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Zhao D, Fang Y, Wei Z, Duan W, Chen Y, Zhou X, Xiao C, Chen W. Proteomics reveals the mechanism of protein degradation and its relationship to sensorial and texture characteristics in dry-cured squid during processing. Food Chem X 2024; 22:101409. [PMID: 38711776 PMCID: PMC11070823 DOI: 10.1016/j.fochx.2024.101409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/27/2024] [Accepted: 04/21/2024] [Indexed: 05/08/2024] Open
Abstract
Proteolysis in dry-cured squid contributes to the development of sensory and textural attributes. In this study, label-free quantitative proteomics was conducted to study the mechanism of proteolysis and its correlation with quality changes. The results showed that the protein profile of dry-cured squid changed markedly during processing, which was confirmed by the quantification of myofibrillar protein, amino nitrogen and total free acids, and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis. Thirty-two key differentially abundant proteins were found to be correlated with sensory and texture characteristics, including myofibrillar protein, tubulin beta chain, collagens, heat shock proteins and cytochrome c. The correlation analysis indicated that myosin regulatory light chain and tubulin beta chain played the most important role in the development of texture and sensory attributes in squid samples during the dry-curing process. The results offered novel insights into proteolysis in dry-cured squid and its relationship to quality changes.
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Affiliation(s)
- Dandan Zhao
- Ecology and Health Institute, Hangzhou Vocational & Technical Collge, Hangzhou, China
- Food Science Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yizhou Fang
- College of Life Sciences, China Jiliang University, Hangzhou 322002, China
| | - Zhengxun Wei
- Ecology and Health Institute, Hangzhou Vocational & Technical Collge, Hangzhou, China
| | - Wenkai Duan
- Ecology and Health Institute, Hangzhou Vocational & Technical Collge, Hangzhou, China
| | - Yu Chen
- Ecology and Health Institute, Hangzhou Vocational & Technical Collge, Hangzhou, China
| | - Xuxia Zhou
- College of Food Science and Technology, Zhejiang University of Technology, Huzhou 313299, China
| | - Chaogeng Xiao
- Food Science Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Wenxuan Chen
- Food Science Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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Taheri A, Wang Z, Singal B, Guo F, Al-Bassam J. Cryo-EM structures of the tubulin cofactors reveal the molecular basis for the biogenesis of alpha/beta-tubulin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.577855. [PMID: 38405852 PMCID: PMC10889022 DOI: 10.1101/2024.01.29.577855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Microtubule polarity and dynamic polymerization originate from the self-association properties of the a-tubulin heterodimer. For decades, it has remained poorly understood how the tubulin cofactors, TBCD, TBCE, TBCC, and the Arl2 GTPase mediate a-tubulin biogenesis from α- and β-tubulins. Here, we use cryogenic electron microscopy to determine structures of tubulin cofactors bound to αβ-tubulin. These structures show that TBCD, TBCE, and Arl2 form a heterotrimeric cage-like TBC-DEG assembly around the a-tubulin heterodimer. TBCD wraps around Arl2 and almost entirely encircles -tubulin, while TBCE forms a lever arm that anchors along the other end of TBCD and rotates α-tubulin. Structures of the TBC-DEG-αβ-tubulin assemblies bound to TBCC reveal the clockwise rotation of the TBCE lever that twists a-tubulin by pulling its C-terminal tail while TBCD holds -tubulin in place. Altogether, these structures uncover transition states in αβ-tubulin biogenesis, suggesting a vise-like mechanism for the GTP-hydrolysis dependent a-tubulin biogenesis mediated by TBC-DEG and TBCC. These structures provide the first evidence of the critical functions of the tubulin cofactors as enzymes that regulate the invariant organization of αβ-tubulin, by catalyzing α- and β-tubulin assembly, disassembly, and subunit exchange which are crucial for regulating the polymerization capacities of αβ-tubulins into microtubules.
