Poly-ADP-ribosylation dynamics, signaling, and analysis

Abstract

ADP-ribosylation is a reversible post-translational modification that plays a role as a signaling mechanism in various cellular processes. This modification is characterized by its structural diversity, highly dynamic nature, and short half-life. Hence, it is tightly regulated at many levels by cellular factors that fine-tune its formation, downstream signaling, and degradation that together impacts cellular outcomes. Poly-ADP-ribosylation is an essential signaling mechanism in the DNA damage response that mediates the recruitment of DNA repair factors to sites of DNA damage via their poly-ADP-ribose (PAR)-binding domains (PBDs). PAR readers, encoding PBDs, convey the PAR signal to mediate cellular outcomes that in some cases can be dictated by PAR structural diversity. Several PBD families have been identified, each with variable PAR-binding affinity and specificity, that also recognize and bind to distinct parts of the PAR chain. PARylation signaling has emerged as an attractive target for the treatment of specific cancer types, as the inhibition of PAR formation or degradation can selectively eliminate cancer cells with specific DNA repair defects and can enhance radiation or chemotherapy response. In this review, we summarize the key players of poly-ADP-ribosylation and its regulation and highlight PBDs as tools for studying PARylation dynamics and the expanding potential to target PARylation signaling in cancer treatment.

Keywords: DNA damage response; PAR readers; PAR‐binding domains; poly‐ADP‐ribose.

Figure 1:

Overview of the key players in ADP-ribosylation signaling. Created with BioRender.com.

Figure 2.

Schematic of protein ADP-ribosylation and binding specificities of various PAR binding domains. The WWE domain recognizes the iso-ADP-ribose part of the chain; the PBZ finger domain recognizes two adjacent ADP-ribose units; the macrodomain recognizes mono-ADP-ribosylated proteins in addition to the terminal ADP-ribose unit of PAR chains. Created with BioRender.com.

Figure 3.

Dynamics of ADP-ribosylation in the DDR. Substrate proteins are poly-ADP-ribosylated by PARP1 and PARP2 and possibly PARP3 by transferring an ADP-ribose unit from NAD⁺ and releasing NAM. Degradation or removal of ADP-ribose units is carried out by hydrolases with various specificities. PARG and ARH3 hydrolyze PAR except for the terminal ADP-ribose unit. TARG1, MacroD1, and MacroD2 hydrolyze the ester bond between the ADP-ribose and the aspartate and glutamate residue side-chains of the modified proteins whereas ARH3 reverses the serine-ADP-ribosylation modification. TARG1 is also capable of removing the whole PAR chain en bloc. Created with BioRender.com.

Figure 4.

Overview of Base Excision Repair (BER)/Single-Strand Break Repair (SSBR) and replication associated BER/SSBR. Created with BioRender.com.

Figure 5:

Regulation of ADP-ribosylation structural diversity by various factors and the consequences of this diversity on downstream effects. Created with BioRender.com.

Figure 6:

Targeting PARylation players in the treatment of cancer. Created with BioRender.com.

Figure 7:

Schematic showing the timeline of various PARylation detection tools. Created with BioRender.com.

Figure 8.

Model of micro irradiation-induced DNA damage and recruitment of EGFP-tagged PAR binding domains to sites of micro-irradiation. 405nm laser is used to induce single strand DNA breaks (SSDB) and double strand DNA breaks (DSDB) which cause activation of PARP1 and PARP2 to form PAR chains. These PAR chains promote the recruitment of various DNA repair factors and can be detected by PBDs fused to fluorescent proteins. Created with BioRender.com.