1
|
Higashi H, Maejima T, Lee LH, Yamazaki Y, Hottiger MO, Singh SA, Aikawa M. A Study into the ADP-Ribosylome of IFN-γ-Stimulated THP-1 Human Macrophage-like Cells Identifies ARTD8/PARP14 and ARTD9/PARP9 ADP-Ribosylation. J Proteome Res 2019; 18:1607-1622. [PMID: 30848916 PMCID: PMC6456868 DOI: 10.1021/acs.jproteome.8b00895] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
ADP-ribosylation is a post-translational modification that, until recently, has remained elusive to study at the cellular level. Previously dependent on radioactive tracers to identify ADP-ribosylation targets, several advances in mass spectrometric workflows now permit global identification of ADP-ribosylated substrates. In this study, we capitalized on two ADP-ribosylation enrichment strategies, and multiple activation methods performed on the Orbitrap Fusion Lumos, to identify IFN-γ-induced ADP-ribosylation substrates in macrophages. The ADP-ribosyl binding protein, Af1521, was used to enrich ADP-ribosylated peptides, and the antipoly-ADP-ribosyl antibody, 10H, was used to enrich ADP-ribosylated proteins. ADP-ribosyl-specific mass spectra were further enriched by an ADP-ribose product ion triggered EThcD and HCD activation strategy, in combination with multiple acquisitions that segmented the survey scan into smaller ranges. HCD and EThcD resulted in overlapping and unique ADP-ribosyl peptide identifications, with HCD providing more peptide identifications but EThcD providing more reliable ADP-ribosyl acceptor sites. Our acquisition strategies also resulted in the first ever characterization of ADP-ribosyl on three poly-ADP-ribose polymerases, ARTD9/PARP9, ARTD10/PARP10, and ARTD8/PARP14. IFN-γ increased the ADP-ribosylation status of ARTD9/PARP9, ARTD8/PARP14, and proteins involved in RNA processes. This study therefore summarizes specific molecular pathways at the intersection of IFN-γ and ADP-ribosylation signaling pathways.
Collapse
Affiliation(s)
- Hideyuki Higashi
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine , Brigham Women's Hospital, Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Takashi Maejima
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine , Brigham Women's Hospital, Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Lang Ho Lee
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine , Brigham Women's Hospital, Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Yukiyoshi Yamazaki
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine , Brigham Women's Hospital, Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Michael O Hottiger
- Department of Molecular Mechanisms of Disease , University of Zurich , 8057 Zurich , Switzerland
| | - Sasha A Singh
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine , Brigham Women's Hospital, Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Masanori Aikawa
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine , Brigham Women's Hospital, Harvard Medical School , Boston , Massachusetts 02115 , United States.,Center for Excellence in Vascular Biology, Cardiovascular Division , Brigham Women's Hospital, Harvard Medical School , Boston , Massachusetts 02115 , United States.,Channing Division of Network Medicine, Department of Medicine , Brigham Women's Hospital, Harvard Medical School , Boston , Massachusetts 02115 , United States
| |
Collapse
|
2
|
Abstract
The molecular events responsible for controlling cell growth and development, as well as their coordinate interaction is only beginning to be revealed. At the basis of these controlling events are hormones, growth factors and mitogens which, through transmembrane signalling trigger an array of cellular responses, initiated by receptor-associated tyrosine kinases, which in turn either directly or indirectly mediate their effects through serine/threonine protein kinases. Utilizing the obligatory response of activation of protein synthesis in cell growth and development, we describe efforts to work backwards along the regulatory pathway to the receptor, identifying those molecular components involved in modulating the rate of translation. We begin by describing the components and steps of protein synthesis and then discuss in detail the regulatory pathways involved in the mitogenic response of eukaryotic cells and during meiotic maturation of oocytes. Finally we discuss possible future work which will further our understanding of these systems.
Collapse
Affiliation(s)
- S J Morley
- Friedrich Miescher-Institut, Basel, Switzerland
| | | |
Collapse
|
3
|
Gschwendt M, Kittstein W, Marks F. The weak immunosuppressant cyclosporine D as well as the immunologically inactive cyclosporine H are potent inhibitors in vivo of phorbol ester TPA-induced biological effects in mouse skin and of Ca2+/calmodulin dependent EF-2 phosphorylation in vitro. Biochem Biophys Res Commun 1988; 150:545-51. [PMID: 3342035 DOI: 10.1016/0006-291x(88)90428-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Various biological effects induced by the tumor promoting phorbol ester TPA in mouse skin are comparably suppressed by the immunologically inactive cyclosporine H (CsH) and by the strongly immunosuppressive cyclosporine A (CsA). These effects inhibited include the development of edema, stimulation of alkaline phosphatase activity, DNA and protein synthesis, as well as tumor promotion. Furthermore, CsH, like CsA, inhibits the Ca2+/calmodulin-dependent phosphorylation of the elongation factor 2 (EF-2) in vitro and the TPA-induced increases in the amount of EF-2 in vivo. Similar observations were made using the weak immunosuppressant CsD. We conclude from these results that the ability of cyclosporines to act as immunosuppressants and their ability to inhibit TPA-effects are based on two different mechanisms of action. Inhibition of TPA-effects may involve suppression of calmodulin-dependent processes, such as augmentation and phosphorylation of EF-2.
