1
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Gauthier CM, LeGallais J, Savic N, Moradi-Fard S, Grew A, Loe M, Kirlikaya B, Cobb J, Nelson CJ. Intrinsic disorder of a nucleoplasmin-like histone chaperone specifies its discrete nuclear and nucleolar functions. FEBS Lett 2024; 598:187-198. [PMID: 38058218 DOI: 10.1002/1873-3468.14783] [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: 10/06/2023] [Revised: 11/16/2023] [Accepted: 11/21/2023] [Indexed: 12/08/2023]
Abstract
Nucleoplasmin (NPM) histone chaperones regulate distinct processes in the nucleus and nucleolus. While intrinsically disordered regions (IDRs) are hallmarks of NPMs, it is not clear whether all NPM functions require these unstructured features. We assessed the importance of IDRs in a yeast NPM-like protein and found that regulation of rDNA copy number and genetic interactions with the nucleolar RNA surveillance machinery require the highly conserved FKBP prolyl isomerase domain, but not the NPM domain or IDRs. By contrast, transcriptional repression in the nucleus requires IDRs. Furthermore, multiple lysines in polyacidic serine/lysine motifs of IDRs are required for both lysine polyphosphorylation and NPM-mediated transcriptional repression. These results demonstrate that this NPM-like protein relies on IDRs only for some of its chromatin-related functions.
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Affiliation(s)
| | - Josey LeGallais
- Department of Biochemistry and Microbiology, University of Victoria, Canada
| | - Neda Savic
- Department of Biochemistry and Microbiology, University of Victoria, Canada
| | - Sarah Moradi-Fard
- Departments of Biochemistry & Molecular Biology and Oncology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Arden Grew
- Department of Biochemistry and Microbiology, University of Victoria, Canada
| | - Martin Loe
- Department of Biochemistry and Microbiology, University of Victoria, Canada
| | - Baran Kirlikaya
- Department of Biochemistry and Microbiology, University of Victoria, Canada
| | - Jennifer Cobb
- Department of Biochemistry and Microbiology, University of Victoria, Canada
- Departments of Biochemistry & Molecular Biology and Oncology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
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2
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Zhang N, Feng S, Tian Y, Zhuang L, Cha G, Duan S, Li H, Nong X, Zhang Z, Tu X, Wang G. Identification, characterization and spatiotemporal expression analysis of the FKBP family genes in Locusta migratoria. Sci Rep 2023; 13:4048. [PMID: 36899085 PMCID: PMC10006077 DOI: 10.1038/s41598-023-30889-1] [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: 09/19/2022] [Accepted: 03/02/2023] [Indexed: 03/12/2023] Open
Abstract
FK506 binding proteins (FKBPs) are a highly-conserved group of proteins known to bind to FK506, an immunosuppressive drug. They play different physiological roles, including transcription regulation, protein folding, signal transduction and immunosuppression. A number of FKBP genes have been identified in eukaryotes; however, very little information about these genes has been reported in Locusta migratoria. Here, we identified and characterized 10 FKBP genes from L. migratoria. Phylogenetic analysis and comparison of domain architectures indicated that the LmFKBP family can be divided into two subfamilies and five subclasses. Developmental and tissue expression pattern analysis revealed that all LmFKBPs transcripts, including LmFKBP46, LmFKBP12, LmFKBP47, LmFKBP79, LmFKBP16, LmFKBP24, LmFKBP44b, LmFKBP53, were periodically expressed during different developmental stages and mainly expressed in the fat body, hemolymph, testis, and ovary. In brief, our work depicts a outline but panoramic picture of LmFKBP family in L. migratoria, and provides a solid foundation to further investigate the molecular functions of LmFKBPs.
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Affiliation(s)
- Neng Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,Scientific Observation and Experimental Station of Pests in Xilingol Rangeland, Ministry of Agriculture and Rural Affairs, Xilinhot, 026000, China
| | - Shiqian Feng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Ye Tian
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Ling Zhuang
- Bayannur Forestry and Grassland Development Center, Bayannur, 015000, China
| | - Gan Cha
- Bayannur Forestry and Grassland Development Center, Bayannur, 015000, China
| | - Saiya Duan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Hongmei Li
- MARA-CABI Joint Laboratory for Bio-Safety, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing, 100193, China
| | - Xiangqun Nong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Zehua Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiongbing Tu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,Scientific Observation and Experimental Station of Pests in Xilingol Rangeland, Ministry of Agriculture and Rural Affairs, Xilinhot, 026000, China
| | - Guangjun Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China. .,Scientific Observation and Experimental Station of Pests in Xilingol Rangeland, Ministry of Agriculture and Rural Affairs, Xilinhot, 026000, China.
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3
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Otero S. HD-tuin proteins, the ugly ducklings of histone deacetylases. THE PLANT CELL 2022; 34:4669-4670. [PMID: 36137216 PMCID: PMC9709961 DOI: 10.1093/plcell/koac277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 09/06/2022] [Indexed: 06/16/2023]
Affiliation(s)
- Sofía Otero
- Assistant Features Editor, The Plant Cell, American Society of Plant Biologists, USA
- Science and Technology Office of the Congress of Deputies, Madrid, Spain
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4
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Bobde RC, Kumar A, Vasudevan D. Plant-specific HDT family histone deacetylases are nucleoplasmins. THE PLANT CELL 2022; 34:4760-4777. [PMID: 36069647 PMCID: PMC9709999 DOI: 10.1093/plcell/koac275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Histone acetyltransferase (HAT)- and histone deacetylase (HDAC)-mediated histone acetylation and deacetylation regulate nucleosome dynamics and gene expression. HDACs are classified into different families, with HD-tuins or HDTs being specific to plants. HDTs show some sequence similarity to nucleoplasmins, the histone chaperones that aid in binding, storing, and loading H2A/H2B dimers to assemble nucleosomes. Here, we solved the crystal structure of the N-terminal domain (NTD) of all four HDTs (HDT1, HDT2, HDT3, and HDT4) from Arabidopsis (Arabidopsis thaliana). The NTDs form a nucleoplasmin fold, exist as pentamers in solution, and are resistant to protease treatment, high temperature, salt, and urea conditions. Structurally, HDTs do not form a decamer, unlike certain classical nucleoplasmins. The HDT-NTD requires an additional A2 acidic tract C-terminal to the nucleoplasmin domain for interaction with histone H3/H4 and H2A/H2B oligomers. We also report the in-solution structures of HDT2 pentamers in complex with histone oligomers. Our study provides a detailed structural and in vitro functional characterization of HDTs, revealing them to be nucleoplasmin family histone chaperones. The experimental confirmation that HDTs are nucleoplasmins may spark new interest in this enigmatic family of proteins.
