A role for PCNA ubiquitination in immunoglobulin hypermutation

Abstract

Proliferating cell nuclear antigen (PCNA) is a DNA polymerase cofactor and regulator of replication-linked functions. Upon DNA damage, yeast and vertebrate PCNA is modified at the conserved lysine K164 by ubiquitin, which mediates error-prone replication across lesions via translesion polymerases. We investigated the role of PCNA ubiquitination in variants of the DT40 B cell line that are mutant in K164 of PCNA or in Rad18, which is involved in PCNA ubiquitination. Remarkably, the PCNA(K164R) mutation not only renders cells sensitive to DNA-damaging agents, but also strongly reduces activation induced deaminase-dependent single-nucleotide substitutions in the immunoglobulin light-chain locus. This is the first evidence, to our knowledge, that vertebrates exploit the PCNA-ubiquitin pathway for immunoglobulin hypermutation, most likely through the recruitment of error-prone DNA polymerases.

Figure 1. Site-Directed Mutagenesis of the PCNA Locus

(A) Alignment of the human, mouse, chicken, Schizosaccharomyces pombe, and S. cerevisiae PCNA amino acid sequences. Amino acid 164 serving as the attachment site for ubiquitination in S. cerevisiae is marked by an asterisk. (B) A physical map of the PCNA locus and the PCNA mutagenesis construct, pPcna^K164RBsr. The targeting strategy of PCNA locus and the genealogy of the mutant clones are shown below and to the right, respectively. (C) Sequence chromatographs covering the PCNA codon 164 which was changed from AAA in the AID^RψV⁻ clone to AGA in the PCNA^K164R/K164R clone.

Figure 2. Ubiquitination and SUMOylation of PCNA

(A) Cells were treated with or without MMS and were analyzed by immunoblotting using an monoclonal antibody to PCNA. The asterisk denotes a band reactive with PCNA antibodies, possibly corresponding to a PCNA modification independent of K164 and Rad18. (B) Analysis of clones stably transfected with His-tagged ubiquitin or SUMO-1 expression vectors. Whole cell lysates (left) and lysates after NiNTA chromatography (right) are shown. The positions expected for unmodified, mono-ubiquitinated, and SUMOylated PCNA are indicated by lines. Due to the low residual level of PCNA ubiquitination in the RAD18 mutant, this modification could not be detected by pull-downs. The bands at the bottom represent low levels of unmodified PCNA unspecifically bound to the beads. (C) Quantification of mono-ubiquitinated and SUMOylated PCNA, histone H3, and AID by immunoblotting. Cells were treated with or without MMS, and immunoblotted using monoclonal antibodies to PCNA (left upper), histone H3 (left middle), and AID (left lower). The values for mono-ubiquitinated and SUMOylated PCNA given in the right hand graphs were calculated as described in the Materials and Methods.

Figure 3. Colony Survival Curves after Exposure to DNA-Damaging Agents

The values of DNA damaging agents, which give 10% cell viability, are also summarized (D ₁₀ values).

Figure 4. FACS Analysis of Ig Hypermutation Activity

(A) FACS profiles of representative subclones derived from a sIgM (+) cell after staining with a monoclonal antibody to IgM. (B) The average percentages of events falling into sIgM (−) gates based on the measurement of 24 subclones are shown by graph.

Figure 5. Ig Hypermutation of the PCNA^K164R/K164R Clone

Ig light-chain sequence variation in the PCNA^K164R/K164R clone. All sequence differences in the region from the first intron to the J-C intron are shown relative to the rearranged light-chain consensus sequence of the AID^RψV⁻ precursor clone. The position of complementary determining regions CDR1, CDR2, and CDR3 and that of Jλ are indicated.

Figure 6. Mutation Spectrum

(A) Frequencies of particular nucleotide substitutions within light-chain gene. (B) A graphical view showing the frequencies of different types of mutations per hundred sequences.