Rise of Adaptive Immunity

8/3/2019 Rise of Adaptive Immunity

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Th adaptiv imm sstm (AIS) is fasciatigt bth scitists ad lam: w hav a spcific ticrdibl divrs sstm that ca fight mriad pathgs ad has a mmr th basis f vacciati that abls a rapid rsps t prvisl ctrd pathgs. Th cmplxit f imm rspsrglati rivals that f th rvs sstm i trmsf th cct is frgd ad spprssd btwclls, bt imm clls mst als travrs th bdthrgh bld, lmph ad tiss til th ctrivadig rgaisms. Hw did sch a sstm aris, adca stdis f mammalia vrtbrats hlp s tdrstad th immit gstalt?

Atibdis wr discvrd vr 100 ars ag, admajr qstis rlatig t th grati f divrsitwr slvd i th 1970s with th dtcti fsomatic

hyprmutation1 advariabldivrsityjoining rarrangmnt(VDJ rarragmt)2 f atibd (r immunoglobulin (Ig) r B cll rcptr (BCR)) gs. I th 1980s, T cllrcptrs (TCRs) wr discvrd ad thr was i

vrsal agrmt that th shard a cmm acstr with BCR gs, basd thir similar dmairgaizati ad rliac th sam rarragmtmchaism t grat divrsit3. Aftr th discvrf zms that ar ivlvd i th rarragmt fBCR ad TCR gs4 ad f hprmtati f BCRgs5, attti shiftd t askig hw a sstm thatis capabl f gratig sch divrsit vlvd. Jawdfish wr fd t hav almst all f ths gs ad

mchaisms, bt jawlss fish (Agathas) appartlhad . This mstifig fidig ld t th big bagthr f AIS mrgc6, which is f th maitpics f this Rviw.

Th discvr i jawlss fish f a lmphid cllbasdsstm f adaptiv immit that is strikigl similar tth sstm i jawd fish was a ttal srpris7. Th sstm i jawlss fish is similar t VDJ rarragmt bthas rarragig rcptrs that ar cdd b athrg famil th variabl lmphct rcptr (VLR)famil. W discss th cmpllig pssibilit that thVLR rarragmt prcss is dr th ctrl fth sam famil f zms that ar rspsibl frsmatic hprmtati f BCR gs8, which pshs thrigis f acqird immit back t th acstr f all

vrtbrats. Hwvr, dspit this w fidig f adap

tiv immit i jawlss fish, th big bag thr ccrig th rigi ad rapid dvlpmt f th highlcmplx BCR ad TCRbasd AIS rmais itact.

I this Rviw, w dscrib th basic fatrs f BCRs,TCRs ad th major histocompatibility complx (MHC)ad strss thir prsrvati ad mdificati vr vltiar tim. W th discss th tw catastrphic,ivativ vts bhid th big bag rigis f thBCRTCRMHCbasd AIS th rcmbiatiactivatig g (RAG) trasps ivasi ad gmwid dplicatis arl i vrtbrat histr ad wdiscss th w tp f AIS that has b discvrdi jawlss fish. Fiall, w spclat th rigis f

*Department of Microbiology

and Immunology, University

of Maryland at Baltimore,655 West Baltimore Street,

Biosciences Research

Building 3056, Baltimore,

Maryland 21201, USA.Department of Pathology,

Hokkaido University

Graduate School of Medicine,

North 15 West 7, Sapporo

0608638, Japan.

emails: mflajnik@som.

umaryland.edu; mkasaha@

med.hokudai.ac.jp

doi:10.1038/nrg2703

Publishd onlin

8 Dcmbr 2009

Somatic hypermutation

Mutation of th variabl gn

aftr matur B clls ar

stimulatd. It rsults in affinity

maturation of th antibody

rspons. Lik th class switch,

it rquirs activation-inducd

cytidin daminas.

Origin and evolution of the adaptiveimmune system: genetic events andselective pressuresMartin F. Flajnik* and Masanori Kasahara

Abstract | The adaptive immune system (AIS)in mammals, which is centred on lymphocytes

bearing antigen receptors that are generated by somatic recombination, arose approximately

500 million years ago in jawed fish. This intricate defence system consists of many molecules,mechanisms and tissues that are not present in jawless vertebrates. Two macroevolutionary

events are believed to have contributed to the genesis of the AIS: the emergence of the

recombination-activating gene (RAG) transposon, and two rounds of whole-genome

duplication. It has recently been discovered that a non-RAG-based AIS with similarities to

the jawed vertebrate AIS including two lymphoid cell lineages arose in jawless fish by

convergent evolution. We offer insights into the latest advances in this field and speculate

on the selective pressures that led to the emergence and maintenance of the AIS.

R E V I E W S

nATuRe ReVIeWS |Genetics VoLuMe 11 | JAnuARy 2010 |47
mailto:[email protected]:[email protected]:[email protected]:[email protected]:[email protected]:[email protected]:[email protected]:[email protected]


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Innate immunity based on pattern-recognition receptors

TCR, BCR and MHC

Adaptive immunity based on rearranging antigen receptors

VLR

(Mya)

APARVLR-like

VCBP

TLR, NLR and SR

NICIR

222

476

326

525

891

652

370

896

794

Bonyfish(sturgeons)

Amphibians(frogs)

Reptiles(snakes)

Birds(chickens)

Mammals(humans)

Bonyfish(zebrafish,me

dakafish)

Cartilaginousfish(shark

s)

Cyclostomes(lampreys)

Echinoderms(seaurchins)

Cephalochordates(amphioxi)

Urochordates(seasquirts)

Cyclostomes(hagfish)

Hemichordates(acornworms)

3R

RAG1 and RAG2RAG1/2-like

RAG1-like

2R

1R

adaptiv immit i all vrtbrats, mphasizig thlsss w hav lard frm xtat imm sstms.

The AIS of jawed vertebrates

Th mst vltiaril acit xtat rgaismsi which th AIS, as dfid i hmas, is fd arth cartilagis fish. It is blivd t hav aris i thfirst jawd vrtbrats (gathstms) th placdrms(FIG. 1). Cmpts f th iat imm sstm, frxampl, pattrrcgiti rcptrs (PRRs) icldig th Tlllik rcptrs (TLRs), ndlik rcptrs (nLRs) ad scavgr rcptrs (SRs) ar fdthrght th aimal kigdm (FIG. 1). I sm ivrtbrats, sch as th sa rchi9, ad i ma plats10thr has b a grat xpasi f PRR familis, whichsggsts that i th absc f a AIS, cmplx iatmchaisms might b rqird fr dfc.

Lmphid clls th cr f th AIS ar firstfd i prvrtbrat dtrstms (that is, thsar th mst vltiaril acit livig phlgticgrp i which lmphid clls ca b fd). Th AIS

rqirs a larg pplati f clls i ach idividal tprmit clal slcti f clls with rcptrs spcific fra particlar pathg. Largbdid vrtbrats wr thfirst rgaisms t flfil this rqirmt (FIG. 1). Hr,w discss imprtat fatrs f th AIS i jawd vrtbrats ad csidr thir csrvati r plasticitvr vltiar tim. Th ccpt f plasticit wasfirst prpsd b Kli ad cllags i th ctxt fMHC mlcls11, bt ca b xtdd t all fatrsf th AIS.

B cell receptors

Immunoglobulin M. Lik mst mlcls f th AIS asdfid i hmas, amg livig aimals Igs ar firstfd i cartilagis fish (sharks, skats, ras adchimaras r ratfish) ad ar gratd b a smaticrcmbiati mchaism. Thir vltiar fatrsar smmarizd i FIG. 2a. IgM is th mst acit atibd class ad has th sam fcti i all gathstms12.Th trasmmbra frm f IgM dfis thB cll liag. Aftr B cll stimlati b a atigad cgat itractis frm T clls this istpis scrtd it th plasma as a mltimric prti.I b fish, IgM is scrtd as a ttramr i diffrt rdcti r xidati stats that sm t mdifth bidig strgth f th atibdis13. I cartilagis fish, IgM is a abdat scrtd mmr; this

scrti crrlats with a switch t a highr affiitrsps14. It is t kw whthr a cll prgrammdt prdc mltimric IgM switchs t prdc thmmric frm r whthr sharks hav liags fB clls that ar spcializd t mak ithr th mltimricr mmric Ig. Dspit ths mdificatis i fish,IgM is grall vltiaril csrvd.