Collapse
Affiliation(s)
- M Gschwendt
- German Cancer Research Center, Institute of Biochemistry, Heidelberg, F.R.G
| | | | | |
Collapse
|
4
|
Takamatsu K, Uchida T, Okada Y. Specific purification of elongation factor 2 and isolation of its antibody. Biochem Biophys Res Commun 1986; 134:1015-21. [PMID: 3511904 DOI: 10.1016/s0006-291x(86)80522-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Elongation factor 2 (EF-2) was purified from rat liver extracts by affinity chromatography using fragment A of diphtheria toxin as the ligand. Purified EF-2 has a molecular weight of 96,000 and isoelectric point of 6.6-6.8. The sequence of the nineteen N-terminal amino acid is Val-Asn-Phe-Thr-Val-Asp-Gln-Ile-Arg-Ala Ile-Met-Asp-Lys-Lys-Ala-Asn and the C-terminal amino acid is leucine. Purified rat EF-2 modified with ADP-ribose was injected into rabbits to prepare antibodies against EF-2. The anti-EF-2 antibodies can immunoprecipitate with EF-2 from various eukaryotic cells.
Collapse
|
5
|
Nilsson L, Nygård O. Localization of the sites of ADP-ribosylation and GTP binding in the eukaryotic elongation factor EF-2. EUROPEAN JOURNAL OF BIOCHEMISTRY 1985; 148:299-304. [PMID: 3987690 DOI: 10.1111/j.1432-1033.1985.tb08839.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Tryptic cleavage of EF-2, molecular mass 93 kDa, produced an 82-kDa polypeptide and a 10-kDa fragment, which was further degraded. By a slower reaction the 82-kDa polypeptide was gradually split into a 48-kDa and a 34-kDa fragment. Similarly, treatment with chymotrypsin resulted in the formation of an 82-kDa polypeptide and a small fragment. In contrast to the tryptic 82-kDa polypeptide the corresponding chymotryptic cleavage product was relatively resistant to further attack. The degradation of the 82-kDa polypeptide with either trypsin or chymotrypsin was facilitated by the presence of guanosine nucleotides, indicating a conformational shift in native EF-2 upon nucleotide binding. No effect was observed in the presence of ATP, indicating that the effect was specific for guanosine nucleotides. After affinity labelling of native EF-2 with oxidized [3H]GTP and subsequent trypsin treatment the radioactivity was recovered in the 48-kDa polypeptide showing that the GTP-binding site was located within this part of the factor. Correspondingly, tryptic degradation of EF-2 labelled with [14C]NAD+ in the presence of diphtheria toxin showed that the site of ADP-ribosylation was within the 34-kDa polypeptide. By cleavage with the tryptophan-specific reagent N-chlorosuccinimide the site of ADP-ribosylation could be located at a distance of 40-60 kDa from the GTP-binding site and about 4-11 kDa from the nearest terminus.
Collapse
|
6
|
Svitkin YV, Agol VI. Translational barrier in central region of encephalomyocarditis virus genome. Modulation by elongation factor 2 (eEF-2). EUROPEAN JOURNAL OF BIOCHEMISTRY 1983; 133:145-54. [PMID: 6303783 DOI: 10.1111/j.1432-1033.1983.tb07440.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A fractionated cell-free system from Krebs-2 cells was prepared which contained ribosomes and a high-speed supernatant. When this system was programmed with encephalomyocarditis virus RNA, the synthesis of a precursor of capsid proteins, polypeptide preA, proceeded at a rate not very different from that observed in unfractionated extracts, whereas the synthesis of more distally encoded proteins, in particular polypeptide F, was greatly retarded, if not abolished. A protein was purified from the cytoplasmic extracts of Krebs-2 cells which greatly enhanced production of polypeptide F as well as other noncapsid proteins in the fractionated system. By several criteria, this protein was identified as eukaryotic elongation factor 2 (eEF-2). By using the ADP-ribosylation assay, it was found that the fractionated system contained about 15% of the amount of eEF-2 present in the unfractionated extracts. The results suggest that changes in the eEF-2 content may affect the elongation rate differently at different regions of the RNA template.
