has been assem- bled from three elements into which it can still be de- marcated-PBD, ILD, and MAD. These elements stem from different families which have evolved in parallel, producing other proteins with diverse functions. The MAD itself may have been put together from sub- units which may also be of independent origin (for simplicity we consider it as being a unit, and ignore the subunits encoded in different exons). Independent origin of PBDs and ILDs has also been postulated by Flajnik et al. 1181.

One possible scheme for the origin of the MHC is de- picted in Figure 2. We assume that early on in MHC evolution, an exon encoding a soluble ILD (perhaps resembling the B2m> was joined by a MAD exon, thus producing a prototypic membrane-anchored member of the Ig-superfamily. An exon coding for a domain with the MHC fold (PBD) and derived from another gene family was then added to the gene and an an- cestral class II-like gene was generated. We assume that the added element consisted of a single PBD exon; had it consisted of two PBD exons then a primitive class I gene would have been generated first. However, the derivation of a class II from a class I gene would require more steps than a derivation the other way around, and so we invoke the parsimony principle to solve this particular form of the chicken-and-egg problem. We assume that the ancestral class II gene was of the A variety (coding for the a-chain), be- cause in phylogenetic trees constructed from MHC- ILD sequences, class II a-chains are usually seen to diverge first, followed by class II &chains and then by class I a-chains 130**1. The order of the chain di- vergence is, however, difficult to decipher because the trees are not very robust and their topology is sensitive to sequence selection and alignment. Also, if any of the chains evolved faster than the rest, the available trees could be misleading. The ‘class II a-chain-first’ postu- late is, however, consistent with the similarity relation- ships between the PBDs (see below and [311X

In our scenario, the undifferentiated ancestral class II a-chains formed homodimers in the plasma mem- branes, and their grooves assumed the function of presenting foreign peptides to T lymphocytes of the CD4 category. The resulting immune response led to the production of Ig-based antibodies. This scheme requires MHC molecules, T-cell receptors, and Igs to have emerged simultaneously during evolution. After subsequent duplication of the ancestral class I A gene, the second copy began to evolve toward a class II B gene encoding class II &chains. In the plasma mem-

’ 926 Genomes and evolution

*

I”rI ’ +2-J&*

ILD lmmunoglobulin-like domain

PBD

Ancestra\;class IIA

1 Duplication

PBD PBD ILD

Ancestra!class IIA Ancestral class II6

Duplication

Ancestral’class IIA Ancestral class II6 Ancestral’class IIA Ancestral’class IIB

1 Deletion

Class IA Class IIA Class IIB

class IB (B2m)

@ 1993 Current Opinion in Genetics and Llevelooment

Ancestral Ig-family protein

Class H-like homodimers

Class II-like heterodimers

Class I Class II

L Fig. 2. Postulated origin of MHC class I and class II genes and proteins. An exon encoding a soluble immunoglobulin-like domain (ILD) is joined with an exon encoding a membrane-anchoring domain (MAD) to produce an ancestral immunoglobulin-family gene. This is joined by an exon encoding a peptide-binding domain (PBD) to produce an ancestral class II-like gene, assumed to be of the A variety (coding for the a-chain). Duplication and deletion events, along with sequence divergence would produce the present day array of class I A and class II A and B genes. The class I B gene is in fact the &-microglobin gene, which is not linked to the main MHC.

brane, homodimers were gradually replaced by as heterodimers which were selectively advantageous be- cause they provided a greater potential for PBR vari- ability. After subsequent duplication of the two-gene segment, and deletion of two exons in the manner shown in Figure 2, an ancestral class I A (a-chain encoding) gene emerged in which two PBD exons be- ‘came associated with single ILD and MAD exons. For steric reasons the class I a-chains probably could not form homodimers or heterodimers with class II chains, but they acquired pz-microglobulin, the product of a separate gene (B~wz), and by then already present

in the body fluids and used for other purposes. The non-covalent association with p2m enabled the class I a-chains to reach the cell surface and thus become functional immediately. The origin of the B2m gene remains a mystery. At least some phylogenetic trees show the fi2rn separating from class II a after the sepa- ration of the latter from class II p and class I a 124,30**1. However, this scheme would leave the ancestral class I a-chains without the p2m for a long evolutionary pe- riod, and hence unexpressed and non-functional. It is unlikely that class I A genes could survive such a pe- riod intact, and we therefore prefer to postulate that

Major histocompatibility complex genes Klein and O’hUigin 927

B2m diverged from class II A before the divergence of class II B and class I A from class II A genes. The cur- rent topologies of the (not very robust) phylogenetic trees could be distorted by differences in evolutionary rates among the genes or some other such factor. The postulate of ancient origin of the B2m also avoids the problems associated with the transposition of the gene to another chromosome (the MHC-ILD is encoded in one exon, the p2rn in three; the expression of the class II ILD is regulated differently from that of the p2m etc.).