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Affiliation(s)
- Ruchir C Bobde
- Institute of Life Sciences, Bhubaneswar, Odisha 751023, India
- Regional Centre for Biotechnology, Faridabad 121001, Haryana, India
| | - Ashish Kumar
- Institute of Life Sciences, Bhubaneswar, Odisha 751023, India
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5
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Singh AK, Saharan K, Baral S, Vasudevan D. The plant nucleoplasmin AtFKBP43 needs its extended arms for histone interaction. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194872. [PMID: 36058470 DOI: 10.1016/j.bbagrm.2022.194872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 08/20/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
The nucleoplasmin family of histone chaperones is a key player in governing the dynamic architecture of chromatin, thereby regulating various DNA-templated processes. The crystal structure of the N-terminal domain of Arabidopsis thaliana FKBP43 (AtFKBP43), an FK506-binding immunophilin protein, revealed a characteristic nucleoplasmin fold, thus confirming it to be a member of the FKBP nucleoplasmin class. Small-Angle X-ray Scattering (SAXS) analyses confirmed its pentameric nature in solution, and additional studies confirmed the nucleoplasmin fold to be highly stable. Unlike its homolog AtFKBP53, the AtFKBP43 nucleoplasmin core domain could not interact with histones and required the acidic arms, C-terminal to the core, for histone association. However, SAXS generated low-resolution envelope structure, ITC, and AUC results revealed that an AtFKBP43 pentamer with C-terminal extensions interacts with H2A/H2B dimer and H3/H4 tetramer in an equimolar ratio, like AtFKBP53. Put together, AtFKBP43 belongs to a hitherto unreported subclass of FKBP nucleoplasmins that requires the C-terminal acidic stretches emanating from the core domain for histone interaction.
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Affiliation(s)
| | - Ketul Saharan
- Institute of Life Sciences, Bhubaneswar 751023, India; Regional Centre for Biotechnology, Faridabad 121001, India
| | - Somanath Baral
- Institute of Life Sciences, Bhubaneswar 751023, India; School of Biotechnology, KIIT University, Bhubaneswar 751024, India
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6
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Wang X, Zhou Y, Guan J, Cheng Y, Lu Y, Wei Y. FKBP39 Controls the Larval Stage JH Activity and Development in Drosophila melanogaster. INSECTS 2022; 13:insects13040330. [PMID: 35447772 PMCID: PMC9030728 DOI: 10.3390/insects13040330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/18/2022] [Accepted: 03/25/2022] [Indexed: 12/10/2022]
Abstract
Simple Summary Two endocrine hormones, ecdysone and juvenile hormone (JH), control insect development and reproduction. Some studies in the literature have suggested that FKBP39 functions as a transcriptional factor and regulates the JH pathway in Drosophila. However, the physiological roles of FKBP39 are still elusive. To determine the FKBP39 roles in vivo, we first developed an antibody to check the FKBP39 expression pattern and then detected JH activity-related phenotypes in fkbp39 mutants, such as pupariation, reproduction, and Kr-h1 expression. We found that FKBP39 expresses at a high level and controls JH activity at the larval stage. Moreover, we found that rp49, the most widely used reference gene for Real-time quantitative PCR (qRT-PCR), significantly decreased in the fkbp39 mutant. This work will provide valuable information for studies on JH activity and insect development. Abstract FK506-binding protein 39kD (FKBP39) localizes in the nucleus and contains multiple functional domains. Structural analysis suggests that FKBP39 might function as a transcriptional factor and control juvenile hormone (JH) activity. Here, we show that FKBP39 expresses at a high level and localizes in the nucleolus of fat body cells during the first two larval stages and early third larval stage. The fkbp39 mutant displays delayed larval-pupal transition and an increased expression of Kr-h1, the main mediator of the JH pathway, at the early third larval stage. Moreover, the fkbp39 mutant has a fertility defect that is independent of JH activity. Interestingly, the expression of rp49, the most widely used reference gene for qRT-PCR in Drosophila, significantly decreased in the fkbp39 mutant, suggesting that FKBP39 might regulate ribosome assembly. Taken together, our data demonstrate the expression pattern and physiological roles of FKBP39 in Drosophila.
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Affiliation(s)
- Xinyu Wang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (X.W.); (Y.Z.); (J.G.); (Y.C.); (Y.L.)
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Ying Zhou
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (X.W.); (Y.Z.); (J.G.); (Y.C.); (Y.L.)
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Jianwen Guan
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (X.W.); (Y.Z.); (J.G.); (Y.C.); (Y.L.)
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Yang Cheng
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (X.W.); (Y.Z.); (J.G.); (Y.C.); (Y.L.)
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Yingying Lu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (X.W.); (Y.Z.); (J.G.); (Y.C.); (Y.L.)
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Youheng Wei
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (X.W.); (Y.Z.); (J.G.); (Y.C.); (Y.L.)
