A systematic analysis of the PARP protein family identifies new functions critical for cell physiology

Abstract

The poly(ADP-ribose) polymerase (PARP) family of proteins use NAD+ as their substrate to modify acceptor proteins with adenosine diphosphate-ribose (ADPr) modifications. The function of most PARPs under physiological conditions is unknown. Here, to better understand this protein family, we systematically analyze the cell cycle localization of each PARP and of poly(ADP-ribose), a product of PARP activity, then identify the knock-down phenotype of each protein and perform secondary assays to elucidate function. We show that most PARPs are cytoplasmic, identify cell cycle differences in the ratio of nuclear to cytoplasmic poly(ADP-ribose), and identify four phenotypic classes of PARP function. These include the regulation of membrane structures, cell viability, cell division, and the actin cytoskeleton. Further analysis of PARP14 shows that it is a component of focal adhesion complexes required for proper cell motility and focal adhesion function. In total, we show that PARP proteins are critical regulators of eukaryotic physiology.

PARPs and ADP-ribosylation: recent advances linking molecular functions to biological outcomes

“…This suggests that cellular NAD + could be present in distinct pools in different subcellular organelles such that the levels of NAD + are locally regulated by the availability and activity of the respective NMNATs. Certain PARPs, such as PARP-2, PARP-3, and PARP-7, exhibit differential localization in the nucleus and the cytoplasm during different phases of the cell cycle (Vyas et al 2013). Moreover, as mentioned in the previous section, the ADP-ribose hydrolases also exhibit distinct subcellular localizations (Niere et al 2012;Jankevicius et al 2013;Sharifi et al 2013).…”

“…They found that the majority of PARP family members localizes to the cytoplasm, with some having a more specific localization to distinct organelles. They also observed that a number of PARPs exhibited cell cycle-dependent shuttling between the nucleus and cytoplasm (Vyas et al 2013). Of the MARTs, loss of PARP-7 resulted in a mitotic defect, while the loss of macrodomain-containing PARP-9, PARP-14, and PARP-15 caused an actin cytoskeletal defect.…”

“…Work by Vyas et al (2013Vyas et al ( , 2014 has been instrumental in systematically characterizing the PARP family, especially the MARTs, on the basis of their cellular localization as well as phenotypes associated with loss of function. They found that the majority of PARP family members localizes to the cytoplasm, with some having a more specific localization to distinct organelles.…”

“…localizations, and functions (Gibson and Kraus 2012;Vyas et al 2013Vyas et al , 2014. PARPs can be thought of as ADP-ribose "writers," that covalently attach ("write") ADP-ribose units on substrate proteins (Fig.…”

“…Based on their structural domains and functions, the different PARPs can be broadly classified as DNA-dependent PARPs (PARP-1, PARP-2, and PARP-3), Tankyrases (PARP-5a and PARP-5b), Cys-Cys-Cys-His zinc finger (CCCH)-containing and WWE PAR-binding domaincontaining PARPs (PARP-7, PARP-12, PARP-13.1, and PARP-13.2), and PAR-binding macrodomain-containing "macro" PARPs (PARP-9, PARP-14, and PARP-15) (Ame et al 2004;Vyas et al 2013). The PARP family members can also be categorized according to their catalytic activities: "mono," "poly," or inactive.…”