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Xu D, Mao L, Deng S, Xie J, Luo H. Tandem Mass Tag Proteomics Provides Insights into the Underlying Mechanism of Flesh Quality Degradation of Litopenaeus vannamei during Refrigerated Waterless Transport at 12 °C. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:20304-20313. [PMID: 38054284 DOI: 10.1021/acs.jafc.3c07146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Refrigerated waterless transport at 12 °C of live shrimp (Litopenaeus vannamei) causes flesh quality deterioration, and the underlying mechanism remains unknown. Herein, proteomics and bioinformatics analyses were used to elucidate the molecular mechanism of flesh quality changes. The result showed that 33 and 44 of the differentially abundant proteins (DAPs) were, respectively, identified in the acute cold (AC) group and the combined stress of acute cold and waterless duration (AC+WD) group, which were mostly involved in the metabolism processes and cellular structure of animal tissues, and notably enriched in biological pathways such as lysosome, glycolysis/gluconeogenesis, and focal adhesion. Furthermore, the changes in color and texture properties were closely associated with tubulin, gelsolin, laminin, trypsin-1, dipeptidyl peptidase, triosephosphate isomerase, and aldehyde dehydrogenase. Therefore, these DAPs could be used as potential biomarkers to monitor the deterioration of shrimp flesh quality during refrigerated waterless transportation.
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Affiliation(s)
- Defeng Xu
- Institute of Marine Medicine, Guangdong Medical University, Zhanjiang 524000, China
| | - Linchun Mao
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Shanggui Deng
- College of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China
| | - Jing Xie
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Hui Luo
- Institute of Marine Medicine, Guangdong Medical University, Zhanjiang 524000, China
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Xia X, Zhao S, Chen W, Xu C, Zhao D. CCT6A promotes esophageal squamous cell carcinoma cell proliferation, invasion and epithelial-mesenchymal transition by activating TGF-β/Smad/c-Myc pathway. Ir J Med Sci 2023; 192:2653-2660. [PMID: 37017854 DOI: 10.1007/s11845-023-03357-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/28/2023] [Indexed: 04/06/2023]
Abstract
OBJECTIVE Chaperonin-containing TCP1 subunit 6A (CCT6A) facilitates several malignant cancer behaviors, but its regulation of esophageal squamous cell carcinoma (ESCC) has not been reported. This study aimed to investigate the effect of CCT6A on cell proliferation, apoptosis, invasion and epithelial-mesenchymal transition (EMT) and its interaction with the TGF-β/Smad/c-Myc pathway in ESCC. METHODS CCT6A expression was detected in ESCC and normal esophageal epithelial cell lines by RT‒qPCR and western blotting. Furthermore, CCT6A siRNA, negative control (NC) siRNA, CCT6A encoding plasmid and NC encoding plasmid were transfected into OE21 and TE-1 cells. Subsequently, CCT6A siRNA- and NC siRNA-transfected cells were treated with TGF-β for rescue experiments. Cell proliferation, apoptosis, invasion, and E-cadherin/N-cadherin and p-Smad2/p-Smad3/c-Myc expression were detected. RESULTS CCT6A expression was increased in KYSE-180, TE-1, TE-4 and OE21 cells compared with HET-1A cells. In both OE21 and TE-1 cells, CCT6A knockdown inhibited cell proliferation, invasion and N-cadherin expression while promoting cell apoptosis and E-cadherin expression; meanwhile, CCT6A overexpression had the opposite effects. Furthermore, in both OE21 and TE-1 cells, CCT6A knockdown decreased p-Smad2/Smad2, p-Smad3/Smad3 and c-Myc/GAPDH expression; CCT6A overexpression had the opposite effects. Next, TGF-β facilitated cell proliferation, invasion, and N-cadherin, p-Smad2/Smad2, p-Smad3/Smad2 and c-Myc/GAPDH expression while repressing cell apoptosis and E-cadherin expression in OE21 and TE-1 cells; importantly, TGF-β could compensate for the regulation of CCT6A knockdown on these activities. CONCLUSION CCT6A facilitates ESCC malignant activities by activating the TGF-β/Smad/c-Myc pathway, which sheds light on the identification of a possible therapeutic target in the management of ESCC.
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Affiliation(s)
- Xiuli Xia
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China
- Department of Gastroenterology, Handan Central Hospital, Handan, 056001, China
| | - Shushan Zhao
- Department of Gastroenterology, Handan Central Hospital, Handan, 056001, China
| | - Wenting Chen
- Department of Endoscopy Center, The First Affiliated Hospital of Hebei North University, Zhangjiakou, 075000, China
| | - Chao Xu
- Department of Gastroenterology, Handan Central Hospital, Handan, 056001, China
| | - Dongqiang Zhao
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China.