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
- Correspondence:
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7
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Tarczewska A, Wycisk K, Orłowski M, Waligórska A, Dobrucki J, Drewniak-Świtalska M, Berlicki Ł, Ożyhar A. Nuclear immunophilin FKBP39 from Drosophila melanogaster drives spontaneous liquid-liquid phase separation. Int J Biol Macromol 2020; 163:108-119. [PMID: 32615218 DOI: 10.1016/j.ijbiomac.2020.06.255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 11/27/2022]
Abstract
The FKBP39 from Drosophila melanogaster is a multifunctional regulatory immunophilin. It contains two globular domains linked by a highly charged disordered region. The N-terminal domain shows homology to the nucleoplasmin core domain, and the C-terminal domain is characteristic for the family of the FKBP immunophilin ligand binding domain. The specific partially disordered structure of the protein inspired us to investigate whether FKBP39 can drive spontaneous liquid-liquid phase separation (LLPS). Preliminary analyses using CatGranule and Pi-Pi contact predictors suggested a propensity for LLPS. Microscopy observations revealed that FKBP39 can self-concentrate to form liquid condensates. We also found that FKBP39 can lead to LLPS in the presence of RNA and peptides containing Arg-rich linear motifs derived from selected nuclear and nucleolar proteins. These heterotypic interactions have a stronger propensity for driving LLPS when compared to the interactions mediated by self-associating FKBP39 molecules. To investigate whether FKBP39 can drive LLPS in the cellular environment, we analysed it in fusion with YFP in COS-7 cells. The specific distribution and diffusion kinetics of FKBP39 examined by FRAP experiments provided evidence that immunophilin is an important driver of phase separation. The ability of FKBP39 to go into heterotypic interaction may be fundamental for ribosome subunits assembly.
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Affiliation(s)
- Aneta Tarczewska
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland.
| | - Krzysztof Wycisk
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Marek Orłowski
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Agnieszka Waligórska
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Jurek Dobrucki
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Magda Drewniak-Świtalska
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Andrzej Ożyhar
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
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8
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Singh AK, Datta A, Jobichen C, Luan S, Vasudevan D. AtFKBP53: a chimeric histone chaperone with functional nucleoplasmin and PPIase domains. Nucleic Acids Res 2020; 48:1531-1550. [PMID: 31807785 PMCID: PMC7026663 DOI: 10.1093/nar/gkz1153] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/20/2019] [Accepted: 12/02/2019] [Indexed: 12/23/2022] Open
Abstract
FKBP53 is one of the seven multi-domain FK506-binding proteins present in Arabidopsis thaliana, and it is known to get targeted to the nucleus. It has a conserved PPIase domain at the C-terminus and a highly charged N-terminal stretch, which has been reported to bind to histone H3 and perform the function of a histone chaperone. To better understand the molecular details of this PPIase with histone chaperoning activity, we have solved the crystal structures of its terminal domains and functionally characterized them. The C-terminal domain showed strong PPIase activity, no role in histone chaperoning and revealed a monomeric five-beta palm-like fold that wrapped over a helix, typical of an FK506-binding domain. The N-terminal domain had a pentameric nucleoplasmin-fold; making this the first report of a plant nucleoplasmin structure. Further characterization revealed the N-terminal nucleoplasmin domain to interact with H2A/H2B and H3/H4 histone oligomers, individually, as well as simultaneously, suggesting two different binding sites for H2A/H2B and H3/H4. The pentameric domain assists nucleosome assembly and forms a discrete complex with pre-formed nucleosomes; wherein two pentamers bind to a nucleosome.
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Affiliation(s)
- Ajit Kumar Singh
- Institute of Life Sciences, Nalco Square, Chandrasekharpur, Bhubaneswar 751023, India.,Manipal Academy of Higher Education, Manipal 576104, India
| | - Aritreyee Datta
- Institute of Life Sciences, Nalco Square, Chandrasekharpur, Bhubaneswar 751023, India
| | - Chacko Jobichen
- Department of Biological Sciences, 14 Science Drive 4, National University of Singapore, Singapore 117543
| | - Sheng Luan
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Dileep Vasudevan
- Institute of Life Sciences, Nalco Square, Chandrasekharpur, Bhubaneswar 751023, India
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9
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Stachowski TR, Snell ME, Snell EH. Structural insights into conformational switching in latency-associated peptide between transforming growth factor β-1 bound and unbound states. IUCRJ 2020; 7:238-252. [PMID: 32148852 PMCID: PMC7055372 DOI: 10.1107/s205225251901707x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 12/20/2019] [Indexed: 06/10/2023]
Abstract
Transforming growth factor β-1 (TGFβ-1) is a secreted signalling protein that directs many cellular processes and is an attractive target for the treatment of several diseases. The primary endogenous activity regulatory mechanism for TGFβ-1 is sequestration by its pro-peptide, latency-associated peptide (LAP), which sterically prohibits receptor binding by caging TGFβ-1. As such, recombinant LAP is promising as a protein-based therapeutic for modulating TGFβ-1 activity; however, the mechanism of binding is incompletely understood. Comparison of the crystal structure of unbound LAP (solved here to 3.5 Å resolution) with that of the bound complex shows that LAP is in a more open and extended conformation when unbound to TGFβ-1. Analysis suggests a mechanism of binding TGFβ-1 through a large-scale conformational change that includes contraction of the inter-monomer interface and caging by the 'straight-jacket' domain that may occur in partnership through a loop-to-helix transition in the core jelly-roll fold. This conformational change does not appear to include a repositioning of the integrin-binding motif as previously proposed. X-ray scattering-based modelling supports this mechanism and reveals possible orientations and ensembles in solution. Although native LAP is heavily glycosylated, solution scattering experiments show that the overall folding and flexibility of unbound LAP are not influenced by glycan modification. The combination of crystallography, solution scattering and biochemical experiments reported here provide insight into the mechanism of LAP sequestration of TGFβ-1 that is of fundamental importance for therapeutic development.
