Gene conversion: Some implications for immunoglobulin genes

Cell, Vol. 24. 592-594.

June

1981,

Copyright

0 1981

by MIT

Gene Conversion: Some Implications for lmmunoglobulin Genes

Minireviews

David Baltimore Center for Cancer Research and Department of Biology Massachusetts Institute of Technology Cambridge, Massachusetts 02139

Among the many changes in our thinking about evolution wrought by the recombinant DNA revolution, a striking one is the new importance given to gene conversion. Gene conversion is one of two classes of mechanisms known that can act on families of genes to maintain their sequence homogeneity; the other class of mechanisms is called unequal crossing-over. Because the implications of these two genetic mechanisms are not widely appreciated, I will first contrast them before considering the importance of gene conversion in other contexts. In gene conversion, gene A interacts with gene B in such a way that the nucleotide sequence of part or all of gene A becomes identical to that of gene B. In the interaction, gene A and gene B retain their integrity and their physical locations but a nonreciprocal alteration in the structure of one partner occurs: this is aptly called conversion. Gene A and gene B could be alleles on homologous chromosomes; tandem copies of a gene on the same chromosome; tandem genes interacting from sister chromatids; or a pair of related genes located anywhere in the chromosomes of an organism. They could interact at mitosis or meiosis. The figure gives a comparison of gene conversion and unequal crossing-over for an idealized case of a twogene family (A and B) constituting the long arm of a single chromosome. The events are shown taking place between sister chromatids; whether gene conversion is any more frequent for tandem genes than for alleles on homologs or randomly placed genes is not known. Unequal-crossing-over events occur in more circumscribed conditions; they can take place only among tandemly arranged genes of a family (a family of genes is two or more genes of very similar sequence that arose by gene duplication). An unequal-crossingover event involves meiotic or mitotic crossing-over between two nonallelic genes of a family. The two interacting genes could be on sister chromatids, as illustrated in the figure, or on homologs. The result of an unequal-crossing-over event is either an increase or a decrease in the size of the gene family-should the family be decreased to one gene, unequal-crossing-over events could no longer take place. Any single unequal-crossing-over event is reciprocal; one segregant has an increased number of genes and the other has a decreased number. Ever since the discovery of gene families, the homogeneity of their sequences has posed an evolutionary puzzle (Hood et al., Ann. Rev. Genet. 9, 305-353,

1975). Given the inevitability of mutation and the difficulty of group selection, how can the members of a family of genes have the same sequence? Some mechanism of rectification of sequences must exist. Unequal crossing-over seemed to offer a way out; multiple occurrences of unequal crossing-over would lead to sequence homogeneity because stochastically one nucleotide sequence would come to dominate the family (Smith, Science 797, 528-535, 1978). Earlier proposals of a master gene converting the sequence of slave genes had been made (Callan, J. Cell Sci. 2, l-8, 1967; Whitehouse, J. Cell Sci. 2, 9-22, 1967), but fell into disfavor when the less complicated unequal-crossing-over proposal was made. The existence of unequal-crossing-over mechanisms was strongly implied by the observations of gene constancy among the ribosomal RNA genes of Drosophila (Tartof, PNAS 77, 1272-l 276, 1974) and has been proved to occur in yeast by the elegant experiments of Szostak and Wu (Nature 284, 426-431,198O) and Petes (Cell 79, 765-774, 19801, both studying the ribosomal RNA genes. Szostak and Wu calculated that the rate of unequal crossing-over they observed would be sufficient to maintain the sequence homogeneity of the ribosomal RNA of yeast. The occurrence of gene conversion was established many years ago, notably in work on various fungi (Radding, Ann. Rev. Biochem. 47, 847-880, 1978). These classical cases involved genes on homologous chromosomes. More recently, yeast workers (Klein and Petes, Nature 289, 144-l 48,198l; Jackson and Fink, Nature, in press) have demonstrated intrachromosomal gene conversion. Also working with yeast, Scherer and Davis (Science 209, 380-384, 1980) have described interchromosomal conversion. There is thus experimental evidence that members of a gene family on sister chromatids, on’the same chromatid or on different chromosomes can pair with one another and one can then convert the sequence of the other. Jackson and Fink (op. cit.) show that between a closely linked pair of virtually identical genes, gene conversion is much more common than homologous recombination. It is evident that gene conversion can explain the maintenance of sequence homogeneity among members of a family in exactly the same way that unequal crossing-over explains it: cross-conversion events will stochastically force identity on a family of sequences. Furthermore, many of the consequences of the unequal-crossing-over proposal are avoided. The num-