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Li M, Peng D, Cao H, Yang X, Li S, Qiu HJ, Li LF. The Host Cytoskeleton Functions as a Pleiotropic Scaffold: Orchestrating Regulation of the Viral Life Cycle and Mediating Host Antiviral Innate Immune Responses. Viruses 2023; 15:1354. [PMID: 37376653 PMCID: PMC10301361 DOI: 10.3390/v15061354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Viruses are obligate intracellular parasites that critically depend on their hosts to initiate infection, complete replication cycles, and generate new progeny virions. To achieve these goals, viruses have evolved numerous elegant strategies to subvert and utilize different cellular machinery. The cytoskeleton is often one of the first components to be hijacked as it provides a convenient transport system for viruses to enter the cell and reach the site of replication. The cytoskeleton is an intricate network involved in controlling the cell shape, cargo transport, signal transduction, and cell division. The host cytoskeleton has complex interactions with viruses during the viral life cycle, as well as cell-to-cell transmission once the life cycle is completed. Additionally, the host also develops unique, cytoskeleton-mediated antiviral innate immune responses. These processes are also involved in pathological damages, although the comprehensive mechanisms remain elusive. In this review, we briefly summarize the functions of some prominent viruses in inducing or hijacking cytoskeletal structures and the related antiviral responses in order to provide new insights into the crosstalk between the cytoskeleton and viruses, which may contribute to the design of novel antivirals targeting the cytoskeleton.
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Affiliation(s)
| | | | | | | | | | - Hua-Ji Qiu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Lian-Feng Li
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
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Han W, Jin M, Liu C, Zhao Q, Wang S, Wang Y, Yin Y, Peng C, Wang Y, Cong Y. Structural basis of plp2-mediated cytoskeletal protein folding by TRiC/CCT. SCIENCE ADVANCES 2023; 9:eade1207. [PMID: 36921056 PMCID: PMC10017041 DOI: 10.1126/sciadv.ade1207] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
The cytoskeletal proteins tubulin and actin are the obligate substrates of TCP-1 ring complex/Chaperonin containing TCP-1 (TRiC/CCT), and their folding involves co-chaperone. Through cryo-electron microscopy analysis, we present a more complete picture of TRiC-assisted tubulin/actin folding along TRiC adenosine triphosphatase cycle, under the coordination of co-chaperone plp2. In the open S1/S2 states, plp2 and tubulin/actin engaged within opposite TRiC chambers. Notably, we captured an unprecedented TRiC-plp2-tubulin complex in the closed S3 state, engaged with a folded full-length β-tubulin and loaded with a guanosine triphosphate, and a plp2 occupying opposite rings. Another closed S4 state revealed an actin in the intermediate folding state and a plp2. Accompanying TRiC ring closure, plp2 translocation could coordinate substrate translocation on the CCT6 hemisphere, facilitating substrate stabilization and folding. Our findings reveal the folding mechanism of the major cytoskeletal proteins tubulin/actin under the coordination of the biogenesis machinery TRiC and plp2 and extend our understanding of the links between cytoskeletal proteostasis and related human diseases.
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Affiliation(s)
- Wenyu Han
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingliang Jin
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Caixuan Liu
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Qiaoyu Zhao
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shutian Wang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yifan Wang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yue Yin
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, CAS, Shanghai 201210, China
| | - Chao Peng
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, CAS, Shanghai 201210, China
| | - Yanxing Wang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yao Cong
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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7
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Pinho-Correia LM, Prokop A. Maintaining essential microtubule bundles in meter-long axons: a role for local tubulin biogenesis? Brain Res Bull 2023; 193:131-145. [PMID: 36535305 DOI: 10.1016/j.brainresbull.2022.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Axons are the narrow, up-to-meter long cellular processes of neurons that form the biological cables wiring our nervous system. Most axons must survive for an organism's lifetime, i.e. up to a century in humans. Axonal maintenance depends on loose bundles of microtubules that run without interruption all along axons. The continued turn-over and the extension of microtubule bundles during developmental, regenerative or plastic growth requires the availability of α/β-tubulin heterodimers up to a meter away from the cell body. The underlying regulation in axons is poorly understood and hardly features in past and contemporary research. Here we discuss potential mechanisms, particularly focussing on the possibility of local tubulin biogenesis in axons. Current knowledge might suggest that local translation of tubulin takes place in axons, but far less is known about the post-translational machinery of tubulin biogenesis involving three chaperone complexes: prefoldin, CCT and TBC. We discuss functional understanding of these chaperones from a range of model organisms including yeast, plants, flies and mice, and explain what is known from human diseases. Microtubules across species depend on these chaperones, and they are clearly required in the nervous system. However, most chaperones display a high degree of functional pleiotropy, partly through independent functions of individual subunits outside their complexes, thus posing a challenge to experimental studies. Notably, we found hardly any studies that investigate their presence and function particularly in axons, thus highlighting an important gap in our understanding of axon biology and pathology.
