Somatic hypermutagenesis in immunoglobulin genes

Rogozin, Igor B.; Колчанов, Н. А.

doi:10.1016/0167-4781(92)90134-l

Cited by 413 publications

(133 citation statements)

References 23 publications

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“…This explains why the intensity of the lower non-hot-spot band is comparable to that of the upper hot-spot band. This preference for WRCY (W ϭ A or T, R ϭ purine, and Y ϭ pyrimidine) hot-spot motifs reflects the targeting of this motif that has been observed in vivo (11) and suggests that purified AID by itself might play a direct role in this process. Although much more data would be required to substantiate this point, the limited data suggest that AID activity depends on sequence context.…”

Section: Resultsmentioning

confidence: 67%

Activation-induced cytidine deaminase deaminates deoxycytidine on single-stranded DNA but requires the action of RNase

Bransteitter

Pham

Scharff

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

620

543

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The expression of activation-induced cytidine deaminase (AID) is prerequisite to a ''trifecta'' of key molecular events in B cells: class-switch recombination and somatic hypermutation in humans and mice and gene conversion in chickens. Although this critically important enzyme shares common sequence motifs with apolipoprotein B mRNA-editing enzyme, and exhibits deaminase activity on free deoxycytidine in solution, it has not been shown to act on either RNA or DNA. Recent mutagenesis data in Escherichia coli suggest that AID may deaminate dC on DNA, but its putative biochemical activities on either DNA or RNA remained a mystery. Here, we show that AID catalyzes deamination of dC residues on single-stranded DNA in vitro but not on double-stranded DNA, RNA-DNA hybrids, or RNA. Remarkably, it has no measurable deaminase activity on single-stranded DNA unless pretreated with RNase to remove inhibitory RNA bound to AID. AID catalyzes dC 3 dU deamination activity most avidly on double-stranded DNA substrates containing a small ''transcription-like'' single-stranded DNA bubble, suggesting a targeting mechanism for this enigmatic enzyme during somatic hypermutation.T he breakthrough discovery of activation-induced cytidine (CR) deaminase (AID) (1, 2) has opened a way to identify the biochemical reactions responsible for generating highaffinity antibodies. Although AID is normally expressed in germinal center B cells, its forced expression in B cells at the wrong stage of differentiation (3), in non-B cells (4, 5), and in Escherichia coli (6, 7) results in enhanced mutagenesis and mutational spectra mimicking somatic hypermutation (SHM). This suggests that AID can operate effectively out of its natural milieu and does not require either B cell-specific V-gene targeting elements or other B cell-specific proteins (8). Based on its similarity to apolipoprotein B mRNA-editing enzyme, which catalyzes the deamination of C on mRNA (9), it has been suggested that conversion of dC 3 dU on DNA, followed by the generation of an abasic site, might account for at least a subset of mutations targeted to SHM hot-spot sequences (6,8,10). Recent data showing that AID-and apolipoprotein B mRNAediting enzyme-generated hypermutation is enhanced in uracil-N-glycosylase-deficient strains of E. coli imply that both AID and apolipoprotein B mRNA-editing enzyme can act on DNA (7).Because previous studies have failed to detect AID activity on either DNA or RNA, the biologically relevant substrate for AID remains an important open question. In this article we identify and characterize AID activity on nucleic acid substrates and provide a surprising explanation for why its activity has been elusive. Materials and MethodsMaterials. Ultrapure dNTP, 2Ј,3Ј-dideoxynucleoside triphosphate, and T4 polynucleotide kinase were purchased from Amersham Pharmacia; RNaseA, CR, deoxycytidine (CdR), uridine, and deoxyuridine were from Sigma; T7 sequenase (version 2.0) and RNase inhibitor were from United States Biochemical; and uracil DNA glycosylase (UDG) and apu...

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Section: Resultsmentioning

confidence: 67%

Activation-induced cytidine deaminase deaminates deoxycytidine on single-stranded DNA but requires the action of RNase

Bransteitter

Pham

Scharff

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

620

543

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“…To simultaneously examine the correlation between three spectra by multiple regression analysis, the ''linear regression module'' of the program STATISTICA was used. Correlation between a distribution of mutable motifs and a distribution of mutations along a target sequence was measured by using a Monte Carlo procedure (5). Small values (Ͻ 0.05) of the probability P(W Յ W random ) indicate a significant correlation between a mutable motif and mutations (5,8).…”

Section: Construction Of New M13mp2mentioning

confidence: 99%

“…Correlation between a distribution of mutable motifs and a distribution of mutations along a target sequence was measured by using a Monte Carlo procedure (5). Small values (Ͻ 0.05) of the probability P(W Յ W random ) indicate a significant correlation between a mutable motif and mutations (5,8). Hotspots were predicted as described (28).…”

