4
Proc. Natl. Acad. Sci. USA Vol. 93, pp. 5380-5383, May 1996 Evolution Ancestral major histocompatibility complex DRB genes beget conserved patterns of localized polymorphisms LAKSHMI K. GAURt#§ AND GERALD T. NEPOMDII tPuget Sound Blood Center, 921 Terry Avenue, Seattle, WA 98104-1256; IVirginia Mason Research Center, 1000 Seneca, Seattle, WA 98101; and Departments of tMicrobiology and Illmmunology, University of Washington School of Medicine, Seattle, WA 98195 Communicated by Hans Neurath, University of Washington School of Medicine, Seattle, WA, January 29, 1996 (received for review September 19, 1995) ABSTRACT Genes within the major histocompatibility complex (MHC) are characterized by extensive polymorphism within species and also by a remarkable conservation of contemporary human allelic sequences in evolutionarily dis- tant primates. Mechanisms proposed to account for strict nucleotide conservation in the context of highly variable genes include the suggestion that intergenic exchange generates repeated sets of MHC DRB polymorphisms [Gyllensten, U. B., Sundvall, M. & Erlich, H. A. (1991) Proc. Nati. Acad. Sci. USA 88,3686-3690; Lundberg, A. S. & McDevitt, H. 0. (1992) Proc. Natl. Acad. Sci. USA 89, 6545-6549]. We analyzed over 50 primate MHC DRB sequences, and identified nucleotide ele- ments within macaque and baboon DRB6-like sequences with deletions corresponding to specific exon 2 hypervariable regions, which encode a discrete ct helical segment of the MHC antigen combining site. This precisely localized deletion pro- vides direct evidence implicating segmental exchange of MHC- encoded DRB gene fragments as one of the evolutionary mechanisms both generating and maintaining MHC diversity. Intergenic exchange at this site may be fundamental to the diversification of immune protection in populations by per- mitting alteration in the specificity of the MHC that deter- mines the repertoire of antigens bound. Extensive variation of major histocompatibility complex (MHC) genes occurs in all vertebrate species, due to a number of structural and genetic features, including gene duplication, heterodimer formation, and extensive allelic polymorphism. Notably, within MHC DRB genes, sequence polymorphism is nonuniform, clustered within "hypervariable" regions of the second exon (1-4), which encodes the antigen-binding portion of the MHC class II molecule. Thus, functional properties of the MHC molecule and the corresponding selective pressures that arise from immunological challenges cluster within a limited set of highly polymorphic nucleotides. Calculations based on sequence variation have indicated that the overall mutation rate of MHC loci is not higher than that of most other genetic loci (5). However, it has been suggested that discrete segments within the second exon may accumulate mutations at different rates (4). Specific mecha- nisms for generating localized variability in the MHC, such as gene conversion and interlocus genetic exchange, have been suggested but they are controversial and indirect (6-8). In- deed, arguments for convergent mechanisms to account for recurrent sequences within otherwise divergent alleles have even been proposed (9). We now provide evidence from an analysis of macaque and baboon MHC DRB-related genes for intragenic segmental loss of specific hypervariable sequences, consistent with evolutionary mechanisms involving exchange of DRB gene segments generating MHC diversity. MATERIALS AND METHODS DRBFP1 (forward) and DRBRP2 (reverse) oligonucleotide primers were used for primary amplification and sequencing of DRB loci in humans and nonhuman primates. Genomic DNA was amplified by PCR for 29 cycles at 55°C, 72°C, and 93°C for 30 sec each. Amplification products were ligated into the TA cloning vector (Invitrogen) before sequencing by the dideoxy termination method. As described, additional allele-specific primers were then derived from these sequences. Nested reverse primers NHP-R0, NHP-R1, and NHP-R2 were used in conjunction with nested forward primers NHP-01, NHP-02, NHP-03, and NHP-04 to confirm the "short" MHC sequences by independent amplification from genomic DNA. Primers used included: NHP-01, TGGAGCAGGCTAAGTGTAAG; NHP-02, TTCTTGGAGTAGGCTAAGTGT; NHP-03, GG- AGCAGGCTAAGTGTGAG; NHP-04, TTGGAGCAGGCT- AAATATGAG; NHP-R0, TGTAACTCTGTGACAGGCCA; NHP-R1, TGTAACITCTGTGACAAGCCG; NHP-R2, TTCC- GTAATTGTAACTCTGTGA; DRBFP1, CCCCACAGCAC- GTTTCTTG; DRBRP2, CCGCTGCACTGTGAAGCTCT. RESULTS AND DISCUSSION Over 50 DRB-like sequences from a wide variety of nonhuman primates were derived by amplification of the second exon homologs using DRB1 consensus primers. Most of the se- quences gave the expected 270-bp product that aligned with DRB second exon sequences. However, four short variants of 208 bp were identified in macaques; these sequences were also homologous to portions of the DRB second exon with a 62-bp gap and were observed in two species of macaques, Macaca fascicularis and Macaca nemestrina (Fig. 1). The deleted nucleotide sequences corresponded to codons 60-80 of the DRB second exon, also creating a frame shift at the junction flanking this gap. Additional polymorphisms distinguished the four short variants, consistent with continued divergence of these sequences subsequent to a common ancestral deletional event. A very similar sequence was also identified in a baboon DRB-like gene shown in Fig. 1, designated Paca-DRB6*pssO2. Again, codons 60-80 were specifically deleted with the same frame-shift mutation at this site. Additional polymorphisms within the baboon-derived sequence, particularly at codon 35-37, indicate that this gene also contains additional muta- tions, consistent with continued accumulation of deleterious nucleotide changes. Abbreviations: MHC, major histocompatibility complex; HVR, vari- able region. Data deposition: The sequences reported in the paper have been deposited in the GenBank data base (accession nos. L76641-L76651, L76675-L76695, L76720-L76725, L76980-L76981, L77100-L77105, and L77110-L77112). §To whom reprint requests should be addressed at: Puget Sound Blood Center, 921 Terry Avenue, Seattle, WA 98104-1256. 5380 The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. §1734 solely to indicate this fact. Downloaded by guest on January 4, 2021