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Affiliation(s)
- Timothy R. Stachowski
- Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
- Cell Stress Biology, Roswell Park Comprehensive Cancer Center, 665 Elm Street, Buffalo, NY 14203, USA
| | - Mary E. Snell
- Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Edward H. Snell
- Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
- Materials Design and Innovation, State University of New York at Buffalo, 700 Ellicott Street, Buffalo, NY 14203, USA
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10
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Kumar A, Vasudevan D. Structure-function relationship of H2A-H2B specific plant histone chaperones. Cell Stress Chaperones 2020; 25:1-17. [PMID: 31707537 PMCID: PMC6985425 DOI: 10.1007/s12192-019-01050-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/15/2019] [Accepted: 10/28/2019] [Indexed: 10/25/2022] Open
Abstract
Studies on chromatin structure and function have gained a revived popularity. Histone chaperones are significant players in chromatin organization. They play a significant role in vital nuclear functions like transcription, DNA replication, DNA repair, DNA recombination, and epigenetic regulation, primarily by aiding processes such as histone shuttling and nucleosome assembly/disassembly. Like the other eukaryotes, plants also have a highly orchestrated and dynamic chromatin organization. Plants seem to have more isoforms within the same family of histone chaperones, as compared with other organisms. As some of these are specific to plants, they must have evolved to perform functions unique to plants. However, it appears that only little effort has gone into understanding the structural features of plant histone chaperones and their structure-function relationships. Studies on plant histone chaperones are essential for understanding their role in plant chromatin organization and how plants respond during stress conditions. This review is on the structural and functional aspects of plant histone chaperone families, specifically those which bind to H2A-H2B, viz nucleosome assembly protein (NAP), nucleoplasmin (NPM), and facilitates chromatin transcription (FACT). Here, we also present comparative analyses of these plant histone chaperones with available histone chaperone structures. The review hopes to incite interest among researchers to pursue further research in the area of plant chromatin and the associated histone chaperones.
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Affiliation(s)
- Ashish Kumar
- Institute of Life Sciences, Bhubaneswar, Odisha, 751023, India
- Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
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11
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Savic N, Shortill SP, Bilenky M, Dobbs JM, Dilworth D, Hirst M, Nelson CJ. Histone Chaperone Paralogs Have Redundant, Cooperative, and Divergent Functions in Yeast. Genetics 2019; 213:1301-1316. [PMID: 31604797 PMCID: PMC6893378 DOI: 10.1534/genetics.119.302235] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/03/2019] [Indexed: 01/03/2023] Open
Abstract
Gene duplications increase organismal robustness by providing freedom for gene divergence or by increasing gene dosage. The yeast histone chaperones Fpr3 and Fpr4 are paralogs that can assemble nucleosomes in vitro; however, the genomic locations they target and their functional relationship is poorly understood. We refined the yeast synthetic genetic array approach to enable the functional dissection of gene paralogs. Applying this method to Fpr3 and Fpr4 uncovered redundant, cooperative, and divergent functions. While Fpr3 is uniquely involved in chromosome segregation, Fpr3 and Fpr4 cooperate to regulate genes involved in polyphosphate metabolism and ribosome biogenesis. We find that the TRAMP5 RNA exosome is critical for fitness in Δfpr3Δfpr4 yeast and leverage this information to identify an important role for Fpr4 at the 5' ends of protein coding genes. Additionally, Fpr4 and TRAMP5 negatively regulate RNAs from the nontranscribed spacers of ribosomal DNA. Yeast lacking Fpr3 and Fpr4 exhibit a genome instability phenotype at the ribosomal DNA, which implies that these histone chaperones regulate chromatin structure and DNA access at this location. Taken together. we provide genetic and transcriptomic evidence that Fpr3 and Fpr4 operate separately, cooperatively, and redundantly to regulate a variety of chromatin environments.
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Affiliation(s)
- Neda Savic
- Department Biochemistry and Microbiology, University of Victoria, BC V8W 3P6, Canada
| | - Shawn P Shortill
- Department Biochemistry and Microbiology, University of Victoria, BC V8W 3P6, Canada
| | - Misha Bilenky
- BC Cancer Agency Genome Sciences Centre and the Department of Microbiology & Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Joseph M Dobbs
- Department Biochemistry and Microbiology, University of Victoria, BC V8W 3P6, Canada
| | - David Dilworth
- Department Biochemistry and Microbiology, University of Victoria, BC V8W 3P6, Canada
| | - Martin Hirst
- BC Cancer Agency Genome Sciences Centre and the Department of Microbiology & Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Christopher J Nelson
- Department Biochemistry and Microbiology, University of Victoria, BC V8W 3P6, Canada
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12
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Dilworth D, Gong F, Miller K, Nelson CJ. FKBP25 participates in DNA double-strand break repair. Biochem Cell Biol 2019; 98:42-49. [PMID: 30620620 PMCID: PMC7457334 DOI: 10.1139/bcb-2018-0328] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
FK506-binding proteins (FKBPs) alter the conformation of proteins via cis-trans isomerization of prolyl-peptide bonds. While this activity can be demonstrated in vitro, the intractability of detecting prolyl isomerization events in cells has limited our understanding of the biological processes regulated by FKBPs. Here we report that FKBP25 is an active participant in the repair of DNA double-strand breaks (DSBs). FKBP25 influences DSB repair pathway choice by promoting homologous recombination (HR) and suppressing single-strand annealing (SSA). Consistent with this observation, cells depleted of FKBP25 form fewer Rad51 repair foci in response to etoposide and ionizing radiation, and they are reliant on the SSA repair factor Rad52 for viability. We find that FKBP25’s catalytic activity is required for promoting DNA repair, which is the first description of a biological function for this enzyme activity. Consistent with the importance of the FKBP catalytic site in HR, rapamycin treatment also impairs homologous recombination, and this effect is at least in part independent of mTor. Taken together these results identify FKBP25 as a component of the DNA DSB repair pathway.