Consistent with the proposed scheme is the similarity between the different PBDs. Both in its primary struc- ture (Fig. 3) and in its postulated 1321 tertiary structure, the amino-terminal PBD (al> of the class I a module is more similar to the PBD (al) of the class II chain than it is either to the class I a2 PBD or the class II pl PBD. By the same token, the class I a2 PBD is more similar to the class II f31 PBD than to the class II al PBD. These similarities suggest that the PBD exon first became associated with a class II ILD exon and that the ancestral class I gene was generated from a class II gene. The class I-first hypothesis would, as already stated, require the association, from the very beginning, of two PBD exons with one ILD exon, and also a more complex mechanism of derivation.

The age of the MHC

It is difficult to place a time scale on the events pos- tulated in Figure 2. Class I and class II molecules are now known to exist in all vertebrate phyla except the agnathan fishes (Table 1). So, the divergence of the dif- ferent chains must have occurred more than 400 mil- lion years ago. From the rate of non-synonymous sub- stitutions, Hughes and Nei [30**1 have calculated that the class II A and B genes separated more than 500 mil- lion years ago. The emergence of the MHC molecules in their present function, of presenting foreign pep- tides to T lymphocytes, must have been tied together with the appearance of the anticipatory system of im- munity and of T-cell receptors and immunoglobulins. We have argued elsewhere i331 that the anticipatory im- mune system .is a vertebrate (chordate) invention. We therefore expect the bona jide MHC to be restricted to vertebrates (chordates). The above age estimates are consistent with this expectation. The proposed scheme explains why class I A, class II A, and class II B genes are clustered in one chromo- somal region, and why the B2m gene is borne by a different chromosome. It is not true, however, as is sometimes claimed, that this is the only MHC clus- ter. MHC genes outside the main cluster have now

1 11 21 31 .l 51 61 71 81 91 ++ + +++ ++ + + +++ + + + ++ ++ +

NLA-DRA Rzwv=11QA rrYLNPoQsc E +*+**nuD rIlm*1,svD w*+***Alm mvNsL**w rGRrAsrEA* ceALA*NI*A VDnNLNnr lmsRYTP1m

--WW VADNVASYGV ULXQSYGPSC Q l ***+YTW WGDZQ,Y”D L**+***GNX LT”NCL**PV LSQPWDP’ WALT*N-I*A VlmNNaILI WsusfllTn WA-WA KADWYGP UYQSYCLSG Q l ****Fl!NS TDWQLWVD La+**•*KKS UVNRL*‘PE I(P?APSDP= QGGLWGPA AI-ILV WSNWWIN

II A SIrA-DPAl KwKv=sTxA AWQTNRPTG E'****nuz nxmluYm L*+****Dlu mvNm.**w rGQmsmA* QGGLA*uI*A ILNNBmmL 1 Q-WTQAm

(al) U*U-DUN t......... . . . . . . . . . . . . . . . . . . . . . . ..Dg- DL. . . . .Q,CJ( L'M(RG..pL ~S~SS~p' QccLR.m& TCKYNLDILI lmsunsms BSm-DSAl QMSR*DWr TGCSDTE*“K D**'**DLn; WGWEYNTD P*+'**IPX WV,‘TL”‘PD TADPYSWGG rRmxAmPL IcKQNLAlm KRYusPLLQL Gild-DAA l *LrD'mQv YnqQRsPrK fv***+mvM tDGnEIrYI5J r**+***nLu -**DE ?ANLnlQGG' WGISANPA WWULKWU NLSGGTPWK

++ + ++ + + + + + + + + ++ + ++ +

[

--Al *GSNS*~W YTSVSRPGRC L’PRIIAVGY VDDTQ- -QRWP NAPNIE*-Q WPCYNDQ~T RNVKAQSQ l * TDRVDIGTLR ‘XYNQSW-

WA-8 l GSNS*I(RW YTAUSRPGRG L*PRIIAVI;I VDDTQ- SDAASPNMAP WPUIL*+*Q WPLWDRRT QISKTNTQ- TWBSLRNLR GYYUQSU- l&A-c l CSNs’lmYr YTAVSIWGRG L*PRrIAvGY vDDTQ- SDAASPFSCP RAPWW***Q WPLYUDIILT QKYSRQAQ l * TDRvs- G X Y U Q S M ”