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Affiliation(s)
- Liliana Maria Pinho-Correia
- The University of Manchester, Manchester Academic Health Science Centre, Faculty of Biology, Medicine and Health, School of Biology, Manchester, UK
| | - Andreas Prokop
- The University of Manchester, Manchester Academic Health Science Centre, Faculty of Biology, Medicine and Health, School of Biology, Manchester, UK.
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8
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Núñez L, Buxbaum AR, Katz ZB, Lopez-Jones M, Nwokafor C, Czaplinski K, Pan F, Rosenberg J, Monday HR, Singer RH. Tagged actin mRNA dysregulation in IGF2BP1[Formula: see text] mice. Proc Natl Acad Sci U S A 2022; 119:e2208465119. [PMID: 36067310 PMCID: PMC9477413 DOI: 10.1073/pnas.2208465119] [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: 05/16/2022] [Accepted: 07/29/2022] [Indexed: 11/18/2022] Open
Abstract
Gene expression is tightly regulated by RNA-binding proteins (RBPs) to facilitate cell survival, differentiation, and migration. Previous reports have shown the importance of the Insulin-like Growth Factor II mRNA-Binding Protein (IGF2BP1/IMP1/ZBP1) in regulating RNA fate, including localization, transport, and translation. Here, we generated and characterized a knockout mouse to study RBP regulation. We report that IGF2BP1 is essential for proper brain development and neonatal survival. Specifically, these mice display disorganization in the developing neocortex, and further investigation revealed a loss of cortical marginal cell density at E17.5. We also investigated migratory cell populations in the IGF2BP1[Formula: see text] mice, using BrdU labeling, and detected fewer mitotically active cells in the cortical plate. Since RNA localization is important for cellular migration and directionality, we investigated the regulation of β-actin messenger RNA (mRNA), a well-characterized target with established roles in cell motility and development. To aid in our understanding of RBP and target mRNA regulation, we generated mice with endogenously labeled β-actin mRNA (IGF2BP1[Formula: see text]; β-actin-MS2[Formula: see text]). Using endogenously labeled β-actin transcripts, we report IGF2BP1[Formula: see text] neurons have increased transcription rates and total β-actin protein content. In addition, we found decreased transport and anchoring in knockout neurons. Overall, we present an important model for understanding RBP regulation of target mRNA.