Ancestral major histocompatibility complex DRB genes beget ...Evolution: GaurandNepom Proc. Natl. Acad. Sci. USA93 (1996) 5381 10 20 30 40 TTC TTG GAG CAG GCT AAG TGT GAG TGT CAT ATC

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Page 1: Ancestral major histocompatibility complex DRB genes beget ...Evolution: GaurandNepom Proc. Natl. Acad. Sci. USA93 (1996) 5381 10 20 30 40 TTC TTG GAG CAG GCT AAG TGT GAG TGT CAT ATC

Proc. Natl. Acad. Sci. USAVol. 93, pp. 5380-5383, May 1996Evolution

Ancestral major histocompatibility complex DRB genes begetconserved patterns of localized polymorphismsLAKSHMI K. GAURt#§ AND GERALD T. NEPOMDIItPuget Sound Blood Center, 921 Terry Avenue, Seattle, WA 98104-1256; IVirginia Mason Research Center, 1000 Seneca, Seattle, WA 98101; and Departments oftMicrobiology and Illmmunology, University of Washington School of Medicine, Seattle, WA 98195

Communicated by Hans Neurath, University of Washington School of Medicine, Seattle, WA, January 29, 1996 (received for reviewSeptember 19, 1995)

ABSTRACT Genes within the major histocompatibilitycomplex (MHC) are characterized by extensive polymorphismwithin species and also by a remarkable conservation ofcontemporary human allelic sequences in evolutionarily dis-tant primates. Mechanisms proposed to account for strictnucleotide conservation in the context of highly variable genesinclude the suggestion that intergenic exchange generatesrepeated sets ofMHCDRB polymorphisms [Gyllensten, U. B.,Sundvall, M. & Erlich, H. A. (1991) Proc. Nati. Acad. Sci. USA88,3686-3690; Lundberg, A. S. & McDevitt, H. 0. (1992) Proc.Natl. Acad. Sci. USA 89, 6545-6549]. We analyzed over 50primate MHC DRB sequences, and identified nucleotide ele-ments within macaque and baboon DRB6-like sequences withdeletions corresponding to specific exon 2 hypervariableregions, which encode a discrete ct helical segment of theMHCantigen combining site. This precisely localized deletion pro-vides direct evidence implicating segmental exchange ofMHC-encoded DRB gene fragments as one of the evolutionarymechanisms both generating and maintaining MHC diversity.Intergenic exchange at this site may be fundamental to thediversification of immune protection in populations by per-mitting alteration in the specificity of the MHC that deter-mines the repertoire of antigens bound.

Extensive variation of major histocompatibility complex(MHC) genes occurs in all vertebrate species, due to a numberof structural and genetic features, including gene duplication,heterodimer formation, and extensive allelic polymorphism.Notably, within MHC DRB genes, sequence polymorphism isnonuniform, clustered within "hypervariable" regions of thesecond exon (1-4), which encodes the antigen-binding portionof the MHC class II molecule. Thus, functional properties ofthe MHC molecule and the corresponding selective pressuresthat arise from immunological challenges cluster within alimited set of highly polymorphic nucleotides.