Immunoglobulin D. Th fcti f IgD rmais prldrstd. It had grall b thght t b a vltiar wcmr, prbabl arisig i mammals (FIG. 2a),bt th dtcti i b fish15 ad frgs16,17 f a Ig istp that rsmbls IgD shwd that this is t th cas

Figure 1 | Ow o ouo o mmu ym uoom.

The stages in phylogeny at which the immune molecules referred to in this Review

emerged. Molecules restricted to jawed and jawless vertebrates are indicated in blue

and green, respectively. Molecules that emerged at the stage of invertebrates are in

pink. Recombination-activating gene (RAG)-like genes (indicated in purple) are of viral

or bacterial origin (from the transib transposon family) and are also present in the

genomes of sea urchins and amphioxi. Agnathan paired receptors resemblingantigen receptors (APAR) and novel immunoreceptor tyrosine-based activation

motif-containing immunoglobulin superfamily receptor (NICIR, also known as T cell

receptor (TCR)-like) are agnathan immunoglobulin superfamily (IgSF) molecules that are

thought to be related to the precursors of TCRs and B cell receptors (BCRs). 1R and 2R

indicate the two rounds of whole-genome duplication (WGD). Whether the 2R, the

second round of WGD, occurred before or after the divergence of jawed and jawless

vertebrates is controversial; the figure places it after the divergence according to the

commonly held view (BOX 2). An ancestor of the majority of ray-finned fish is thought to

have experienced an additional, lineage-specific WGD (designated as 3R) ~320 million

years ago134,135. The divergence time of animals (shown in Mya (million years ago)) is

based on Blair and Hedges136. MHC, major histocompatibility complex; NLR, Nod-like

receptor; SR, scavenger receptor; TLR, Toll-like receptor; VCBP, V-region containing

chitin-binding protein; VLR, variable lymphocyte receptor.

R E V I E W S

48 | JAnuARy 2010 | VoLuMe 11 www.au.om/w/g


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Vn

Dn

Jn

Dn

C CCJn

Mammal Vn

Dn

Jn

C C C others

V D D J C/

C

Mammal

CJV

Mammal C

Mammal

Mammal

Mammal

Translocon

Cluster

Translocon

Cluster:some germline-joined

Translocon

Translocon or cluster

Translocon

Double V (one rearranging):cluster + germline-joined

Double V (two rearranging):cluster + translocon

Mammal

n

V D D D J CNAR

Vn

Dn

Jn

CVn

Jn

Vn

V D J V D J

V D J V Vn

Jn

CD

Vn

Jn

Jmany

D13 C C

Primordial Ig Transmembrane

form defines B cells Pentamer/hexamer

in most vertebrates Tetramer in teleosts Secreted monomer

in cartilaginous fish (associated with

affinity increase)

Primordial Ig Highly plastic in

evolution Lost in several

species Known as IgW

in several fish Secreted form

associated withgranulocytes andinflammation

Derived fromIgY-likeancestor

First appearedin amphibiansand the classswitch

Derived fromIgY-likeancestor

First foundin reptiles

Dimer insecretions,monomer in sera

Mucosal Igs inother vertebratesvia convergence(e.g. IgX in frogs)

Derived formofbona fide IgG

Single-chain Vconvergentwith a similarform, IgNAR, incartilaginousfish

IgM

a

b

IgD IgG IgE IgA Camelid IgG

Ig H chain, amphibians

Ig H chain, bony fish

Ig H chain, cartilaginous fish

Ig L chain, bony fish

Ig L chain, bony and cartilaginous fish

TCR, cartilaginous fish

TCR, cartilaginous fish

TCR, bony fish

TCR, marsupials(form of)

NAR-TCR, cartilaginousfish (form of)

n

n

n

n

n

V, , J, , C,,

V, , J, , C,,

n n

Variablediversityjoining

rearrangement(VDJ rarrangmnt.) Th

rcombination-activating gn

(RAG)-mdiatd ligation of

T cll rcptor or B cll

rcptor variabl (V), divrsity

(D) and joining (J) gn

sgmnts during lymphocyt

ontogny, which gnrats th

antign rcptor rprtoir.

Immunoglobulins

Also known as antibodis or

B cll rcptors, thy ar

composd of two idntical

havy (H) and light (L) chains

that ar covalntly linkd by

disulphid bonds. Monomric

immunoglobulins ar bivalnt,

and th binding sit is mad up

of th amino-trminal variabl

domains of on H and on L

chain. Th class or isotyp of

an immunoglobulin is dfind

by its H chain.

Jawless fish

Primordial vrtbrats without

jaws, of which th only two

xtant forms ar lamprys

and hagfish.

Major histocompatibility

complexA larg complx of tightly

linkd gns, many of which

ar involvd in immunity. It

ncods th polymorphic class

I and class II molculs, which

prsnt antigns in th form of

pptids to cytotoxic and

hlpr T clls, rspctivly.

Jawed vertebrates

Vrtbrats from cartilaginous

fish to mammals. Th first

class of vrtbrats with

jaws, th placodrms, all

bcam xtinct.

(FIG. 2b). Frthrmr, phlgtic aalss sggst thatathr istp i cartilagis fish ad sm b fish,IgW1820, is rlatd t IgD. Thrfr, a IgDlik istpwas prst i th acstr f all gathstms. I frgsad mammals, IgD/IgW ccrs prdmiatl i thtrasmmbra frm, bt i b fish thr ar highlvls f scrtd IgD, which is mstl bd t th srfac f gralcts. This wrk i fish prmptd a rctrxamiati f th fcti f IgD i hmas, adit was fd that th scrtd frm f IgD is bd tth srfac f basphils ad has strg priflammatrprprtis21. Thrfr, althgh this w std ds taddrss th fcti f cllsrfac IgD, th wrk i fishhraldd a tirl w drstadig f scrtr IgD

fcti i hmas. Lik IgM, IgD is a acit atibd class, bt lik IgM, it has b xtrardiarilmallabl i strctr ad (prsmabl) i fcti vrvltiar tim.

Other immunoglobulins. Bsids IgM ad IgD, mammals hav thr Ig istps: IgG, which is ivlvd ihighaffiit mmr rspss; Ige, which fctisi iflammatr (ad allrgic) rspss at pithlialsrfacs; ad th mcsal atibd IgA (FIG. 2a). IgGad Ige rigiat frm a istp kw as Igy, whichis first fd i amphibias ad has th sam fctias IgG (at last i frgs ad birds17,22). Shrtr frms fIgy, which ar frmd ithr b altrativ splicig r

Figure 2 | Ag o o a g jaw ba. a | The different B cell receptor (BCR) isotypes

in mammals and their features in other vertebrates. Each oval represents an immunoglobulin superfamily (IgSF) domain

consisting of 90100 amino acids. Immunoglobulin D (IgD) is represented in two forms, mouse (left) and human (right);

note that even in mammals the IgD structure is highly plastic. Major phylogenetic features are described in the text.

b | BCR genes (which are defined by their heavy (H) chain) and T cell receptor (TCR) genes throughout phylogeny.

Recombination signal sequences are located at the 3 end of all variable (V) loci, and the 5 end of joining (J) seqments and

on both sides of diversity (D) segments. Note that in both the bony fish Ig H chain and vertebrate TCRs, entire antigenreceptor families are deleted upon rearrangement of the V segment to the downstream D and J segments ( genes aredeleted in bony fish and is deleted at the TCR locus). Note also that, despite its name, TCR in marsupials is related to TCR and not the IgM constant region. L chain, light chain; NAR, new antigen receptor.

R E V I E W S



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Mucosal immunity

Immun rsponss mad

across pithlial surfacs, such

as th gut and lung.

Immunoglobulin new

antigen receptor

(IgNAR.) A spcializd antibody

in sharks that is composd of

disulphid-linkd havy chains

and no associatd light chains.

Translocon organization

An organization of

immunoglobulin gns in whichthr ar multipl variabl (V),

divrsity (D) and joining (J)

sgmnts upstram of a singl

constant gn.