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Affiliation(s)
- David Dilworth
- The Department of Biochemistry & Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada
| | - Fade Gong
- Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, 2506 Speedway Stop A5000, Austin, TX 78712 USA
| | - Kyle Miller
- Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, 2506 Speedway Stop A5000, Austin, TX 78712 USA
| | - Christopher J Nelson
- The Department of Biochemistry & Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada
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13
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Chu J, Chen Z. Molecular identification of histone acetyltransferases and deacetylases in lower plant Marchantia polymorpha. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 132:612-622. [PMID: 30336381 DOI: 10.1016/j.plaphy.2018.10.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 09/18/2018] [Accepted: 10/10/2018] [Indexed: 06/08/2023]
Abstract
Histone is the core component of nucleosome and modification of amino acid residues on histone tails is one of the most pivotal epigenetic regulatory mechanisms. Histone acetylation or deacetylation is carried out by two groups of proteins: histone acetyltransferases (HATs) or histone deacetylases (HDACs), and has been proven to be tightly linked to regulation of gene expression in animals and vascular plants. The biological functions of HATs and HDACs in non-flowering plants remain largely unknown. We found that there are seven MpHAT genes and twelve MpHDAC genes present in the Marchantia genome, and the comprehensive protein sequence analysis of the HAT and HDAC families was introduced to investigate their potential functions. On the basis of the functional domain analysis, eight MpHATs and twelve MpHDACs contain the conserved functional domains as the defining feature of each family. Phylogenetic trees of all families of MpHATs and MpHDACs along with their homologs from different plant and green algae species were constructed to illustrate evolutionary relationship of HAT and HDAC proteins. We found both SIR2 family and RPD3/HDA1 superfamily possess lower plant-specific proteins indicating the potential unknown functions of HATs and HDACs in Marchantia and other lower plant or algae species. Subcellular localization prediction suggests that MpHATs and MpHDACs are likely functioning in various organelles. Expression analysis shows that all MpHAT and MpHDAC genes are expressed in all tissues with differences at the transcriptional level. In addition, their expression patterns were altered in response to various treatments with plant hormones and environmental stress. We concluded that all MpHATs and MpHDACs are functional proteins in Marchantia and involved in various signaling pathways. Marchantia could have developed a complex histone acetylation epigenetic mechanism to regulate growth and development, as well as responses to environment.
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Affiliation(s)
- Jiashu Chu
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, 1 Nanyang Walk, Singapore, 637616, Singapore
| | - Zhong Chen
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, 1 Nanyang Walk, Singapore, 637616, Singapore.
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14
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Orłowski M, Popławska K, Pieprzyk J, Szczygieł-Sommer A, Więch A, Zarębski M, Tarczewska A, Dobrucki J, Ożyhar A. Molecular determinants of Drosophila immunophilin FKBP39 nuclear localization. Biol Chem 2018; 399:467-484. [PMID: 29337690 DOI: 10.1515/hsz-2017-0251] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 01/04/2018] [Indexed: 12/27/2022]
Abstract
FK506-binding proteins (FKBPs) belong to a distinct class of immunophilins that interact with immunosuppressants. They use their peptidyl-prolyl isomerase (PPIase) activity to catalyze the cis-trans conversion of prolyl bonds in proteins during protein-folding events. FKBPs also act as a unique group of chaperones. The Drosophila melanogaster peptidyl-prolyl cis-trans isomerase FK506-binding protein of 39 kDa (FKBP39) is thought to act as a transcriptional modulator of gene expression in 20-hydroxyecdysone and juvenile hormone signal transduction. The aim of this study was to analyze the molecular determinants responsible for the subcellular distribution of an FKBP39-yellow fluorescent protein (YFP) fusion construct (YFP-FKBP39). We found that YFP-FKBP39 was predominantly nucleolar. To identify the nuclear localization signal (NLS), a series of YFP-tagged FKBP39 deletion mutants were prepared and examined in vivo. The identified NLS signal is located in a basic domain. Detailed mutagenesis studies revealed that residues K188 and K191 are crucial for the nuclear targeting of FKBP39 and its nucleoplasmin-like (NPL) domain contains the sequence that controls the nucleolar-specific translocation of the protein. These results show that FKBP39 possesses a specific NLS in close proximity to a putative helix-turn-helix (HTH) motif and FKBP39 may bind DNA in vivo and in vitro.
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Affiliation(s)
- Marek Orłowski
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Katarzyna Popławska
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Joanna Pieprzyk
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Aleksandra Szczygieł-Sommer
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Anna Więch
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Mirosław Zarębski
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Aneta Tarczewska
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Jurek Dobrucki
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Andrzej Ożyhar
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
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15
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Ghartey-Kwansah G, Li Z, Feng R, Wang L, Zhou X, Chen FZ, Xu MM, Jones O, Mu Y, Chen S, Bryant J, Isaacs WB, Ma J, Xu X. Comparative analysis of FKBP family protein: evaluation, structure, and function in mammals and Drosophila melanogaster. BMC DEVELOPMENTAL BIOLOGY 2018; 18:7. [PMID: 29587629 PMCID: PMC5870485 DOI: 10.1186/s12861-018-0167-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 03/12/2018] [Indexed: 12/19/2022]
Abstract
Background FK506-binding proteins (FKBPs) have become the subject of considerable interest in several fields, leading to the identification of several cellular and molecular pathways in which FKBPs impact prenatal development and pathogenesis of many human diseases. Main body This analysis revealed differences between how mammalian and Drosophila FKBPs mechanisms function in relation to the immunosuppressant drugs, FK506 and rapamycin. Differences that could be used to design insect-specific pesticides. (1) Molecular phylogenetic analysis of FKBP family proteins revealed that the eight known Drosophila FKBPs share homology with the human FKBP12. This indicates a close evolutionary relationship, and possible origination from a common ancestor. (2) The known FKBPs contain FK domains, that is, a prolyl cis/trans isomerase (PPIase) domain that mediates immune suppression through inhibition of calcineurin. The dFKBP59, CG4735/Shutdown, CG1847, and CG5482 have a Tetratricopeptide receptor domain at the C-terminus, which regulates transcription and protein transportation. (3) FKBP51 and FKBP52 (dFKBP59), along with Cyclophilin 40 and protein phosphatase 5, function as Hsp90 immunophilin co-chaperones within steroid receptor-Hsp90 heterocomplexes. These immunophilins are potential drug targets in pathways associated with normal physiology and may be used to treat a variety of steroid-based diseases by targeting exocytic/endocytic cycling and vesicular trafficking. (4) By associating with presinilin, a critical component of the Notch signaling pathway, FKBP14 is a downstream effector of Notch activation at the membrane. Meanwhile, Shutdown associates with transposons in the PIWI-interacting RNA pathway, playing a crucial role in both germ cells and ovarian somas. Mutations in or silencing of dFKBPs lead to early embryonic lethality in Drosophila. Therefore, further understanding the mechanisms of FK506 and rapamycin binding to immunophilin FKBPs in endocrine, cardiovascular, and neurological function in both mammals and Drosophila would provide prospects in generating unique, insect specific therapeutics targeting the above cellular signaling pathways. Conclusion This review will evaluate the functional roles of FKBP family proteins, and systematically summarize the similarities and differences between FKBP proteins in Drosophila and Mammals. Specific therapeutics targeting cellular signaling pathways will also be discussed.