Section: Construction Of New M13mp2mentioning

confidence: 99%

“…Although the mechanism for introducing these sequence changes is currently unknown, several features of SHM specificity offer clues to the DNA transactions that might be involved. For example, SHM primarily occurs in two highly mutable DNA sequence motifs (5)(6)(7)(8)(9). One is the RGYW sequence (the underlined G is mutated, R ϭ A or G, Y ϭ T or C, and W ϭ A or T), which is found in SHM substitution spectra in equal proportions in both DNA strands.…”

mentioning

confidence: 99%

“…One is the RGYW sequence (the underlined G is mutated, R ϭ A or G, Y ϭ T or C, and W ϭ A or T), which is found in SHM substitution spectra in equal proportions in both DNA strands. The other is the WA motif, where substitutions are more likely in one strand than the other (5,(7)(8)(9)(10). A clue to the origins of the substitutions in the WA motif is the observation that their type and location correlates with the base substitution error specificity of human DNA polymerase when copying a bacterial gene sequence in a model system in vitro (8).…”

mentioning

confidence: 99%

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Correlation of somatic hypermutation specificity and A-T base pair substitution errors by DNA polymerase η during copying of a mouse immunoglobulin κ light chain transgene

Pavlov

Rogozin

Galkin

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

118

110

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To test the hypothesis that inaccurate DNA synthesis by mammalian DNA polymerase (pol ) contributes to somatic hypermutation (SHM) of Ig genes, we measured the error specificity of mouse pol during synthesis of each strand of a mouse Ig light chain transgene. We then compared the results to the base substitution specificity of SHM of this same gene in the mouse. The in vitro and in vivo base substitution spectra shared a number of common features. A highly significant correlation was observed for overall substitutions at A-T pairs but not for substitutions at G-C pairs. Sixteen mutational hotspots at A-T pairs observed in vivo were also found in spectra generated by mouse pol in vitro. The correlation was strongest for errors made by pol during synthesis of the non-transcribed strand, but it was also observed for synthesis of the transcribed strand. These facts, and the distribution of substitutions generated in vivo, support the hypothesis that pol contributes to SHM of Ig genes at A-T pairs via short patches of low fidelity DNA synthesis of both strands, but with a preference for the non-transcribed strand.H igh affinity antibodies result from somatic hypermutation (SHM) of Ig genes followed by selection. The SHM process introduces base substitutions at a very high rate into DNA encoding the variable regions of immunoglobulins (1-4). Although the mechanism for introducing these sequence changes is currently unknown, several features of SHM specificity offer clues to the DNA transactions that might be involved. For example, SHM primarily occurs in two highly mutable DNA sequence motifs (5-9). One is the RGYW sequence (the underlined G is mutated, R ϭ A or G, Y ϭ T or C, and W ϭ A or T), which is found in SHM substitution spectra in equal proportions in both DNA strands. The other is the WA motif, where substitutions are more likely in one strand than the other (5, 7-10). A clue to the origins of the substitutions in the WA motif is the observation that their type and location correlates with the base substitution error specificity of human DNA polymerase when copying a bacterial gene sequence in a model system in vitro (8). Based on that correlation and additional considerations of the two mutable motifs (11), we suggested that errors at A-T base pairs by pol may contribute to as much as one third of somatic mutations in Ig genes, preferentially during synthesis of the non-transcribed strand. This hypothesis is supported by the observation that XP-V patients lacking active polymerase have a lower proportion of somatic substitutions at A-T base pairs in Ig genes (12). Because pol error specificity does not correlate with substitutions in the RGYW sequence motif, and because those substitutions are distributed equally on both strands, we further suggested that SHM may involve more than one DNA transaction and more than one DNA polymerase (8). This finding is consistent with the two-phase model of SHM proposed earlier (9, 13). Other DNA polymerases suggested to participate in SHM include pol (14-16), pol (17, 18) ...

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Somatic hypermutation and B-cell malignancies

Spencer

Dunn-Walters

1999

J. Pathol.

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Somatic hypermutagenesis in immunoglobulin genes

Cited by 413 publications

References 23 publications

Activation-induced cytidine deaminase deaminates deoxycytidine on single-stranded DNA but requires the action of RNase

Activation-induced cytidine deaminase deaminates deoxycytidine on single-stranded DNA but requires the action of RNase

Correlation of somatic hypermutation specificity and A-T base pair substitution errors by DNA polymerase η during copying of a mouse immunoglobulin κ light chain transgene

Somatic hypermutation and B-cell malignancies

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