Phosphorylation Targets of DNA-PK and Their Role in HIV-1 Replication

Abstract

The DNA dependent protein kinase (DNA-PK) is a trimeric nuclear complex consisting of a large protein kinase and the Ku heterodimer. The kinase activity of DNA-PK is required for efficient repair of DNA double-strand breaks (DSB) by non-homologous end joining (NHEJ). We also showed that the kinase activity of DNA-PK is essential for post-integrational DNA repair in the case of HIV-1 infection. Besides, DNA-PK is known to participate in such cellular processes as protection of mammalian telomeres, transcription, and some others where the need for its phosphorylating activity is not clearly elucidated. We carried out a systematic search and analysis of DNA-PK targets described in the literature and identified 67 unique DNA-PK targets phosphorylated in response to various in vitro and/or in vivo stimuli. A functional enrichment analysis of DNA-PK targets and determination of protein–protein associations among them were performed. For 27 proteins from these 67 DNA-PK targets, their participation in the HIV-1 life cycle was demonstrated. This information may be useful for studying the functioning of DNA-PK in various cellular processes, as well as in various stages of HIV-1 replication.

Predicted Cellular Interactors of the Endogenous Retrovirus-K Integrase Enzyme

“…One interaction that was not predicted was with LEDGF/p75, and indeed, this interactor is limited to partnership with lentiviral integrases [ 147 , 148 ]. Another set of DDR proteins commonly found to impact retroviral integration and replication is the DNA-PK complex [ 99 , 149 ]. HIV integrase directly interacts with Ku70 [ 120 ]; while ERVK IN was predicted to be phosphorylated by DNA-PKcs (PRKDC), it contained no ELMs to suggest direct interaction with Ku80 or Ku70.…”

“…133-137 in ERVK, MMTV, ENTV, and JRSV) that binds Pex13 and Pex14 for peroxisomal import [63], a SxIP motif (aa. [137][138][139][140][141][142][143][144][145][146][147][148][149][150] that binds to EBH domains in end-binding proteins involved in microtubule transport [64], and a tyrosine-based YXXØ sorting signal (aa. [75][76][77][78] for interaction with the µ-subunit of adaptor protein complex [65] and a PEXEL-like motif [66].…”

Crosstalk between Different DNA Repair Pathways Contributes to Neurodegenerative Diseases

“…For example, ATM is also a regulator of mitophagy, oxidative stress responses and insulin signaling [ 36 , 37 ]. DNA-PKcs is activated by the Ku70/Ku80-DNA complex and is required for NHEJ [ 13 , 38 ]. Through its participation in NHEJ, DNA-PKcs plays a role in lymphocyte and neuronal differentiation, and also functions in post-integrational DNA repair in the case of human immunodeficiency virus-1 (HIV-1) infection [ 38 , 39 , 40 ].…”

“…DNA-PKcs is activated by the Ku70/Ku80-DNA complex and is required for NHEJ [ 13 , 38 ]. Through its participation in NHEJ, DNA-PKcs plays a role in lymphocyte and neuronal differentiation, and also functions in post-integrational DNA repair in the case of human immunodeficiency virus-1 (HIV-1) infection [ 38 , 39 , 40 ]. During lymphocyte development, DSBs are generated in immunoglobulin and T cell receptor loci to generate immune-receptor diversity by V(D)J and class-switch recombination.…”

Structural insights into the role of DNA-PK as a master regulator in NHEJ

“…DNA-PKcs and Artemis are also required for opening DNA hairpin coding ends during V(D)J recombination and cells lacking DNA-PKcs, Ku, XRCC4 or DNA ligase IV are radiation sensitive and defective in NHEJ and V(D)J recombination (Pannunzio et al, 2018). Recently, additional roles for DNA-PKcs, outside DSB repair have been reported (Yue et al, 2020), including mitosis (Douglas et al, 2014(Douglas et al, , 2020Jette & Lees-Miller, 2015;Lee et al, 2011), transcription (Goodwin et al, 2015;Ju et al, 2006), RNA processing (Shao et al, 2020), metastasis (Goodwin et al, 2015), metabolism (Chung, 2018;Park et al, 2017), the innate immune response (Yang et al, 2020) and HIV replication (Anisenko et al, 2020), but its most well-characterized role is in NHEJ.…”