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Orndorff KS, Veltri EJ, Hoitsma NM, Williams IL, Hall I, Jaworski GE, Majeres GE, Kallepalli S, Vito AF, Struble LR, Borgstahl GEO, Dieckman LM. Structural Basis for the Interaction Between Yeast Chromatin Assembly Factor 1 and Proliferating Cell Nuclear Antigen. J Mol Biol 2024; 436:168695. [PMID: 38969056 PMCID: PMC11305522 DOI: 10.1016/j.jmb.2024.168695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 06/13/2024] [Accepted: 07/01/2024] [Indexed: 07/07/2024]
Abstract
Proliferating cell nuclear antigen (PCNA), the homotrimeric eukaryotic sliding clamp protein, recruits and coordinates the activities of a multitude of proteins that function on DNA at the replication fork. Chromatin assembly factor 1 (CAF-1), one such protein, is a histone chaperone that deposits histone proteins onto DNA immediately following replication. The interaction between CAF-1 and PCNA is essential for proper nucleosome assembly at silenced genomic regions. Most proteins that bind PCNA contain a PCNA-interacting peptide (PIP) motif, a conserved motif containing only eight amino acids. Precisely how PCNA is able to discriminate between binding partners at the replication fork using only these small motifs remains unclear. Yeast CAF-1 contains a PIP motif on its largest subunit, Cac1. We solved the crystal structure of the PIP motif of CAF-1 bound to PCNA using a new strategy to produce stoichiometric quantities of one PIP motif bound to each monomer of PCNA. The PIP motif of CAF-1 binds to the hydrophobic pocket on the front face of PCNA in a similar manner to most known PIP-PCNA interactions. However, several amino acids immediately flanking either side of the PIP motif bind the IDCL or C-terminus of PCNA, as observed for only a couple other known PIP-PCNA interactions. Furthermore, mutational analysis suggests positively charged amino acids in these flanking regions are responsible for the low micromolar affinity of CAF-1 for PCNA, whereas the presence of a negative charge upstream of the PIP prevents a more robust interaction with PCNA. These results provide additional evidence that positive charges within PIP-flanking regions of PCNA-interacting proteins are crucial for specificity and affinity of their recruitment to PCNA at the replication fork.
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Affiliation(s)
- Keely S Orndorff
- Department of Chemistry and Biochemistry, Creighton University, Omaha, NE, USA
| | - Evan J Veltri
- Department of Chemistry and Biochemistry, Creighton University, Omaha, NE, USA
| | - Nicole M Hoitsma
- Department of Biochemistry and Molecular Biology, Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, USA; Department of Biochemistry, University of Colorado at Boulder, Boulder, Colorado; Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Ivy L Williams
- Department of Chemistry and Biochemistry, Creighton University, Omaha, NE, USA
| | - Ian Hall
- Department of Chemistry and Biochemistry, Creighton University, Omaha, NE, USA
| | - Grace E Jaworski
- Department of Chemistry and Biochemistry, Creighton University, Omaha, NE, USA
| | - Grace E Majeres
- Department of Chemistry and Biochemistry, Creighton University, Omaha, NE, USA
| | - Samaya Kallepalli
- Department of Chemistry and Biochemistry, Creighton University, Omaha, NE, USA
| | - Abigayle F Vito
- Department of Chemistry and Biochemistry, Creighton University, Omaha, NE, USA
| | - Lucas R Struble
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Gloria E O Borgstahl
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Lynne M Dieckman
- Department of Chemistry and Biochemistry, Creighton University, Omaha, NE, USA.
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2
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Kwan A, Mcdermott-Brown I, Muthana M. Proliferating Cell Nuclear Antigen in the Era of Oncolytic Virotherapy. Viruses 2024; 16:1264. [PMID: 39205238 PMCID: PMC11359830 DOI: 10.3390/v16081264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 07/01/2024] [Accepted: 07/22/2024] [Indexed: 09/04/2024] Open
Abstract
Proliferating cell nuclear antigen (PCNA) is a well-documented accessory protein of DNA repair and replication. It belongs to the sliding clamp family of proteins that encircle DNA and acts as a mobile docking platform for interacting proteins to mount and perform their metabolic tasks. PCNA presence is ubiquitous to all cells, and when located in the nucleus it plays a role in DNA replication and repair, cell cycle control and apoptosis in proliferating cells. It also plays a crucial role in the infectivity of some viruses, such as herpes simplex viruses (HSVs). However, more recently it has been found in the cytoplasm of immune cells such as neutrophils and macrophages where it has been shown to be involved in the development of a pro-inflammatory state. PCNA is also expressed on the surface of certain cancer cells and can play a role in preventing immune cells from killing tumours, as well as being associated with cancer virulence. Given the growing interest in oncolytic viruses (OVs) as a novel cancer therapeutic, this review considers the role of PCNA in healthy, cancerous, and immune cells to gain an understanding of how PCNA targeted therapy and oncolytic virotherapy may interact in the future.
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Affiliation(s)
| | | | - Munitta Muthana
- Medical School, University of Sheffield, Beech Hill Road, Sheffield S10 2RX, UK; (A.K.)
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3
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Schumacher MA, Singh RR, Salinas R. Structure of the E. coli nucleoid-associated protein YejK reveals a novel DNA binding clamp. Nucleic Acids Res 2024; 52:7354-7366. [PMID: 38832628 PMCID: PMC11229321 DOI: 10.1093/nar/gkae459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/02/2024] [Accepted: 05/15/2024] [Indexed: 06/05/2024] Open
Abstract
Nucleoid-associated proteins (NAPs) play central roles in bacterial chromosome organization and DNA processes. The Escherichia coli YejK protein is a highly abundant, yet poorly understood NAP. YejK proteins are conserved among Gram-negative bacteria but show no homology to any previously characterized DNA-binding protein. Hence, how YejK binds DNA is unknown. To gain insight into YejK structure and its DNA binding mechanism we performed biochemical and structural analyses on the E. coli YejK protein. Biochemical assays demonstrate that, unlike many NAPs, YejK does not show a preference for AT-rich DNA and binds non-sequence specifically. A crystal structure revealed YejK adopts a novel fold comprised of two domains. Strikingly, each of the domains harbors an extended arm that mediates dimerization, creating an asymmetric clamp with a 30 Å diameter pore. The lining of the pore is electropositive and mutagenesis combined with fluorescence polarization assays support DNA binding within the pore. Finally, our biochemical analyses on truncated YejK proteins suggest a mechanism for YejK clamp loading. Thus, these data reveal YejK contains a newly described DNA-binding motif that functions as a novel clamp.
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Affiliation(s)
- Maria A Schumacher
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC 27710, USA
| | - Rajiv R Singh
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC 27710, USA
| | - Raul Salinas
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC 27710, USA
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4
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Hardebeck S, Jácobo Goebbels N, Michalski C, Schreiber S, Jose J. Identification of a potent PCNA-p15-interaction inhibitor by autodisplay-based peptide library screening. Microb Biotechnol 2024; 17:e14471. [PMID: 38646975 PMCID: PMC11033925 DOI: 10.1111/1751-7915.14471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/04/2024] [Accepted: 04/04/2024] [Indexed: 04/25/2024] Open
Abstract
Proliferating cell nuclear antigen (PCNA) is an essential factor for DNA metabolism. The influence of PCNA on DNA replication and repair, combined with the high expression rate of PCNA in various tumours renders PCNA a promising target for cancer therapy. In this context, an autodisplay-based screening method was developed to identify peptidic PCNA interaction inhibitors. A 12-mer randomized peptide library consisting of 2.54 × 106 colony-forming units was constructed and displayed at the surface of Escherichia coli BL21 (DE3) cells by autodisplay. Cells exhibiting an enhanced binding to fluorescent mScarlet-I-PCNA were enriched in four sorting rounds by flow cytometry. This led to the discovery of five peptide variants with affinity to mScarlet-I-PCNA. Among these, P3 (TCPLRWITHDHP) exhibited the highest binding signal. Subsequent flow cytometric analysis revealed a dissociation constant of 0.62 μM for PCNA-P3 interaction. Furthermore, the inhibition of PCNA interactions was investigated using p15, a PIP-box containing protein involved in DNA replication and repair. P3 inhibited the PCNA-p1551-70 interaction with a half maximal inhibitory activity of 16.2 μM, characterizing P3 as a potent inhibitor of the PCNA-p15 interaction.
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Affiliation(s)
- Sarah Hardebeck
- University of MünsterInstitute of Pharmaceutical and Medicinal ChemistryMünsterGermany
| | | | - Caroline Michalski
- University of MünsterInstitute of Pharmaceutical and Medicinal ChemistryMünsterGermany
| | - Sebastian Schreiber
- University of MünsterInstitute of Pharmaceutical and Medicinal ChemistryMünsterGermany
| | - Joachim Jose
- University of MünsterInstitute of Pharmaceutical and Medicinal ChemistryMünsterGermany
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5
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Gharouni M, Mosaddeghi H. Evaluation of mutations on O 6-methylguanine methyl transferase structure and its interactions: molecular dynamics simulation study. J Biomol Struct Dyn 2024:1-13. [PMID: 38166600 DOI: 10.1080/07391102.2023.2300133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024]
Abstract
O6-methylguanine DNA methyl transferase (MGMT) is a significant vehicle for the cellular clearance of alkyl lesions, particularly the methyl group of the O-6 and O-4 positions of guanine and thymine, respectively. Many publications have studied the correlation between polymorphisms in MGMT and susceptibility to various cancers. In the present study, we investigated the consequence of L84F, common single-nucleotide polymorphism, K125E, site-specific mutagenesis, and L84F/K125E on conformation, stability, and behavior of MGMT in the free form and interaction with proliferating cell nuclear antigen (PCNA) and DNA as partners in the biochemical network by using molecular dynamics simulation method. Our results showed that all free variants of MGMT differed from the native form. However, among all free variants of MGMT, the L84F/K125E variant exhibited similar properties compared with the wild-type. In contrast, in complex modes, only amino acid residues of the L84F variant are involved in the interactions with PCNA and DNA somewhat differently relative to the wild-type. Furthermore, L84F SNP showed the highest binding free energy compared to other variants and native forms. These alterations in the amino acids and binding free energy of L84F relative to the native are the reasons for changing its region connection compared to the native form. Therefore, we propose conducting further investigations into the impact of inhibitors or chemotherapeutic agents to assess their effectiveness on MGMT variants compared to the wild-type, aiming to reduce the cost of cancer treatment that will depend on inhibiting native MGMT protein.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Marzieh Gharouni
- Department of Biochemistry, Neyshabur Branch, Islamic Azad University, Neyshabur, Iran
| | - Hamid Mosaddeghi
- Department of Chemistry, Isfahan University of Technology, Isfahan, Iran
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Wendel SO, Snow JA, Gu L, Banerjee NS, Malkas L, Wallace NA. The potential of PCNA inhibition as a therapeutic strategy in cervical cancer. J Med Virol 2023; 95:e29244. [PMID: 38010649 PMCID: PMC10683864 DOI: 10.1002/jmv.29244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/01/2023] [Accepted: 11/02/2023] [Indexed: 11/29/2023]
Abstract
Cervical cancers are the fourth most common and most deadly cancer in women worldwide. Despite being a tremendous public health burden, few novel approaches to improve care for these malignancies have been introduced. We discuss the potential for proliferating cell nuclear antigen (PCNA) inhibition to address this need as well as the advantages and disadvantages for compounds that can therapeutically inhibit PCNA with a specific focus on cervical cancer.
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Affiliation(s)
| | - Jazmine A Snow
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Long Gu
- Beckman Research Institute of City of Hope, Duarte, California, USA
| | - Nilam Sanjib Banerjee
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Linda Malkas
- Beckman Research Institute of City of Hope, Duarte, California, USA
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7
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Li S, Ge H, Li Y, Zhang K, Yu S, Cao H, Wang Y, Deng H, Li J, Dai J, Li LF, Luo Y, Sun Y, Geng Z, Dong Y, Zhang H, Qiu HJ. The E301R protein of African swine fever virus functions as a sliding clamp involved in viral genome replication. mBio 2023; 14:e0164523. [PMID: 37772878 PMCID: PMC10653895 DOI: 10.1128/mbio.01645-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 08/22/2023] [Indexed: 09/30/2023] Open
Abstract
IMPORTANCE Sliding clamp is a highly conserved protein in the evolution of prokaryotic and eukaryotic cells. The sliding clamp is required for genomic replication as a critical co-factor of DNA polymerases. However, the sliding clamp analogs in viruses remain largely unknown. We found that the ASFV E301R protein (pE301R) exhibited a sliding clamp-like structure and similar functions during ASFV replication. Interestingly, pE301R is assembled into a unique ring-shaped homotetramer distinct from sliding clamps or proliferating cell nuclear antigens (PCNAs) from other species. Notably, the E301R gene is required for viral life cycle, but the pE301R function can be partially restored by the porcine PCNA. This study not only highlights the functional role of the ASFV pE301R as a viral sliding clamp analog, but also facilitates the dissection of the complex replication mechanism of ASFV, which provides novel clues for developing antivirals against ASF.