Calculations based on sequence variation have indicatedthat the overall mutation rate of MHC loci is not higher thanthat of most other genetic loci (5). However, it has beensuggested that discrete segments within the second exon mayaccumulate mutations at different rates (4). Specific mecha-nisms for generating localized variability in the MHC, such asgene conversion and interlocus genetic exchange, have beensuggested but they are controversial and indirect (6-8). In-deed, arguments for convergent mechanisms to account forrecurrent sequences within otherwise divergent alleles haveeven been proposed (9). We now provide evidence from ananalysis of macaque and baboon MHC DRB-related genes forintragenic segmental loss of specific hypervariable sequences,consistent with evolutionary mechanisms involving exchangeof DRB gene segments generating MHC diversity.

MATERIALS AND METHODS

DRBFP1 (forward) and DRBRP2 (reverse) oligonucleotideprimers were used for primary amplification and sequencing ofDRB loci in humans and nonhuman primates. Genomic DNAwas amplified by PCR for 29 cycles at 55°C, 72°C, and 93°C for30 sec each. Amplification products were ligated into the TAcloning vector (Invitrogen) before sequencing by the dideoxytermination method. As described, additional allele-specificprimers were then derived from these sequences. Nestedreverse primers NHP-R0, NHP-R1, and NHP-R2 were usedin conjunction with nested forward primers NHP-01, NHP-02,NHP-03, and NHP-04 to confirm the "short" MHC sequencesby independent amplification from genomic DNA. Primersused included: NHP-01, TGGAGCAGGCTAAGTGTAAG;NHP-02, TTCTTGGAGTAGGCTAAGTGT; NHP-03, GG-AGCAGGCTAAGTGTGAG; NHP-04, TTGGAGCAGGCT-AAATATGAG; NHP-R0, TGTAACTCTGTGACAGGCCA;NHP-R1, TGTAACITCTGTGACAAGCCG; NHP-R2, TTCC-GTAATTGTAACTCTGTGA; DRBFP1, CCCCACAGCAC-GTTTCTTG; DRBRP2, CCGCTGCACTGTGAAGCTCT.

RESULTS AND DISCUSSIONOver 50 DRB-like sequences from a wide variety of nonhumanprimates were derived by amplification of the second exonhomologs using DRB1 consensus primers. Most of the se-quences gave the expected 270-bp product that aligned withDRB second exon sequences. However, four short variants of208 bp were identified in macaques; these sequences were alsohomologous to portions of the DRB second exon with a 62-bpgap and were observed in two species of macaques, Macacafascicularis and Macaca nemestrina (Fig. 1). The deletednucleotide sequences corresponded to codons 60-80 of theDRB second exon, also creating a frame shift at the junctionflanking this gap. Additional polymorphisms distinguished thefour short variants, consistent with continued divergence ofthese sequences subsequent to a common ancestral deletionalevent.A very similar sequence was also identified in a baboon

DRB-like gene shown in Fig. 1, designated Paca-DRB6*pssO2.Again, codons 60-80 were specifically deleted with the sameframe-shift mutation at this site. Additional polymorphismswithin the baboon-derived sequence, particularly at codon35-37, indicate that this gene also contains additional muta-tions, consistent with continued accumulation of deleteriousnucleotide changes.

