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. 2010 Jul 14;132(27):9363-72.
doi: 10.1021/ja101588r.

Clickable NAD analogues for labeling substrate proteins of poly(ADP-ribose) polymerases

Affiliations

"VSports注册入口" Clickable NAD analogues for labeling substrate proteins of poly(ADP-ribose) polymerases

Hong Jiang et al. J Am Chem Soc. .

Abstract

Poly(ADP-ribose) polymerases (PARPs) catalyze the transfer of multiple adenine diphosphate ribose (ADP-ribose) units from nicotinamide adenine dinucleotide (NAD) to substrate proteins VSports手机版. There are 17 PARPs in humans. Several PARPs, such as PARP-1 and Tankyrase-1, are known to play important roles in DNA repair, transcription, mitosis, and telomere length maintenance. To better understand the functions of PARPs at a molecular level, it is necessary to know what substrate proteins PARPs modify. Here we report clickable NAD analogues that can be used to label PARP substrate proteins. The clickable NAD analogues have a terminal alkyne group which allows the conjugation of fluorescent or affinity tags to the substrate proteins. Using this method, PARP-1 and tankyrase-1 substrate proteins were labeled by a fluorescent tag and visualized on SDS-PAGE gel. Using a biotin affinity tag, we were able to isolate and identify a total of 79 proteins as potential PARP-1 substrates. These include known PARP-1 substrate proteins, including histones and heterogeneous nuclear ribonucleoproteins. About 40% of the proteins were also identified in recent proteomic studies as potential PARP-1 substrates. Among the identified potential substrates, we further demonstrated that tubulin and three mitochondrial proteins, TRAP1 (TNF receptor-associated protein 1), citrate synthase, and GDH (glutamate dehydrogenase 1), are substrates of PARP-1 in vitro. These results demonstrate that the clickable NAD analogue is useful for labeling, in-gel detection, isolation, and identification of the substrate proteins of PARPs and will help to understand the biological functions of PARPs. .

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Figures (V体育官网入口)

Figure 1
Figure 1
Poly(ADP-ribosyl)ation reaction catalyzed by PARPs.
Figure 2
Figure 2
(A) Labeling of poly(ADP-ribosyl)ated proteins with NAD analogs. NAD analogs bearing an alkyne group will be used in PARP-catalyzed reactions. An affinity tag can be added using click chemistry after the substrate protein is labeled. The labeled protein can then be affinity purified, separated on 1D/2D protein gel, and then the sequence identified by MS. (B) Structure of 6-/8-alkyne-NAD, Rh-N3, and Biotin-N3, which were used in labeling reactions.
Figure 3
Figure 3
Labeling of PARP-1 auto-(ADP-ribosyl)ation with 6- or 8-alkyne-NAD. The panel on the left shows the image of Rhodamine fluorescence and the panel on the right is the same gel stained with Coomassie blue. The arrow points at the position of unmodified PARP-1. All lanes contain PARP-1 (0.15 μM) and all lanes except 7 and 8 contain ssDNA (0.25 μg/μL). Lane 1, control without NAD; lane 2, control with normal NAD (100 μM); lane 3, 6-alkyne-NAD (100 μM); lane 4, 8-alkyne-NAD (100 μM); lane 5, 6-alkyne-NAD (100 μM) and NAD (100 μM); lane 6, 8-alkyne-NAD (100 μM) and NAD (100 μM); lane 7, control with 6-alkyne-NAD (100 μM), NAD (100 μM), and no ssDNA; lane 8, control with 8-alkyne-NAD (100 μM), NAD (100 μM), and no ssDNA. The fluorescence signal below 116 kDa in lane 5 and 6 is likely due to the hydrolysis of poly(ADP-ribose) chain resulting in poly(ADP-ribose) polymers that are not covalently bound to proteins. The linkage between different ADP-ribose units is a relatively labile ester bond.
Figure 4
Figure 4
Labeling of p53 and RAP74 subunit of TFIIF by PARP-1 using 6-alkyne-NAD (A) and 8-alkyne-NAD (B). The panel on the left shows the image of Rhodamine fluorescence recorded by Typhoon 9400 Variable Mode Imager, and the panel on the right is the same gels stained with Coomassie blue. In addition to 6- or 8-alkyne NAD (100 μM), the following were present in different lanes: 1 and 2, PARP-1 (0.15 μM); 3 and 4, PARP-1 (0.15 μM) and p53 (2.8 μM); 5 and 6, PARP-1 (0.15 μM) and RAP74 (0.59 μM); 7 and 8, p53 (2.8 μM); 9 and 10, RAP74 (0.59 μM). ssDNA were present in all lanes, and normal NAD (100 μM) were present in lanes 2, 4, 6, 8, and 10. The fluorescence signal in the loading wells likely came from poly(ADP-ribosyl)ated PARP-1.
Figure 5
Figure 5
Labeling of TRF1 by tankyrase-1 using 6-alkyne-NAD. The panel on the left shows the image of Rhodamine fluorescence, and the panel on the right is the same gels stained with Coomassie blue. Lanes 1 and 2: tankyrase-1 suspension (0.09 μg/μL) with 6-alkyne-NAD (100 μM); 3 and 4: tankyrase-1 suspension (0.09 μg/μL) and TRF1 (1.1 μM) with 6-alkyne-NAD (100 μM); 5 and 6: TRF1 (1.1 μM) with 6-alkyne-NAD (100 μM); 7 and 8: suspension of the insoluble fraction of non-infected SF9 cell lysate (0.15 μg/μL, negative control) and TRF1 (1.1 μM) with 6-alkyne-NAD (100 μM). Lanes 2, 4, 6, and 8 contained normal NAD (100 μM).
Figure 6
Figure 6
Labeling of MCF-7 wild type and PARP-1 KD cell lysate with PARP1 and 6-alkyne-NAD. The panel on the left shows the image of Rhodamine fluorescence, and the panel on the right is the same gels stained with Coomassie blue. PARP-1 (0.075 μM), MCF-7 wild type cell lysate (2 μg/μL) and PARP-1 KD cell lysate (2 μg/μL) were used in the labeling reactions. All lanes contain 6-alkyne-NAD (100 μM) and ssDNA (0.25 μg/μL). Lanes 6–10 contained normal NAD (100 μM).
Figure 7
Figure 7
Labeling of TRAP1 (A), GDH (B), citrate Synthase (C) and tubulin (D) by PARP-1 using 6-alkyne-NAD. The panel on the left shows the image of Rhodamine fluorescence, and the panel on the right is the same gels stained with Coomassie blue. All lanes contain 6-alkyne-NAD (100 μM) and ssDNA (0.25 μg/μL). Lanes 1 and 2: PARP-1 (0.05 μM); 3 and 4: PARP-1 (0.05 μM) with TRAP1 (1.0 μM, A) or GDH (3.1 μM, B) or citrate synthase (3.37 μM, C) or tubulin (3.64 μM, D); 5 and 6: TRAP1 (1.0 μM, A), GDH (3.1 μM, B), citrate synthase (3.37 μM, C), or tubulin (3.64 μM, D). Lanes 2, 4 and 6 contained normal NAD (100 μM).

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