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Affiliation(s)
- Su Li
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High-Containment Facilities for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Hailiang Ge
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High-Containment Facilities for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
- College of Animal Sciences, Yangtze University, Jingzhou, China
| | - Yanhua Li
- Multidiscipline Research Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Kehui Zhang
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High-Containment Facilities for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Shaoxiong Yu
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High-Containment Facilities for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Hongwei Cao
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High-Containment Facilities for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yanjin Wang
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High-Containment Facilities for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Hao Deng
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High-Containment Facilities for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Jiaqi Li
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High-Containment Facilities for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Jingwen Dai
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High-Containment Facilities for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Lian-Feng Li
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High-Containment Facilities for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yuzi Luo
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High-Containment Facilities for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yuan Sun
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High-Containment Facilities for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Zhi Geng
- Multidiscipline Research Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Yuhui Dong
- Multidiscipline Research Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Heng Zhang
- Multidiscipline Research Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Hua-Ji Qiu
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High-Containment Facilities for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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8
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Ghouil R, Miron S, Sato K, Ristic D, van Rossum-Fikkert SE, Legrand P, Ouldali M, Winter JM, Ropars V, David G, Arteni AA, Wyman C, Knipscheer P, Kanaar R, Zelensky AN, Zinn-Justin S. BRCA2-HSF2BP oligomeric ring disassembly by BRME1 promotes homologous recombination. SCIENCE ADVANCES 2023; 9:eadi7352. [PMID: 37889963 PMCID: PMC10610910 DOI: 10.1126/sciadv.adi7352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 09/20/2023] [Indexed: 10/29/2023]
Abstract
In meiotic homologous recombination (HR), BRCA2 facilitates loading of the recombinases RAD51 and DMC1 at the sites of double-strand breaks (DSBs). The HSF2BP-BRME1 complex interacts with BRCA2. Its absence causes a severe reduction in recombinase loading at meiotic DSB. We previously showed that, in somatic cancer cells ectopically producing HSF2BP, DNA damage can trigger HSF2BP-dependent degradation of BRCA2, which prevents HR. Here, we report that, upon binding to BRCA2, HSF2BP forms octameric rings that are able to interlock into a large ring-shaped 24-mer. Addition of BRME1 leads to dissociation of both of these ring structures and cancels the disruptive effect of HSF2BP on cancer cell resistance to DNA damage. It also prevents BRCA2 degradation during interstrand DNA crosslink repair in Xenopus egg extracts. We propose that, during meiosis, the control of HSF2BPBRCA2 oligomerization by BRME1 ensures timely assembly of the ring complex that concentrates BRCA2 and controls its turnover, thus promoting HR.
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Affiliation(s)
- Rania Ghouil
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Simona Miron
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Koichi Sato
- Oncode Institute, Hubrecht Institute–KNAW and University Medical Center Utrecht, Utrecht, Netherlands
| | - Dejan Ristic
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA, Rotterdam, Netherlands
| | - Sari E. van Rossum-Fikkert
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA, Rotterdam, Netherlands
| | - Pierre Legrand
- Synchrotron SOLEIL, HelioBio group, L’Orme des Merisiers, Gif sur-Yvette, France
| | - Malika Ouldali
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | | | - Virginie Ropars
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Gabriel David
- Synchrotron SOLEIL, HelioBio group, L’Orme des Merisiers, Gif sur-Yvette, France
| | - Ana-Andreea Arteni
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Claire Wyman
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA, Rotterdam, Netherlands
- Department of Radiation Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA, Rotterdam, Netherlands
| | - Puck Knipscheer
- Oncode Institute, Hubrecht Institute–KNAW and University Medical Center Utrecht, Utrecht, Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Roland Kanaar
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA, Rotterdam, Netherlands
| | - Alex N. Zelensky
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA, Rotterdam, Netherlands
| | - Sophie Zinn-Justin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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Shao Z, Yang J, Gao Y, Zhang Y, Zhao X, Shao Q, Zhang W, Cao C, Liu H, Gan J. Structural and functional studies of PCNA from African swine fever virus. J Virol 2023; 97:e0074823. [PMID: 37534905 PMCID: PMC10506467 DOI: 10.1128/jvi.00748-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 06/16/2023] [Indexed: 08/04/2023] Open
Abstract
Proliferating cell nuclear antigen (PCNA) belongs to the DNA sliding clamp family. Via interacting with various partner proteins, PCNA plays critical roles in DNA replication, DNA repair, chromatin assembly, epigenetic inheritance, chromatin remodeling, and many other fundamental biological processes. Although PCNA and PCNA-interacting partner networks are conserved across species, PCNA of a given species is rarely functional in heterologous systems, emphasizing the importance of more representative PCNA studies. Here, we report two crystal structures of PCNA from African swine fever virus (ASFV), which is the only member of the Asfarviridae family. Compared to the eukaryotic and archaeal PCNAs and the sliding clamp structural homologs from other viruses, AsfvPCNA possesses unique sequences and/or conformations at several regions, such as the J-loop, interdomain-connecting loop (IDCL), P-loop, and C-tail, which are involved in partner recognition or modification of sliding clamps. In addition to double-stranded DNA binding, we also demonstrate that AsfvPCNA can modestly enhance the ligation activity of the AsfvLIG protein. The unique structural features of AsfvPCNA can serve as a potential target for the development of ASFV-specific inhibitors and help combat the deadly virus. IMPORTANCE Two high-resolution crystal structures of African swine fever virus proliferating cell nuclear antigen (AsfvPCNA) are presented here. Structural comparison revealed that AsfvPCNA is unique at several regions, such as the J-loop, the interdomain-connecting loop linker, and the P-loop, which may play important roles in ASFV-specific partner selection of AsfvPCNA. Unlike eukaryotic and archaeal PCNAs, AsfvPCNA possesses high double-stranded DNA-binding affinity. Besides DNA binding, AsfvPCNA can also modestly enhance the ligation activity of the AsfvLIG protein, which is essential for the replication and repair of ASFV genome. The unique structural features make AsfvPCNA a potential target for drug development, which will help combat the deadly virus.
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Affiliation(s)
- Zhiwei Shao
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Jie Yang
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Yanqing Gao
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Yixi Zhang
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Xin Zhao
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Qiyuan Shao
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Weizhen Zhang
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Chulei Cao
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Hehua Liu
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Jianhua Gan
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
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10
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Wu J, Zheng H, Gong P. Crystal structure of African swine fever virus pE301R reveals a ring-shaped trimeric DNA sliding clamp. J Biol Chem 2023:104872. [PMID: 37257822 PMCID: PMC10320598 DOI: 10.1016/j.jbc.2023.104872] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 05/11/2023] [Accepted: 05/23/2023] [Indexed: 06/02/2023] Open
Abstract
African swine fever virus (ASFV) is an important animal pathogen that is causing a current ASF pandemic and affecting pork industry globally. ASFV encodes at least 150 proteins, and the functions of many of them remain to be clarified. The ASFV protein E301R (pE301R) was predicted to be a DNA sliding clamp protein homolog working as a DNA replication processivity factor. However, structural evidence was lacking to support the existence of a ring-shaped sliding clamp in large eukaryotic DNA viruses. Here we have solved a high-resolution crystal structure of pE301R and identified a canonical ring-shaped clamp comprising a pE301R trimer. Interestingly, this complete-toroidal structure is different from those of the monomeric clamp protein homolog, herpes simplex virus UL42, and the C-shaped dimeric human cytomegalovirus UL44, but highly homologous to that of the eukaryotic clamp homolog proliferating cell nuclear antigen. Moreover, pE301R has a unique N-terminal extension (NE) that is important in maintaining the trimeric form of the protein in solution, while specific features in length and surface electrostatic potential of its inter-domain connector (IDC) implies specificity in interactions with binding partners such as the viral DNA polymerase. Thus, our data pave the way for further dissection of the processivity clamp protein structural and functional diversity and ASFV DNA replication mechanisms.
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Affiliation(s)
- Jiqin Wu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, No.262 Jin Long Street, Wuhan, Hubei, 430207, China
| | - Haixue Zheng
- State Key Laboratory of Veterinary Etiological Biology and OIE/National Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, China
| | - Peng Gong
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, No.262 Jin Long Street, Wuhan, Hubei, 430207, China; Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, 300350, China; Hubei Jiangxia Laboratory, Wuhan, Hubei 430207, China.
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11
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Ling JA, Gildenberg MS, Honda M, Kondratick CM, Spies M, Washington MT. Fork-Remodeling Helicase Rad5 Preferentially Reverses Replication Forks with Gaps in the Leading Strand. J Mol Biol 2023; 435:167946. [PMID: 36623584 PMCID: PMC9915103 DOI: 10.1016/j.jmb.2023.167946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/15/2022] [Accepted: 01/02/2023] [Indexed: 01/09/2023]
Abstract
DNA damage bypass pathways promote the replication of damaged DNA when replication forks stall at sites of DNA damage. Template switching is a DNA damage bypass pathway in which fork-reversal helicases convert stalled replication forks into four-way DNA junctions called chicken foot intermediates, which are subsequently extended by replicative DNA polymerases. In yeast, fork-reversal is carried out by the Rad5 helicase using an unknown mechanism. To better understand the mechanism of Rad5 and its specificity for different fork DNA substrates, we used a FRET-based assay to observe fork reversal in real time. We examined the ability of Rad5 to bind and catalyze the reversal of various fork DNA substrates in the presence of short gaps in the leading or lagging strand as well as in the presence or absence of RPA and RNA primers in the lagging strand. We found that Rad5 preferentially reverses fork DNA substrates with short gaps (10 to 30 nt.) in the leading strand. Thus, Rad5 preferentially reverses fork DNA substrates that form chicken foot intermediates with 5' overhangs that can be extended by replicative DNA polymerases during the subsequent steps of template switching.
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Affiliation(s)
- Justin A Ling
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA 52242-1109, United States. https://twitter.com/Biochem_Ling
| | - Melissa S Gildenberg
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA 52242-1109, United States. https://twitter.com/MGild01
| | - Masayoshi Honda
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA 52242-1109, United States
| | - Christine M Kondratick
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA 52242-1109, United States
| | - Maria Spies
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA 52242-1109, United States. https://twitter.com/maria_spies
| | - M Todd Washington
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA 52242-1109, United States.
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12
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FGF9 promotes cell proliferation and tumorigenesis in TM3 mouse Leydig progenitor cells. Am J Cancer Res 2022; 12:5613-5630. [PMID: 36628285 PMCID: PMC9827084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 12/06/2022] [Indexed: 01/12/2023] Open
Abstract
Fibroblast growth factor 9 (FGF9) modulates cell proliferation, differentiation and motility for development and tissue repair in normal cells. Growing evidence shows that abnormal activation of FGF9 signaling is associated with tumor malignancy. We have previously reported that FGF9 increases MA-10 mouse Leydig tumor cell proliferation, in vitro, and tumor growth, in vivo. Also, FGF9 promotes the tumor growth and liver metastasis of mouse Lewis lung cancer cells, in vivo. However, the effects of FGF9 in the early stage of tumorigenesis remains elusive. In this study, TM3 mouse Leydig progenitor cells, that are not tumorigenic in immunocompromised mice, were used as a model cell line to investigate the role of FGF9 in tumorigenesis. The results demonstrated that FGF9 significantly induced cell proliferation and activated the MAPK, PI3K and PLCγ signaling pathways in TM3 cells. The percentage of the cell number in G1 phase was reduced and that in S and G2/M phases was increased after FGF9 stimulation in TM3 cells. Cyclin D1, cyclin A1, CDK2, CDK1, and p21 expressions and the phosphorylation level of Rb were all induced in FGF9-treated TM3 cells. In addition, FGF9 increased the expression of FGF receptor 1-4 in TM3 cells, suggesting the positive feedback loop between FGF9 and FGFRs. Furthermore, in the allograft mouse model, FGF9 promoted the tumorigenesis of TM3 cells characterized by higher expression of tumor markers, such as tumor necrosis factor alpha (TNFα) and α-fetoprotein (AFP), in the subcutaneously inoculated TM3 cell tissue. Conclusively, FGF9 induced cell cycle to increase cell proliferation of TM3 cells through FAK, MAPK, PI3K/Akt and PLCγ signaling pathways, in vitro, and promoted the tumorigenesis of TM3 cell allograft tissue, in vivo, which is a potential marker for tumor as well as a target for cancer therapeutic strategies.