Abbreviations: MHC, major histocompatibility complex; HVR, vari-able region.Data deposition: The sequences reported in the paper have beendeposited in the GenBank data base (accession nos. L76641-L76651,L76675-L76695, L76720-L76725, L76980-L76981, L77100-L77105,and L77110-L77112).§To whom reprint requests should be addressed at: Puget Sound BloodCenter, 921 Terry Avenue, Seattle, WA 98104-1256.

5380

The publication costs of this article were defrayed in part by page chargepayment. This article must therefore be hereby marked "advertisement" inaccordance with 18 U.S.C. §1734 solely to indicate this fact.

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Page 2: Ancestral major histocompatibility complex DRB genes beget ...Evolution: GaurandNepom Proc. Natl. Acad. Sci. USA93 (1996) 5381 10 20 30 40 TTC TTG GAG CAG GCT AAG TGT GAG TGT CAT ATC

Evolution: Gaur and Nepom Proc. Natl. Acad. Sci. USA 93 (1996) 5381

10 20 30 40

TTC TTG GAG CAG GCT AAG TGT GAG TGT CAT ATC TTC AAT GGG ATG AAG CGG GTG CAG TAC CTG AAC AGA TAC ATC CAT AAA CGG GAG GAG AAC CTG CCC TTC GAC AGC GAC GTG

--- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- -G- --- --- --- A-- ---

--- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- -G- --- --- --- A- ---

-- -- --- --- --- --- --- --- a-- --- --- --- --- --A --- -CT a-- --- --- --- --G --- --- --- --- --- --- --- --- --- --- --- -G_ c-- --- --- --c

--- --- --- --- T-- --- --- --- --- --- --- --- --- --- --- -CT G-- --- --- -a- --- --- --- --- A-- --- --- -A- -G- C-- --- --- ---

--- --- --- --- --- --- --- --- --- --- -C- --- --- --- --- -CT G-- -C- --- --- --- --- --- --- --- --- --- A-- --- --- --- --- -G- -A- A-- --- --- C--

--- --- --- --- --- --- --A -A- --- --- --- --- --- --- --- -CTOG-- --- --- --- --- --AA --- --- -- --- --- G-- --- A-- --- --- - C-C-G --- --- --CGAG

--- --- --- A-C- --- --- --- --- --- --- --- --- --- --- -- - CT G-- -A- - --- ------ --- --- -- A-- --- --- --- ---G--^-c-- --- -G -C-- --- --- ---

--- --- --- --- --- --- --- --- --- --- --- T-- --- --- --- -CT G-- A-C G-- --- --- --- --- --- --- --- --- --- --- --- --- -CG-C-- --- --- ---

--- --- --- --- --- --- --- --- --- --- --- T-- --- --- --- -CT G-- A-- --- --- --- --- --- --- --- --- --- --- --- --- --- -CG-C -- --- --- ---

--- --- --- --- --- -G- --C-- --- --- --A --- --- --C ---G- G-- --- --- -G- --- --- --- --- --- --- --- --- --- --- --- --- -G- --- --- --- --- ---

--- --- --- --- --- -G- --C-- --- --- --A --- --- --C ---G- G-- --- --- -G- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ---

--- --- --- --- --- -T- --- --- A-C --- -G- --- --- --- --- -CT G-- -A- --- --- --- --- --- --- A-- --- --- --- --- --- --- --- -G- --- C-- --- A- C--

50 60 70 80

GAG GAG TTC CAG GCA GTT ACG GAA CTG GGG CGG CCT GTC GCA GAG AAC TGG AAC AGC CAG AAG GGA ATC CTG GAG GAG AAT CGG GAC AAG GTG GAC ACC TAC TGC AGA TAC AGT

--- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --C --- --- --- --- --G --- --- --- A-- - GA- -- -- -- ---A-

--- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --C --- --- --- --- --G --- --- --- A-- - GA- --- --- --- --- -A-

-a- --- --- --- -AG - - -- --- --- -T- --- A-- I --- -A-

-o- --- --- --- --G --G --- --- --- --- T-- --- --- A-- T --- GA-

- --- --- --- --a --G --- --- --- ---- T-- --- --- CT -A-

-a- --- --- - - --G--G --- ---G TG-- --- --- IT ---A-

-a - --- --- --- -A --a --- --- --- --- --- -- - A- --AG -T -A-

-G- - --- - -- - -- - -G - -G - -C --- - -- - -- - -- - -- --A- - -G --- - -- - -- - -- - -- - -- - -- - --C --- - -- - -- - -- ---G - -- - -- - -- - -- - -- - -- - -- - -- - -- --- - -A-

-G- --- --T --- --G --G --- C-- --- --- --- --- --- --G --- --- --- --- --- --- --- --C --- --- --- --- -GC G-- --- --- --- --- --- --- --- --- --- -A-

-G- --- --- --- --G --G --- --- --- --- --- --- --- --G ------ --- --- --- --- --- -- C --- --- --- --- --G ------ --- --- --- --- --- --- --- -- A-

-G- - --- - -- - -- - -G - -G --- - -- - -- - -- - -- - -- - -- - --G --- - -- - -- - -- - -- - -- - -- - --C --- - -- - -- - -- ---G - -- - -- - -- - -- - -- - -- - -- - -- - -- --- - -A-

-G- --- --- --- --G --G --- --- *-- --- --- --- --- --G --- --- --- --- --- --- --- --- --- --- --- --- --G -C- --- --- --- --- --- --- --- --- --- -A-

TAC GGG GTT TTT GAG AG

- -- T-

A-----

A-- --- ---T--- --

O

--- -----_ --- --

--T - --

S- --- - --

-- --

_ --__

--A C-- --- --- --- --

--A C-- --- --- --- --

FIG. 1. MHC DRB6 second exon sequence alignments. Primate DRB6 alleles identified with a gap

corresponding to codons 60-80 are aligned with previously described human DRB6 sequences. Representativeadditional macaque DRB6 full-length alleles are also listed for comparison; provisional locus and allelicnomenclature assignments are based on overall homology with published human and nonhuman primateDRB6 sequences (10, 11).

To confirm the presence of the short sequences in genomicDNA, additional primer oligonucleotides (NHP-R0, NHP-Rl, NHP-R2) were constructed that annealed to the predictedjunctional sequence linking codons 59 and 81 when codons60-80 are deleted. Specifically amplified DNA of the pre-

dicted length was obtained from all four macaque samples andnucleotide sequences confirmed the previously identified genes.

Because the deleted gene segments corresponded to most ofthe distal portion of the second exon, sequences in the proximalportion of the exon were used for alignment comparisons.Conserved lineage motifs in this region for each of the fivedeleted DRB sequences corresponded to homology with theDRB6 locus. This alignment is shown in Fig. 1. DRB6 genes

have been identified in prosimians and most primate species,suggesting that it is one of the oldest ancestral DRB homologs(11). In modern primate and human lineages, DRB6 analogs

are pseudogenes with, for example, deletions of the first exoncommonly found (12). Indeed, one of the short DRB6 se-

quences observed in the macaques contains an additionalsequence polymorphism at codon 10 that encodes a stop

codon, consistent with the interpretation that these represent

ancestral pseudogenes.DNA from a variety of human MHC haplotypes was also

studied, using both the amplification primers originally used inthis study as well as primers corresponding to the predictedjunctional sequences; no short human homologs were iden-tified.The boundaries of the deleted DNA segment from codon

60-80 are of interest because they have a specific topologicalalignment within the DRB molecule. Codons 7-54 encode a