Cluster organization

An organization of

immunoglobulin gns in which

thr ar singl variabl (V),

divrsity (D), joining (J) and

constant gn sgmnts,

although somtims two or

thr divrsity sgmnts occur

togthr. Also known as

minilocus organization.

Receptor editingTh r-rarrangmnt of

antign rcptor gns to

avoid slf ractivity in th cas

of B clls or to xprss nw

rcptors that can b positivly

slctd in th cas of T cl ls.

Class switch

Th rarrangmnt of an

xisting variabldivrsity

joining (VDJ) xon from th 5

nd of th immunoglobulin M

gn to downstram constant

(C) gns. Lik somatic

hyprmutation, it rquirs

activation-inducdcytidin daminas.

Major histocompatibility

complex restriction

T cll rcptors rcogniz

antigns in th form of small

pptids ranging from 922

amino acids that ar bound to

major histocompatibility

complx (MHC) class I or class

II molculs. Th T cll rcptor

rcognizs both th MHC

protin and th pptid

antign this is known as

MHC rstriction.

frm sparat gs, ar prst i mltipl taxa; thsshrt frms ar blivd t traliz pathgs withtactivati f iflammatr rspss. IgA is fd firsti rptils ad sms t srv th sam fctis i allaimals. Itrstigl, i lwr taxa, thr istps fr xampl, IgX i frgs23 prvid mucosal immunity.Fiall, i camlids, thr is a mdifid frm f IgG thatds t assciat with light (L) chais, ad its V rgisar fr t itract with atigs; a similar frm calldimmunoglobulin nw antign rcptor (IgnAR) is fd icartilagis fish; th IgnAR V rgi is als csrvdi sm TCRs24,25 (s blw). I smmar, i vltiar trms all vrtbrats hav mltipl istps thatprvid distict ffctr fctis. Amphibias ar thmst primitiv class, with a classical mmr rspsthat is basd istp switchig t IgG ad Igy aftratig stimlati.

B cell receptor light chains. It was prvisl blivdthat th tw istps f th BCR L chais i hmas ad ars lat i vlti, prbabl i th

mammalia liag (FIGS 2,3a). Hwvr, gm adeST prjcts ad stdis f mdl vrtbrat spcishav shw that ths tw istps mrgd i th cmm acstr f all livig vrtbrats2629. Frthrmr,athr L chai idtifid i frgs ad amd 30 als ars arl i vlti ad has b rtaidi all cldbldd gathstms. Th ras(s) frth mrgc ad maitac f mltipl L chais is(ar) t kw, bt it might b rlatd t th frmatif spcific bidig sits b particlar cmbiatis fL chais ad hav (H) chais.

B cell receptor heavy chains. Frm b fish t mammals, BCR H chai gs ar arragd i a scalldtraslc rgaizati (FIGS 2b,3a): mltipl V gsccr pstram f mltipl D ad J sgmts, fllwdb sigl gs that cd th diffrt cstat (C)rgis. Th primar H chai rprtir is gratdb rarragmt i th primar lmphid tisss (frxampl, b marrw), which ivlvs a sigl V g(t f ts t hdrds f V gs) big rarragdt th dwstram D ad J sgmts31. I sm spcis,sch as chicks ad rabbits, aftr th rarragmtf a sigl V g, g cvrsi vts ivlvigarb fctial V gs grat divrsit ith primar rprtir32,33. I cartilagis fish, th Iggs ar i a clstr cfigrati with a sigl V, D, J

ad C g i ach clstr34. RAGmdiatd rarragmt ccrs withi a clstr, bt divrsit is gratd b jctial divrsit at th VD, DD ad DJrarragmt jits ad b smatic hprmtatiaftr atigic stimlati f B clls3537. Th sitatiis similar fr th L chai gs, xcpt th lack D sgmts (FIG. 2b). Als, i b fish th L chai gs caccr i translocon organization r clustr organization;this sggsts that xtsiv rcptor diting that is,rrarragmt f BCR gs ca ccr fr L chaigs i all fish3841(FIG. 2b).

Th H chai class switch first vlvd i amphibias,which hav a mammalialik Ig H chai lcs. I b

fish, th Ig H chai istps IgM ad IgD ar gratd b altrativ splicig. Th rctl discvrdIgT istp is gratd b altrativ rarragmt:th IgT D, J ad C g sgmts ar lcatd btw thV gs ad th IgM ad IgD D, J ad C sgmts42,43(FIG. 2b), ad rarragmt that jis V gs t th IgMD sgmts dlts th IgT gs, a sitati similar tthat at th TCR lcs. Thr is switchig appart btw clstrs i cartilagis fish, ithr withith IgM class r btw th IgM ad cartilagisfishspcific IgnAR/IgW classs.

Amphibias, which hav class switchig ad Igy,mark a majr trasiti frm th AIS i fish. A sigl B cll has th capacit t mdif th ffctr fcti f its scrtd mlcl ad t prvid a mmrrsps. I sharks, a switch at th bichmical lvlfrm mltimric t mmric IgM prvids at lastsm f th fctis f a IgG fr xampl, thcapacit t tr xtravasclar sits ad a icrasi affiit, bt th mmr rsps is clarl ifrirt that f th highr vrtbrats.

T cell receptors

T cell receptors. TCRs rcgiz bth th atig(i th frm f a pptid) ad th MHC class I r IImlcl t which it is bd. This is kw as majorhistocompatibility complx rstriction (MHC rstricti)44.T clls dvlp i th thms, ad th basic vlti fth thms ad T cll dvlpmt is csrvd fr allgathstms, xcpt i sm spcis i which th sstm sms t hav dgratd (FIG. 1 ad s blw). Atraslc rgaizati f bth th ad TCR gsis fd i all aimals (FIG. 2b). Th prsc f a D sgmt i th TCRlcs ad th absc f D sgmtsad th prsc f a larg mbr f J sgmts i th TCR lcs ar als vltiaril csrvd, at lastfrm mammals t b fish45(FIG. 2b). Th ma J sgmts i th lcs allw xtsiv rcptr ditigi dvlpig T clls, rsltig i gratr pprtitis fr mdificati f th atig rcptr, fllwdb pttial slcti f slfMHCrstrictd TCRs ith thms46.

T cell receptors. TCRs ar qit diffrt frm TCRs. Th basic g rgaizati is csrvd igathstms, with l J sgmts i th g, sall tw D sgmts i th g, ad a cls likagf th ad TCR gs. Hwvr, th rcptr ca

b adaptd i svral was. It was shw i mic that T clls that ars arl i tg bar ivariatrcptrs ad hm t sits, sch as th ski, whrth frm a first li f dfc ad slfrw fr thlif f th rgaism47. Similarl, i hmas, T cllswith caical rcptrs mak p a larg prctag f lmphcts i th bld ad bcm highlxpadd p ifcti. Ths clls rspd t thmtablit isprlphsphat, which is prdcd ball clls bt is prdcd i a mr immgic frmb iclllar pathgs48. Th iatlik T cllsca mak p th majrit f T clls i sm spcis,bt i thrs T clls d t bar caical rcptrs,

R E V I E W S



5/13

ba

SP

Germline VLR gene

5-LRRCT

Heavy chain gene Light chain gene

Transcriptionand translation

LRRVe

LRR

3-terminus5-LRRNT3-LRRNT

3-LRRCTLRR1 CPSP

LRRCTLRRNT LRR

3-terminusCP

J CV V V D DD JJ

JV V V JJ C

CV D J CV J

Membrane-bound Igs

Secreted Igs

Transcription and translation

Membrane-bound VLRs

Secreted VLRs

Rearranged gene

RAG-independent rearrangementRAG-mediated rearrangement

Rearranged gene

Complementarity-

determining region 3

A loop in th variabl (V)

rgion of th B cll rcptor

and T cll rcptor chains that

is ncodd by th variabl

divrsityjoining (VDJ)

intrsction that is gnratd

by rcombination-activating

gn (RAG)-mdiatd somatic

rarrangmnt. It is th part of

th antign-binding sit that is

most divrs in amino acid

squnc and lngth.

ar a larg prprti f th T clls i th bd, adsm t b mr adaptiv i atr49. Th bidigsits f ths rcptrs (v f sm f th iatrcptrs) ar mr lik BCR bidig sits: th hav lg ad shrt complmntarity-dtrminingrgion 3 (CDR3), whras TCRs hav similarl sizdCDR3s fr bth chais50.