--OIL ‘GPNSWNlW YTGLTWGSG l *AlWLAVGY VDDQQ- TDSPSQRBW R*-VDQ WPG¶ltWQT GIISQTAQ'* TD-TSA GWNQSAG- Gaga-B-l

CIalA, Z-E&i

l CLNT*LRYI QTAUTDPGPG QWIWVWGY WC- ST’*APAWP RTSNI.W*AK AWQYNDGQT QIGQGUEQ l * IDWUIGIW RRYNQT’G”

l PSNS’LQW YTGVSEPGQG L*PQmnrcY VDGQLWQYD SU=*TREW.P RVSNIK*QN WSKINWQT QNLQGMP- VPWNINTAU NRXNQT*G** l GSILS*LRYI YTAVSDRUG L*PWSTVGY VDDIQIWYS SD’*TGWW AW*QK EGPI-T QKSKGIW** - DWNQS*T*+

.%SWXAl AVTNA*LKW YTASSKL’PUP l *P- WGVQWNW sIp”SQRAW KQDNVN**KR WPQYNWMT GIIIOCSQQ- -IAK QWUQS*G** ++ + ++ ++ + ++ +

[

WA-A *GSllT’IQIN YGCDVGPDGR I* -& YDGWYIALN sD**LwNTA ADUUQIk -*NME ‘*QQRAYLEG + ++

irLmnlmYL EucIILTLQ** NIA-B l GSN'IQRI( YccDvcpDGR L*LRGWQSA YDGKDYIALU W'*LSNTA NkTAAQITQR -*RIuL l *QLilAYLEG LcvmLRnrL KuGKwLQ** NLA-c l GSET*I&# YGCDLGPDGR L*LRGWQSA YDGWYIALN LB**LWCTA ADTAWITpR -*RAM -QQNAYLW TCWNLRRYL mGPzrLQ** Wuu-1TM ‘GVWPLQSM YGCEVSPZLR ?+QRW”QYA YDGQD- TL*‘TLl.“!A AWPAVSTW -+FSTA S*-YLW TCVLNWKYL EKKWLW’

(‘a23

Gmga-s-r l GSUT~ Yc(pII.EGGP I-RGYXOQ YDGRD~TAW KW’TUTYTA AWUWTKR KNEW*SW* ~‘INIWYLW TCVWLWYV LYGKULG** ham-XA *GLST*IIPIO( Y MLRI;DGS K-GGWQIG YDGWFZALD Io+*TLTNTA ADSEAQWKS IOID1L.W Q*- 1c1nlLQKm RYGNKTLL*’ Kda-UAA ‘GTNNWQw( YWLI;DM;S I**RCYLQNV YSESSIALD TV*WWVP SvRtAQLm XNNSP’NM PwnwYLQN ICIu3rmrL sYGQsDw** SaSa-KAl l GVNV*NQW‘ IGCBWDDEAG \rTEcrrp*c YDGWrIAW LK*‘TKSNI.A PTlmsvITw WDsn’TAQN WNWNYYTQ ICIZNUWXV DYGKSTIM-

++ + +++ ++ + + ++ ++ ++ + + ++ ++ +t rmwLwvKlucNw NGT EmRrLDRW YNQUYVRPD SD-VGWRA V’FSLGWDAS l-NNSQWLL* I*QSRAAVDT Y-tXTE WtVQ+****

WSPWWYQm QCWT’NGT WVRLVSRSI YMlpIVRPD SD*- VTLLGLPMm YNNsQwIL' t*-VDR v R-....’ l 'D#'PIQAK ADCWT*ffiT KPXQWVWI -- SD*- LTwGQPDAt QI(IsRLDLL* EwlsRQAvDG - PmuG***** l +UYLWQGR QECXAPWGT Q**RJI.WtYI YNWUARW SD*- -ME XNNSQKDIL+ L*-WDR YaslRpicc Pttl’I@*‘**

-LIL* t*-VDT LCNENWILE mw***** II B

hnl-DAB1 “D?L*WJAK SECWWUGT QNVNIWRW v SD+- VSWGRLQU l *WQ- ucNYL*lKx ERANFLERNI YnTlcQnmPD sD*wGKxvA DTPLGWQM INNSNAEIL* WD0mVDT TCRWXWW srrvp+*...

(Pl) ++DWWQNK SQCZYR*ffiT DNVRYLECYA UNQUTNPD SD-VGSYXA WD?GWQSK YNUSQKDLL* WQWAVVDT vcF2uIxQLxK PrTvD*‘**’ l =W**- TQCRYSSWL QGIWITSW WIFSN ST*- I- ABNlKGPL*L* AWXLGVLtR Y- ID1 sAIID*****