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Affiliation(s)
- Leti Núñez
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, NY 10461
| | | | | | - Melissa Lopez-Jones
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, NY 10461
| | - Chiso Nwokafor
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, NY 10461
| | | | - Feng Pan
- Eli Lilly and Company, Indianapolis, IN 46285
| | | | | | - Robert H. Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, NY 10461
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, New York, NY 10461
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9
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Payán-Bravo L, Fontalva S, Peñate X, Cases I, Guerrero-Martínez J, Pareja-Sánchez Y, Odriozola-Gil Y, Lara E, Jimeno-González S, Suñé C, Muñoz-Centeno M, Reyes J, Chávez S. Human prefoldin modulates co-transcriptional pre-mRNA splicing. Nucleic Acids Res 2021; 49:6267-6280. [PMID: 34096575 PMCID: PMC8216451 DOI: 10.1093/nar/gkab446] [Citation(s) in RCA: 3] [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: 09/07/2020] [Revised: 05/01/2021] [Accepted: 05/07/2021] [Indexed: 11/14/2022] Open
Abstract
Prefoldin is a heterohexameric complex conserved from archaea to humans that plays a cochaperone role during the co-translational folding of actin and tubulin monomers. Additional functions of prefoldin have been described, including a positive contribution to transcription elongation and chromatin dynamics in yeast. Here we show that prefoldin perturbations provoked transcriptional alterations across the human genome. Severe pre-mRNA splicing defects were also detected, particularly after serum stimulation. We found impairment of co-transcriptional splicing during transcription elongation, which explains why the induction of long genes with a high number of introns was affected the most. We detected genome-wide prefoldin binding to transcribed genes and found that it correlated with the negative impact of prefoldin depletion on gene expression. Lack of prefoldin caused global decrease in Ser2 and Ser5 phosphorylation of the RNA polymerase II carboxy-terminal domain. It also reduced the recruitment of the CTD kinase CDK9 to transcribed genes, and the association of splicing factors PRP19 and U2AF65 to chromatin, which is known to depend on CTD phosphorylation. Altogether the reported results indicate that human prefoldin is able to act locally on the genome to modulate gene expression by influencing phosphorylation of elongating RNA polymerase II, and thereby regulating co-transcriptional splicing.
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Affiliation(s)
- Laura Payán-Bravo
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Sara Fontalva
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Xenia Peñate
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Ildefonso Cases
- Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide, Seville, Spain
| | - José Antonio Guerrero-Martínez
- Andalusian Center of Molecular Biology and Regenerative Medicine-CABIMER, Junta de Andalucia-University of Pablo de Olavide-University of Seville-CSIC, Seville, Spain
| | - Yerma Pareja-Sánchez
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain
| | - Yosu Odriozola-Gil
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain
| | - Esther Lara
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain
| | - Silvia Jimeno-González
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
- Andalusian Center of Molecular Biology and Regenerative Medicine-CABIMER, Junta de Andalucia-University of Pablo de Olavide-University of Seville-CSIC, Seville, Spain
| | - Carles Suñé
- Department of Molecular Biology, Institute of Parasitology and Biomedicine “López Neyra” IPBLN-CSIC, PTS, Granada, Spain
| | - Mari Cruz Muñoz-Centeno
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - José C Reyes
- Andalusian Center of Molecular Biology and Regenerative Medicine-CABIMER, Junta de Andalucia-University of Pablo de Olavide-University of Seville-CSIC, Seville, Spain
| | - Sebastián Chávez
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
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10
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Manifestations of gene expression profiles in human right atrial myocardium caused by mechanical stretch. Heart Vessels 2020; 36:577-588. [PMID: 33180177 DOI: 10.1007/s00380-020-01724-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 10/30/2020] [Indexed: 10/23/2022]
Abstract
This investigation was aimed to identify gene profiles in human atrial myocardium in response to chronic mechanical stretch. Right atrial appendages from 21 patients were divided into 2 groups based on the size of right atrial volume. The microarray DATA analyses differentially identified 335 genes (> 2.0-fold, corrected P < 0.05) including "functionally unknown genes". This study identified 26 up-regulated genes (natriuretic peptide B, G protein subunit gamma 13, thyroid stimulating hormone beta, etc.) and 23 down-regulated genes (oligodendrocyte transcription factor 1, carbonic anhydrase 12, etc.), which could be responsible for chronic stretch-mediated structural remodeling in the atrium.
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11
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Fourel G, Boscheron C. Tubulin mutations in neurodevelopmental disorders as a tool to decipher microtubule function. FEBS Lett 2020; 594:3409-3438. [PMID: 33064843 DOI: 10.1002/1873-3468.13958] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 09/28/2020] [Accepted: 10/05/2020] [Indexed: 01/08/2023]
Abstract
Malformations of cortical development (MCDs) are a group of severe brain malformations associated with intellectual disability and refractory childhood epilepsy. Human missense heterozygous mutations in the 9 α-tubulin and 10 β-tubulin isoforms forming the heterodimers that assemble into microtubules (MTs) were found to cause MCDs. However, how a single mutated residue in a given tubulin isoform can perturb the entire microtubule population in a neuronal cell remains a crucial question. Here, we examined 85 MCD-associated tubulin mutations occurring in TUBA1A, TUBB2, and TUBB3 and their location in a three-dimensional (3D) microtubule cylinder. Mutations hitting residues exposed on the outer microtubule surface are likely to alter microtubule association with partners, while alteration of intradimer contacts may impair dimer stability and straightness. Other types of mutations are predicted to alter interdimer and lateral contacts, which are responsible for microtubule cohesion, rigidity, and dynamics. MCD-associated tubulin mutations surprisingly fall into all categories, thus providing unexpected insights into how a single mutation may impair microtubule function and elicit dominant effects in neurons.
