Molecular evolution of VH9 germline genes isolated from DBA, BALB, 129 and C57BL mouse strains and sublines

Abstract

We have used the polymerase chain reaction (PCR) in an attempt to clone and sequence the exons and hitherto unavailable contiguous flanks of all members of the small V(H) 9 germline gene family from inbred mouse strains and sublines that have had a common ancestry within the last century, and to analyze the molecular evolution of these sequences. Fifteen genuine germline genes were isolated (designated V(H) 9.1 through V(H) 9.15) from strains and sublines of DBA, BALB, 129 and C57BL inbred mice. Of the 15 genuine isolates, nine are novel: seven sequences from DBA strains and sublines ( V(H) 9.3 to V(H) 9.9) and two sequences from C57BL strains ( V(H) 9.13 and V(H) 9.14). We have identified sequencing errors and PCR recombinant artefacts in previously published sequences. We detected no sequence divergence of individual genes shared by the strains and sublines studied. However, we isolated two genes from DBA strains and sublines, V(H) 9.1 and V(H) 9.3, that differ only by five nucleotides encoding three amino acid changes that are concentrated within a 33 nucleotide (11 codon) region. Of these 11 codons, eight encode a putative antigen binding site. There were no differences in the remaining 733 nucleotides sequenced (including both 5' and 3' flanking regions). Potential explanations for the generation of V(H) 9.1 and V(H) 9.3 are discussed.

Soma‐to‐germline feedback is implied by the extreme polymorphism at IGHV relative to MHC

“…This has been observed in all vertebrate germline V arrays analyzed including pseudogenes, particularly the chicken V pseudogene arrays . These data suggest SHM mutation patterns are physically written into the homologous sequences in the germline V arrays , Fig. .…”

“…The rearranged somatic DNA, V(D)J, is the substrate for SHM . We will use the two sequenced human heavy chain IGHV loci as the germline references throughout this section with citation to mouse germline VH systems where necessary .…”

“…Functional and pseudogene V elements encoding about 98 amino acids are themselves highly similar within V families both in their V segments and in the surrounding 5’ and 3’ flanks (∼10–20 Kb), with ≥80% similarity in DNA sequence. The greatest sequence diversity within a V family resides in CDR1 and CDR2, which is highly non‐random and indicative of V‐ and CDR‐targeted point mutations and strong antigen‐mediated selection . Paradoxically germline V segments are never expressed as protein so they cannot be subjected to direct antigen‐binding selection, as would normally be expected for B cell Ig receptors.…”

The R109H Variant of Fascin-2, a Developmentally Regulated Actin Crosslinker in Hair-Cell Stereocilia, Underlies Early-Onset Hearing Loss of DBA/2J Mice

“…Little in 1909. Shown are the approximate dates when these DBA-related inbred strains were separated from one another (Bailey, 1978; Zylstra et al, 2003). DBA/2J is the only strain with the G>A missense mutation in Fscn2 ; this mutation occurred sometime between 1951 and 1975, as deduced from archived DNA samples of DBA/2J strain mice.…”

The boundaries of the distribution of somatic hypermutation of rearranged immunoglobulin variable genes

“…For example, the L intron of V κ Ox, the gene used to define the 5 ′ border of SHM by the Milstein laboratory, 16 is 171 bases long. In contrast, the L intron of V H 9-related genes is 81 bases, 19 and that of V H 186.2-related genes is 82 bases. 15 These H locus introns each contain a single pyrimidine-rich tract of 18 and 20 bases, respectively, preceded by the CURA 2 ′ OH Y branch point consensus, albeit incomplete in each case (CUXA 2 ′ OH Y in V H 9 and XURA 2′OH Y in V H 186.2, where X is a non-consensus base).…”