Auha-23la wGrL*SYsv DPsQrN.¶Tn WINIRKW -1IRIs ss**LmmG YTEYGvKQAD rmlNDKAIL* s+saQaQluT YtzmtNxGvDY SAILS*.*** &x9-Mm l *GR*QIP( LECIYSTWY WWLLWGS -VQXN ST-VGKYVG YTEQGVIrAR MPUWQNL+ Q*QPXUWS -1SD SAVW-•**

l GYY*Nsm TKcINsswr wlFrnDNYI FNWWIQFU ST*- YTALGWWK RWWPNIL* Q*QKMQWR KSNNAWYQ SAIW***” D-•CISL BRM**19T GWWLF@W WQXLIAYYD lN**QRIPIA VKANWWW NNNWGAU* Q*YWG**UA I CLBIIPIVY wAIA*****

Fig. 3. Alignment of amino acid sequences of class I al and a2, as well as class II al and 61, domains from nucleotide sequences of vertebrate genes. Amino acid residues are abbreviated according to the international single-letter code. Gaps (9 have been introduced to improve the alignment. The amino acid sequences have been translated from nucleotide sequences stored in the GenBank. Amam, Amieva amieva (Amieva lizard); Auha, Aulonocara hansbaenschi (cichlid fish); Brre, Brachydanio rerio (zebrafish); Cyca, Cyprinus carpio (carp); Caga, Gal/us gal/us (domestic fowl); Cici, Ging/ymostoma cirrafum (nurse shark); HLA, human leukocyte antigen; Maeu, Macropus eugenii (tammar wallaby); Maru, Macropus ru@@eus (red-necked wallaby); Sasa, Saalmo salar (Atlantic salmon); Xele, Xenopus laevis (clawed frog). For references. see Table 1.

928 Cenomes and evolution

Tablel. Current status of cloning MUC genes in different vertebrate groups.

Class I Class II

Group A f3 A B

Pisces Agnatha Chondrichthyes +[42*] +[43*,44*]

Osteichthyes ’ +[26,45] +[46*,47*] +[48*] +[26,49,50-,511 [52*,53,54**,55]

Choanichthyes +(a) Tetrapoda Amphibia +(b)[56,57**,58*] +ISS’l Reptilia +[58*,60*] Aves +[37*,61] +]62,63] +[64-67] Mammalia +[ll +I1 1 +I11 +I11

MHC genes have been cloned from representatives of all vertebrate classes except Agnatha. + indicates that the particular genes have been cloned and sequenced. References are to the original papers except in the case of mammals, for which a review reference is given. (a) U Betz, W Mayer and J Klein, unpublished data. (b) MF Flajnik, personal communication.

been found in mammals 134-361, birds 137’1, and am- References and recommended reading phibians (MF Flajnik, personal communication). Some of these genes are inactive and may be functionless (MF Flajnik, personal communication), while others appear to have acquired new functions. An example of the latter is the gene encoding the F? receptor involved in the transport of IgG molecules across the epithelium in suckling mammals [351. Other examples might be the CD1 [38,391 and zinc-a2-glycoprotein 1361 genes, whose functions are still not known, but which apparently evolved under functional constraints differ- ent from those imposed on the bona fide MHC genes [391. The Fc+ receptor genes apparently acquired their new function at the time of adaptive radiation of pla- cental mammals more than 70 million years ago [30**1, whereas the CD1 made the functional switch 250 mil- lion years ago, at the time of (or shortly before) the divergence of birds and mammals [30**1. Occasionally, MHCgenes are also acquired by viruses and then ap- parently ‘misused’ to thwart the immune response of the host [401. Evolution toward acquisition of a new function may also occur within the bona fide MHC In most species the cluster contains many more genes than are required for the presentation of foreign pep- tides to T cells. The extra genes could become harm- ful to the immune system were they expressed fully, as are the functional genes. Therefore, most of the supernumerary genes are inactivated and turned into pseudogenes, but some may become free to assume specialized tasks for the immune system [411 and per- haps even new tasks altogether.

Papers of particular interest, published within the annual period of review, have been highlighted hs:

of special interest of outstanding interest

KLEIN J: Nar~rrul Hisroy of rhe Major Hislocomprrtihility Compkx. New York: John Wiley; 1986.

BJORKMAN PJ, SAPER MA, SAMRAOUI B, BENN~II’ WS, STROMIN(;ER JL, WILEY DC: The Foreign Antigen Binding Site and T Cell Recognition Regions of Class I Histocompatibility Antigens. Nufzlre 1987, 329:512-518.

3. POI.JAK RJ, AMZEL LM, AMY HP, CHEN BL, PHUACKERLEY RP, SAUL F: Three-Dimensional Structure of the Fab’ Fragment o’ a Human Immunoglobulin at 2.8i Resolution. Prcx Narl Acad Sci USA 1973. 70:330%3310.

4. ?AOWN EA, SECAL DM, SPAND~: TF, DAVIS DR. RU~IKOFF S, POllFR M: Structure at 4.5fi Resolution of a Phusphorylcholinc-Sinding Fab. Nat New Btol 1973, 245:16%i67.