,B-pleated sheet platform structure underlying the MHC-

antigen binding groove, and codons 60-80 encode a long a

HLA-DRB6*0101

HLA-DRB6*0201

HLA-DRB6* 02 02

Mne-DR26*pxsO3

Mai-DRBC^ps0Ol

Kane-DRB6*pap02

Kafa-DR36*psu01

Paca-DRB6*pssl1

Mane-DRB6*02a

Mane-DRB6*02b

Mane-DRB6*03a

Mafa-DRB6*03a

Mane-DRB6*psOl

HLA-DRB6*0101

HLA-DRB6*0201

HLA-DRB6*0202

Kaa-DRB6*pmuO3

Kane-DR36*poaO1

Kane-DR36*psu02

Kafa-D336*p&sOl

Paca-DRn6*pms1

Mane-DRB6*02a

Mane-DRB6*02b

Mane-DRB6*03a

Mafa-DR16*03a

Mane-DRB6*psOl

HLA-DRB6*0101

HLA-DRB6*0201

HLA-DRB6*0202

-ane-DRB6*psaO3

Maza-DRB6*psaO1

Kane-DRB6*pssO2

Kafa-DRB6*pasO1

Paca-DRB6*psaOl

Mane-DRB6*02a

Mane-DRB6*02b

Mane-DRB6*03a

Mafa-DRB6*03a

Mane-DRB6*psOl

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Page 3: Ancestral major histocompatibility complex DRB genes beget ...Evolution: GaurandNepom Proc. Natl. Acad. Sci. USA93 (1996) 5381 10 20 30 40 TTC TTG GAG CAG GCT AAG TGT GAG TGT CAT ATC

5382 Evolution: Gaur and Nepom

helical loop that forms the lateral boundary of the antigen

binding MHC groove (13). Previous sequence comparisons of

full-length DRB genes have suggested that these two regionshave distinct evolutionary histories. Statistical analyses of the

relative frequencies of replacement and silent substitutions

(14), as well as phylogenetic analysis (4, 15), have been used to

argue that the proximal (f3 sheet portion) second exon contains

Proc. Natl. Acad. Sci. USA 93 (1996)

most of the stable allelic lineage-related sequence motifs, with

a slow conventional accumulation of additional mutations over

time. In contrast, the distal (a helical portion) second exon

represents a fixed sequence element that occurs in the context

of multiple different allelic lineages. We believe we have

identified in the short DRB6 macaque and baboon sequences

direct evidence consistent with a mechanism of intergenic

HLA-DRtB1*0101HLA-DRB1*1501

HLA-DRB1*0301HIA-DRB1*1101

HLA-DRB1*0801

EMA-DRB1*1301Nane-DRB1*13aMane..DRB1*03b

Man.-DRB1*03cNafa-DRB1*03aMane-DRB1*13b

HL&-DRB1*0401Kafa-DRB1*04aMafa-DRB1*04bMane-DRB1*04aHLL-..RB4*0101Name-DEB4*04cNane-DRB4*05bI4ane-DRB4*05cMane-DRB4*05dHafa-DRB4*05aMafa-DRB4*05bMafa-DRB4*05c

Mafa-DRB5*OlaMafa-DRB5*09a

Mane-DRBS*OlaHIUA-RB6*0101Xane-DRB6*02aMane-DRB6*02bMane-DRB6*03aMane-DEB6*03bMane-DRB6*03cMafa-DRB6*03aHr&AflB7*0101Mane-DRB7*02aI4afa-DRB*02aMane-DRB*02bMafa-DRB*02bMane-DRB*02a

Mafa-DRB*03aGamin-DEB*02Lefs-DRB*01Lefs-DRB*02

Lefs-DRB*03Gaga-DRB*01Gaga-DRB*02Mane-DRB4*05aKane-DRB5*02aUEane-DRB5*03aLefa-DRB5*03aGasmnDRB5*03aMane..DRB*05a

Mane-DRB*05bI4ane-tSB?*psOlMane-DE4B6*pssOlMane-DMA6*pssO2

HVR1

9 14

TOG CAG CTT ADG TTT OAA

-- -AGO --G

HVRi26 35.