Rctl, w tps f TCR gs hav b dis

cvrd i diffrt vrtbrat taxa. I abt a qartr f thir TCR gs, sharks hav a thrdmaircptr chai with tw amitrmial V dmaisad a mmbraprximal C dmai calld nARTCR51 (FIG. 2b). Bth V dmais ar gratd b VDJrarragmt: th ntrmial dmai is cdd ba IgnARlik clstr, ad th thr is gratdb rarragmt f V t caical D ad J lmts.It is likl that this TCR chai rcgizs atigs i asimilar wa t th bona fide IgnAR, which is prsmdt hav a sigldmai bidig sit. I marspials,th TCR lcs has b dplicatd. A appartlacit trans rarragmt f IgV rgis t this lcs

i grm clls52 has rsltd i st f V, D ad J sgmts that rarrag i a clstr that is pstram fa prrarragd (that is, grmlijid) VDJ g.This is prdictd t rslt i a thrdmai TCR chaithat has tw V dmais ad C dmai ad is similar t th TCR chai i sharks (FIG. 2b). Althgh thfcti f ths rcptrs is t kw, it is prpsdthat lik th MHCrstrictd TCRs th rc

giz slbl atigs, which wld giv thm a similar fcti t Igs53. Csistt with this ida, shark TCR gs hav rctl b shw t hprmtatlik BCR gs bt lik TCR gs54. Thrfr, aw paradigm mrgig frm th cmparativ stdisis that TCRs prbabl hav th capacit t itractwith fr atigs i a similar wa t Igs. Additiall,wh cmparig TCRs ad TCRs, th frmrclarl ar th mr vltiaril csrvd, prbablbcas th ar cstraid b MHC rstricti. Bctrast, TCRs ar mr vltiaril labil adhav adaptiv imm ad iat imm fctisthat diffr v btw vrtbrats i th sam class.

Figure 3 | two om o aa mmuy ba. a | Immunoglobulin (Ig) genes in jawed

vertebrates. Ig genes generate repertoire diversity by recombining variable (V), diversity (D) and joining (J) gene

segments with the help of the recombination-activating gene (RAG) recombinase. D gene segments occur only in

the heavy chain genes. T cell receptors generate diversity in a similar manner (not shown). They occur only in a

membrane-bound form. b | Variable lymphocyte receptors (VLRs) in jawless vertebrates. Multiple amino-terminal

leucine-rich repeat (LRRNT)-, leucine-rich repeat (LRR)-, connecting peptide (CP)- and carboxy-terminal LRR

(LRRCT)-encoding modules are located adjacent to the germline VLR gene. During the development of lymphoid cells,

these modules are incorporated into the VLR gene. The rearranged VLR gene encodes a membrane-bound protein.

VLRB has a secreted form and functions as an antibody, whereas VLRA apparently occurs only in a membrane-bound

form. Whether membrane-bound VLRs occur as monomers or multimers is not known. LRR1 and LRRVe denote LRR

modules located at the N- and C-termini, respectively. The organization of the VLR locus shows minor variations

depending on loci and species. The figure is intended to emphasize the essential features ofVLR assembly and does not

accurately reproduce the organization of a specific VLR locus. SP, signal peptide.

R E V I E W S



6/13

Transporter associated with

antigen processing(TAP). A transportr of th

ATP-binding casstt

suprfamily that is involvd

in th transport of pptids

from th cytosol into th lumn

of th ndoplasmic rticulum.

It is a htrodimr composd

of TAP1 and TAP2 subunits

and has a crucial rol in

th transport of major

histocompatibility complx

class I-binding pptids.

Tapasin

A protin that facilitats th

binding of pptids to majorhistocompatibility complx

(MHC) class I molculs by

forming a bridg btwn

MHC class I molculs and

transportr associatd with

antign procssing (TAP).

Recombination signal

sequences

Consrvd nuclotid

squncs flanking variabl (V),

divrsity (D) and joining (J)

sgmnts that ar rcognizd

by th rcombination-activating

gn (RAG) protins to

induc rarrangmnt.

Immunoglobulin

superfamily

Domains of 90100 amino

acids composd of 79

strands forming two shts,

gnrally stabilizd by a

disulphid bond. Found in B

cll rcptor, T cll rcptor

and major histocompatibility

complx molculs.

Ohnologues

Paralogus, namd aftr

Susumu Ohno, that ar

thought to hav mrgd clos

to th origin of vrtbrats bywhol-gnom duplication.

Paralogy group

A st of paralogons that

ar drivd from a singl

ancstral rgion.

Paralogues

(Also known as paralogous

gns.) Gns within a singl

spcis that blong to th

sam gn family. In contrast

to paralogus, orthologus

rfrs to gns that divrgd

by spciation vnts.

Major histocompatibility complex

Th MHC is dfid b: MHC class I ad class II gs;gs that cd transportr associatd with antignprocssing (TAP) ad tapasin, which ar ivlvd iprcssig atigs fr prstati b MHC class Imlcls; ad gs that ar ivlvd i gral immit (s blw). Th MHC, lik TCRs ad BCRs, is firstfd i cartilagis fish55. Gs ivlvd i class Iprcssig ad prstati ar clsl likd i almstall vrtbrats (xcpt i plactal mammals, i whichthr is cls likag f th class I prcssig gs adclass II gs) ad ar blivd t hav cvlvd55,56. Asdscribd blw, gs that cd atral killr (nK) cllrcptrs ar assciatd with th MHC f varis livig

vrtbrats, ad ths srv as cctis t what smst hav b a primrdial g cmplx cmpsd frcptrs ad ligads55,57,58. Thrfr, it sms likl thatnK rcptrs (ad prhaps als th frrrs f atig rcptrs) wr phsicall likd t th primrdialMHC i a similar wa t th liks btw rcptrs adligads i th mriad histcmpatibilit sstms f md

rda lwr dtrstms ad prtstms59; thsliks wr sbsqtl fragmtd i gathstms.

How did the jawed vertebrate AIS arise?

As discssd abv, th BCRTCRMHCbasd AIS isprst i cartilagis fish bt abst i lwr chrdats. Tw macrvltiar vts th ivasi fth RAG trasps ad tw whlgm dplicatis (WGDs) ar blivd t hav prvidd th i

vati ad raw matrial, rspctivl, fr th rlativlrapid mrgc f th AIS i jawd vrtbrats. I thisscti w discss th pttial ctribti f thstw vts.

The recombination-activating gene transposon. I thlat 1970s, Saka ad Tgawa discvrd rcombi-nation signal squncs (RSSs) flakig V, D ad J rarragig sgmts60, ad th ticd that th ivrtdrpats withi th RSSs wr rmiisct f a trasps. This sggstd that a g cdig a immunoglob-ulin suprfamily (IgSF) x was ivadd b a trasps.Thrfr, th g cld t b xprssd lss it wasstitchd back tgthr thrgh th acti f a rcmbias. Thr ar ma IgSF gs i lwr chrdats thatar rlatd t BCR ad TCR V rgis (th scalld VJtp f IgSF g; FIG. 1), s thr ar ma cadidatgs that cld hav b ivadd b th RAG tras

ps i a vrtbrat acstr61. Fr xampl, th gfamil cdig th variabl rgi ctaiig chitibidig prtis (VCBPs) i amphixs is prsmd tb ivlvd i dfc ad cld b rlatd t th rarragig acstr f th BCR ad TCR gs62. othrgs that might b rlatd t th acstral VJ g (frxampl, ReFS6365) ar dscribd blw.