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Affiliation(s)
- George Ghartey-Kwansah
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Xi'an, 710062, China.,Laboratory of Cell Biology, Genetics and Developmental Biology, Shaanxi Normal University College of Life Sciences, Xi'an, 710062, China
| | - Zhongguang Li
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Xi'an, 710062, China.,Laboratory of Cell Biology, Genetics and Developmental Biology, Shaanxi Normal University College of Life Sciences, Xi'an, 710062, China
| | - Rui Feng
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Xi'an, 710062, China.,Laboratory of Cell Biology, Genetics and Developmental Biology, Shaanxi Normal University College of Life Sciences, Xi'an, 710062, China
| | - Liyang Wang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Xi'an, 710062, China.,Laboratory of Cell Biology, Genetics and Developmental Biology, Shaanxi Normal University College of Life Sciences, Xi'an, 710062, China
| | - Xin Zhou
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Xi'an, 710062, China.,Laboratory of Cell Biology, Genetics and Developmental Biology, Shaanxi Normal University College of Life Sciences, Xi'an, 710062, China.,Ohio State University College of Medicine, Columbus, OH, USA
| | | | - Meng Meng Xu
- Department of Pharmacology, Duke University Medical Center, Durham, NC, USA
| | - Odell Jones
- University of Maryland School of Medicine, Baltimore, MD, USA
| | - Yulian Mu
- State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | | | - Joseph Bryant
- University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Jianjie Ma
- Ohio State University College of Medicine, Columbus, OH, USA
| | - Xuehong Xu
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Xi'an, 710062, China. .,Laboratory of Cell Biology, Genetics and Developmental Biology, Shaanxi Normal University College of Life Sciences, Xi'an, 710062, China.
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16
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Moulin M, Strohmeier GA, Hirz M, Thompson KC, Rennie AR, Campbell RA, Pichler H, Maric S, Forsyth VT, Haertlein M. Perdeuteration of cholesterol for neutron scattering applications using recombinant Pichia pastoris. Chem Phys Lipids 2018; 212:80-87. [PMID: 29357283 DOI: 10.1016/j.chemphyslip.2018.01.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 12/20/2017] [Accepted: 01/15/2018] [Indexed: 02/08/2023]
Abstract
Deuteration of biomolecules has a major impact on both quality and scope of neutron scattering experiments. Cholesterol is a major component of mammalian cells, where it plays a critical role in membrane permeability, rigidity and dynamics, and contributes to specific membrane structures such as lipid rafts. Cholesterol is the main cargo in low and high-density lipoprotein complexes (i.e. LDL, HDL) and is directly implicated in several pathogenic conditions such as coronary artery disease which leads to 17 million deaths annually. Neutron scattering studies on membranes or lipid-protein complexes exploiting contrast variation have been limited by the lack of availability of fully deuterated biomolecules and especially perdeuterated cholesterol. The availability of perdeuterated cholesterol provides a unique way of probing the structural and dynamical properties of the lipoprotein complexes that underly many of these disease conditions. Here we describe a procedure for in vivo production of perdeuterated recombinant cholesterol in lipid-engineered Pichia pastoris using flask and fed-batch fermenter cultures in deuterated minimal medium. Perdeuteration of the purified cholesterol was verified by mass spectrometry and its use in a neutron scattering study was demonstrated by neutron reflectometry measurements using the FIGARO instrument at the ILL.
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Affiliation(s)
- Martine Moulin
- Institut Laue-Langevin, 71, Avenue des Martyrs, Grenoble 38042, France; Faculty of Natural Sciences, Keele University, Keele, Staffordshire ST5 5BG, United Kingdom
| | - Gernot A Strohmeier
- acib, Austrian Centre of Industrial Biotechnology GmbH, 8010 Graz, Austria; Institute of Organic Chemistry, NAWI Graz, Graz University of Technology, 8010 Graz, Austria
| | - Melanie Hirz
- Institute of Molecular Biotechnology, NAWI Graz, BioTechMed Graz, Graz University of Technology, 8010 Graz, Austria
| | - Katherine C Thompson
- Department of Biological Sciences and Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London WC1E 7HX, United Kingdom
| | - Adrian R Rennie
- Centre for Neutron Scattering, Uppsala University, 751 20 Uppsala, Sweden
| | | | - Harald Pichler
- acib, Austrian Centre of Industrial Biotechnology GmbH, 8010 Graz, Austria; Institute of Molecular Biotechnology, NAWI Graz, BioTechMed Graz, Graz University of Technology, 8010 Graz, Austria
| | - Selma Maric
- Biofilms - Research Centre for Biointerfaces and Biomedical Science Department, Faculty of Health and Society, Malmö University, Malmö 20506, Sweden
| | - V Trevor Forsyth
- Institut Laue-Langevin, 71, Avenue des Martyrs, Grenoble 38042, France; Faculty of Natural Sciences, Keele University, Keele, Staffordshire ST5 5BG, United Kingdom
| | - Michael Haertlein
- Institut Laue-Langevin, 71, Avenue des Martyrs, Grenoble 38042, France.