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ber of genes is not constantly changing and thus gene dosage can be selected as an independent variable. Also, the loss of the whole family by an event that leaves only one gene is avoided. Finally, unequal crossing-over is limited in occurrence to a tandem family of genes: for both progeny chromosomes of an unequal-crossing-over event to be viable, the minimal requirement is that no sequences necessary to the survival of an organism occur among the genes of the family. Gene conversion, however, can occur between genes located anywhere in the genome, because neither gene loss nor rearrangement occurs during gene conversion. For that reason, gene conversion could be the process that maintains the relative homogeneity of species-specific, interspersed repetitive DNA, as well as the homogeneity of tandem gene families. The occurrence of gene conversion among tandem mammalian genes has recently been suggested by Slightom et al. (Cell 27, 627-638, 1980). They found regions of homology between adjacent ,&like globin genes on one human chromosome that were not reflected on the homologous chromosome, and they interpreted their result as a consequence of gene conversion. They persuasively argued that unequal crossing-over was an unlikely cause of the homology they detected. Their results extend the concept of gene conversion by demonstrating that it might cause localized conversion of a segment of a mammalian gene. These results suggest the following thoughts. The immunoglobulin (lg) genes consist of a complicated, hierarchically related set of related sequences. All of the lg domains, both constant and variable regions, appear to be derived from a single ancestral gene by multiple levels of duplication events. If gene conversion is a reasonably common event during evolutionary time, then it might be expected to be obvious in the structure of the lg genes. One recent observation, very similar to that of Slightom et al. (op. cit.), suggests that gene conversion has occurred among the lg genes. Schreier et al. (PNAS, in press)

have shown that two nonallelic y-constant-region genes of the BALB/c mouse have obviously homologous segments that are not shared by an apparently allelic gene of the C57BL/6 mouse strain. Although there is some difficulty in being absolutely certain in this system that the genes considered allelic are actually so, this appears to be a very strong case for gene conversion, and is especially interesting because the interconverting genes are not members of a repeated family but were duplicated sufficiently long ago that they have individual characteristics. Miyata et al. (PNAS 77, 2143-2147, 1980) have noted homology among subregions of another pair of lg y genes, and have suggested unequal crossing-over as its origin; gene conversion is as likely the cause of that homology. Similarly, the segmental homology between a mouse pseudo cu-globin gene and a true mouse cY-globin gene discussed by Miyata and Yasunaga (PNAS 78, 450-453, 1981) could result from gene-conversion events as suggested by Liebhaker et al. (Nature 290, 21-29, 1981) for human a-globin genes. The apparent detection of gene conversion among lg constant-region genes raises the question of whether gene conversion might not have been a very frequent event during the evolution of the genes of the immune system. An apparently paradoxical situation in the analysis of variable-region (V-region) sequences could be resolved by postulating just such an extensive occurrence of gene conversion. Kabat% al. (J. Exp. Med. 149, 1299-l 313, 1979; 152, 72-84, 1980) and Capra and Kindt (Immunogenetics 7, 417422, 1975) have presented striking evidence that Vregion genes have subregions of homology. (“Variable region” is used here to denote only the encoded sequence from amino acid 1 to about 97 and is not meant to refer to the D or J regions that are joined to it.) From amino acid sequence data indicating independent assortment of framework and complementarity-determining segments of V regions, Kabat et al.