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13
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Gopinathan Nair A, Rabas N, Lejon S, Homiski C, Osborne MJ, Cyr N, Sverzhinsky A, Melendy T, Pascal JM, Laue ED, Borden KLB, Omichinski JG, Verreault A. Unorthodox PCNA Binding by Chromatin Assembly Factor 1. Int J Mol Sci 2022; 23:ijms231911099. [PMID: 36232396 PMCID: PMC9570017 DOI: 10.3390/ijms231911099] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/12/2022] [Accepted: 09/15/2022] [Indexed: 11/29/2022] Open
Abstract
The eukaryotic DNA replication fork is a hub of enzymes that continuously act to synthesize DNA, propagate DNA methylation and other epigenetic marks, perform quality control, repair nascent DNA, and package this DNA into chromatin. Many of the enzymes involved in these spatiotemporally correlated processes perform their functions by binding to proliferating cell nuclear antigen (PCNA). A long-standing question has been how the plethora of PCNA-binding enzymes exert their activities without interfering with each other. As a first step towards deciphering this complex regulation, we studied how Chromatin Assembly Factor 1 (CAF-1) binds to PCNA. We demonstrate that CAF-1 binds to PCNA in a heretofore uncharacterized manner that depends upon a cation-pi (π) interaction. An arginine residue, conserved among CAF-1 homologs but absent from other PCNA-binding proteins, inserts into the hydrophobic pocket normally occupied by proteins that contain canonical PCNA interaction peptides (PIPs). Mutation of this arginine disrupts the ability of CAF-1 to bind PCNA and to assemble chromatin. The PIP of the CAF-1 p150 subunit resides at the extreme C-terminus of an apparent long α-helix (119 amino acids) that has been reported to bind DNA. The length of that helix and the presence of a PIP at the C-terminus are evolutionarily conserved among numerous species, ranging from yeast to humans. This arrangement of a very long DNA-binding coiled-coil that terminates in PIPs may serve to coordinate DNA and PCNA binding by CAF-1.
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Affiliation(s)
- Amogh Gopinathan Nair
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC H3T 1J4, Canada
- Molecular Biology Program, University of Montreal, Montreal, QC H3T 1J4, Canada
- Correspondence: (A.G.N.); (A.V.)
| | - Nick Rabas
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Sara Lejon
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Caleb Homiski
- Departments of Biochemistry and Microbiology & Immunology, University at Buffalo Jacobs School of Medicine & Biomedical Sciences, 955 Main Street, Buffalo, NY 14210, USA
| | - Michael J. Osborne
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Normand Cyr
- Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, QC H3C 3J7, Canada
| | - Aleksandr Sverzhinsky
- Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, QC H3C 3J7, Canada
| | - Thomas Melendy
- Departments of Biochemistry and Microbiology & Immunology, University at Buffalo Jacobs School of Medicine & Biomedical Sciences, 955 Main Street, Buffalo, NY 14210, USA
| | - John M. Pascal
- Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, QC H3C 3J7, Canada
| | - Ernest D. Laue
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Katherine L. B. Borden
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC H3T 1J4, Canada
- Department of Pathology and Cell Biology, University of Montreal, Montreal, QC H3T 1J4, Canada
| | - James G. Omichinski
- Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, QC H3C 3J7, Canada
| | - Alain Verreault
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC H3T 1J4, Canada
- Department of Pathology and Cell Biology, University of Montreal, Montreal, QC H3T 1J4, Canada
- Correspondence: (A.G.N.); (A.V.)
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14
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Fenteany G, Sharma G, Gaur P, Borics A, Wéber E, Kiss E, Haracska L. A series of xanthenes inhibiting Rad6 function and Rad6-Rad18 interaction in the PCNA ubiquitination cascade. iScience 2022; 25:104053. [PMID: 35355521 PMCID: PMC8958325 DOI: 10.1016/j.isci.2022.104053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 12/13/2021] [Accepted: 03/08/2022] [Indexed: 11/24/2022] Open
Abstract
Ubiquitination of proliferating cell nuclear antigen (PCNA) triggers pathways of DNA damage tolerance, including mutagenic translesion DNA synthesis, and comprises a cascade of reactions involving the E1 ubiquitin-activating enzyme Uba1, the E2 ubiquitin-conjugating enzyme Rad6, and the E3 ubiquitin ligase Rad18. We report here the discovery of a series of xanthenes that inhibit PCNA ubiquitination, Rad6∼ubiquitin thioester formation, and the Rad6–Rad18 interaction. Structure-activity relationship experiments across multiple assays reveal chemical and structural features important for different activities along the pathway to PCNA ubiquitination. The compounds that inhibit these processes are all a subset of the xanthen-3-ones we tested. These small molecules thus represent first-in-class probes of Rad6 function and the association of Rad6 and Rad18, the latter being a new inhibitory activity discovered for a small molecule, in the PCNA ubiquitination cascade and potential therapeutic agents to contain cancer progression. Alpha-based HTS for PCNA ubiquitination modulators Target-based characterization of hits A series of xanthenes that inhibit Rad6 functions and Rad6–Rad18 interaction
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15
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Gharouni M, Mosaddeghi H, Mehrzad J, Es-haghi A, Motavalizadehkakhky A. Detecting a novel motif of O6-methyl guanine DNA methyltransferase, a DNA repair enzyme, involved in interaction with proliferating cell nuclear antigen through a computer modeling approach. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2021.113471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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16
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Araújo TG, Mota STS, Ferreira HSV, Ribeiro MA, Goulart LR, Vecchi L. Annexin A1 as a Regulator of Immune Response in Cancer. Cells 2021; 10:2245. [PMID: 34571894 PMCID: PMC8464935 DOI: 10.3390/cells10092245] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/05/2021] [Accepted: 08/07/2021] [Indexed: 01/01/2023] Open
Abstract
Annexin A1 is a 37 kDa phospholipid-binding protein that is expressed in many tissues and cell types, including leukocytes, lymphocytes and epithelial cells. Although Annexin A1 has been extensively studied for its anti-inflammatory activity, it has been shown that, in the cancer context, its activity switches from anti-inflammatory to pro-inflammatory. Remarkably, Annexin A1 shows pro-invasive and pro-tumoral properties in several cancers either by eliciting autocrine signaling in cancer cells or by inducing a favorable tumor microenvironment. Indeed, the signaling of the N-terminal peptide of AnxA1 has been described to promote the switching of macrophages to the pro-tumoral M2 phenotype. Moreover, AnxA1 has been described to prevent the induction of antigen-specific cytotoxic T cell response and to play an essential role in the induction of regulatory T lymphocytes. In this way, Annexin A1 inhibits the anti-tumor immunity and supports the formation of an immunosuppressed tumor microenvironment that promotes tumor growth and metastasis. For these reasons, in this review we aim to describe the role of Annexin A1 in the establishment of the tumor microenvironment, focusing on the immunosuppressive and immunomodulatory activities of Annexin A1 and on its interaction with the epidermal growth factor receptor.
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Affiliation(s)
- Thaise Gonçalves Araújo
- Laboratory of Genetics and Biotechnology, Federal University of Uberlandia, Patos de Minas 387400-128, MG, Brazil; (T.G.A.); (S.T.S.M.); (H.S.V.F.); (M.A.R.)
- Laboratory of Nanobiotechnology, Federal University of Uberlandia, Uberlandia 38400-902, MG, Brazil;
| | - Sara Teixeira Soares Mota
- Laboratory of Genetics and Biotechnology, Federal University of Uberlandia, Patos de Minas 387400-128, MG, Brazil; (T.G.A.); (S.T.S.M.); (H.S.V.F.); (M.A.R.)
- Laboratory of Nanobiotechnology, Federal University of Uberlandia, Uberlandia 38400-902, MG, Brazil;
| | - Helen Soares Valença Ferreira
- Laboratory of Genetics and Biotechnology, Federal University of Uberlandia, Patos de Minas 387400-128, MG, Brazil; (T.G.A.); (S.T.S.M.); (H.S.V.F.); (M.A.R.)
| | - Matheus Alves Ribeiro
- Laboratory of Genetics and Biotechnology, Federal University of Uberlandia, Patos de Minas 387400-128, MG, Brazil; (T.G.A.); (S.T.S.M.); (H.S.V.F.); (M.A.R.)
| | - Luiz Ricardo Goulart
- Laboratory of Nanobiotechnology, Federal University of Uberlandia, Uberlandia 38400-902, MG, Brazil;
| | - Lara Vecchi
- Laboratory of Nanobiotechnology, Federal University of Uberlandia, Uberlandia 38400-902, MG, Brazil;
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17
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Dieckman L. Something’s gotta give: How PCNA alters its structure in response to mutations and the implications on cellular processes. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 163:46-59. [DOI: 10.1016/j.pbiomolbio.2020.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 10/19/2020] [Accepted: 10/29/2020] [Indexed: 12/19/2022]
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18
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Structural insight into FANCI-FANCD2 monoubiquitination. Essays Biochem 2021; 64:807-817. [PMID: 32725171 PMCID: PMC7588663 DOI: 10.1042/ebc20200001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/10/2020] [Accepted: 07/07/2020] [Indexed: 12/13/2022]
Abstract
The Fanconi anemia (FA) pathway coordinates a faithful repair mechanism for DNA damage that blocks DNA replication, such as interstrand cross-links. A key step in the FA pathway is the conjugation of ubiquitin on to FANCD2 and FANCI, which is facilitated by a large E3 ubiquitin ligase complex called the FA core complex. Mutations in FANCD2, FANCI or FA core complex components cause the FA bone marrow failure syndrome. Despite the importance of these proteins to DNA repair and human disease, our molecular understanding of the FA pathway has been limited due to a deficit in structural studies. With the recent development in cryo-electron microscopy (EM), significant advances have been made in structural characterization of these proteins in the last 6 months. These structures, combined with new biochemical studies, now provide a more detailed understanding of how FANCD2 and FANCI are monoubiquitinated and how DNA repair may occur. In this review, we summarize these recent advances in the structural and molecular understanding of these key components in the FA pathway, compare the activation steps of FANCD2 and FANCI monoubiquitination and suggest molecular steps that are likely to be involved in regulating its activity.
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19
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Zhou R, Wang M, Zhang X, Chen A, Fei Y, Zhao Q, Guo D, Chen H, Zheng S. Therapeutic effect of concentrated growth factor preparation on skin photoaging in a mouse model. J Int Med Res 2021; 48:300060520962946. [PMID: 33115316 PMCID: PMC7645418 DOI: 10.1177/0300060520962946] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVE To establish a nude mouse model of photoaging and study the therapeutic effect of a concentrated growth factor preparation (CGF) on skin photoaging. METHODS CGF was prepared from blood from Sprague-Dawley rats. A skin photoaging nude mouse model was developed using UV irradiation combined with the photosensitizer, 8-methoxypsoralen. Mice were divided randomly into seven groups (n = 6 per group): normal control, photoaging, mock treatment, saline treatment, CGF treatment, Filoca 135HA treatment, and plasma skin regeneration system irradiation (the latter two were positive controls). Body weight and skin appearance were observed and pathological changes were determined by hematoxylin and eosin staining. Fiber elasticity was evaluated by Weigert staining. Expression levels of proliferating cell nuclear antigen (PCNA) and matrix metalloproteinase 1 (MMP1) were determined by immunohistochemistry. RESULTS A mouse model with typical features of photoaging skin was successfully developed. CGF significantly improved the skin appearance, wrinkle scores, pathological changes, and fiber elasticity, and increased PCNA and decreased MMP1 expression levels in photoaging mice, comparable to the two positive controls. CONCLUSION CGF can improve the symptoms of skin photoaging in mice, suggesting that it may have applications in the treatment of skin aging in humans.