Th RAG1 ad RAG2 gs hav hmlgsrgis ad itrs bt ar clsl likd t ach thr,which sggsts that th cld hav b acqird b vrtbrats as part f th rigial trasps4,66. CmpltRAG gs hav b islatd frm all gathstmsstdid, bt t frm jawlss fish. This is csistt with

th ida that acqisiti f th RAG trasps hlpdt triggr BCR ad TCRbasd immit. Srprisigl,likd RAG1 ad RAG2 gs wr fd i th gmf th sa rchi (a chidrm)67(FIG. 1), which implisithr that th RAG trasps ivadd th gm 100milli ars bfr th mrgc f adaptiv immitad rmaid drmat, r that it had ivadd at mltipl tims. Th athrs sggstd that a RAG1lik givadd th gm ad isrtd ar a RAG2likg that was sbsqtl icldd i th rigial trasps. Th RAG1lik g cld hav rigiatd frmtrasib a trasps that cds th RAG1 cr adthat has b fd i ma rgaisms68 r, as Drfshas rctl sggstd69, frm a viral gtic lmt.RAG2 th lst its rigial fcti ad was cptdt th VDJ rarragmt prcss. This prpsiti iscsistt with rct wrk shwig that RAG2 ds tctribt t rarragmtper se, bt istad itractswith mdifid hists at sits f activ trascripti70. Wprps a wrkig mdl i which RAG2 bids t activrgis f trascripti ad RAG1 bids t th xpsd

RSS. RAG1 itracts with, ad is dpdt , RAG2 tiitiat VDJ rarragmt, bt RAG1 prfrms all f thmajr fctis assciatd with rcmbiati.

Rgardlss f th rt f its mrgc i chrdats,th RAG trasps ivasi mst hav b crcialfr adaptiv immit, as all f th BCR ad TCRgs s th sam mchaism f VDJ rarragmt.Frthrmr, dspit argmts t th ctrar71, RAGactivit was likl t hav b a ivativ vt fradaptiv immit, as jawd vrtbrats hav ma vlmchaisms ad mlcls that ar ivlvd i immit i gral, ad adaptiv immit i particlar,cmpard with jawlss fish (discssd frthr blw)72.

Whole-genome duplication. narl 40 ars ag, Ssmoh prpsd that th vrtbrat gm drwt r tw rds f WGD at th stag f fish r amphibias thrgh a ttraplidizati prcss73. Althgh thisprpsal was a mattr f ht dbat til rctl(BOX 1),it is w widl accptd that th vrtbrat gmxpricd tw rds f WGD aftr th mrgcf rchrdats ad bfr th radiati f jawd vrtbrats7477(FIGS 1,4). WGDs sm t hav had a crcialrl i th mrgc f jawd vrtbrattp adaptivimmit78,79. This is idicatd b th fact that maohnologus, which ars as a rslt f WGDs, ar sstialcmpts f th jawd vrtbrattp AIS80,81.

Th MHC paralogy group(FIG. 4a) ad th HoX paralg grp (Spplmtar ifrmati S1 (figr)) arillstrativ xampls. I th cas f th MHC paralggrp8284, paralogus f mr tha 100 g familis ardistribtd i fr sts fparalogons (fr a list f gfamilis, s ReF. 85). As wld b xpctd frm ohsthr f WGD, th gms f ivrtbrats, sch asamphixi84,86 ad Ciona intestinalis87, d t hav mltipl sts f MHC paralgs ad ctai l MHClik rgi, which is dvid f class I ad II gs(a prtMHC).

Rctl, oliski et al.85 sggstd that th rtrphi paralg grp (FIG. 4, lft) ad th MHC

R E V I E W S

http://www.ncbi.nlm.nih.gov/gene/5896http://www.ncbi.nlm.nih.gov/gene/5897http://www.nature.com/nrg/journal/v11/n1/suppinfo/nrg2703.htmlhttp://www.nature.com/nrg/journal/v11/n1/suppinfo/nrg2703.htmlhttp://www.ncbi.nlm.nih.gov/gene/5897http://www.ncbi.nlm.nih.gov/gene/5896


7/13

Paralogons

Chromosomal sgmnts that

contain closly linkd sts of

paralogus. Also known as

paralogous rgions.

Agglutinin

Any substanc that can

clump particls togthr.

AID-APOBEC

A family of cytidin

daminass that ar involvdin th hyprmutation of

variabldivrsityjoining

(VDJ) sgmnts, in th

immunoglobulin class switch

and in dfnc against viruss.

Two mmbrs of th family

ar implicatd in gnrating

divrsity in variabl

lymphocyt rcptors.

Allelic exclusion

Th xprssion of a singl

rcptor in clls with th

potntial to xprss mor

than two rcptors.

paralg grp (FIG. 4, right) wr drivd frm ighbrig rgis th sam acstral chrmsm.This sggsti is basd th bsrvati that svral gs f th MHC ad rtrphiparalggrps ar likd i th gms fC. intestinalis85ad amphixi88. Itrstigl, chrmsmal rgis12p13.2p12.3 ad 19q13.4, which cd th hmanK cmplx (nKC) ad lkct rcptr cmplx(LRC), rspctivl(BOX 2), ar mbddd i th rtrphi paralgs89. Thrfr, oliski et al.s sggsti prvids a lgical basis fr th arlir prpsals thatth acstrs f nK rcptr gs cdd i th nKCad LRC wr lcatd i th prtMHC55,57,90,91.

Strikigl, th itgratd MHC/rtrphi paralg grp cds ma hlgs that hav imprtatfctis i th AIS, particlarl i atig prstatib MHC class I ad II mlcls (FIG. 4; Spplmtarifrmati S2 (tabl)). I additi t TAP ad tapasi,

thr prtasm sbits that ar spcializd fr atigprstati ar cdd i this paralg grp, tgthrwith sm f thir paralgs. Similarl, th itgratdparalg grp cds 10 f th 11 cathpsi hlgs, icldig cathpsis S ad L, which hav crcialrls i atig prstati b class II mlcls adi thmic slcti. othr xampls icld: rtiidX rcptr (RXRB) ad rglatr factr X5 (RFX5),which cd prtis that rglat th xprssi fclass I ad II mlcls, rspctivl; NOTCH1, which isivlvd i lmphct diffrtiati; ad VAV1, whichis rqird fr T ad B cll dvlpmt ad activati(Spplmtar ifrmati S2 (tabl)).

The convergent AIS of jawless vertebrates

With sm xcptis, ad dspit th ivlvmtf th wllcsrvd ad rapidl vlvig mlclarfatrs dscribd abv, th AIS f jawd vrtbratshas b rmarkabl ifrm vr 500 milli ars.Fctial assas f jawlss vrtbrats (lamprs adhagfish) hav shw sigs f adaptiv immit, btithr adaptiv imm mlclar charactristics rtisss, sch as a thms r spl, wr dtctd iths aimals. Fr xampl, jawlss vrtbrats prdcspcific agglutinins wh immizd with particlatad slbl atigs9295, bt xtsiv trascriptmaalsis f jawlss fish lkcts prvidd vidc fr th prsc f MHC, BCR r TCR mlcls9698. Thir absc has b rctl cfirmdb th aalsis f th sa lampr (Petromyzon marinus)draft gm sqc. Hw ca th mt adaptivimm rspss i th absc f BCR, TCR adMHC mlcls? Th discvr f a VLR g, whichgrats divrsit b smaticall rarragig lcirich rpat (LRR) mdls7, prvidd a aswr99. Th

grmli VLR g lacks g sgmts cdig fr LRRmdls ad is t capabl f cdig fctial prtis (FIG. 3b). Drig th dvlpmt f lmphid clls,LRR mdls that flak th g ar sqtiall icrpratd it VLR b a prcss calld cp chic100.Icrprati is prsmabl mdiatd b ctididamiass f th AID-APOBeC famil8. Th matr VLRg cds a glcslphsphatidlisitlachrdplpptid. Th sqc f idividal LRR mdlsassmbld it th VLR g is highl divrs, ad thmbr f LRR mdls prst i a rarragd g

varis frm t i. Thrfr a sigl VLR g cahav cmbiatrial divrsit cmparabl t that f Igs(~1014 cmbiatis)101. Th crstal strctrs f hagfish VLR mmrs idicat that th adpt a hrsshlik slid strctr that is charactristic f LRRfamil prtis. Th majrit f variabl rsids i thVLR ar lcatd th ccav srfac, which sggststhat this srfac is ivlvd i atig bidig 102. Thiswas rctl cfirmd bin vitro mtagsis xprimts103 ad th crstal strctr aalsis f VLR icmplx with th hma bld grp Htrisaccharid104r with h gg lszm105.

