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Li Z, Huang RYC, Yopp DC, Hileman TH, Santangelo TJ, Hurwitz J, Hudgens JW, Kelman Z. A novel mechanism for regulating the activity of proliferating cell nuclear antigen by a small protein. Nucleic Acids Res 2014; 42:5776-89. [PMID: 24728986 PMCID: PMC4027161 DOI: 10.1093/nar/gku239] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Proliferating cell nuclear antigen (PCNA) forms a trimeric ring that associates with and influences the activity of many proteins participating in DNA metabolic processes and cell cycle progression. Previously, an uncharacterized small protein, encoded by TK0808 in the archaeon Thermococcus kodakarensis, was shown to stably interact with PCNA in vivo. Here, we show that this protein, designated Thermococcales inhibitor of PCNA (TIP), binds to PCNA in vitro and inhibits PCNA-dependent activities likely by preventing PCNA trimerization. Using hydrogen/deuterium exchange mass spectrometry and site-directed mutagenesis, the interacting regions of PCNA and TIP were identified. Most proteins bind to PCNA via a PCNA-interacting peptide (PIP) motif that interacts with the inter domain connecting loop (IDCL) on PCNA. TIP, however, lacks any known PCNA-interacting motif, suggesting a new mechanism for PCNA binding and regulation of PCNA-dependent activities, which may support the development of a new subclass of therapeutic biomolecules for inhibiting PCNA.
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Affiliation(s)
- Zhuo Li
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Richard Y-C Huang
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Daniel C Yopp
- Department of Microbiology and Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
| | - Travis H Hileman
- Department of Microbiology and Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
| | - Thomas J Santangelo
- Department of Microbiology and Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
| | - Jerard Hurwitz
- Program of Molecular Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Jeffrey W Hudgens
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Zvi Kelman
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, USA
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Abstract
Thermococcus kodakarensis (T. kodakarensis) has emerged as a premier model system for studies of archaeal biochemistry, genetics, and hyperthermophily. This prominence is derived largely from the natural competence of T. kodakarensis and the comprehensive, rapid, and facile techniques available for manipulation of the T. kodakarensis genome. These genetic capacities are complemented by robust planktonic growth, simple selections, and screens, defined in vitro transcription and translation systems, replicative expression plasmids, in vivo reporter constructs, and an ever-expanding knowledge of the regulatory mechanisms underlying T. kodakarensis metabolism. Here we review the existing techniques for genetic and biochemical manipulation of T. kodakarensis. We also introduce a universal platform to generate the first comprehensive deletion and epitope/affinity tagged archaeal strain libraries.
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Affiliation(s)
- Travis H Hileman
- Department of Microbiology, Center for RNA Biology, Ohio State University Columbus, OH, USA
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