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Affiliation(s)
- Rongrong Zhou
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Joint Service Support Force 903 Hospital, Hangzhou, China
| | - Miao Wang
- ArtBeauty Cosmetology Clinic, Guangzhou, China
| | - Xudong Zhang
- Joint Service Support Force 903 Hospital, Hangzhou, China
| | - Aifen Chen
- Joint Service Support Force 903 Hospital, Hangzhou, China
| | | | | | - Danjing Guo
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Hui Chen
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Shusen Zheng
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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20
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Sundaram R, Manohar K, Patel SK, Acharya N, Vasudevan D. Structural analyses of PCNA from the fungal pathogen Candida albicans identify three regions with species-specific conformations. FEBS Lett 2021; 595:1328-1349. [PMID: 33544878 DOI: 10.1002/1873-3468.14055] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 01/11/2023]
Abstract
An assembly of multiprotein complexes achieves chromosomal DNA replication at the replication fork. In eukaryotes, proliferating cell nuclear antigen (PCNA) plays a vital role in the assembly of multiprotein complexes at the replication fork and is essential for cell viability. PCNA from several organisms, including Saccharomyces cerevisiae, has been structurally characterised. However, the structural analyses of PCNA from fungal pathogens are limited. Recently, we have reported that PCNA from the opportunistic fungal pathogen Candida albicans complements the essential functions of ScPCNA in S. cerevisiae. Still, it only partially rescues the loss of ScPCNA when the yeast cells are under genotoxic stress. To understand this further, herein, we have determined the crystal structure of CaPCNA and compared that with the existing structures of other fungal and human PCNA. Our comparative structural and in-solution small-angle X-ray scattering (SAXS) analyses reveal that CaPCNA forms a stable homotrimer, both in crystal and in solution. It displays noticeable structural alterations in the oligomerisation interface, P-loop and hydrophobic pocket regions, suggesting its differential function in a heterologous system and avenues for developing specific therapeutics. DATABASES: The PDB and SASBDB accession codes for CaPCNA are 7BUP and SASDHQ9, respectively.
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Affiliation(s)
- Rajivgandhi Sundaram
- Laboratory of Macromolecular Crystallography, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India.,Manipal Academy of Higher Education, India
| | - Kodavati Manohar
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Shraddheya Kumar Patel
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Narottam Acharya
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Dileep Vasudevan
- Laboratory of Macromolecular Crystallography, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
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21
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Ripley BM, Reusch DT, Washington MT. Yeast DNA polymerase η possesses two PIP-like motifs that bind PCNA and Rad6-Rad18 with different specificities. DNA Repair (Amst) 2020; 95:102968. [PMID: 32932109 DOI: 10.1016/j.dnarep.2020.102968] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 08/21/2020] [Accepted: 08/31/2020] [Indexed: 11/29/2022]
Abstract
In translesion synthesis (TLS), specialized DNA polymerases, such as polymerase (pol) η and Rev1, are recruited to stalled replication forks. These polymerases form a multi-protein complex with PCNA, Rad6-Rad18, and other specialized polymerases. Pol η interacts with PCNA and Rev1 via a PCNA-interacting protein (PIP) motif in its C-terminal unstructured region. Here we report the discovery of a second PIP-like motif in the C-terminal region of pol η, which we have designated as PIP2. We have designated the original PIP motif as PIP1. We show that the pol η PIP1 and PIP2 motifs bind PCNA with different affinities and kinetics. PIP1 binds with higher affinity than does PIP2, and PIP1 dissociates more slowly than does PIP2. In addition, we show that the interaction between pol η and Rad6-Rad18 is also mediated by the pol η PIP1 and PIP2 motifs. Again, we show that the affinity and kinetics by which these motifs bind Rad6-Rad18 is different. These findings are significant, because the multiple PIP-like motifs on pol η likely play quite different roles within the multi-protein complex formed at stalled replication forks. PIP1 likely plays a critical role in the recruiting pol η to this multi-protein complex. PIP2, by contrast, likely plays a critical role in maintaining the architecture and the dynamics of this multi-protein complex needed to maximize the efficiency and accuracy of TLS.
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Affiliation(s)
- Brittany M Ripley
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA 52242-1109, United States
| | - Devin T Reusch
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA 52242-1109, United States
| | - M Todd Washington
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA 52242-1109, United States.
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22
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Binding-Induced Conformational Changes Involved in Sliding Clamp PCNA and DNA Polymerase DPO4. iScience 2020; 23:101117. [PMID: 32422591 PMCID: PMC7229285 DOI: 10.1016/j.isci.2020.101117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 03/22/2020] [Accepted: 04/26/2020] [Indexed: 11/29/2022] Open
Abstract
Cooperation between DNA polymerases and DNA sliding clamp proteins is essential for DNA replication and repair. However, it is still challenging to clarify the binding mechanism and the movements of Y-family DNA polymerase IV (DPO4) on the proliferating cell nuclear antigen (PCNA) ring. Here we develop the simulation models of DPO4–PCNA123 and DPO4–PCNA12 complexes and uncover the underlying dynamics of DPO4 during binding and the binding order of the DPO4 domains. Two important intermediate states are found on the free energy surface before reaching the final bound state. Our results suggest that both PCNA3 and DPO4 can influence the PCNA12 planar conformation, whereas the impact of PCNA3 on PCNA12 is more significant than DPO4. These findings provide the crucial information of the conformational dynamics of DPO4 and PCNA, as well as the clue of the underlying mechanism of the cooperation between DPO4 and PCNA during DNA replication. The mechanism of DPO4 binding to PCNA ring and PCNA dimer is investigated Two important intermediate states are found before reaching the final bound state Both PCNA3 and DPO4 can influence the PCNA12 planar conformation
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23
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A Multifunctional Protein PolDIP2 in DNA Translesion Synthesis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1241:35-45. [PMID: 32383114 DOI: 10.1007/978-3-030-41283-8_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Polymerase δ-interacting protein 2 (PolDIP2) is involved in the multiple protein-protein interactions and plays roles in many cellular processes including regulation of the nuclear redox environment, organization of the mitotic spindle and chromosome segregation, pre-mRNA processing, mitochondrial morphology and functions, cell migration and cellular adhesion. PolDIP2 is also a binding partner of high-fidelity DNA polymerase delta, PCNA and a number of translesion and repair DNA polymerases. The growing evidence suggests that PolDIP2 is a general regulatory protein in DNA damage response. However PolDIP2 functions in DNA translesion synthesis and repair are not fully understood. In this review, we address the functional interaction of PolDIP2 with human DNA polymerases and discuss the possible functions in DNA damage response.
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24
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Fenteany G, Gaur P, Sharma G, Pintér L, Kiss E, Haracska L. Robust high-throughput assays to assess discrete steps in ubiquitination and related cascades. BMC Mol Cell Biol 2020; 21:21. [PMID: 32228444 PMCID: PMC7106726 DOI: 10.1186/s12860-020-00262-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 03/12/2020] [Indexed: 01/21/2023] Open
Abstract
Background Ubiquitination and ubiquitin-like protein post-translational modifications play an enormous number of roles in cellular processes. These modifications are constituted of multistep reaction cascades. Readily implementable and robust methods to evaluate each step of the overall process, while presently limited, are critical to the understanding and modulation of the reaction sequence at any desired level, both in terms of basic research and potential therapeutic drug discovery and development. Results We developed multiple robust and reliable high-throughput assays to interrogate each of the sequential discrete steps in the reaction cascade leading to protein ubiquitination. As models for the E1 ubiquitin-activating enzyme, the E2 ubiquitin-conjugating enzyme, the E3 ubiquitin ligase, and their ultimate substrate of ubiquitination in a cascade, we examined Uba1, Rad6, Rad18, and proliferating cell nuclear antigen (PCNA), respectively, in reconstituted systems. Identification of inhibitors of this pathway holds promise in cancer therapy since PCNA ubiquitination plays a central role in DNA damage tolerance and resulting mutagenesis. The luminescence-based assays we developed allow for the quantitative determination of the degree of formation of ubiquitin thioester conjugate intermediates with both E1 and E2 proteins, autoubiquitination of the E3 protein involved, and ubiquitination of the final substrate. Thus, all covalent adducts along the cascade can be individually probed. We tested previously identified inhibitors of this ubiquitination cascade, finding generally good correspondence between compound potency trends determined by more traditional low-throughput methods and the present high-throughput ones. Conclusions These approaches are readily adaptable to other E1, E2, and E3 systems, and their substrates in both ubiquitination and ubiquitin-like post-translational modification cascades.
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Affiliation(s)
- Gabriel Fenteany
- HCEMM-BRC Mutagenesis and Carcinogenesis Research Group, Institute of Genetics, Biological Research Centre, Szeged, Temesvári krt. 62, Szeged, 6726, Hungary.
| | - Paras Gaur
- HCEMM-BRC Mutagenesis and Carcinogenesis Research Group, Institute of Genetics, Biological Research Centre, Szeged, Temesvári krt. 62, Szeged, 6726, Hungary.,Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, Szeged, 6726, Hungary
| | - Gaurav Sharma
- HCEMM-BRC Mutagenesis and Carcinogenesis Research Group, Institute of Genetics, Biological Research Centre, Szeged, Temesvári krt. 62, Szeged, 6726, Hungary.,Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, Szeged, 6726, Hungary
| | - Lajos Pintér
- Visal Plus Ltd., Temesvári krt. 62, Szeged, 6726, Hungary
| | - Ernő Kiss
- HCEMM-BRC Mutagenesis and Carcinogenesis Research Group, Institute of Genetics, Biological Research Centre, Szeged, Temesvári krt. 62, Szeged, 6726, Hungary
| | - Lajos Haracska
- HCEMM-BRC Mutagenesis and Carcinogenesis Research Group, Institute of Genetics, Biological Research Centre, Szeged, Temesvári krt. 62, Szeged, 6726, Hungary.
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25
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Zhang W, Feng J, Li Q. The replisome guides nucleosome assembly during DNA replication. Cell Biosci 2020; 10:37. [PMID: 32190287 PMCID: PMC7066812 DOI: 10.1186/s13578-020-00398-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 02/29/2020] [Indexed: 12/18/2022] Open
Abstract
Nucleosome assembly during DNA replication is tightly coupled to ongoing DNA synthesis. This process, termed DNA replication-coupled (RC) nucleosome assembly, is essential for chromatin replication and has a great impact on both genome stability maintenance and epigenetic inheritance. This review discusses a set of recent findings regarding the role of replisome components contributing to RC nucleosome assembly. Starting with a brief introduction to the factors involved in nucleosome assembly and some aspects of the architecture of the eukaryotic replisome, we discuss studies from yeast to mammalian cells and the interactions of replisome components with histones and histone chaperones. We describe the proposed functions of replisome components during RC nucleosome assembly and discuss their impacts on histone segregation and implications for epigenetic inheritance.
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Affiliation(s)
- Wenshuo Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China
| | - Jianxun Feng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China
| | - Qing Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China
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26
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Control of DNA Damage Bypass by Ubiquitylation of PCNA. Genes (Basel) 2020; 11:genes11020138. [PMID: 32013080 PMCID: PMC7074500 DOI: 10.3390/genes11020138] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 01/23/2020] [Accepted: 01/27/2020] [Indexed: 02/01/2023] Open
Abstract
DNA damage leads to genome instability by interfering with DNA replication. Cells possess several damage bypass pathways that mitigate the effects of DNA damage during replication. These pathways include translesion synthesis and template switching. These pathways are regulated largely through post-translational modifications of proliferating cell nuclear antigen (PCNA), an essential replication accessory factor. Mono-ubiquitylation of PCNA promotes translesion synthesis, and K63-linked poly-ubiquitylation promotes template switching. This article will discuss the mechanisms of how these post-translational modifications of PCNA control these bypass pathways from a structural and biochemical perspective. We will focus on the structure and function of the E3 ubiquitin ligases Rad18 and Rad5 that facilitate the mono-ubiquitylation and poly-ubiquitylation of PCNA, respectively. We conclude by reviewing alternative ideas about how these post-translational modifications of PCNA regulate the assembly of the multi-protein complexes that promote damage bypass pathways.