TTG CTG ORA AGA TOC ATC_

-AC - -C --- -A- T----C ----C.--- -A- T-----C --. -C ----A- T--

--C -_C --- -A- T----C -- -C --- -A- T---AC--

-AC ---

-AC ---

GA-T-CTO - 0 AA-C --AC - -A- T--OK- T-C 0- -G -AC ---AC --A- T--

OK- T~~-C0 - 0 -AC ---AC ---A- T--0 ~~--C--AC--T ?-A-T--~

GA- T-C 0G--- --- --0 -AC-- ATC ---G- T--GM?-'C0--0 ~-AC --- MTC --- 0GT- T'--

GM?-CG------0 -AC --- ATC --- GT- T--

CA6- GA6-Q--- -

CA-----AA --- GC- --G

rq~."

GA- O;C----A-

Q----- 0--

CA6T AT- -0-

- - -

- - -

- - -

-A CO- --O

--A CO- --G

C- C-

--0G

HVRIII67 74

c Tm G C C a

---------OC- - -

I

A- - - - A ----- GA- - - - A -----CG

--- --- --- - - - - - - - - A-

-- - - -- - - - - - -CA-

-A

A--------A-- - CO.-

T-- - - ----------

--C C-C ---QGA- ---I-- - -G - - - - - - - - - - - -A--CA---C --- C-C --- G&---- A- ----G-------A-

I--C--c---( - A -

-- - - - - - - -

V--C ----C----TC-C --- -GC-0--G---

GA -- - -T CA---AA----C---GC---GO -----C CG--- CA-T--AA---AC---- C -O ------ C --- CA-T--

AA---AC----GC---O------C --- CA-T--

o-- GC- --A CO---G --C--C -Ao-- GC- --A CG- --G --C--C -A -

GAT.0---- --C --C -A -

OA- T--G C" 0- -AC A-C--AA---

GA-~w QC-

Mafa-DRB6tpssOl GA- OC- --A -A- --0

Mane-DRB6tpssO3 GA- GC-0---- A-0

Paca-DRB6tpssOl AA- GC-o---G -

-AC --A A-C --- AA----

-A- A-C -- ---

-AC --- A-C --- hA- -

j T ----- A-- -T AAT-G---O T T-C OC-------

I ---------A - -TT

A- - - QC -------

FIo. 2. Selected human (HIA), macaque, baboon, and prosimian (lemur and galago) sequence alignment representing the three variable regions(HVR) within the DRB second exon. Mane, M. nemestrina; Mafa, M. fascicularis; Lefa, Lemurfulvus albifons; Lefs, L. fulvus sanfordi; Gaga, Galagogarnetti; Gasm, Galago senegalensis moholi; Paca, Papic cynocephalus anubis. The allelic designation for the primates is provisional; allelic designationps" indicates a pseudogene with a stop codon and "pss" indicates pseudogenes with a short sequence due to the 62-bp gap in the a helical region.

I

IIIIIIIIME12 II I

1.

.. .- -- ... -- .I ---J.-I

--C --- -A- T----- --- -A- T----C --- -A- T--

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Page 4: Ancestral major histocompatibility complex DRB genes beget ...Evolution: GaurandNepom Proc. Natl. Acad. Sci. USA93 (1996) 5381 10 20 30 40 TTC TTG GAG CAG GCT AAG TGT GAG TGT CAT ATC

Proc. Natl. Acad. Sci. USA 93 (1996) 5383

segmental interchange for the distal (a helical portion) DRBsecond exon. The short macaque DRB6 pseudogenes appear torepresent the donor sites from such an exchange, which inthese cases was apparently nonreciprocal, leading to the evo-lutionary remnants found.