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have proposed that the V-region genes are actually encoded as families of “minigenes” and that a V region is constructed by joining seven such minigenes together as an event of somatic differentiation. This proposalalthough subsequently shown to be correct for the J and D regions of lg chains (Early et al., Cell 19, 981-992, 1980)-is directly counter to the observation that V regions occur in the genome as uninterrupted sequences, not as fragments (Tonegawa et al., PNAS 75, 1488-l 492, 1978). V regions have no intervening sequences that might allow minigene joining. Thus far, those V-region genes that have been sequenced, both as cDNAs and from the genome, have shown no occurrences of recombination among V-region genes during the events that form the expressed V region (at least ten such comparisons have been made; these will be reviewed separately). Thus the strong evidence for conserved subregions of the lg V region seems inconsistent with the available evidence about the structure and expression of the V regions. One proposal that would explain the segmental homologies of V regions, but would not require postulating their somatic assembly into V regions, is that over evolutionary time the V regions have often participated in gene-conversion events with each other in such a way that segments of sequence have been transferred from one gene to another. Selection as well as stochastic processes could then be invoked to explain why certain segments are found commonly and certain segments are rare. The apparent coincidence of the homologous sequences with the functional segments of the V region either could indicate that gene-conversion events tend to initiate or terminate at the borders of such functional segments, or could be a consequence of the different selective pressures on framework as opposed to complementarity-determining residues. Bothwell et al. (Cell 24, 625-637, 1981) have sequenced seven closely related germline VH regions, and have demonstrated in the sequences subsegments of homology that could well have been a consequence of gene-conversion events. Studies of k-light-chain V-region sequences by Komaromy and Wall (J. Supramol. Struct. S(suppl.), 12, 1981) also apparently indicate that segments of sequence are held in common by multiple Vregion genes. The utility of gene-conversion events to the evolution of the V genes is evident from a consideration of the requirements for maintaining a large library of V genes (perhaps 200-l 000 in size). One of the major difficulties in evolving and maintaining this large library of related but subtly and crucially different V regions is loss of function in a gene by mutations that cripple

the gene (such as small deletions, point mutations that create terminators or loss of residues that are critical to maintenance of structure). Because of the multiplicity of genes, selection may act only weakly on any one gene, implying that much of the library could badly degrade before evolutionary forces could come into play. Gene conversion allows the results of selection on a few indispensable V regions to become distributed through the entire library. It could repair defective genes and return them to the library. Gene conversion also allows the mixing of segments of V regions that have evolved independently. In more general terms, extensive gene conversion could be important to the evolution of any gene library that maintains microdiversity in a set of otherwise very similar molecules. The genes of the major histocompatibility complex (MHC) come to mind here-gene conversion could well be the explanation both for the shared specificities of the K- and D-region products and for the species-specific residues in the sequences of MHC products analyzed from different species (Klein, Biology of the Mouse H-2 Complex, SpringerVerlag, 1975; Science 203, 516-521, 1979). Put more generally, gene conversion can, by combining elements of genes, make a new gene from parts of previous ones. Gene conversion differs from the shuffling of exons during evolution (Gilbert, Nature 277, 501-502, 1978) in that gene conversion requires preexisting homology, while the recombination of exons may occur with little homology by illegitimate recombination events occurring in intervening sequences. The suggestion that gene conversion may have played an extensive role in the evolution of lg V regions adds yet another mechanism to those known to determine the extent of variability of this remarkable gene family. V-region heterogeneity is a consequence of a large number of encoded differences interacting with systems that generate various forms of combinatorial diversity and somatic point mutations. Much progress has been made recently towards understanding the somatic mechanisms, but the evolutionary forces and genetic structures that maintain the extent of and alter the structure of the encoded library of V regions still require elucidation. Because of the enormous size and diversity of the V-region family, we can expect to find encoded in and around the V regions signals that are important to the evolution of the family. I thank Elvin Kabat. Gerry Fink, David Sotstein. Lee Hood, Phillip Sharp and members of my laboratory for stimulating discussions of these ideas. Egel (Nature 290, 191-l 92, 1981) has independently reviewed gene conversion and discusses some of the issues raised here.