5.

5 t .

C S.<WN P. BONIFACINO JS: Role of Transmcmbranc Domain Interactions in the Ajsembly of Class II MHC Molecules. Scfence 1992, 258:65+662.

BALDWIN ET, WEUER IT, ST CHARLU R, Xuruv J-C, APPELLA E, YAMADA M. MATSUSHIMA K, EDWARDS BFP, CLORE GM, GRONENUORN AM, WLODA\VER A: Crystal Structure of Intcr- lcukin 8: Symbiosis of NMR and Crystallography. Proc NutI Acsd Sci USA 1991, 88:502-506.

7. ST CHARLFS ;‘., WALZ DA, EDWARDS BFP: The Three Dimcn- sional Stuctunz of Bovine Platclct Factor 4 at 3.Oi Resole tion. J Bfol Chem 1989. 264:2092-2099.

8. FURUTANI Y, NOMURA H, NOTAKE M, OYAMADA Y, FUKU T, YAMADA M, LARSEN CG, OPPENHEIM JJ, MATSUSHIMA K: Cloning and Sequencing of the cDNA for Human Mane cytc Chcmotactic and Activating Factor. Bfocbem Stopby Res Comm 1989. 159:249-255.

Acknowledgqnents

We thank Lynne Yakes for editorial assistance and Anita Milosev for the preparation of the computer graphics.

9. ANISOWICZ A, BARDWELL L. SAGER R: Constitutive Overcxprcs sion of a Growth-Regulated Gene in Transformed Chinese Hamster and Human Cells. Proc Narl Acad Scl USA 1987, 84:7188-7192.

Major hi&compatibility complex genes Klein and O’hUigin 929

10.

11.

12.

13.

14.

15.

16.

17.

18.

19.

20.

21.

22.

23.

24.

25.

26.

27.

28.

29.

WOLPE SD, SHERRY B, JUERS D, DAVA~‘EI.IS G, YuR’r RW, CEKAMI A: Identification and Characterization of Macrophagc Inflammatory Protein 2. Proc Nat1 Acad Set USA 1989, 86:612416.

SUCANO S, SI’OEKLE Y, HANAFUSA H: Transformation by Rous Sarcoma virus Induces a Novel Gene with Homology to a Mitogcnic Platelet Protein. Cell 1987. 49:321-328.

HOLT JC. HARRIS ME, Hoi.‘r AM, LANCE E, NENSCHEN A, NIEWIAROSWSKI S: Characterization of Human Platelet Basic Protein. a Precursor Form of Low-Affinity Platelet Factor 4 and BThromboglobulin. Bfocbemlstty 1986, 25:1988-1996.

LUSXR AD, UNKELE%% JC, RAV~XH JV: Gamma-Interferon Transcriptionally Regulates an Early-Response Gcnc Con- taining Homology to Platelet Proteins. Nature 1985, 315:672-676.

LINI~IJISI’ S, CRAIG, EA: The Heat Shock Proteins. Annu Rev &net 1988, 22:631-677.

FIAHER’I~ KM, DELUCA-FIAHEKIY C, MCKAY DB: Three-Di- mcnsional Structure of the ATPasc Fragment of a 70K Heat-Shock Cognate Protein. Nature 1990, 346:623-628.

KAI~CH W, MANNHE~~Z HG, SUCK D, PAI EF, HOI.YFS KC: Atomic Structure of the Actin:DNase I Complex. Nature 1990, 347L37-44.

KIPPMANN F, TAYLOR WR, R~XHIIARI) JB, GREEN NM: A Hy- pothetical Model for the Pcptidc Binding Domain of Hsp70 Based on the Pcptidc Binding Domain of HIA. IzMBO J 1991. 10:10531059.

FIAJNIK MF, CANEL C, KIXA.MER J. KASAHARA M: Which Came First, MHC Class I or Class II? Immtrnogmetics 1991, 33:29>300.

SARGENT CA, DUNHAM I, TR~WSI,AI.E J, CAMPIIEI.L RD: Human Major Histocompatibility Complex Contains Genes for the Major Heat Shock Protein HSP70. hoc Nat1 Acud Scf USA 1989. 86:196t?-1972.

WILLIAMS AF, BARCLAY, AN: The Immunoglobulin Supcrfam- ily - Domains for Cell Surface Recognition. Annzc Rev Itn- munol 1988, 6381405.

HUNKAPII.LER T, HOOD L: Diversity of the lmmunoglobulin Gene SupcrfamiIy. Adv Immrrnol 1989, 44:1-63.

BENIAN GM, KIFF, JE, NECK~LMANN N, MOERMAN DG, WAIFRSI’ON RI-I: Sequence of an Unusually Large Protein Implicated in Regulation of Myosin Activity in C. elegans. Nature 1989, 342:45-50.

