Interaction with the CCT chaperonin complex limits APOBEC3A cytidine deaminase cytotoxicity

Abstract

The APOBEC3 cytidine deaminases are implicated as the cause of a prevalent somatic mutation pattern found in cancer genomes. The APOBEC3 enzymes act as viral restriction factors by mutating viral genomes. Mutation of the cellular genome is presumed to be an off‐target activity of the enzymes, although the regulatory measures for APOBEC3 expression and activity remain undefined. It is therefore difficult to predict circumstances that enable APOBEC3 interaction with cellular DNA that leads to mutagenesis. The APOBEC3A (A3A) enzyme is the most potent deaminase of the family. Using proteomics, we evaluate protein interactors of A3A to identify potential regulators. We find that A3A interacts with the chaperonin‐containing TCP‐1 (CCT) complex, a cellular machine that assists in protein folding and function. Importantly, depletion of CCT results in A3A‐induced DNA damage and cytotoxicity. Evaluation of cancer genomes demonstrates an enrichment of A3A mutational signatures in cancers with silencing mutations in CCT subunit genes. Together, these data suggest that the CCT complex interacts with A3A, and that disruption of CCT function results in increased A3A mutational activity.

Protein interaction map of APOBEC3 enzyme family reveals deamination-independent role in cellular function

“…Consistent with the proteomics results of the previous study, in our hands the CCT complex binding is specific to A3A and does not co-purify with other A3 proteins. A3C shares some functional overlap with other A3 proteins including mRNA and ncRNA metabolic processes ( Figure 1E ) (58). The top A3C-specific functional enrichment is the Replication Protein A (RPA) complex, a heterotrimeric complex that binds to ssDNA.…”

“…protein folding, with A3B, A3D, and A3F, it is for different complexes and specific proteins (PDCL3, PHLP, TXND9, TCPA, TCPH, and TCPZ) related to protein folding functions ( Figure S4C ). The A3A-specific functional enrichment is for PDCL and TRiC/CCT in G-protein beta folding, and in a recent study it was shown that A3A interaction with the CCT complex inhibits its deaminase activity (58). Consistent with the proteomics results of the previous study, in our hands the CCT complex binding is specific to A3A and does not co-purify with other A3 proteins.…”

“…If a protein had more than one BP and one CC, the term with a larger population was selected to represent it in the network ( Table S8 ). Several PPIs captured in this network have been described in previous studies, or have been reported in interaction databases ( Table S8 ) (51, 52, 58, 70, 71), though we capture a number of novel interactors as well. The most interconnected A3 interacting proteins were RNA binding proteins including proteins involved in splicing, ribonucleoprotein complexes (RNP), and RNA modification.…”

“…However, it is also interesting that A3A interacts with proteins of another chaperone complex, the CCT complex that includes TCPA, TCPZ, and TCPH. For A3A, it was found that interaction with the CCT complex inhibits A3A deamination activity, which may be a mechanism to protect from unwanted deamination of genomic DNA (58). We did not find that the PFD proteins specifically inhibited the activity of A3D, A3F, or A3B (data not shown).…”

Similar deamination activities but different phenotypic outcomes induced by APOBEC3 enzymes in breast epithelial cells

“…Suppression of A3 mRNA transcription provides the main protective measure against somatic mutagenesis, although A3B and A3A transcription is upregulated in response to DNA replication stress, an early sign of cellular transformation and viral infection ( Kanu et al, 2016 ; Oh et al, 2021 ). A3A activity also appears to be regulated by binding partners that suppress catalytic activity, such as Human Tribbles 3 or chaperonin-containing TCP-1 (CCT) complex ( Aynaud et al, 2012 ; Green et al, 2021 ). A3H Hap I is ubiquitinated in cells, and the resulting short half-life decreases its catalytic activity ( Chesarino and Emerman, 2020 ).…”