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17
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Chen X, Lu L, Qian S, Scalf M, Smith LM, Zhong X. Canonical and Noncanonical Actions of Arabidopsis Histone Deacetylases in Ribosomal RNA Processing. THE PLANT CELL 2018; 30:134-152. [PMID: 29343504 PMCID: PMC5810568 DOI: 10.1105/tpc.17.00626] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 12/11/2017] [Accepted: 01/12/2018] [Indexed: 05/13/2023]
Abstract
Ribosome biogenesis is a fundamental process required for all cellular activities. Histone deacetylases play critical roles in many biological processes including transcriptional repression and rDNA silencing. However, their function in pre-rRNA processing remains poorly understood. Here, we discovered a previously uncharacterized role of Arabidopsis thaliana histone deacetylase HD2C in pre-rRNA processing via both canonical and noncanonical manners. HD2C interacts with another histone deacetylase HD2B and forms homo- and/or hetero-oligomers in the nucleolus. Depletion of HD2C and HD2B induces a ribosome-biogenesis deficient phenotype and aberrant accumulation of 18S pre-rRNA intermediates. Our genome-wide analysis revealed that HD2C binds and represses the expression of key genes involved in ribosome biogenesis. Using RNA immunoprecipitation and sequencing, we further uncovered a noncanonical mechanism of HD2C directly associating with pre-rRNA and small nucleolar RNAs to regulate rRNA methylation. Together, this study reveals a multifaceted role of HD2C in ribosome biogenesis and provides mechanistic insights into how histone deacetylases modulate rRNA maturation at the transcriptional and posttranscriptional levels.
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Affiliation(s)
- Xiangsong Chen
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Li Lu
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Shuiming Qian
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Xuehua Zhong
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53706
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18
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Abstract
The nucleoplasmin family of histone chaperones is identified by a pentamer-forming domain and multiple acidic tracts that mediate histone binding and chaperone activity. Within this family, a novel domain organization was recently discovered that consists of an N-terminal nucleoplasmin-like (NPL) domain and a C-terminal FKBP peptidyl-proline isomerase domain. Saccharomyces cerevisiae Fpr4 is one such protein. Here we report that in addition to its known histone prolyl isomerase activities, the Fpr4 FKBP domain binds to nucleosomes and nucleosome arrays in vitro. This ability is mediated by a collection of basic patches that enable the enzyme to stably associate with linker DNA. The interaction of the Fpr4 FKBP with recombinant chromatin complexes condenses nucleosome arrays independently of its catalytic activity. Based on phylogenetic comparisons we propose that the chromatin binding ability of ‘basic’ FKBPs is shared amongst related orthologues present in fungi, plants, and insects. Thus, a subclass of FKBP prolyl isomerase enzymes is recruited to linker regions of chromatin.
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19
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Warren C, Shechter D. Fly Fishing for Histones: Catch and Release by Histone Chaperone Intrinsically Disordered Regions and Acidic Stretches. J Mol Biol 2017; 429:2401-2426. [PMID: 28610839 DOI: 10.1016/j.jmb.2017.06.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 06/05/2017] [Accepted: 06/06/2017] [Indexed: 01/21/2023]
Abstract
Chromatin is the complex of eukaryotic DNA and proteins required for the efficient compaction of the nearly 2-meter-long human genome into a roughly 10-micron-diameter cell nucleus. The fundamental repeating unit of chromatin is the nucleosome: 147bp of DNA wrapped about an octamer of histone proteins. Nucleosomes are stable enough to organize the genome yet must be dynamically displaced and reassembled to allow access to the underlying DNA for transcription, replication, and DNA damage repair. Histone chaperones are a non-catalytic group of proteins that are central to the processes of nucleosome assembly and disassembly and thus the fluidity of the ever-changing chromatin landscape. Histone chaperones are responsible for binding the highly basic histone proteins, shielding them from non-specific interactions, facilitating their deposition onto DNA, and aiding in their eviction from DNA. Although most histone chaperones perform these common functions, recent structural studies of many different histone chaperones reveal that there are few commonalities in their folds. Importantly, sequence-based predictions show that histone chaperones are highly enriched in intrinsically disordered regions (IDRs) and acidic stretches. In this review, we focus on the molecular mechanisms underpinning histone binding, selectivity, and regulation of these highly dynamic protein regions. We highlight new evidence suggesting that IDRs are often critical for histone chaperone function and play key roles in chromatin assembly and disassembly pathways.
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Affiliation(s)
- Christopher Warren
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - David Shechter
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA.
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20
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Reddy BA, Jeronimo C, Robert F. Recent Perspectives on the Roles of Histone Chaperones in Transcription Regulation. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/s40610-017-0049-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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21
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Nucleoplasmin-like domain of FKBP39 from Drosophila melanogaster forms a tetramer with partly disordered tentacle-like C-terminal segments. Sci Rep 2017; 7:40405. [PMID: 28074868 PMCID: PMC5225439 DOI: 10.1038/srep40405] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 12/06/2016] [Indexed: 11/22/2022] Open
Abstract
Nucleoplasmins are a nuclear chaperone family defined by the presence of a highly conserved N-terminal core domain. X-ray crystallographic studies of isolated nucleoplasmin core domains revealed a β-propeller structure consisting of a set of five monomers that together form a stable pentamer. Recent studies on isolated N-terminal domains from Drosophila 39-kDa FK506-binding protein (FKBP39) and from other chromatin-associated proteins showed analogous, nucleoplasmin-like (NPL) pentameric structures. Here, we report that the NPL domain of the full-length FKBP39 does not form pentameric complexes. Multi-angle light scattering (MALS) and sedimentation equilibrium ultracentrifugation (SE AUC) analyses of the molecular mass of the full-length protein indicated that FKBP39 forms homotetrameric complexes. Molecular models reconstructed from small-angle X-ray scattering (SAXS) revealed that the NPL domain forms a stable, tetrameric core and that FK506-binding domains are linked to it by intrinsically disordered, flexible chains that form tentacle-like segments. Analyses of full-length FKBP39 and its isolated NPL domain suggested that the distal regions of the polypeptide chain influence and determine the quaternary conformation of the nucleoplasmin-like protein. These results provide new insights regarding the conserved structure of nucleoplasmin core domains and provide a potential explanation for the importance of the tetrameric structural organization of full-length nucleoplasmins.