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27
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Bender D, Da Silva EML, Chen J, Poss A, Gawey L, Rulon Z, Rankin S. Multivalent interaction of ESCO2 with the replication machinery is required for sister chromatid cohesion in vertebrates. Proc Natl Acad Sci U S A 2020; 117:1081-1089. [PMID: 31879348 PMCID: PMC6969535 DOI: 10.1073/pnas.1911936117] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The tethering together of sister chromatids by the cohesin complex ensures their accurate alignment and segregation during cell division. In vertebrates, sister chromatid cohesion requires the activity of the ESCO2 acetyltransferase, which modifies the Smc3 subunit of cohesin. It was shown recently that ESCO2 promotes cohesion through interaction with the MCM replicative helicase. However, ESCO2 does not significantly colocalize with the MCM complex, suggesting there are additional interactions important for ESCO2 function. Here we show that ESCO2 is recruited to replication factories, sites of DNA replication, through interaction with PCNA. We show that ESCO2 contains multiple PCNA-interaction motifs in its N terminus, each of which is essential to its ability to establish cohesion. We propose that multiple PCNA-interaction motifs embedded in a largely flexible and disordered region of the protein underlie the unique ability of ESCO2 to establish cohesion between sister chromatids precisely as they are born during DNA replication.
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Affiliation(s)
- Dawn Bender
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
- Department of Cell Biology, Oklahoma University Health Science Center, Oklahoma City, OK 73104
| | | | - Jingrong Chen
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
| | - Annelise Poss
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
| | - Lauren Gawey
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
| | - Zane Rulon
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
| | - Susannah Rankin
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104;
- Department of Cell Biology, Oklahoma University Health Science Center, Oklahoma City, OK 73104
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28
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Costa P, Somensi LB, da Silva RDCMVDAF, Mariano LNB, Boeing T, Longo B, Perfoll E, de Souza P, Gushiken LFS, Pellizzon CH, Rodrigues DM, Bastos JK, de Andrade SF, da Silva LM. Role of the antioxidant properties in the gastroprotective and gastric healing activity promoted by Brazilian green propolis and the healing efficacy of Artepillin C. Inflammopharmacology 2019; 28:1009-1025. [PMID: 31745698 DOI: 10.1007/s10787-019-00649-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 09/16/2019] [Indexed: 12/11/2022]
Abstract
Green propolis is a resinous substance used in folk medicine given its anti-inflammatory, antibacterial, and anti-ulcer effects. Our research group has already confirmed the gastroprotective activity of hydroalcoholic extract from green propolis (HEGP), as well as of its main isolated compounds. In continuity, this study evaluated the antioxidant mode of action involved in the preventive effect induced by HEGP, and its therapeutic gastric healing potential on installed ulcers. In addition, the healing effect of its main compound Artepillin C was also investigated. Acute and chronic ulcers were induced in rats by given ethanol or acetic acid, respectively. In acute model, the rats were orally pre-treated with vehicle (water plus 1% Tween, 1 mL/kg), HEGP (30-300 mg/kg), or carbenoxolone (200 mg/kg) 1 h prior the ulcer induction. In the chronic ulcer protocol, the rats received vehicle (water plus 1% Tween, 1 mL/kg), HEGP (300 mg/kg), or omeprazole (20 mg/kg) twice a day by 7 days, whereas groups of mice received vehicle (water plus 1% Tween, 1 mL/kg), Artepillin C (18 mg/kg), or ranitidine (20 mg/kg) twice a day by 4 days. Ulcerated tissue was collected for histological, histochemical, immunostaining, oxidative, and inflammatory analyses. The in vitro scavenger activity of HEGP was also verified using the DPPH assay. The oral pre-treatment with HEGP (100 and 300 mg/kg) prevented the gastric epithelial damage promoted by ethanol. Besides, HEGP (100 and 300 mg/kg) reduced SOD activity about 11% and 26%, respectively, and increased the activity of GST around 20% and CAT in 80%. HEGP (300 mg/kg) also reduced the production of reactive oxygen species, as well as lipoperoxidation levels in the ethanol-ulcerated tissue. In the acetic acid-induced chronic ulcer, the daily treatment with HEGP (300 mg/kg) accelerates the healing process by 71%. In this model, HEGP normalized SOD and CAT activity and increased GST activity by 109% when compared to non-ulcerated rats. In both models, the extract administration increased the mucin PAS staining and reduced the myeloperoxidase activity at the ulcer site. Moreover, the treatment with HEGP enhanced the PCNA immunostaining, but did not alter the concentration of collagen in the acetic acid-ulcerated tissue. The extract had a direct DPPH radical-scavenging ability (LogIC50: 0.56). Besides, as expected, HPLC analysis showed Artepillin C as a major compound and its administration at 18 mg/kg also accelerated the gastric healing ulcer process in mice. Our findings confirm that HEGP displays both gastroprotective and gastric healing properties, contributing to the validation of its popular use as preventive and therapeutic approaches. These actions occur through the increase in mucin production and the reestablishment of the oxidative balance due to a reduction in gastric inflammation.
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Affiliation(s)
- Philipe Costa
- Programa de Pós-Graduação em Ciências Farmacêuticas, Núcleo de Investigações Químico-Farmacêuticas (NIQFAR), Universidade do Vale do Itajaí (UNIVALI), Rua Uruguai, 458, Santa Catarina, SC, 88302-901, Brazil.,Departamento de Morfologia, Universidade do Estado de São Paulo (Unesp), Instituto de Biociências, Botucatu, Rua Professor Antônio Celso Wagner Zanin s/n, São Paulo, SP, 18618-689, Brazil.,Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo (USP), Avenida do Café, s/n, Ribeirão Preto, SP, 14040-903, Brazil
| | - Lincon Bordignon Somensi
- Programa de Pós-Graduação em Ciências Farmacêuticas, Núcleo de Investigações Químico-Farmacêuticas (NIQFAR), Universidade do Vale do Itajaí (UNIVALI), Rua Uruguai, 458, Santa Catarina, SC, 88302-901, Brazil
| | | | - Luísa Nathalia Bolda Mariano
- Programa de Pós-Graduação em Ciências Farmacêuticas, Núcleo de Investigações Químico-Farmacêuticas (NIQFAR), Universidade do Vale do Itajaí (UNIVALI), Rua Uruguai, 458, Santa Catarina, SC, 88302-901, Brazil
| | - Thaise Boeing
- Programa de Pós-Graduação em Ciências Farmacêuticas, Núcleo de Investigações Químico-Farmacêuticas (NIQFAR), Universidade do Vale do Itajaí (UNIVALI), Rua Uruguai, 458, Santa Catarina, SC, 88302-901, Brazil
| | - Bruna Longo
- Programa de Pós-Graduação em Ciências Farmacêuticas, Núcleo de Investigações Químico-Farmacêuticas (NIQFAR), Universidade do Vale do Itajaí (UNIVALI), Rua Uruguai, 458, Santa Catarina, SC, 88302-901, Brazil.,Departamento de Morfologia, Universidade do Estado de São Paulo (Unesp), Instituto de Biociências, Botucatu, Rua Professor Antônio Celso Wagner Zanin s/n, São Paulo, SP, 18618-689, Brazil.,Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo (USP), Avenida do Café, s/n, Ribeirão Preto, SP, 14040-903, Brazil
| | - Ellen Perfoll
- Programa de Pós-Graduação em Ciências Farmacêuticas, Núcleo de Investigações Químico-Farmacêuticas (NIQFAR), Universidade do Vale do Itajaí (UNIVALI), Rua Uruguai, 458, Santa Catarina, SC, 88302-901, Brazil
| | - Priscila de Souza
- Programa de Pós-Graduação em Ciências Farmacêuticas, Núcleo de Investigações Químico-Farmacêuticas (NIQFAR), Universidade do Vale do Itajaí (UNIVALI), Rua Uruguai, 458, Santa Catarina, SC, 88302-901, Brazil
| | - Lucas Fernando Sérgio Gushiken
- Departamento de Morfologia, Universidade do Estado de São Paulo (Unesp), Instituto de Biociências, Botucatu, Rua Professor Antônio Celso Wagner Zanin s/n, São Paulo, SP, 18618-689, Brazil
| | - Cláudia Helena Pellizzon
- Departamento de Morfologia, Universidade do Estado de São Paulo (Unesp), Instituto de Biociências, Botucatu, Rua Professor Antônio Celso Wagner Zanin s/n, São Paulo, SP, 18618-689, Brazil
| | - Débora Munhoz Rodrigues
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo (USP), Avenida do Café, s/n, Ribeirão Preto, SP, 14040-903, Brazil
| | - Jairo Kenupp Bastos
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo (USP), Avenida do Café, s/n, Ribeirão Preto, SP, 14040-903, Brazil
| | - Sérgio Faloni de Andrade
- Programa de Pós-Graduação em Ciências Farmacêuticas, Núcleo de Investigações Químico-Farmacêuticas (NIQFAR), Universidade do Vale do Itajaí (UNIVALI), Rua Uruguai, 458, Santa Catarina, SC, 88302-901, Brazil
| | - Luísa Mota da Silva
- Programa de Pós-Graduação em Ciências Farmacêuticas, Núcleo de Investigações Químico-Farmacêuticas (NIQFAR), Universidade do Vale do Itajaí (UNIVALI), Rua Uruguai, 458, Santa Catarina, SC, 88302-901, Brazil.
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29
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Gildenberg MS, Washington MT. Conformational flexibility of fork-remodeling helicase Rad5 shown by full-ensemble hybrid methods. PLoS One 2019; 14:e0223875. [PMID: 31626633 PMCID: PMC6799953 DOI: 10.1371/journal.pone.0223875] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 10/01/2019] [Indexed: 12/17/2022] Open
Abstract
Several pathways exist to bypass DNA damage during replication. One such pathway is template switching. The Rad5 protein plays two important roles in template switching: it is an E3 ubiquitin ligase that catalyzes PCNA poly-ubiquitylation and it is a helicase that converts replication forks to chicken foot structures. To understand the structure, conformational flexibility, and mechanism of Rad5, we used a full-ensemble hybrid method combining Langevin dynamics simulations and small-angle X-ray scattering. From these studies, we generated the first experimentally validated, high-resolution structural model of Rad5. We found that Rad5 is more compact and less extended than is suggested by its large amount of predicted intrinsic disorder. Thus, Rad5 likely has a novel intra-molecular interaction that limits the range of conformational space it can sample. We provide evidence for a novel interaction between the HIRAN and the helicase domains of Rad5, and we discuss the biological and mechanistic implications of this.
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Affiliation(s)
- Melissa S. Gildenberg
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, Iowa, United States of America
| | - M. Todd Washington
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, Iowa, United States of America
- * E-mail:
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30
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Horsfall AJ, Abell AD, Bruning JB. Targeting PCNA with Peptide Mimetics for Therapeutic Purposes. Chembiochem 2019; 21:442-450. [DOI: 10.1002/cbic.201900275] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Aimee J. Horsfall
- ARC Centre of Excellence for Nanoscale BioPhotonicsInstitute for Photonics and Advanced Sensing (IPAS)Department of ChemistryUniversity of Adelaide Nth Tce Adelaide 5005 Australia
| | - Andrew D. Abell
- ARC Centre of Excellence for Nanoscale BioPhotonicsInstitute for Photonics and Advanced Sensing (IPAS)Department of ChemistryUniversity of Adelaide Nth Tce Adelaide 5005 Australia
| | - John B. Bruning
- Institute of Photonics and Advanced Sensing (IPAS)School of Biological SciencesUniversity of Adelaide Nth Tce Adelaide 5005 Australia
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31
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Tehseen M, Raducanu VS, Rashid F, Shirbini A, Takahashi M, Hamdan SM. Proliferating cell nuclear antigen-agarose column: A tag-free and tag-dependent tool for protein purification affinity chromatography. J Chromatogr A 2019; 1602:341-349. [DOI: 10.1016/j.chroma.2019.06.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 06/01/2019] [Accepted: 06/03/2019] [Indexed: 10/26/2022]
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32
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Jiang Q, Zhang W, Liu C, Lin Y, Wu Q, Dai J. Dissecting PCNA function with a systematically designed mutant library in yeast. J Genet Genomics 2019; 46:301-313. [PMID: 31281030 DOI: 10.1016/j.jgg.2019.03.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 02/27/2019] [Accepted: 03/07/2019] [Indexed: 11/26/2022]
Abstract
Proliferating cell nuclear antigen (PCNA), encoded by POL30 in Saccharomyces cerevisiae, is a key component of DNA metabolism. Here, a library consisting of 304 PCNA mutants was designed and constructed to probe the contribution of each residue to the biological function of PCNA. Five regions with elevated sensitivity to DNA damaging reagents were identified using high-throughput phenotype screening. Using a series of genetic and biochemical analyses, we demonstrated that one particular mutant, K168A, has defects in the DNA damage tolerance (DDT) pathway by disrupting the interaction between PCNA and Rad5. Subsequent domain analysis showed that the PCNA-Rad5 interaction is a prerequisite for the function of Rad5 in DDT. Our study not only provides a resource in the form of a library of versatile mutants to study the functions of PCNA, but also reveals a key residue on PCNA (K168) which highlights the importance of the PCNA-Rad5 interaction in the template switching (TS) pathway.