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12
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Gholkar AA, Schmollinger S, Velasquez EF, Lo YC, Cohn W, Capri J, Dharmarajan H, Deardorff WJ, Gao LW, Abdusamad M, Whitelegge JP, Torres JZ. Regulation of Iron Homeostasis through Parkin-Mediated Lactoferrin Ubiquitylation. Biochemistry 2020; 59:2916-2921. [PMID: 32786404 PMCID: PMC7803182 DOI: 10.1021/acs.biochem.0c00504] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Somatic mutations that perturb Parkin ubiquitin ligase activity and the misregulation of iron homeostasis have both been linked to Parkinson's disease. Lactotransferrin (LTF) is a member of the family of transferrin iron binding proteins that regulate iron homeostasis, and increased levels of LTF and its receptor have been observed in neurodegenerative disorders like Parkinson's disease. Here, we report that Parkin binds to LTF and ubiquitylates LTF to influence iron homeostasis. Parkin-dependent ubiquitylation of LTF occurred most often on lysines (K) 182 and 649. Substitution of K182 or K649 with alanine (K182A or K649A, respectively) led to a decrease in the level of LTF ubiquitylation, and substitution at both sites led to a major decrease in the level of LTF ubiquitylation. Importantly, Parkin-mediated ubiquitylation of LTF was critical for regulating intracellular iron levels as overexpression of LTF ubiquitylation site point mutants (K649A or K182A/K649A) led to an increase in intracellular iron levels measured by ICP-MS/MS. Consistently, RNAi-mediated depletion of Parkin led to an increase in intracellular iron levels in contrast to overexpression of Parkin that led to a decrease in intracellular iron levels. Together, these results indicate that Parkin binds to and ubiquitylates LTF to regulate intracellular iron levels. These results expand our understanding of the cellular processes that are perturbed when Parkin activity is disrupted and more broadly the mechanisms that contribute to Parkinson's disease.
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Affiliation(s)
- Ankur A. Gholkar
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Stefan Schmollinger
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
| | - Erick F. Velasquez
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Yu-Chen Lo
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Whitaker Cohn
- Pasarow Mass Spectrometry Laboratory, University of California, Los Angeles, CA 90095, USA
| | - Joseph Capri
- Pasarow Mass Spectrometry Laboratory, University of California, Los Angeles, CA 90095, USA
| | - Harish Dharmarajan
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - William J. Deardorff
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Lucy W. Gao
- Pasarow Mass Spectrometry Laboratory, University of California, Los Angeles, CA 90095, USA
| | - Mai Abdusamad
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Julian P. Whitelegge
- Pasarow Mass Spectrometry Laboratory, University of California, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| | - Jorge Z. Torres
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
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13
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Liang J, Xia L, Oyang L, Lin J, Tan S, Yi P, Han Y, Luo X, Wang H, Tang L, Pan Q, Tian Y, Rao S, Su M, Shi Y, Cao D, Zhou Y, Liao Q. The functions and mechanisms of prefoldin complex and prefoldin-subunits. Cell Biosci 2020; 10:87. [PMID: 32699605 PMCID: PMC7370476 DOI: 10.1186/s13578-020-00446-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/15/2020] [Indexed: 12/26/2022] Open
Abstract
The correct folding is a key process for a protein to acquire its functional structure and conformation. Prefoldin is a well-known chaperone protein that regulates the correct folding of proteins. Prefoldin plays a crucial role in the pathogenesis of common neurodegenerative diseases (Alzheimer's disease, Parkinson's disease, and Huntington's disease). The important role of prefoldin in emerging fields (such as nanoparticles, biomaterials) and tumors has attracted widespread attention. Also, each of the prefoldin subunits has different and independent functions from the prefoldin complex. It has abnormal expression in different tumors and plays an important role in tumorigenesis and development, especially c-Myc binding protein MM-1. MM-1 can inhibit the activity of c-Myc through various mechanisms to regulate tumor growth. Therefore, an in-depth analysis of the complex functions of prefoldin and their subunits is helpful to understand the mechanisms of protein misfolding and the pathogenesis of diseases caused by misfolded aggregation.