Lamprs hav tw VLR gs: VLRA ad VLRB8.Bth sm t b xprssd xclsivl i lmphid clls,ad th sall xhibit alllic xclusion. Stimlati withatigs cass lmphid clls xprssig spcific VLRB

mlcls t drg clal xpasi ad t scrtVLRs i a mar aalgs t th scrti f Igs bB clls7,101. Scrtd VLRB mlcls ccr as ptamrsr ttramrs f dimrs ad hav ight t t atigbidig sits103. Thrfr, th sbit rgaizati fscrtd VLRB mlcls rsmbls that f IgM atibdis. Th mltivalt strctr f VLRB abls itt bid atigs carrig rptitiv pitps with highavidit ad spcificit, ad it displas strg aggltiatig activitis106. It has b sggstd that, lik sbclasssf IgM, VLRB might prfrtiall r xclsivl rcgiz thmsidpdt atigs106. B ctrast,VLRA sms t ccr l i a cllbd frm ad is

Box 1 | Controversies surrounding whole-genome duplication

The idea that the vertebrate genome underwent two rounds of whole-genome

duplication (WGD) at a time close to the origin of vertebrates known as the

two-round (2R) hypothesis caused hot debate for more than a decade. The major

evidence in favour of this hypothesis was that paralogues that emerged close to the

origin of vertebrates are not distributed at random in the human genome, but have a

strong tendency to occur in clusters, known as paralogons, on multiple typically four

chromosomes. The major arguments against this hypothesis were twofold127,128

. First,ohnologues (for example, A, B, C and D) generated by two rounds of WGD should

display the tree topology (that is, A and B together and C and D together), which is not

always the case127. Second, paralogons occasionally contain paralogues that duplicated

much earlier than the origin of vertebrates. We now know that incongruent tree

topologies can occur if two waves of genome doubling occurred in close succession129,

if paralogues have evolved at different evolutionary rates130 or if the resolving power of

phylogenetic trees is not sufficient129. Also, the divergence time of paralogues can be

much older than the age of WGD if tandem duplication preceded WGD and the

duplicated genes were lost differentially after WGD. Therefore, neither of these two

counterarguments contradicts the 2R hypothesis.

Recently, comparison of the human and amphioxus (Branchiostoma floridae) genomes

revealed widespread quadruple conserved synteny, in which four sets of human

paralogons corresponded to one set of linked genes in B. floridae131. This observation

provided definitive evidence for the 2R hypothesis and settled the long-standing

debate. The exact timing of WGD relative to the emergence of jawless vertebrates(FIG. 1) is still controversial. A commonly held view, which we also favour, is that the first

round of WGD occurred in a common ancestor of jawed and jawless vertebrates, and

the second round in a common ancestor of jawed vertebrates76. However, recent

analysis of 55 gene families in jawless vertebrates suggested that both rounds of WGD

might have taken place in a common ancestor of all vertebrates, although this analysis

could not discount the idea that the second round of WGD occurred in a common

ancestor of jawed vertebrates132, as depicted in FIG. 1.

R E V I E W S

http://www.nature.com/nrg/journal/v11/n1/suppinfo/nrg2703.htmlhttp://www.nature.com/nrg/journal/v11/n1/suppinfo/nrg2703.htmlhttp://www.nature.com/nrg/journal/v11/n1/suppinfo/nrg2703.htmlhttp://pre.ensembl.org/Petromyzon_marinus/Info/Indexhttp://pre.ensembl.org/Petromyzon_marinus/Info/Indexhttp://pre.ensembl.org/Petromyzon_marinus/Info/Indexhttp://pre.ensembl.org/Petromyzon_marinus/Info/Indexhttp://pre.ensembl.org/Petromyzon_marinus/Info/Indexhttp://pre.ensembl.org/Petromyzon_marinus/Info/Indexhttp://www.nature.com/nrg/journal/v11/n1/suppinfo/nrg2703.htmlhttp://www.nature.com/nrg/journal/v11/n1/suppinfo/nrg2703.htmlhttp://www.nature.com/nrg/journal/v11/n1/suppinfo/nrg2703.html


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TAPBPL

MHC

NOTCH3

ABL2

RXRG

TNFSF4, 6, 18PIAS3SHC1

19q13q14

LRC

A2M

KRAS

NRAS

NKC

TAPL

RFX4SPIC

AKT3

TICAM2ERAP1

CD74

Two rounds of WGD

Proto-MHC chromosome

PSME1, 2TCRA/D

14q11q32

AKT1NFKBIA

2

IGKCCD8A, B2

p12p23

20p11p12

HRASSPI1

11q12q13

6p21p22

PIK3R1

CTSH

15

5

15q13q26

5q11q23

PIAS1CSKMAP2K1SHC4B7H3B2M

6

9

CTSL2

CTSL

C5

PSMB7

VAV2TNFSF8SHC3

ABL1NOTCH1RXRA

RFX3

9q32q34

9p13p

24

TAPBPTAP

PSMB8, 9

C4

JAK2

MHC class I, II

TNFSF1, 2, 3NOTCH4RXRB

19

114

11

12

1

20

19

RFX1, 2

C3

JAK3VAV1IL12RB1TNFSF4, 7, 9TICAM1PIAS4MATKJUNB, JUNDMAP2K2SHC2

RFX5

CTSK, CTSS

NOTCH2JAK1VAV3IL12RB2JUNB7H4

19p13.1p13.3

1q21q25

1p11p32

CTSD

CTSC, F, W

11p12p15

11q23q24

CTSG

PSMB5, 11

LGMN

NKG2

CD4LAG3

12p11p13

12q22q24

PIK3R3

1p13

1q32q44

PIK3R2

KIRSPIBBCL3AKT2NFKBIB

RXR

PSMB

TAP-like

TAPBP-like

RFXCTS

NOTCH

A2M/C3/4/5

VAV

TNFSF

JAKMHCprecurso

NKRprecursor

PDCD1LG1

PDCD1LG2

xprssd lmphid clls that fctiall rsmblT clls. Thrfr lamprs hav tw pplatis flmphid clls that sm t b fctiall similar t thT ad B clls f jawd vrtbrats107.

Hagfish als hav tw VLR gs108, VLRA adVLRB, which ar prsmd t b rthlgs t lamprVLRA ad VLRB, basd sqc cmparis.Th map t th sam chrmsm bt ar distat frmach thr, which idicats that th fcti as sparat its109. Csistt with this, th rarragd VLRAad VLRB gs d t shar a LRR mdl with a

idtical cltid sqc. It rmais t b dtrmid whthr hagfish VLRA adVLRB ar fctiallsimilar t th crrspdig lampr gs.

Origin of the two distinct forms of AIS

Bth VLRs ad BCRs/TCRs rl cmbiatrial divrsit t grat a vast rprtir f bidig spcificitis;hwvr, th gs f VLRs shw strctral similaritt ths f BCRs r TCRs (FIG. 3). Thir rcmbiatimachiris mst diffr bcas RAG1 ad RAG2 arrqird l fr BCR/TCRs. Ths bsrvatis sggst

Figure 4 | t majo oomaby omx aaogy gou a uoo aaogy gou

uma gom. Four sets of major histocompatibility complex (MHC) paralogons are located on chromosomes 1, 6,

9 and 19 (ReFS 55,137,138). A number of smaller-sized MHC paralogons, which presumably originated from fragmentation

and subsequent translocation of the major paralogons, have been identified55. Among them, those located on

15q13q26 and 5q11q23 seem to have broken off from the paralogons on chromosomes 6 and 9, respectively130. Four sets

of major neurotrophin paralogons are located on chromosomes 1, 11, 12 and 19 (ReF. 89).The MHC paralogy group (right)and neurotrophin paralogy group (left) are thought to have descended from neighbouring regions on a single ancestral

chromosome. Paralogues that are distributed across the two paralogy groups are indicated by blue highlighted text. In

addition to genes that share paralogues among the relevant paralogons, immunologically important genes, such as those

encoding MHC class I, MHC class II, T cell receptors (TCRs), and immunoglobulins (Igs) are shown. A2M, 2-macroglobulin;B2M, 2-microglobulin; BCL, B cell leukaemia/lymphoma; CSK, cytoplasmic tyrosine kinase; CTS, cathepsin; ERAP,endoplasmic reticulum aminopeptidase; IL12RB, interleukin 12 receptor,-subunit; JAK, Janus kinase; KIR, killer Ig-likereceptor; LAG3, lymphocyte activation gene 3; LGMN, legumain; LRC, leukocyte receptor complex; MAP2K,

mitogen-activated protein kinase kinase; MATK, megakaryocyte-associated tyrosine kinase; NFKBIA, nuclear factor-Binhibitor; NKC, natural killer complex; NKR, NK receptor; NRAS, neuroblastoma RAS; PD, programmed cell death 1 ligand;

PIAS, protein inhibitors of activated STAT; PIK3R, phosphatidylinositol 3-kinase, regulatory subunit; PSMB, proteasome

subunits, -type; PSME, proteasome activator subunits; RFX, regulatory factor X; RXR, retinoid X receptor; SPI1, spleenfocus forming virus proviral integration oncogene; TAP, transporter associated with antigen processing; TAPBP, TAP-binding

protein (also known as tapasin); TAPBPL, TAPBP-like; TAPL, TAP-like (also known as ABCB9); TICAM, TIR domain-containing

adaptor molecule; TNFSF, tumour necrosis factor ligand superfamily; WGD, whole-genome duplication.