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Affiliation(s)
- Qingwen Jiang
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China; Shenzhen Key Laboratory of Synthetic Genomics and Center for Synthetic Genomics, Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Weimin Zhang
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China; Shenzhen Key Laboratory of Synthetic Genomics and Center for Synthetic Genomics, Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Chenghao Liu
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yicong Lin
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China; Shenzhen Key Laboratory of Synthetic Genomics and Center for Synthetic Genomics, Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Qingyu Wu
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Junbiao Dai
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China; Shenzhen Key Laboratory of Synthetic Genomics and Center for Synthetic Genomics, Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
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33
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Interaction between Two Iridovirus Core Proteins and Their Effects on Ranavirus (RGV) Replication in Cells from Different Species. Viruses 2019; 11:v11050416. [PMID: 31060251 PMCID: PMC6563300 DOI: 10.3390/v11050416] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/28/2019] [Accepted: 04/30/2019] [Indexed: 12/16/2022] Open
Abstract
The two putative proteins RGV-63R and RGV-91R encoded by Rana grylio virus (RGV) are DNA polymerase and proliferating cell nuclear antigen (PCNA) respectively, and are core proteins of iridoviruses. Here, the interaction between RGV-63R and RGV-91R was detected by a yeast two-hybrid (Y2H) assay and further confirmed by co-immunoprecipitation (co-IP) assays. Subsequently, RGV-63R or RGV-91R were expressed alone or co-expressed in two kinds of aquatic animal cells including amphibian Chinese giant salamander thymus cells (GSTCs) and fish Epithelioma papulosum cyprinid cells (EPCs) to investigate their localizations and effects on RGV genome replication. The results showed that their localizations in the two kinds of cells are consistent. RGV-63R localized in the cytoplasm, while RGV-91R localized in the nucleus. However, when co-expressed, RGV-63R localized in both the cytoplasm and the nucleus, and colocalized with RGV-91R in the nucleus. 91R△NLS represents the RGV-91R deleting nuclear localization signal, which is localized in the cytoplasm and colocalized with RGV-63R in the cytoplasm. qPCR analysis revealed that sole expression and co-expression of the two proteins in the cells of two species significantly promoted RGV genome replication, while varying degrees of viral genome replication levels may be linked to the cell types. This study provides novel molecular evidence for ranavirus cross-species infection and replication.
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34
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Tian P, Lv P, Shi W, Zhu M, Cong B, Wen B. Chronic stress reduces spermatogenic cell proliferation in rat testis. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2019; 12:1921-1931. [PMID: 31934015 PMCID: PMC6947124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 02/20/2019] [Indexed: 06/10/2023]
Abstract
Male reproductive dysfunction induced by mental stress and environmental factors has increased greatly in recent years. Previous studies of the male rat reproductive system under stress conditions evaluated changes in physiology and pathophysiology. However, no genome-wide study has been applied to such models. Here we studied the histopathologic changes in testes of rats under different durations of stress and used RNA sequencing (RNA-seq) to investigate the testicular transcriptome and detect differentially expressed genes. Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) and immunohistochemistry were used to verify these. Chronic stress resulted in significant histopathologic changes in seminiferous tubules and RNA-seq showed that growing numbers of genes were dysregulated with increasing stress exposure. Gene Ontology (GO) analysis showed that many biological processes of cell proliferation-associated terms were highly significantly enriched among downregulated genes, from chronically stressed groups. Proliferating cell nuclear antigen (PCNA) was used as a key marker of cell proliferation. RT-qPCR and immunohistochemistry indicated that PCNA mRNA and protein expression levels were greatly decreased with prolonged stress, thereby contributing to the attenuation of spermatogenic cell proliferation in the rat testis. This could provide a new scientific basis for the study of male reproductive dysfunction caused by stress.
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Affiliation(s)
- Pengxiang Tian
- Institutes of Biomedical Sciences, MOE Key Laboratory of Metabolism and Molecular Medicine, School of Basic Medical Sciences, Fudan University Shanghai Medical CollegeShanghai 200032, China
| | - Pin Lv
- Institutes of Biomedical Sciences, MOE Key Laboratory of Metabolism and Molecular Medicine, School of Basic Medical Sciences, Fudan University Shanghai Medical CollegeShanghai 200032, China
| | - Weibo Shi
- Department of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular IdentificationShijiazhuang 050017, China
| | - Minzhe Zhu
- Institutes of Biomedical Sciences, MOE Key Laboratory of Metabolism and Molecular Medicine, School of Basic Medical Sciences, Fudan University Shanghai Medical CollegeShanghai 200032, China
| | - Bin Cong
- Department of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular IdentificationShijiazhuang 050017, China
| | - Bo Wen
- The Fifth People’s Hospital of Shanghai, Institutes of Biomedical Sciences, Fudan UniversityShanghai 200032, China
- MOE Key Laboratory of Metabolism and Molecular Medicine and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan UniversityShanghai 200032, China
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35
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Powers KT, Gildenberg MS, Washington MT. Modeling Conformationally Flexible Proteins With X-ray Scattering and Molecular Simulations. Comput Struct Biotechnol J 2019; 17:570-578. [PMID: 31073392 PMCID: PMC6495069 DOI: 10.1016/j.csbj.2019.04.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/15/2019] [Accepted: 04/17/2019] [Indexed: 01/03/2023] Open
Abstract
Proteins and protein complexes with high conformational flexibility participate in a wide range of biological processes. These processes include genome maintenance, gene expression, signal transduction, cell cycle regulation, and many others. Gaining a structural understanding of conformationally flexible proteins and protein complexes is arguably the greatest problem facing structural biologists today. Over the last decade, some progress has been made toward understanding the conformational flexibility of such systems using hybrid approaches. One particularly fruitful strategy has been the combination of small-angle X-ray scattering (SAXS) and molecular simulations. In this article, we provide a brief overview of SAXS and molecular simulations and then discuss two general approaches for combining SAXS data and molecular simulations: minimal ensemble approaches and full ensemble approaches. In minimal ensemble approaches, one selects a minimal ensemble of structures from the simulations that best fit the SAXS data. In full ensemble approaches, one validates a full ensemble of structures from the simulations using SAXS data. We argue that full ensemble models are more realistic than minimal ensemble searches models and that full ensemble approaches should be used wherever possible.
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Key Words
- BD, Brownian dynamics
- CG, coarse-grained
- Cryo-EM, cryo-electron microscopy
- DNA polymerase
- DNA replication
- Dmax, maximal distance
- LD, Langevin dynamics
- MD, molecular dynamics
- Minimal ensemble search
- NMR, nuclear magnetic resonance
- PCNA, proliferating cell nuclear antigen
- Pol η, DNA polymerase eta
- Protein structure
- RPA, replication protein A
- Rg, radius of gyration
- SANS
- SANS, small-angle neutron scattering
- SAXS
- SAXS, small-angle X-ray scattering
- SEC, size exclusion chromatography
- SUMO, small ubiquitin-like modifie
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Affiliation(s)
| | | | - M. Todd Washington
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA 52242-1109, United States of America
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36
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Hlavac N, VandeVord PJ. Astrocyte Mechano-Activation by High-Rate Overpressure Involves Alterations in Structural and Junctional Proteins. Front Neurol 2019; 10:99. [PMID: 30853931 PMCID: PMC6395392 DOI: 10.3389/fneur.2019.00099] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 01/24/2019] [Indexed: 11/13/2022] Open
Abstract
Primary blast neurotrauma represents a unique injury paradigm characterized by high-rate overpressure effects on brain tissue. One major hallmark of blast neurotrauma is glial reactivity, notably prolonged astrocyte activation. This cellular response has been mainly defined in primary blast neurotrauma by increased intermediate filament expression. Because the intermediate filament networks physically interface with transmembrane proteins for junctional support, it was hypothesized that cell junction regulation is altered in the reactive phenotype as well. This would have implications for downstream transcriptional regulation via signal transduction pathways like nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB). Therefore, a custom high-rate overpressure simulator was built for in vitro testing using mechanical conditions based on intracranial pressure measurements in a rat model of blast neurotrauma. Primary rat astrocytes were exposed to isolated high-rate mechanical stimulation to study cell junction dynamics in relation to their mechano-activation. First, a time course for "classical" features of reactivity was devised by evaluation of glial fibrillary acidic protein (GFAP) and proliferating cell nuclear antigen (PCNA) expression. This was followed by gene and protein expression for both gap junction (connexins) and anchoring junction proteins (integrins and cadherins). Signal transduction analysis was carried out by nuclear localization of two molecules, NF-κB p65 and mitogen-activated protein kinase (MAPK) p38. Results indicated significant increases in connexin-43 expression and PCNA first at 24 h post-overpressure (p < 0.05), followed by structural reactivity (via increased GFAP, p < 0.05) corresponding to increased anchoring junction dynamics at 48 h post-overpressure (p < 0.05). Moreover, increased phosphorylation of focal adhesion kinase (FAK) was observed in addition to increased nuclear localization of both p65 and p38 (p < 0.05) during the period of structural reactivity. To evaluate the transcriptional activity of p65 in the nucleus, electrophoretic mobility shift assay was conducted for a binding site on the promoter region for intracellular adhesion molecule-1 (ICAM-1), an antagonist of tight junctions. A significant increase in the interaction of nuclear proteins with the NF-κB site on the ICAM-1 corresponded to increased gene and protein expression of ICAM-1 (p < 0.05). Altogether, these results indicate multiple targets and corresponding signaling pathways which involve cell junction dynamics in the mechano-activation of astrocytes following high-rate overpressure.
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Affiliation(s)
- Nora Hlavac
- Department of Biomedical Engineering and Mechanics, Virginia Polytechnic Institute, Blacksburg, VA, United States
| | - Pamela J VandeVord
- Department of Biomedical Engineering and Mechanics, Virginia Polytechnic Institute, Blacksburg, VA, United States.,Department of Research, Salem Veterans Affairs Medical Center, Salem, VA, United States
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Zatopek KM, Gardner AF, Kelman Z. Archaeal DNA replication and repair: new genetic, biophysical and molecular tools for discovering and characterizing enzymes, pathways and mechanisms. FEMS Microbiol Rev 2018; 42:477-488. [PMID: 29912309 DOI: 10.1093/femsre/fuy017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 04/17/2018] [Indexed: 01/03/2023] Open
Abstract
DNA replication and repair are essential biological processes needed for the survival of all organisms. Although these processes are fundamentally conserved in the three domains, archaea, bacteria and eukarya, the proteins and complexes involved differ. The genetic and biophysical tools developed for archaea in the last several years have accelerated the study of DNA replication and repair in this domain. In this review, the current knowledge of DNA replication and repair processes in archaea will be summarized, with emphasis on the contribution of genetics and other recently developed biophysical and molecular tools, including capillary gel electrophoresis, next-generation sequencing and single-molecule approaches. How these new tools will continue to drive archaeal DNA replication and repair research will also be discussed.
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Affiliation(s)
| | | | - Zvi Kelman
- Biomolecular Labeling Laboratory, Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
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Powers KT, Lavering ED, Washington MT. Conformational Flexibility of Ubiquitin-Modified and SUMO-Modified PCNA Shown by Full-Ensemble Hybrid Methods. J Mol Biol 2018; 430:5294-5303. [PMID: 30381149 DOI: 10.1016/j.jmb.2018.10.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 10/10/2018] [Accepted: 10/23/2018] [Indexed: 01/22/2023]
Abstract
Ubiquitin-modified proliferating cell nuclear antigen (PCNA) and small ubiquitin-like modifier (SUMO)-modified PCNA regulate DNA damage tolerance pathways. X-ray crystal structures of these proteins suggested that they do not have much conformational flexibility because the modifiers have preferred binding sites on the surface of PCNA. By contrast, small-angle X-ray scattering analyses of these proteins suggested that they have different degrees of conformational flexibility, with SUMO-modified PCNA being more flexible. These conclusions were based on minimal-ensemble hybrid approaches, which produce unrealistic models by representing flexible proteins with only a few static structures. To overcome the limitations of minimal-ensemble hybrid approaches and to determine the degree of conformational flexibility of ubiquitin-modified PCNA and SUMO-modified PCNA, we utilized a novel full-ensemble hybrid approach. We carried out molecular simulations and small-angle X-ray scattering analyses of both proteins and obtained outstanding agreement between the full ensembles generated by the simulations and the experimental data. We found that both proteins have a high degree of conformational flexibility. The modifiers occupy many positions around the back and side of the PCNA ring. Moreover, we found no preferred ubiquitin-binding or SUMO-binding sites on PCNA. This conformational flexibility likely facilitates the recognition of downstream effector proteins and the formation of PCNA tool belts.
