Evolution of V genes: DNA sequence structure of functional germline genes and pseudogenes

Abstract

In this review we have examined the features of germline sequences of IgV genes from a number of species in an attempt to identify the "signature" of molecular mechanisms responsible for generating and maintaining diversity in the germline repertoire (after gene duplication by meiotic unequal crossover). We now summarize the relevant features point by point: 1. Codon analysis reveals a significant deficit of stop codons below the numbers that would be expected under random point mutational change. This implies that the majority of individual V genes have each been selected for the possession of open reading frames able to encode a functional Ig molecule. There is an extraordinarily high rate of apparent rescue of potential stop codons in both V genes and pseudogenes. Other (non-Ig) pseudogene sequences studied thus far do not show this high rate of rescue of stop codons. 2. The distribution of changes is concentrated in most cases in the 5' half of CDR2 (CDR2a), and coincides with the patterns of antigen-selected mutations in B lymphocytes. It does not coincide with expected non-antigen-selected (random) changes, as exemplified by hypermutated but unexpressed passenger V transgenes in B cells in Peyer's patches of unimmunized mice (Gonzalez-Fernandez and Milstein 1993). 3. In germline V genes of mice, there is no evidence of triplet codon insertion (or multiples thereof) as a mechanism generating germline diversity. This parallels a known absence of gene conversion as a mechanism generating somatic diversity in mice. In contrast, in germline chicken pseudogenes which are known to contribute to somatic generation of diversity by gene conversion, frequent examples of triplet codon insertions and deletions in CDRs are present. 4. The pattern of unique insertions and deletions in all species with sufficient sequence data available is consistent with hyper-recombination events targeting the transcription and/or coding unit. The distribution of these events does not correlate with known inducers of gene conversion, for example, inverted or direct repeats and palindromes. Furthermore, the 5' boundaries of somatic hypermutation and the 5' peak of germline nucleotide insertions and deletions coincide in IghV (Rothenfluh et al. 1993, 1994; Rogerson 1994) and in IgkV (Rogerson 1994; Rada et al. 1994, and analyses herein). It will be interesting to see how these features relate to each other in other gene sets as data become available.(ABSTRACT TRUNCATED AT 400 WORDS)

Pseudogenes: Are They “Junk” or Functional DNA?

“…In chicken, IglV and IghV pseudogenes have been identified that include crippling mutations (182). However, only a few IglV and IghV pseudogenes contain more than one crippling mutation and, notably, very few are crippled because of stop codons or frameshift mutations.…”

Molecular evolution of the vertebrate immune system

“…(50) have argued that Ig V region genes cannot be under direct positive selection favoring diversity at the amino acid level. They base their argument on the fact that somatic hypermutation serves to diversify these molecules further; thus the germline sequence does not directly encode the final protein product.…”

Pseudogenes: Pseudo-functional or key regulators in health and disease?

“…It has been reported recently (for review, see that synonymous point mutations occur far more frequently than do nonsynonymous base changes in the Drosophila Est-6 pseudogene . In chickens, it has been observed that, within the multiple IglV and IghV pseudogenes, the number of stop codons contained in the ''coding'' sequence is far lower than would be expected were nucleotide substitutions occurring at random; in addition, the majority of stop codons introduced by point mutations are then ''corrected'' and eliminated by further point mutations within the same codon (Rothenfluh et al 1995). This feature, which is also observed in V H pseudogenes in mice (Schiff et al 1985), may indicate either that some presumed pseudogenes are, in fact, protein-coding, or that the conservation of open reading frames plays a role in any putative function of pseudogenes involved in somatic gene rearrangements .…”