Collapse
|
7
|
Chinali G, Sacchi A, Ferrini U. Determination of elongation factor 2 associated with native mammalian ribosomes. BIOCHIMICA ET BIOPHYSICA ACTA 1982; 697:193-201. [PMID: 7104356 DOI: 10.1016/0167-4781(82)90077-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
|
8
|
|
9
|
|
10
|
|
11
|
Isolation and properties of the trypsin-derived ADP-ribosyl peptide from diphtheria toxin-modified yeast elongation factor 2. J Biol Chem 1978. [DOI: 10.1016/s0021-9258(17)34230-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
|
12
|
Nakamura S, Ohta S, Arai K, Arai N, Oshima T, Kaziro Y. Studies on polypeptide-chain-elongation factors from an extreme thermophile, Thermus thermophilus HB8. 3. Molecular properties. EUROPEAN JOURNAL OF BIOCHEMISTRY 1978; 92:533-43. [PMID: 33049 DOI: 10.1111/j.1432-1033.1978.tb12775.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Molecular properties of the polypeptide chain elongation factors from Thermus thermophilus HB8 have been investigated and compared with those from Escherichia coli. 1. As expected, the factors purified from T. thermophilus were exceedingly heat-stable. Even free EF-Tu not complexed with GDP was stable after heating for 5 min at 60 degrees C. 2. GDP binding activity of T. thermophilus EF-Tu was also stable in various protein denaturants, such as 5.5 M urea, 1.5 M guanidine-HCl, and 4 M LiCl. 3. Amino acid compositions of EF-Tu and EF-G from T. thermophilus were similar to those from E. coli. On the other hand, amino acid composition of T. thermophilus EF-Ts was considerably different from that of E. coli EF-Ts. 4. In contrast to E. coli EF-Tu, T. thermophilus EF-Tu contained no free sulfhydryl group, but one disulfide bond. The disulfide bond was cleaved by sodium borohydride or sodium sulfite under native conditions. The heat stability of the reduced EF-Tu . GDP, as measured by GDP binding activity, did not differ from that of the untreated EF-Tu . GDP. 5. T. thermophilus EF-Ts contained, in addition to one disulfide bond, a sulfhydryl group which could be titrated only after complete denaturation of the protein. 6. Under native conditions one sulfhydryl group of T. thermophilus EF-G was titrated with p-chloromercuribenzoate, while the rate of reaction was very sluggish. The sulfhydryl group appears to be essential for interaction with ribosomes, whereas the ability to form a binary GDP . EF-G complex was not affected by its modification. The protein contained also one disulfide bond. 7. Circular dichroic spectra of EF-Tu from T. thermophilus and E. coli were very similar. Binding of GDP or GTP caused a similar spectral change in both. T. thermophilus and E. coli EF-Tu. On the other hand, the spectra of T. thermophilus EF-G and E. coli EF-G were significantly different, the content of ordered structure being higher in the former as compared to the latter.
Collapse
|
13
|
Isolation of eukaryotic ribosomal proteins. Purification and characterization of the 60 S ribosomal subunit proteins La, Lb, Lf, P1, P2, L13‘, L14, L18‘, L20, and L38. J Biol Chem 1978. [DOI: 10.1016/s0021-9258(17)38196-6] [Citation(s) in RCA: 87] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
14
|
Bermek E. Mechanisms in polypeptide chain elongation on ribosomes. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1978; 21:63-100. [PMID: 358280 DOI: 10.1016/s0079-6603(08)60267-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
15
|
Comstock JP, Van NT. Purification and characterization of homogeneous protein synthesis elongation factor 2 from hen oviduct. BIOCHIMICA ET BIOPHYSICA ACTA 1977; 477:199-220. [PMID: 884114 DOI: 10.1016/0005-2787(77)90046-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
16
|
Richter D, Isono K. The mechanism of protein synthesis-initiation, elongation and termination in translation of genetic messeges. Curr Top Microbiol Immunol 1977; 76:83-125. [PMID: 334484 DOI: 10.1007/978-3-642-66653-7_3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
17
|
Simpson RJ, Neuberger MR, Liu TY. Complete amino acid analysis of proteins from a single hydrolysate. J Biol Chem 1976. [DOI: 10.1016/s0021-9258(17)33637-2] [Citation(s) in RCA: 604] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
18
|
Marsh RC, Chinali G, Parmeggiani A. Function of sulfhydryl groups in ribosome-elongation factor G reactions. Assignment of guanine nucleotide binding site to elongation factor G. J Biol Chem 1975. [DOI: 10.1016/s0021-9258(19)40765-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
19
|
Clegg JC, Kennedy SI. Initiation of synthesis of the structural proteins of Semliki Forest virus. J Mol Biol 1975; 97:401-11. [PMID: 171418 DOI: 10.1016/s0022-2836(75)80050-7] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
20
|
Kirschenbaum DM. A compilation of amino acid analyses of proteins. VII. Residues per molecule-5. Anal Biochem 1975; 66:123-50. [PMID: 1096669 DOI: 10.1016/0003-2697(75)90732-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|
21
|
Merrick WC, Kemper WM, Kantor JA, Anderson WF. Purification and properties of rabbit reticulocyte protein synthesis elongation factor 2. J Biol Chem 1975. [DOI: 10.1016/s0021-9258(19)41646-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
|
22
|
|
23
|
|
24
|
|
25
|
Kirschenbaum DM. Molar absorptivity and A 1 per cent-1 cm values for proteins at selected wavelengths of the ultraviolet and visible regions. 8. Anal Biochem 1973; 55:166-92. [PMID: 4753144 DOI: 10.1016/0003-2697(73)90302-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
|