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Affiliation(s)
- Kyle T Powers
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA 52242-1109, USA
| | - Emily D Lavering
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA 52242-1109, USA
| | - M Todd Washington
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA 52242-1109, USA.
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Powers KT, Washington MT. Eukaryotic translesion synthesis: Choosing the right tool for the job. DNA Repair (Amst) 2018; 71:127-134. [PMID: 30174299 DOI: 10.1016/j.dnarep.2018.08.016] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Normal DNA replication is blocked by DNA damage in the template strand. Translesion synthesis is a major pathway for overcoming these replication blocks. In this process, multiple non-classical DNA polymerases are thought to form a complex at the stalled replication fork that we refer to as the mutasome. This hypothetical multi-protein complex is structurally organized by the replication accessory factor PCNA and the non-classical polymerase Rev1. One of the non-classical polymerases within this complex then catalyzes replication through the damage. Each non-classical polymerase has one or more cognate lesions, which the enzyme bypasses with high accuracy and efficiency. Thus, the accuracy and efficiency of translesion synthesis depends on which non-classical polymerase is chosen to bypass the damage. In this review article, we discuss how the most appropriate polymerase is chosen. In so doing, we examine the structural motifs that mediate the protein interactions in the mutasome; the multiple architectures that the mutasome can adopt, such as PCNA tool belts and Rev1 bridges; the intrinsically disordered regions that tether the polymerases to PCNA and to one another; and the kinetic selection model in which the most appropriate polymerase is chosen via a competition among the multiple polymerases within the mutasome.
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Affiliation(s)
- Kyle T Powers
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA 52242-1109, United States
| | - M Todd Washington
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA 52242-1109, United States.
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40
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Kondratick CM, Litman JM, Shaffer KV, Washington MT, Dieckman LM. Crystal structures of PCNA mutant proteins defective in gene silencing suggest a novel interaction site on the front face of the PCNA ring. PLoS One 2018; 13:e0193333. [PMID: 29499038 PMCID: PMC5834165 DOI: 10.1371/journal.pone.0193333] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 02/08/2018] [Indexed: 11/19/2022] Open
Abstract
Proliferating cell nuclear antigen (PCNA), a homotrimeric protein, is the eukaryotic sliding clamp that functions as a processivity factor for polymerases during DNA replication. Chromatin association factor 1 (CAF-1) is a heterotrimeric histone chaperone protein that is required for coupling chromatin assembly with DNA replication in eukaryotes. CAF-1 association with replicating DNA, and the targeting of newly synthesized histones to sites of DNA replication and repair requires its interaction with PCNA. Genetic studies have identified three mutant forms of PCNA in yeast that cause defects in gene silencing and exhibit altered association of CAF-1 to chromatin in vivo, as well as inhibit binding to CAF-1 in vitro. Three of these mutant forms of PCNA, encoded by the pol30-6, pol30-8, and the pol30-79 alleles, direct the synthesis of PCNA proteins with the amino acid substitutions D41A/D42A, R61A/D63A, and L126A/I128A, respectively. Interestingly, these double alanine substitutions are located far away from each other within the PCNA protein. To understand the structural basis of the interaction between PCNA and CAF-1 and how disruption of this interaction leads to reduced gene silencing, we determined the X-ray crystal structures of each of these mutant PCNA proteins. All three of the substitutions caused disruptions of a surface cavity on the front face of the PCNA ring, which is formed in part by three loops comprised of residues 21–24, 41–44, and 118–134. We suggest that this cavity is a novel binding pocket required for the interaction between PCNA and CAF-1, and that this region in PCNA also represents a potential binding site for other PCNA-binding proteins.
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Affiliation(s)
- Christine M. Kondratick
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA, United States of America
| | - Jacob M. Litman
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA, United States of America
| | - Kurt V. Shaffer
- Department of Chemistry, Creighton University, Omaha, NE, United States of America
| | - M. Todd Washington
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA, United States of America
| | - Lynne M. Dieckman
- Department of Chemistry, Creighton University, Omaha, NE, United States of America
- * E-mail:
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Shi W, Wang R, Niu S, Li Y, Ma C, Zhang G, Cong B. Dynamaic changes of proliferation and apoptosis in rat retina development. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2017; 10:11679-11684. [PMID: 31966527 PMCID: PMC6966058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 10/24/2017] [Indexed: 06/10/2023]
Abstract
Precise coordination of cell proliferation and apoptosis is essential for proper organ morphogenesis and function during mammalian development. The retina is a part of the central nervous system, with a function in capture and conversion of light particles into nerve signals. However, the dynamical changes of cell proliferation and apoptosis during the retinal development is unclear. Thus, this study was to observe the changes of proliferating cell nuclear antigen expression and apoptosis during the retina development in rats. Rats from different developmental stages (embryonic days 14-20 (E14-20), postnatal days 0-15 (P0-15) and adult (P36)) were used. The eyeballs were removed and fixed immediately in formalin. The tissues were embedded in paraffin. Sections were prepared for immunohistochemical staining and terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling (TUNEL). PCNA expression appeared in large quantities in rat retina from E14 to P7, decreased obviously since P9, and could not be observed since P15. Apoptotic cells appeared in small quantities since E18. And then apoptotic cells dramatically increased during the retina development, and peaked at P7. As maturation continued, these cells decreased gradually. Apoptotic cells could not be found in the mature retina. Cell proliferation and apoptosis shows orderly and dynamic changes during the retina development, which is essential for the development of normal structure and function of the retina.
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Affiliation(s)
- Weibo Shi
- Department of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular IdentificationShijiazhuang, China
| | - Ran Wang
- Department of Psychiatry, The First Hospital of Hebei Medical UniversityShijiazhuang, China
| | - Shiba Niu
- Department of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular IdentificationShijiazhuang, China
| | - Yingmin Li
- Department of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular IdentificationShijiazhuang, China
| | - Chunling Ma
- Department of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular IdentificationShijiazhuang, China
| | - Guozhong Zhang
- Department of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular IdentificationShijiazhuang, China
| | - Bin Cong
- Department of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular IdentificationShijiazhuang, China
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Liu X, Ren W, Jiang Z, Su Z, Ma X, Li Y, Jiang R, Zhang J, Yang X. Hypothermia inhibits the proliferation of bone marrow-derived mesenchymal stem cells and increases tolerance to hypoxia by enhancing SUMOylation. Int J Mol Med 2017; 40:1631-1638. [PMID: 29039464 PMCID: PMC5716456 DOI: 10.3892/ijmm.2017.3167] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 09/05/2017] [Indexed: 11/23/2022] Open
Abstract
Hypothermia therapy has a positive effect on patients with severe brain injury. Recent studies have shown that mild hypothermia increases the survival of bone marrow-derived mesenchymal stem cells (BMSCs) in a hypoxic environment; however, the underlying mechanisms are not yet fully understood. Small ubiquitin-like modifiers (SUMOs) are sensitive to temperature stress reactions and are considered to exert a protective effect. In this study, we examined the protective effects of hypothermia on BMSCs in terms of SUMO protein modification. First, we found that mild hypothermia inhibited the proliferation and differentiation of BMSCs and increased cell tolerance to a hypoxic environment. Second, hypothermia significantly increased the levels of SUMO modification of multiple proteins in BMSCs. The knockdown of SUMO1/2/3 induced the rapid aging of the BMSCs, while the inhibition of the SUMO-conjugating enzyme, Ubc9, reduced cell proliferation and increased the proportion of BMSCs differentiating into nerve cells. Moreover, the tolerance of BMSCs to the hypoxic environment was significantly decreased. Lastly, we investigated 4 reported SUMO target proteins, anti-proliferating cell nuclear antigen, octamer-binding transcription factor 4, p53 and hypoxia-inducible factor-1α, to confirm that SUMO modification was indeed involved in maintaining the proliferation, inhibiting differentiation and enhancing the resistance of BMSCs against adverse conditions. Taken together, our results indicate that the SUMO pathway is involved in the response to hypothermic stress, and that SUMOylation may be an important protective mechanism against hypothermia for the survival of BMSCs under unfavorable conditions.
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Affiliation(s)
- Xiaozhi Liu
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, P.R. China
| | - Wenbo Ren
- Department of Neurology, The Fifth Central Hospital of Tianjin, Tianjin 300450, P.R. China
| | - Zhongmin Jiang
- Department of Pathology, The Fifth Central Hospital of Tianjin, Tianjin 300450, P.R. China
| | - Zhiguo Su
- Department of Neurosurgery, The Fifth Central Hospital of Tianjin, Tianjin 300450, P.R. China
| | - Xiaofang Ma
- Central Laboratory, The Fifth Central Hospital of Tianjin, Tianjin 300450, P.R. China
| | - Yanxia Li
- Central Laboratory, The Fifth Central Hospital of Tianjin, Tianjin 300450, P.R. China
| | - Rongcai Jiang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, P.R. China
| | - Jianning Zhang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, P.R. China
| | - Xinyu Yang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, P.R. China
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43
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Choe KN, Moldovan GL. Forging Ahead through Darkness: PCNA, Still the Principal Conductor at the Replication Fork. Mol Cell 2017; 65:380-392. [PMID: 28157503 DOI: 10.1016/j.molcel.2016.12.020] [Citation(s) in RCA: 203] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 11/28/2016] [Accepted: 12/21/2016] [Indexed: 10/20/2022]
Abstract
Proliferating cell nuclear antigen (PCNA) lies at the center of the faithful duplication of eukaryotic genomes. With its distinctive doughnut-shaped molecular structure, PCNA was originally studied for its role in stimulating DNA polymerases. However, we now know that PCNA does much more than promote processive DNA synthesis. Because of the complexity of the events involved, cellular DNA replication poses major threats to genomic integrity. Whatever predicament lies ahead for the replication fork, PCNA is there to orchestrate the events necessary to handle it. Through its many protein interactions and various post-translational modifications, PCNA has far-reaching impacts on a myriad of cellular functions.
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Affiliation(s)
- Katherine N Choe
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.
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Belyakova NV, Pantina RA, Kovalev RA, Filatov MV, Naryzhny SN. [Quaternary structures of human cytoplasmic and nuclear PCNA are the same]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2017; 63:356-360. [PMID: 28862608 DOI: 10.18097/pbmc20176304356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Properties and mechanisms of PCNA (proliferating cell nuclear antigen) functions have been investigated for a long time and are studied in great detail. As follows from its name, most known PCNA functions (DNA replication, DNA repair, DNA recombination and others) are connected with cell proliferation and localization of this protein in nuclei. In addition, there is good reason to believe that PCNA also performs some functions in the cytoplasm. However, the possible role and mechanisms of PCNA action in the cytoplasm require careful study and clarification. Interestingly, such cells as neutrophils differ in that they are non-dividing on one hand and on the other hand contain a rather large amount of PCNA, which is localized only in the cytoplasm, that is, they are an ideal model for the study of cytoplasmic PCNA. Using cross-linkages with formaldehyde, we showed that this cytoplasmic PCNA is cross-linked in a similar way, that is, organized in the same way as the nuclear PCNA that is present in the proliferating cells. Previously, we showed that PCNA in such cells is organized into a dynamic complex of double trimer on the basis of the back-to-back principle (Naryzhny S.N. et al. (2005) J. Biol. Chem., 280, 13888). Apparently, such organization of this hub-protein allows it to better coordinate the processes taking place in the cytoplasm as well.