R E V I E W S



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Vertebrate ancestors

Jawless vertebrates Jawed vertebrates

Ig V-like domain closely relatedto the BCR and TCR domains

BCR TCR

T cellsB cells

BCR/TCR ancestor

T-like lymphoid cellsB-like lymphoid cells

VLRAVLRB

T-like lymphoid cellsB-like lymphoid cells T-like lymphoid cellsB-like lymphoid cells

VLR ancestor

2R

1R

RAG activity

Differential recruitment of receptors

GPIb- B-like lymphoid cel ls T-like lymphoid cel ls

S

SV

J

that th acstrs f jawd ad jawlss vrtbratsdvlpd thir atig rcptrs idpdtl.

Althgh VLRs prbabl xist l i lamprs ad

hagfish, th rigi f LRR mdls is acit; LRR mdl rpats ar fd i ma aimal ad plat prtis,i which th sm t mdiat prti itractis rmicrbial rcgiti. It has b prpsd, th basisf th similarit f g strctrs ad a charactristicisrti i th LRR carbxtrmial (LRRCT) dmai,that a acstr f VLR might hav mrgd frm a glcprti Ib (GPIb)lik prti (GPIb is a cmpt f th platlt glcprti rcptr cmplx thatis csrvd i all vrtbrats)8. Frthrmr, sarchsfr IgSF prtis i jawlss vrtbrats hav idtifidmlcls that ar thght t b rlatd t th pttialvltiar prcrsrs f BCRs ad TCRs6365. Ths

ar: th agatha paird rcptrs rsmblig atigrcptrs (APAR) famil f iat imm rcptrs,which cd a grp f mmbra prtis carrig a

sigl xtraclllar Vtp Iglik dmai with a caical J sgmt64; ad a immrcptr trsibasdihibiti mtifbarig mmbra prti, amdTCRlik65, which has VC2tp dmai rgaizatiad sms t b clsl rlatd t th vl immrcptr trsibasd activati mtifctaiigIgSF rcptr (nICIR) famil f activatig iatimm rcptrs110. Th ccrrc f ths rcptrsi jawlss vrtbrats sggsts that a cmm acstrf all vrtbrats had Vtp Iglik dmais that vlvdit th Iglik dmais f BCRs ad TCRs. Hc, asmtid abv, it sms that a vrtbrat acstr hadbth BCR/TCR ad VLR prcrsrs (FIG. 5). I a jawd

Figure 5 | A yoa mo o og o wo majo om o aa mmu ym.

The occurrence of B- and T-like lymphoid cells in jawless vertebrates indicates that they were likely to be present in

a common ancestor of all vertebrates107. Similarly, the occurrence of a V-type immunoglobulin (Ig)-like domain with a

canonical joining (J) segment in jawless vertebrates indicates that a common ancestor of all vertebrates had V-type Ig-like

domains that could be converted to B cell receptor (BCR) or T cell receptor (TCR) Ig-like domains. Amphioxus, a basalchordate, has a glycoprotein Ib- (GPIb-)-like protein, which is the most likely precursor to the variable lymphocytereceptor (VLR)8. Therefore, a common ancestor of all vertebrates presumably had all of the key structural elements of the

two radically different antigen receptors. Acquisition of recombination-activating gene (RAG) recombinase activities and

the second round of whole-genome duplication (WGD; indicated as 2R) are thought to have had a crucial role in the

emergence of the BCRTCRMHC-based adaptive immune system (AIS). Little is known about the genetic events that

contributed to the emergence of the VLR-based AIS in jawless vertebrates. It is possible that the first round of WGD

(indicated as 1R) contributed to the emergence of the two lineages of lymphoid cells; however, we cannot rule out the

possibility that their origin predates the emergence of vertebrates.

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vrtbrat liag i which RAG isrti ccrrd, aIgSF prti was chs as a atig rcptr, whichld t th BCRs ad TCRs. I a jawlss vrtbrat liagwith apprpriat RAG isrti, a LRR prti famil that cld mdiat micrbial rcgiti was chsas a atig rcptr, which ld t th VLRs.

Th ccrrc f strctrall rlatd rcptrsthat ar sd fr th sam r similar prpss is tprcdtd (BOX 2). Fr xampl, i primats thnK rcptrs that itract with classical MHC class Imlcls ar mmbrs f th killr cll Iglik rcptr(KIR) famil, bt i rdts th crrspdig rcptrsar Ctp lctilik mlcls kw as L49 rcptrs111. A cmm acstr f primats ad rdts isthght t hav had prcrsr gs fr bth tps fnK rcptrs; th KIR g famil xpadd i th primat liag ad th L49 famil xpadd i th rdtliag112,113. W sggst that th acstrs f jawd ad

jawlss vrtbrats adptd distict mlcls as thiratig rcptrs i a aalgs mar.

Th bsrvati that jawlss vrtbrats hav B ad

Tlik lmphid clls107 idicats that th tw liagsf lmphid clls mrgd bfr th divrgc f

jawd ad jawlss vrtbrats (FIG. 5). Thrfr, thrigi f B ad Tlik lmphid clls is likl t bmr acit tha prvisl thght. This is cmpatibl with rct bsrvatis that B ad T clls d tshar a immdiat cmm prgitr, bt diffrtiat frm mlid B prgitrs ad mlid T prgitrs, rspctivl88,113115. This sggsts that B ad Tliklmphid clls divrgd bfr th divrgc f mlidad lmphid clls. Althgh w mst b catis whsig cll liag ifrmati as a prx fr th rdr f

vltiar mrgc, it sms likl that th bildigblcks fr bth tps f atig rcptrs ad als thtw liags f lmphid clls wr prst i a cmmacstr f all vrtbrats (FIG. 5).

Pressures for adaptive immunity

Wh did th AIS aris? As td abv, ivrtbratsad plats maag with iat mchaisms f dfc(hwvr, it shld b mtid that primitiv adaptiv sstms hav b dscribd i svral ivrtbrattaxa116 ad that a RnAilik mchaism prvids aptt adaptiv rsps i ma rgaisms117). Idd,it has b argd that a aticipatr sstm f dfcis mr trbl tha it is wrth, as it cssitats thgrati f tlrac t slf drig th tg flmphcts, ad failr t rglat ths dfc mchaisms ca rslt i atimmit118. Frthrmr, thadaptiv sstm might l b maitaid wh drstrg slctiv prssr: rgaisms sch as cd119, sahrss120 ad axltl121, which might t b dr strgprssr frm pathgs, sm t hav lst th capacit

t mt ffctiv imm rspss, at last as far asth ca b masrd xprimtall121.

