Progress and outlook in studying the substrate specificities of PARPs and related enzymes

Abstract

Despite decades of research on ADP-ribosyltransferases (ARTs) from the poly(ADP-ribose) polymerase (PARP) family, one key aspect of these enzymestheir substrate specificityhas remained unclear. Here, we briefly discuss the history of this area and, more extensively, the recent breakthroughs, including the identification of protein serine residues as a major substrate of PARP1 and PARP2 in human cells and of cysteine and tyrosine as potential targets of specific PARPs. On the molecular level, the modification of serine residues requires a composite active site formed by PARP1 or PARP2 together with a specificity-determining factor, HPF1; this represents a new paradigm not only for PARPs but generally for posttranslational modification (PTM) catalysis. Additionally, we discuss the identification of DNA as a substrate of PARP1, PARP2 and PARP3, and some bacterial ARTs and the discovery of noncanonical RNA capping by several PARP family members. Together, these recent findings shed new light on PARP-mediated catalysis and caution to 'expect the unexpected' when it comes to further potential substrates.

HPF1 and nucleosomes mediate a dramatic switch in activity of PARP1 from polymerase to hydrolase

“…[18][19][20][21] . The lack of specificity for a particular site (or protein) has been frustrating and confusing the field for decades 18,22 . In the presence of HPF1, the specificity of PARP1 switches to serine side chains, again located primarily in the automodification regions between the end of the BRCT domain and the WGR domain for autoPARylation, and in histone tails for transPARylation 7,23 .…”

Behavioural Characterisation of Macrod1 and Macrod2 Knockout Mice

“…Removal of ADPr is performed by two main types of ADPr hydrolase families: the macrodomains and ARHs (ADP-ribosylhydrolases) [ 12 ]. There many different specificities for hydrolases, dependent upon specific macromolecule modification and the nature of the chemical bond on the macromolecular targets [ 12 , 13 , 14 , 15 , 16 ]. Among the macrodomain family are three enzymes, MACROD1, MACROD2 and TARG1 (terminal ADP-ribose protein glycohydrolase); these share very similar biochemical activities and are responsible for removal of the terminal ADP-ribose moiety from acidic residues [ 17 , 18 , 19 ].…”

Mono(ADP-ribosyl)ation Enzymes and NAD+ Metabolism: A Focus on Diseases and Therapeutic Perspectives

“…Studies focused on the investigation of ARTD1/PARP1 and ARTD2/PARP2 mechanisms of DNA damage repair uncover serine residues of target proteins as the most abundant acceptor sites for PARylation [ 11 , 95 , 96 , 97 , 98 , 99 , 100 , 101 ], with a minor contribution of tyrosine, lysine, and acidic residues [ 101 , 102 ]. By contrast, for MARylation, which is the major ADP-ribosylation under physiological conditions, the most abundant target residues are depicted by arginine, cysteine, and histidine [ 102 , 103 , 104 ].…”

“…Based on the chemical analysis of the reaction products, it was proposed that ARTD10 selectively modifies acidic amino acids. It was proposed that ARTD family members may also be capable of modifying serine residues proximal to lysine on account of the KS recognition motif [ 10 , 11 ]. ARTD10 contains several additional domains and motifs, including a RNA recognition motif (RRM), two functional ubiquitin interaction motifs (UIM), sequences capable of promoting nuclear targeting and nuclear export, and a small motif that mediates interaction with PCNA [ 138 ] and with ubiquitin receptor p62/SQSTM1 [ 133 , 139 , 140 ].…”

“…Indeed, NAD + depletion easily occurs in response to excessive DNA damage, which is one of the well-known activation mechanisms of the main PARPs involved in DNA damage repair, namely PARP1 and PARP2 (also named ARTD1 and ARTD2, respectively) [ 3 , 4 , 5 ]. Specifically, ARTs utilize NAD + as a donor to transfer single or multiple units of ADP-ribose to substrate molecules, which can be proteins and, in some cases, nucleic acids [ 6 , 7 , 8 , 9 , 10 , 11 ]. Such enzymatic reaction is reversible and takes the name of ADP-ribosylation, a type of post-translational modification (PTM) [ 12 , 13 ].…”