Segmental recombination at this site in DRB second exonsis presumably not limited to the DRB6 pseudogene. Sequenceidentities between the a helical portion of the DRB moleculeamong different alleles have been noted by many investigatorsand are present in most of the functional allelic lineages inmodern primates and man. For example, the humanDRB1 *1414 gene sequence is consistent with a recombinationbetween DRB1 *1404 and DRBJ *0802 or DRB1 *0804 alleles atthis second exon site (16), and similarly the DRB1 *0415sequence may derive from a DRB1 *0401/DRBl *11 recombi-nant (17). Analysis of additional sequences derived fromnonhuman primates identified some striking examples thatalso appear to represent this diversification mechanism. Asshown in Fig. 2, polymorphism among DRB genes can beviewed as a patchwork of distinct clusters of variable sequenceelements (HVR) that occur in three sites, including the HVRII,cluster encoding residues 67-74 within the a helical loopregion. Conserved sequence motifs from this region occur

interspersed among loci, alleles, and even between species, as

highlighted in Fig. 2.An example of this segmental conservation is shown for the

HVRII, sequence TAC CTG GAG CAG AGG CGG GCCGCG (Fig. 2, dark blue), which is found in DRB4-like, DRBS-like, and DRB6-like loci in several different alleles distributedacross macaque, lemur, and galago species, and is present inthe context of a least four different HVRI and HVRI, se-

quences. Although it is not possible to definitively identify thecodon 60-80 segment currently "missing" from the shortmacaque DRB6 sequences, it may be noteworthy that somecontemporary DRB6 genes have identical HVRI and HVRI,segments (i.e., compare Mane-DRB6*pssO2 with Mane-DRB6*02a and Mane-DRB6*02b), suggesting the possibilitythat the DRB6*02 HVR1II sequence ATC CTG GAG GAGAAG CGG GAC AAG (Fig. 2, grey) could correspond to thehypervariable segment deleted in the short sequences. If thisis the case, we can speculate that potential acceptor genes forthis sequence, if indeed it was donated in a nonreciprocalexchange, might be the macaque DRB6*03a or even the humanHLA-DRB7 pseudogene sequences, which share contempo-rary HVRII homologs. Most likely, this form of segmentalexchange is frequently reciprocal, yielding gene products ofnormal length; the existence of the short DRB6 homologs mayrepresent an exception to this reciprocal recombination that,nevertheless, provides direct evidence for this form of diver-sification mechanism.

Strong selective pressures encourage both diversification ofMHC DRB alleles within a species as well as conservation offunctionally successful motifs, not only within a species but alsobetween species (18, 19). It is possible that a mechanism ofsegmental recombination for the a helical portion of thesecond exon represents an evolutionary adaptation favoringthe exchange of successful structural motifs in this regionamong different alleles. Indeed, Gyllensten et al. (15) havenoted that DRB sequences between codons 51-55 are partiallyhomologous to bacterial x-like recombination signals and havesuggested this as a basis for the distinct evolutionary historiesof the a-sheet region compared with the a helical portions ofthe second exon (4). Because this x-like sequence occurs in a

nonpolymorphic portion of the exon, it raises the possibility

that conservation of a mechanism for localized segmentalexchange is one of the underlying evolutionary features ac-counting for MHC DRB diversity.

Localization of DRB1 segmental variation to the secondexon implies functional selection mechanisms, because thissegment encodes the class II MHC domain that interacts withhighly variable peptide antigens. Indeed, the comparablefunctional site in the third exon of the MHC class I HLA-Blocus has also been suggested to arise by similar mechanisms,based on sequence comparisons that suggest recombinantorigins (20). As pointed out by others (21), there are alsoexamples of sequence variation in DRB genes consistent withconcepts of convergent evolution. However, the specific local-ization of the deleted DRB6 gene segment described here ismost consistent with the interpretation that the evolutionaryhistory of the a helical portion of the second exon likelyinvolves specialized recombinational events.

We thank Kathy Snyder, Jeanne Anderson, and Emily Schultz fortheir excellent technical assistance, and Nicolette Ducommun forpreparing the manuscript. We also thank the Washington RegionalPrimate Center (Seattle) for the old world monkey blood samples andDuke Primate Center (Durham, NC), for the prosimian blood samples.This work is supported in part by a grant to the Washington RegionalPrimate Research Center from the National Institutes of Health(RRO0116).

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