Hwvr, w thik that at last th BCRTCRMHCsstm ars as a ptt sstm f dfc. It is blivdthat this sstm mrgd i aimals with jaws, which arlikl t hav b prdatr. Larg prdatrs gralld t hav ma ffsprig, thrb maitaiig a ratif prdatrtpr that prptats th status quo122.Sharks, th ldst livig vrtbrats with this adaptivsstm, hav ma w mchaisms f rprdctit prtct g ffsprig sch as imptrabl ggcass ad mds f viviparit that hav cvrgd thmchaisms i mammals. Thrfr it ca b prpsdthat a ptt sstm f dfc ars i cjctiwith th d t prtct ffsprig. I jawlss fish, thAIDAPoBeC famil mmbrs might hav abld thdivrsificati f a primm rprtir f IgSF gs,as sms t b th cas fr th VLR sstm. Th additif th RAG trasps t this adaptiv sstm wld havprvidd a grat advatag, casig a brak drig rarragmt that wld hav cratd th pttial fr larg

variatis i th siz f f th CDR lps that itractwith atigs37. This advatag, alg with th raw matrial f a larg mbr f wl dplicatd gs that cldb cptd fr imm fctis, prbabl rsltdi th highl cmplx AIS s tda i gathstms.

ConclusionsThr ar ma charactristics f th AIS that ca grall b agrd p: jawlss ad jawd fish bth hav aAIS basd diffrt g familis, bt th BCRTCRMHCbasd sstm is mr cmplx; th RAG trasps ad WGDs had majr rls i th mrgc fth jawd vrtbrat AIS, ad th majr fatrs f thsstm ars arl i a big bag ad hav b mdifidl slightl vr vltiar tim; ad th jawd vrtbrat AIS displas bth csrvd ad plastic fatrs,th frmr prsmabl t allw fr a gral fctiigf th sstm ad th lattr t prmit rapid chags vrvltiar tim t rspd t pathgs11.

Box 2 | Natural killer cell receptors

Natural killer (NK) cells are part of the innate immune system. They can produce

cytokines and kill virally infected cells without a clonal proliferation phase. NK cells

share many characteristics with T cells, including most cell-surface markers,

elaboration of the same effector functions and origins from a similar haematopoietic

precursor111. However, the NK cell receptor (NKR) recognition strategy is different

from that of T cells (although the signalling cascades are homologous). When cells

become virally infected, major histocompatibility complex (MHC) class I molecules

are often downregulated, making the cells invisible to cytotoxic T cells. Inhibitory

NKRs on NK cells recognize MHC class I molecules; when the inhibitory NKRs are not

engaged, the NK cells can be stimulated by activating receptors that often recognize

stress-induced molecules that are upregulated on viral infection. This is known as the

missing self hypothesis133.

Unlike T cell receptors (TCRs), NKRs are not generated by recombination-activating

gene (RAG)-mediated recombination, but rather through stochastic, clonal expressionof a few receptors from a cluster of genes encoding activating and inhibitory NKRs.

These receptors are encoded by the NK complex (NKC) and leukocyte receptor

complex (LRC), found on different chromosomes in all mammals examined. The NKRs

that recognize classical (polymorphic) class I molecules are encoded by genes in

different gene families in various species, for example the C-type lectin Ly49 genes

found in the NKC in mice and the killer immunoglobulin superfamily (IgSF) receptor

(KIR) genes found in the LRC of humans. This is the only known case in the immune

system in which receptors from different gene families perform precisely the same

functions in closely related species, and it is a testament to the rapid evolution of the

NK system of defence. Evidence from comparative studies of the MHC, LRC and NKC

strongly suggest that the three complexes were originally linked and that their

polymorphic receptors and ligands have co-evolved, as has been found in many

histocompatibility systems in plants and invertebrates59.

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Ma qstis still d t b addrssd, mst fwhich will rqir icrmtal prgrss. Fr xampl,what is th atr f th RAG trasps? What ar thfctis f atig rcptrs i diffrt rgaisms,spciall th TCR? Ad hw is th VLR sstm rglatd? Hwvr, thr ar tw glarig qstis: did Tad Blik lmphid clls rall mrg i th cmmacstr f jawlss ad jawd vrtbrats, ad what wrth prssrs that slctd fr th mrgc f th AIS?Rgardig th first f ths qstis, bsids what whav discssd abv ccrig th atig rcptrs,it is sstial t dtrmi whthr, lik gathstm T clls, th Tlik lmphid clls f jawlss vrtbrats rcgiz prcssd atigs, prhaps thrghprstati a cvrgt tp f MHC mlcl.Istad, th might rcgiz ativ atigs i a cllbd frm, prhaps i a wa similar t th rcgitithat ccrs fr sm sbsts f gathstm T clls.Bcas th lampr T cll atig rcptr VLRAhas b shw t bid slbl atigs ad bcasits g appartl mtats aftr atigic stimlati,

r prdicti is that th TCRlik mchaism willprv t b crrct123. Rgardig th scd qsti, wwill vr b abl t rslv this prblm xprimtall.

nw idas ccrig slcti prssrs sggst that thcapacit f th imm sstm t distigish btwcmmsal ad pathgic micrrgaisms rsltd ith grat cmplxit f th gathstm AIS124,125. Thdrstadig f th imm sstms itractis withcmmsal rgaisms is i its ifac, ad prhaps wca dvlp dfid hpthss as this fild dvlps.o hpthsis, which mphasizs th imprtac fth gt, sggsts that with th advt f jaws, digstdmatrial cld ijr th itsti ad thrfr rslti massiv ifctis. Th sahrs, which has smigl lst fatrs f adaptiv immit, is a filtrfdig aimal, s it is spclatd t hav rvrtd ta pradaptiv stat120. or viw is that th AIS ars as asstm f dfc ad bcam mr crcial ad mrsphisticatd with th mrgc f th larg prdatr

jawd vrtbrats that br fw ffsprig. W thik thatr psiti has b strgthd b rct vidcthat has shw that th jawd vrtbrats i which it isblivd that th AIS first mrgd th placdrms had itral frtilizati126. W hp that this Rviw

will spark frthr itrst i this ara, spciall amgimmlgists wh might s th prblm frm afrsh prspctiv.

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AcknowledgementsM.F.F. has been funded by the US National Institutes of

Health grants AI027877 and RR006603. M.K. has been

funded by a KAKENHI grant for the priority area Comparative

Genomics from the Ministry of Education, Culture, Sports,

Science and Technology of Japan.

Competing interests statementThe authors declare no competing financial interests.

DATABASESEntrez Gene:http://www.ncbi.nlm.nih.gov/geneRAG1 | RAG2

FURTHER INFORMATIONMasanori Kasaharas homepage:http://www.med.hokudai.

ac.jp/en/dept/outline/path/index.html

Pre-Ensembl genome database:http://pre.ensembl.org

Lamprey (Petromyzon marinus) draft genome sequence

SUPPLEMENTARY INFORMATIONSee online article:S1 (figure) |S2 (table)

All links Are Active in the Online pdf

R E V I E W S
http://www.ncbi.nlm.nih.gov/genehttp://www.ncbi.nlm.nih.gov/gene/5896http://www.ncbi.nlm.nih.gov/gene/5897http://www.med.hokudai.ac.jp/en/dept/outline/path/index.htmlhttp://www.med.hokudai.ac.jp/en/dept/outline/path/index.htmlhttp://pre.ensembl.org/http://pre.ensembl.org/http://pre.ensembl.org/Petromyzon_marinus/Info/Indexhttp://pre.ensembl.org/Petromyzon_marinus/Info/Indexhttp://pre.ensembl.org/Petromyzon_marinus/Info/Indexhttp://www.nature.com/nrg/journal/v11/n1/suppinfo/nrg2703.htmlhttp://www.nature.com/nrg/journal/v11/n1/suppinfo/nrg2703.htmlhttp://www.nature.com/nrg/journal/v11/n1/suppinfo/nrg2703.htmlhttp://www.nature.com/nrg/journal/v11/n1/suppinfo/nrg2703.htmlhttp://www.nature.com/nrg/journal/v11/n1/suppinfo/nrg2703.htmlhttp://pre.ensembl.org/Petromyzon_marinus/Info/Indexhttp://pre.ensembl.org/http://www.med.hokudai.ac.jp/en/dept/outline/path/index.htmlhttp://www.med.hokudai.ac.jp/en/dept/outline/path/index.htmlhttp://www.ncbi.nlm.nih.gov/gene/5897http://www.ncbi.nlm.nih.gov/gene/5896http://www.ncbi.nlm.nih.gov/gene

Rise of Adaptive Immunity

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