BRANDEN C. Toox J: Introduction to Prorein Stnrctwe. New York: Garland Publishers; 1991.

HOOD L, KRONENBERG M, HUNKMILLER T: T Cell Antigen Receptors and the ImmunogIobuIin Supcrgcnc Family. Cell 1985, 40:225-229.

OHNISHI K: Domain Structure and Molecular Evolution of Class 1 and Class 11 Major Histocompatibihty Gene Complex. MHC Products Dcduccd from Amino Acid and Nuclcotidc Homologies. O@fn.s 01 Ll/e 1984, 14:707-716.

HASHIMOTO K, NAKANISHI T, KUROSAWA Y: Isolation of Carp Gcncs Encoding Major Histocompatibility Complex Antigens. Proc Narl Acad Sci USA 1990. 87: 6863-6867.

GEARING DP, KING JA, GOUGH NM, NICOLA NA: Expression Cloning of a Rcccptor for Human GranttIocytc-Macrophagc ColonyStimulating Factor. EMBO J 1989, 8:3667-3676.

KORNBIJHIT AR, UME~WA K, VIBE-PEDERSEN K, BARALLE FE: Primary Structure of Human Fibroncctin: Differential Splic- ing May Generate at Last 10 Polypcptidcs from a Single Gcnc. EMBO J 1985, 4:1755-1759.

RICHARDSON JS, RXHARDSON DC, THOMAS KA, SILVERTON EW, DAVIES DR: Similarity of Three-Dimensional Stntcturc Ftctwccn the 1mmunogIobulin Domain and the Copper,

Zinc Supcr-Oxidc Dismutasc Subunit. J Mol Blol 1976, 102:221-235.

30. HUGHES AL, NEI M: Evolutionary Relationships of the Classes . . of Major Histocompatibility Complex Gcncs. Immtinogener-

its 1993, 37:337-346. This pper represents an attempt fo construct the phylogenetic tree of the MHC and rebdted proteins. Class II a-chains are found to be related to &microglobulin and class II bhains to class I a-chains. The authors argue that MHC class I did not evolve by recombination with HSWO. and that MHC class II evolved first.

31.

32.

33.

34.

35.

36.

37. .

KAUFMAN J: Vertebrates and the Evolution of the Major Histo compatibility Complex (MHC) Class I and Class II Molecules. Verb Dtscb Zoo1 Ges 1988, 81:131-144.

BROU~N JH, JARDIXKY T, SAPER MA, SAMRAOUI B, BJORKMAN PJ, WILEY DC: A Hypothetical Model of the Foreign Antigen Binding Site of Class II Histocompatibility Molecules. Nurtcre 1988, 3323845-850.

KLEIN J: ti Invcncbratcs Capable of Anticipatory Immune Response? Stand J Immtinol 1989, 29~499-505.

MARION LH, CALABI F, MILSTEIN C: Isolation of CD1 Genes: A Family of Major Histocompatibiity Complac-Related Dii fcrcntiation Antigens. Proc Nat1 Acad Sci USA 1986, 83:9154-9158.

SIMI~R NE, Moslpv KE: An Fc Receptor Structurally Rc- latcd to MHC Class I Antigens. Nature 1989, 3373184-187.

ARAKI T, GEJYO F, TAKAGAKI K, HAUPT H, SCH\WICK G, BURGI W, MARTI T, SCHMLER J. RICKLI E. BROSSM~R R, m AL.: Corn plctc Amino Acid Sequence of Human Plasma Znafilycc+ protein and its Homology to Histocompatibility Antigens. Proc Natl Acud Set USA 1988, 85~679-683.

BRILE~ WE, Golo RM, AUFFRAY C, MILLER MM: A Polymor phic System R&ted to but Genetically Indcpcndcnt of the Chicken Major Histocompatibility Compla. Immunogenel- fci 1993, 37:408-414.

Evidence is provided that the domestic fowl has at least two inde- pendently segregating MHC systems.

38.

39.

40.

41.

42. .

CALAL)I F, JAR~IS JM, MAR~N L, MIUXIN C: %o Classes of CD1 Gcncs. Eur J Immwtol 1989, 19:28%292.

HUGHES AL Evolutionary Origin and Diversification of the Mammalian CD1 Antigen Genes. Mol Bfol Et& 1991, 8:18%201.

BECK S, BARRELL BG: Human Cytomcgalovirus Encodes A Glycoprotcin Homologous to IMHC Class I-Antigens. Nature 1988, 331:269-272.