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Affiliation(s)
- N V Belyakova
- Petersburg Nuclear Physics Institute NRC Kurchatov Institute, Leningrad region (PNPI), Gatchina, Russia
| | - R A Pantina
- Petersburg Nuclear Physics Institute NRC Kurchatov Institute, Leningrad region (PNPI), Gatchina, Russia
| | - R A Kovalev
- Petersburg Nuclear Physics Institute NRC Kurchatov Institute, Leningrad region (PNPI), Gatchina, Russia
| | - M V Filatov
- Petersburg Nuclear Physics Institute NRC Kurchatov Institute, Leningrad region (PNPI), Gatchina, Russia
| | - S N Naryzhny
- Petersburg Nuclear Physics Institute NRC Kurchatov Institute, Leningrad region (PNPI), Gatchina, Russia
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45
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Hedglin M, Benkovic SJ. Eukaryotic Translesion DNA Synthesis on the Leading and Lagging Strands: Unique Detours around the Same Obstacle. Chem Rev 2017; 117:7857-7877. [PMID: 28497687 PMCID: PMC5662946 DOI: 10.1021/acs.chemrev.7b00046] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
During S-phase, minor DNA damage may be overcome by DNA damage tolerance (DDT) pathways that bypass such obstacles, postponing repair of the offending damage to complete the cell cycle and maintain cell survival. In translesion DNA synthesis (TLS), specialized DNA polymerases replicate the damaged DNA, allowing stringent DNA synthesis by a replicative polymerase to resume beyond the offending damage. Dysregulation of this DDT pathway in human cells leads to increased mutation rates that may contribute to the onset of cancer. Furthermore, TLS affords human cancer cells the ability to counteract chemotherapeutic agents that elicit cell death by damaging DNA in actively replicating cells. Currently, it is unclear how this critical pathway unfolds, in particular, where and when TLS occurs on each template strand. Given the semidiscontinuous nature of DNA replication, it is likely that TLS on the leading and lagging strand templates is unique for each strand. Since the discovery of DDT in the late 1960s, most studies on TLS in eukaryotes have focused on DNA lesions resulting from ultraviolet (UV) radiation exposure. In this review, we revisit these and other related studies to dissect the step-by-step intricacies of this complex process, provide our current understanding of TLS on leading and lagging strand templates, and propose testable hypotheses to gain further insights.
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Affiliation(s)
- Mark Hedglin
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Stephen J. Benkovic
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, U.S.A
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Kim Y, de la Torre A, Leal AA, Finkelstein IJ. Efficient modification of λ-DNA substrates for single-molecule studies. Sci Rep 2017; 7:2071. [PMID: 28522818 PMCID: PMC5437064 DOI: 10.1038/s41598-017-01984-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 04/05/2017] [Indexed: 01/15/2023] Open
Abstract
Single-molecule studies of protein-nucleic acid interactions frequently require site-specific modification of long DNA substrates. The bacteriophage λ is a convenient source of high quality long (48.5 kb) DNA. However, introducing specific sequences, tertiary structures, and chemical modifications into λ-DNA remains technically challenging. Most current approaches rely on multi-step ligations with low yields and incomplete products. Here, we describe a molecular toolkit for rapid preparation of modified λ-DNA. A set of PCR cassettes facilitates the introduction of recombinant DNA sequences into the λ-phage genome with 90-100% yield. Extrahelical structures and chemical modifications can be inserted at user-defined sites via an improved nicking enzyme-based strategy. As a proof-of-principle, we explore the interactions of S. cerevisiae Proliferating Cell Nuclear Antigen (yPCNA) with modified DNA sequences and structures incorporated within λ-DNA. Our results demonstrate that S. cerevisiae Replication Factor C (yRFC) can load yPCNA onto 5'-ssDNA flaps, (CAG)13 triplet repeats, and homoduplex DNA. However, yPCNA remains trapped on the (CAG)13 structure, confirming a proposed mechanism for triplet repeat expansion. We anticipate that this molecular toolbox will be broadly useful for other studies that require site-specific modification of long DNA substrates.
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Affiliation(s)
- Yoori Kim
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Armando de la Torre
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Andrew A Leal
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, 78712, USA.
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, 78712, USA.
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Prakash A, Moharana K, Wallace SS, Doublié S. Destabilization of the PCNA trimer mediated by its interaction with the NEIL1 DNA glycosylase. Nucleic Acids Res 2017; 45:2897-2909. [PMID: 27994037 PMCID: PMC5389659 DOI: 10.1093/nar/gkw1282] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 11/11/2016] [Accepted: 12/12/2016] [Indexed: 12/12/2022] Open
Abstract
The base excision repair (BER) pathway repairs oxidized lesions in the DNA that result from reactive oxygen species generated in cells. If left unrepaired, these damaged DNA bases can disrupt cellular processes such as replication. NEIL1 is one of the 11 human DNA glycosylases that catalyze the first step of the BER pathway, i.e. recognition and excision of DNA lesions. NEIL1 interacts with essential replication proteins such as the ring-shaped homotrimeric proliferating cellular nuclear antigen (PCNA). We isolated a complex formed between NEIL1 and PCNA (±DNA) using size exclusion chromatography (SEC). This interaction was confirmed using native gel electrophoresis and mass spectrometry. Stokes radii measured by SEC hinted that PCNA in complex with NEIL1 (±DNA) was no longer a trimer. Height measurements and images obtained by atomic force microscopy also demonstrated the dissociation of the PCNA homotrimer in the presence of NEIL1 and DNA, while small-angle X-ray scattering analysis confirmed the NEIL1 mediated PCNA trimer dissociation and formation of a 1:1:1 NEIL1-DNA-PCNA(monomer) complex. Furthermore, ab initio shape reconstruction provides insights into the solution structure of this previously unreported complex. Together, these data point to a potential mechanistic switch between replication and BER.
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Affiliation(s)
- Aishwarya Prakash
- Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, 1660 Springhill Avenue, Mobile, AL 36604-1405, USA
| | - Kedar Moharana
- Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, VT 05405-0068, USA
| | - Susan S. Wallace
- Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, VT 05405-0068, USA
| | - Sylvie Doublié
- Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, VT 05405-0068, USA
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Wang Q, Li Y, Dong H, Wang L, Peng J, An T, Yang X, Tian Z, Cai X. Identification of host cellular proteins that interact with the M protein of a highly pathogenic porcine reproductive and respiratory syndrome virus vaccine strain. Virol J 2017; 14:39. [PMID: 28222748 PMCID: PMC5320790 DOI: 10.1186/s12985-017-0700-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 02/06/2017] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) continues to pose one of the greatest threats to the swine industry. M protein is the most conserved and important structural protein of PRRSV. However, information about the host cellular proteins that interact with M protein remains limited. METHODS Host cellular proteins that interact with the M protein of HP-PRRSV were immunoprecipitated from MARC-145 cells infected with PRRSV HuN4-F112 using the M monoclonal antibody (mAb). The differentially expressed proteins were identified by LC-MS/MS. The screened proteins were used for bioinformatics analysis including Gene Ontology, the interaction network, and the enriched KEGG pathways. Some interested cellular proteins were validated to interact with M protein by CO-IP. RESULTS The PRRSV HuN4-F112 infection group had 10 bands compared with the control group. The bands included 219 non-redundant cellular proteins that interact with M protein, which were identified by LC-MS/MS with high confidence. The gene ontology and Kyoto encyclopedia of genes and genomes (KEGG) pathway bioinformatic analyses indicated that the identified proteins could be assigned to several different subcellular locations and functional classes. Functional analysis of the interactome profile highlighted cellular pathways associated with protein translation, infectious disease, and signal transduction. Two interested cellular proteins-nuclear factor of activated T cells 45 kDa (NF45) and proliferating cell nuclear antigen (PCNA)-that could interact with M protein were validated by Co-IP and confocal analyses. CONCLUSIONS The interactome data between PRRSV M protein and cellular proteins were identified and contribute to the understanding of the roles of M protein in the replication and pathogenesis of PRRSV. The interactome of M protein will aid studies of virus/host interactions and provide means to decrease the threat of PRRSV to the swine industry in the future.
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Affiliation(s)
- Qian Wang
- Division of Swine Infectious Diseases, National Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No.678, Haping street, Xiangfang District, Harbin, 150069, China
| | - Yanwei Li
- National Engineering Research Center of Veterinary Biologics, Harbin, 150001, China
| | - Hong Dong
- Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, College of Veterinary Medicine and State Key Laboratory of Agribiotechnology, China Agricultural University, Beijing, 100193, China
| | - Li Wang
- Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, College of Veterinary Medicine and State Key Laboratory of Agribiotechnology, China Agricultural University, Beijing, 100193, China
| | - Jinmei Peng
- Division of Swine Infectious Diseases, National Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No.678, Haping street, Xiangfang District, Harbin, 150069, China
| | - Tongqing An
- Division of Swine Infectious Diseases, National Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No.678, Haping street, Xiangfang District, Harbin, 150069, China
| | - Xufu Yang
- North Guangdong Collaborative Innovation and Development Center of Pig Farming and Disease Control, Shaoguan University, Shaoguan, 512005, China
| | - Zhijun Tian
- Division of Swine Infectious Diseases, National Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No.678, Haping street, Xiangfang District, Harbin, 150069, China.
| | - Xuehui Cai
- Division of Swine Infectious Diseases, National Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No.678, Haping street, Xiangfang District, Harbin, 150069, China.
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Billon P, Li J, Lambert JP, Chen Y, Tremblay V, Brunzelle JS, Gingras AC, Verreault A, Sugiyama T, Couture JF, Côté J. Acetylation of PCNA Sliding Surface by Eco1 Promotes Genome Stability through Homologous Recombination. Mol Cell 2016; 65:78-90. [PMID: 27916662 DOI: 10.1016/j.molcel.2016.10.033] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 10/09/2016] [Accepted: 10/24/2016] [Indexed: 11/19/2022]
Abstract
During DNA replication, proliferating cell nuclear antigen (PCNA) adopts a ring-shaped structure to promote processive DNA synthesis, acting as a sliding clamp for polymerases. Known posttranslational modifications function at the outer surface of the PCNA ring to favor DNA damage bypass. Here, we demonstrate that acetylation of lysine residues at the inner surface of PCNA is induced by DNA lesions. We show that cohesin acetyltransferase Eco1 targets lysine 20 at the sliding surface of the PCNA ring in vitro and in vivo in response to DNA damage. Mimicking constitutive acetylation stimulates homologous recombination and robustly suppresses the DNA damage sensitivity of mutations in damage tolerance pathways. In comparison to the unmodified trimer, structural differences are observed at the interface between protomers in the crystal structure of the PCNA-K20ac ring. Thus, acetylation regulates PCNA sliding on DNA in the presence of DNA damage, favoring homologous recombination linked to sister-chromatid cohesion.
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Affiliation(s)
- Pierre Billon
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Centre de Recherche du CHU de Québec-Axe Oncologie, Quebec City, QC G1R 3S3, Canada
| | - Jian Li
- Department of Biological Sciences and Molecular and Cellular Biology Graduate Program, Ohio University, Athens, OH 45701, USA
| | - Jean-Philippe Lambert
- The Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Yizhang Chen
- Department of Biological Sciences and Molecular and Cellular Biology Graduate Program, Ohio University, Athens, OH 45701, USA
| | - Véronique Tremblay
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Joseph S Brunzelle
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Anne-Claude Gingras
- The Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Alain Verreault
- Institute for Research in Immunology and Cancer and Département de Pathologie et Biologie Cellulaire, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Tomohiko Sugiyama
- Department of Biological Sciences and Molecular and Cellular Biology Graduate Program, Ohio University, Athens, OH 45701, USA
| | - Jean-Francois Couture
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Centre de Recherche du CHU de Québec-Axe Oncologie, Quebec City, QC G1R 3S3, Canada.
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50
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Hedglin M, Pandey B, Benkovic SJ. Characterization of human translesion DNA synthesis across a UV-induced DNA lesion. eLife 2016; 5. [PMID: 27770570 PMCID: PMC5123862 DOI: 10.7554/elife.19788] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 10/21/2016] [Indexed: 12/11/2022] Open
Abstract
Translesion DNA synthesis (TLS) during S-phase uses specialized TLS DNA polymerases to replicate a DNA lesion, allowing stringent DNA synthesis to resume beyond the offending damage. Human TLS involves the conjugation of ubiquitin to PCNA clamps encircling damaged DNA and the role of this post-translational modification is under scrutiny. A widely-accepted model purports that ubiquitinated PCNA recruits TLS polymerases such as pol η to sites of DNA damage where they may also displace a blocked replicative polymerase. We provide extensive quantitative evidence that the binding of pol η to PCNA and the ensuing TLS are both independent of PCNA ubiquitination. Rather, the unique properties of pols η and δ are attuned to promote an efficient and passive exchange of polymerases during TLS on the lagging strand. DOI:http://dx.doi.org/10.7554/eLife.19788.001
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Affiliation(s)
- Mark Hedglin
- Department of Chemistry, The Pennsylvania State University, University Park, United States
| | - Binod Pandey
- Department of Chemistry, The Pennsylvania State University, University Park, United States
| | - Stephen J Benkovic
- Department of Chemistry, The Pennsylvania State University, University Park, United States
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