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22
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Bourque S, Jeandroz S, Grandperret V, Lehotai N, Aimé S, Soltis DE, Miles NW, Melkonian M, Deyholos MK, Leebens-Mack JH, Chase MW, Rothfels CJ, Stevenson DW, Graham SW, Wang X, Wu S, Pires JC, Edger PP, Yan Z, Xie Y, Carpenter EJ, Wong GKS, Wendehenne D, Nicolas-Francès V. The Evolution of HD2 Proteins in Green Plants. TRENDS IN PLANT SCIENCE 2016; 21:1008-1016. [PMID: 27789157 DOI: 10.1016/j.tplants.2016.10.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 09/28/2016] [Accepted: 10/04/2016] [Indexed: 05/18/2023]
Abstract
In eukaryotes, protein deacetylation is carried out by two well-conserved histone deacetylase (HDAC) families: RPD3/HDA1 and SIR2. Intriguingly, model plants such as Arabidopsis express an additional plant-specific HDAC family, termed type-2 HDACs (HD2s). Transcriptomic analyses from more than 1300 green plants generated by the 1000 plants (1KP) consortium showed that HD2s appeared early in green plant evolution, the first members being detected in several streptophyte green alga. The HD2 family has expanded via several rounds of successive duplication; members are expressed in all major green plant clades. Interestingly, angiosperm species express new HD2 genes devoid of a zinc-finger domain, one of the main structural features of HD2s. These variants may have been associated with the origin and/or the biology of the ovule/seed.
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Affiliation(s)
- S Bourque
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, 21000 Dijon, France.
| | - S Jeandroz
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, 21000 Dijon, France
| | - V Grandperret
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, 21000 Dijon, France
| | - N Lehotai
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, 21000 Dijon, France
| | - S Aimé
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, 21000 Dijon, France
| | - D E Soltis
- Department of Biology, Florida Museum of Natural History, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - N W Miles
- Department of Biological Sciences, University of North Texas, 1155 Union Circle, Denton, TX 76201, USA
| | - M Melkonian
- Botanical Institute, Cologne Biocenter, University of Cologne, 50674 Cologne, Germany
| | - M K Deyholos
- Department of Biology, University of British Columbia, Kelowna, BC V1V 1V7, Canada
| | - J H Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - M W Chase
- Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, Surrey, UK; Plant Biology, University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Western Australia
| | - C J Rothfels
- University Herbarium and Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - D W Stevenson
- New York Botanical Garden, 2900 Southern Boulevard, Bronx, NY 10458, USA
| | - S W Graham
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - X Wang
- Chinese Academy of Sciences (CAS) Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, CAS, 1-104 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - S Wu
- Chinese Academy of Sciences (CAS) Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, CAS, 1-104 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - J C Pires
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - P P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI 48823, USA
| | - Z Yan
- Beijing Genomics Institute (BGI)-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Y Xie
- Beijing Genomics Institute (BGI)-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - E J Carpenter
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - G K S Wong
- Beijing Genomics Institute (BGI)-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China; Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada; Department of Medicine, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - D Wendehenne
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, 21000 Dijon, France
| | - V Nicolas-Francès
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, 21000 Dijon, France
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Scott DD, Oeffinger M. Nucleolin and nucleophosmin: nucleolar proteins with multiple functions in DNA repair. Biochem Cell Biol 2016; 94:419-432. [PMID: 27673355 DOI: 10.1139/bcb-2016-0068] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The nucleolus represents a highly multifunctional intranuclear organelle in which, in addition to the canonical ribosome assembly, numerous processes such as transcription, DNA repair and replication, the cell cycle, and apoptosis are coordinated. The nucleolus is further a key hub in the sensing of cellular stress and undergoes major structural and compositional changes in response to cellular perturbations. Numerous nucleolar proteins have been identified that, upon sensing nucleolar stress, deploy additional, non-ribosomal roles in the regulation of varied cell processes including cell cycle arrest, arrest of DNA replication, induction of DNA repair, and apoptosis, among others. The highly abundant proteins nucleophosmin (NPM1) and nucleolin (NCL) are two such factors that transit to the nucleoplasm in response to stress, and participate directly in the repair of numerous different DNA damages. This review discusses the contributions made by NCL and (or) NPM1 to the different DNA repair pathways employed by mammalian cells to repair DNA insults, and examines the implications of such activities for the regulation, pathogenesis, and therapeutic targeting of NPM1 and NCL.
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Affiliation(s)
- Daniel D Scott
- a Laboratory of RNP Biochemistry, Institut de recherches cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
- b Division of Experimental Medicine, Faculty of Medicine, McGill University, Montréal, QC H3A 2A3, Canada
| | - Marlene Oeffinger
- a Laboratory of RNP Biochemistry, Institut de recherches cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
- b Division of Experimental Medicine, Faculty of Medicine, McGill University, Montréal, QC H3A 2A3, Canada
- c Département de biochimie et médecine moléculaire, Faculté de Médecine, Université de Montréal, QC H3T 1J4, Canada
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Swenson JM, Colmenares SU, Strom AR, Costes SV, Karpen GH. The composition and organization of Drosophila heterochromatin are heterogeneous and dynamic. eLife 2016; 5. [PMID: 27514026 PMCID: PMC4981497 DOI: 10.7554/elife.16096] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 07/06/2016] [Indexed: 12/13/2022] Open
Abstract
Heterochromatin is enriched for specific epigenetic factors including Heterochromatin Protein 1a (HP1a), and is essential for many organismal functions. To elucidate heterochromatin organization and regulation, we purified Drosophila melanogaster HP1a interactors, and performed a genome-wide RNAi screen to identify genes that impact HP1a levels or localization. The majority of the over four hundred putative HP1a interactors and regulators identified were previously unknown. We found that 13 of 16 tested candidates (83%) are required for gene silencing, providing a substantial increase in the number of identified components that impact heterochromatin properties. Surprisingly, image analysis revealed that although some HP1a interactors and regulators are broadly distributed within the heterochromatin domain, most localize to discrete subdomains that display dynamic localization patterns during the cell cycle. We conclude that heterochromatin composition and architecture is more spatially complex and dynamic than previously suggested, and propose that a network of subdomains regulates diverse heterochromatin functions.
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Affiliation(s)
- Joel M Swenson
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Serafin U Colmenares
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Amy R Strom
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Sylvain V Costes
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Gary H Karpen
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
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25
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Haertlein M, Moulin M, Devos JM, Laux V, Dunne O, Trevor Forsyth V. Biomolecular Deuteration for Neutron Structural Biology and Dynamics. Methods Enzymol 2016; 566:113-57. [DOI: 10.1016/bs.mie.2015.11.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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