WANG C-R, LIVING.STONE A, BUTCHER GW, HERMEL E, HOWARD JC, FISCHER LINDAHL K: Antigen Prcscntation by Neoclv sical MHC Class I Gcnc Products in Mutinc Rodents. In Molecular E~lirtion of rbe Major Histocompatibility Com- plex. Edited by Klein J, Klein D. Heidelberg: Springer Verlag; 1991:441-462.

HASHIMOTO K, NAKANISHI T, KUROSAWA Y: Identification of a Shark Scqucncc Rcscmbling the Major Histocompatibility Compla Class I a3 Domain. Proc Natl Acad Scl USA 1992, 8922-2212.

A short nucleotide sequence (exon 41, interpreted by the authors to be that of a shark class 1 gene, is presented.

43. USAHARA M, VAZQIJEZ M, SATO K, MCKINNEY EC, ~AJNIK . MF: Evolution of the Major Iiistocompatibility Compla: b

lation of a CIass II A Gcnc from the Cartilaginous Fnh. &oc Nat1 Acad Set USA 1992, 89:6688&92.

Description of the entire coding sequence of a shark class II A gene and thus a demonstration that cartilaginous fishes possess both class I and class II genes.

44. KASAHARA M, MCK~NNEY EC, FLAJNIK MF, ISHIDASHI T: The . Evolutionary Origin of the Major Histocompatibiity Cotn-

pla. Eur J Immtrnol 1993, in press.

930 Genomes and evolution

The shark class 11 A genes were found to be polymorphic with much of the polymorphism concentrated in exon 2. The genes are there- fore likely to be functional.

45. GIUMHOLT U, HORDVIK I, Foss~. VM, OWAKER I, ENDHE~:SEN C. LIE: Molcular Cloning of Major Histocompatibility Corn pla Class 1 cDNAs from Atlantic Salmon (S&no salar). Immunogenetics 1993, 37:46w73.

46. DIXON B. STI?I’ RJM. VAN ERP SHM. POHAJUAK W: Charac- . tcrization of BzMicroglobulin Transcripts from ho Tclcost

Species. Immrrnogenetics 1993, 38~27-34. see 147.1.

47. ONO H, FIGLJ$ROA F, O’HUIGIN C, KLEIN J: Cloning of the fir . Microglobulin Cknc in the Zebra&h. Immunogenetics 1993.

3&l-10. This and [46*1 provide the first evidence for the existence of flz-mi- croglobulin In teleost fishes.

43. SOLTMANN H. MAYER WE, FICLIEROA F, O’HUIGIN C, ICLEIN . J: Zebrafish MHC Class 11 a Chain-Encoding Genes: Poly-

morphism, Expression and Function. Immunogenefiu- 1993, 38:4OW20.

This is the first demonstration of class II A genes in teleost fishes. The promoter region of the gene is conserved, the gene is transcribed and polymorphic. Like the DMA gene, but unlike the mammalian class 11 A genes, the zebrafish gene codes for two cysteine residues which might potentially be involved in the formation of a disuffide bond in the al domain.

49. JUUL-MADSEN HR. GLAMANN J, MADSEN HO, SIMONSEN M: MHC Class II beta<hain Expression in the Rainbow Trout. Stand J Immunol 1992, 35687694.

50. ONO H, KLEIN D, VINC~K V, FICUEROA F. O’HUIGIN C, . . TICHY H, KLEIN J: Major Histocompatibility Compla Class

II Genes of the Zebrafish. Proc Nat1 Acad Scl USA 1992. l39:11~11890.

A class 11 E locus of a teleost fish is highly polymorphic and the polymorphism is concentmted In positions corresponding to the peptide-binding region of the mammalian class 11 B genes. The fish gene evolves under positive selection pressure. Hence the fish and mammalian genes are functionally equivalent.

51. ONO H, O’HUIGIN C, VINCEK V, Sill- RJM, FIGUEROA F, KLEIN J: New p Chain-Encoding MHC Class 11 Genes in the Carp. Immrcnogenetkzs 1993, 38~146149.

52. ONO H, O’HUIGIN C. VINCEK V, KLEIN J: Axon-lntron Orga- . nization of Fish Major Histocompatibility Compla Class 11

B Genes. Immunogenetics 1993, 38:223234. The organization of class 11 Egenes in teleost fishes (cichlids) is sIm- IIar to that found In mammalian genes. The introns are, however, considerably shorter than those of mammalian genes. Some teleost fishes have an extra intron that splits the 62 domain-encoding exon Info two.

53. 0~0 H, O’HUIGIN C, TICHY H, KLEIN J: Major Histocompat- ibIIly Compla Variation In lkvo Species of Cichlid Fishes from Lake Malawi. Mol Bfol EL& 1993, 10:1060-1072.

54. KLEIN D, ONO H, GOLD~CHMIDT T, O’HUIGIN C, VINCEK V, . . KLEIN J: Extensive MHC Variability in Cichlid Fishes of Lake

Malawi. Nancre 1993, 364:330-334. This paper and 1531 demonstrate that MHC polymorphism present in the founding population segregates Into adaptively radiating species which have orIgIIted from this population. MHCgenes could rhere- fore become Important markers for the study of speciation.

55. HORDWK I, GRIMHOLT U, F~SSE VM, LIE 0, ENDRESEN C: Cloning and Sequence Analysis of cDNAs Encoding the

MHC Class 11 fi Chain in Atlantic Salmon (tilmo salar). Immwtogenetlcs 1993, 37:437441.

56. FLAJNIK MF, CANAL C, KRAMER J, KASAHARA M: Evolution of the Major Histocompatibility Complex: ~Molccular Cloning of Major Histocompatibility Complex Class 1 from the Amphib ian Xenopus. PIW Nat1 Acad Sci USA 1991, 88:537-541.

57. SHUM BP, AVILA D, Du PA.SQUIER L, KASAHARA M, FIAJNIK . . MF: Isolation of a Classical MHC Class 1 cDNA from an

Amphibian: Evidence for Only One Class 1 Locus in the Xenopus MHC. J lmmunol 1993, in press.

In polyploid Xenopzu- species, the duplicated class 1 genes are inac- tivated during evolution so that only one gene remains functional. 58. GROSSBERGER D, PAHHAM P: Reptilian Class 1 Major Histo . compatibility Complex Genes Reveal Conserved Elements

in Class 1 Structure. Immllnogenetia 1992, 36:166-174. The first repon on cloning reptilian class 1 genes.

59. SAIW K, FL.4JNlK MF, DU PASQIJIER L, KATAGIRI M, KA.~AHNIA . M: Evolution of the IMHC: Isolation of Class 11 whain

cDNA Clones from the Amphibian Xenopus laevls. J Im munol 1993, 150:2831-2843.

The first report on the cloning and characterization of amphibian CkIss II B genes.

60. BECKER 13, CASE 7. MILLER RD, lirn1.k~ R: Comparisons of . Class 1 Variation in Sexual and Parthenogenetic Geckos. &CJC

Nat1 Acad Sci USA 1993, in press. Asexual lineages in geckos show little or no MHC class 1 A Rcne diversification over thousands of generations. 61.

62.

63.

64.

65.

66.

67.

KROEMER G, ZOORO~ R, AUPPRAY C: Structure and Expression of a Chicken IMHC Class I Gene. Immtrnogeneflcs 1990, 3 1:405-w. WELINDER KG, J~PRRSEN HM, WALTHER-KAS#USSEN J, SKJ~DT K: Amino Acid Sequences and Structure of Chicken and Turkey bcta2 Microglobulin. Moi Immrcnoll991, 28:177-182. KAUFMANN J, ANIIEHSEN R, AVILA D, ENGBERG J, LAMURIS J, SALOWONSEN J, WELIND~IR K, SKJ@DT K: Different Features of the MHC Class 1 Hctcrodimcr have Evolved at Different Rates. J Immunol 1992, 148:1532-1546. BOLJRL~ Y, BI?HAR G, GUILLEMOT F, FRECHIN N, BILWLJLT A, CHAUSSC A-M, ZWROR R, AuFYRAY C: Isolation of Chicken Major Histocompatibility Compla Class 11 (BL) fl Chain Sequences: Comparison with Mammalian p Chains and Ex- pression in Lymphoid Organs. EMBO J 1988, 7:1031-1039. GLJILLEMOT F, BILLALILT A, POURQLJI~ 0, BIHAR G, CHAUSSC A-M, Z~~ROB R, KREIBICH G. AUFFRAY C: A Molecular Map of the Chicken Major Histocompatibiliry Compla: the Class II b Genes are Closely Linked to the Class 1 Genes and the Nuclcolar Organizer. !%fBO J 1988,7:2775-2785. Xu Y, PITCOVSKI J, Pt?n%oN L, ALJITRAY C, BOLIRL~ Y, GERNDT BM. NORDSKOG AW, LAMONT SJ, WARNER CM: lsola don and Characterization of Three Class 11 MHC Genomic Clones from the Chicken. J Immunol 1989, 142:2122-2158. ZOOROB R, BI?HAR G, KROEMER G, AUFFRAY C: Organization of a Functional Chicken Class 11 B Gene. Immrmogeneflcs 1990, 31:179-187.

J Klein, Department of Microbiology and Immunology, University of Miami School of Medicine (R-1381, Room No. 3152, 1600 NW 10th Avenue, Miami, Florida 33136, USA. C O’hUigin, Max-Planck-lnstitut fir Biologie. Abteilung lmmun- genetik, Corrensstrasse 42, D-72076 Tiibingen, Germany.