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Affiliation(s)
- Jiaxin Liang
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013 Hunan China
| | - Longzheng Xia
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013 Hunan China
| | - Linda Oyang
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013 Hunan China
| | - Jinguan Lin
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013 Hunan China
| | - Shiming Tan
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013 Hunan China
| | - Pin Yi
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013 Hunan China
| | - Yaqian Han
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013 Hunan China
| | - Xia Luo
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013 Hunan China
| | - Hui Wang
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013 Hunan China
| | - Lu Tang
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013 Hunan China
- Department of Medical Microbiology Immunology & Cell Biology, Simmons Cancer Institute, Southern Illinois University School of Medicine, 913 N. Rutledge Street, Springfield, IL 62794 USA
| | - Qing Pan
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013 Hunan China
- Department of Medical Microbiology Immunology & Cell Biology, Simmons Cancer Institute, Southern Illinois University School of Medicine, 913 N. Rutledge Street, Springfield, IL 62794 USA
| | - Yutong Tian
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013 Hunan China
- Department of Medical Microbiology Immunology & Cell Biology, Simmons Cancer Institute, Southern Illinois University School of Medicine, 913 N. Rutledge Street, Springfield, IL 62794 USA
| | - Shan Rao
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013 Hunan China
| | - Min Su
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013 Hunan China
| | - Yingrui Shi
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013 Hunan China
| | - Deliang Cao
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013 Hunan China
- Department of Medical Microbiology Immunology & Cell Biology, Simmons Cancer Institute, Southern Illinois University School of Medicine, 913 N. Rutledge Street, Springfield, IL 62794 USA
| | - Yujuan Zhou
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013 Hunan China
| | - Qianjin Liao
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013 Hunan China
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14
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Zhang T, Shi W, Tian K, Kong Y. Chaperonin containing t-complex polypeptide 1 subunit 6A correlates with lymph node metastasis, abnormal carcinoembryonic antigen and poor survival profiles in non-small cell lung carcinoma. World J Surg Oncol 2020; 18:156. [PMID: 32631353 PMCID: PMC7339415 DOI: 10.1186/s12957-020-01911-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 06/10/2020] [Indexed: 12/25/2022] Open
Abstract
Background This study aimed to investigate the correlation of chaperonin containing t-complex polypeptide 1 subunit 6A (CCT6A) expression with clinicopathological features and survival profiles in non-small cell lung carcinoma (NSCLC) patients. Methods A total of 381 NSCLC patients with Tumor, Node, Metastasis (TNM) stage I–IIIA who underwent tumor resection were retrospectively screened. Immunohistochemistry staining and semi-quantitative scoring were used to evaluate CCT6A expression in tumor and adjacent tissues. Clinicopathological features were retrieved. Disease-free survival (DFS) and overall survival (OS) were calculated. Results CCT6A expression was elevated in tumor tissue (CCT6A high 47.5% vs. low 52.5%) compared with adjacent tissue (CCT6A high 30.4% vs. low 69.6%) (P < 0.001), and ROC curve displayed that CCT6A could distinguish tumor tissue from adjacent tissue. Moreover, tumor CCT6A high expression was associated with lymph node metastasis (P = 0.001), elevated TNM stage (P = 0.002), and abnormal carcinoembryonic antigen (P = 0.022). Kaplan–Meier curves displayed that tumor CCT6A high expression was negatively correlated with DFS and OS (all P < 0.001). Cox’s regression analysis disclosed that tumor CCT6A high expression independently predicted worse DFS (P < 0.001) (hazard ratio (HR) 1.659 (95% confidence interval (CI) 1.318–2.089)), and OS (P < 0.001) (HR 1.779 (95%CI 1.378–2.298)). Conclusions CCT6A may present some clinical value in the management of NSCLC.
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Affiliation(s)
- Ting Zhang
- Department of Pulmonary and Critical Care Medicine, Affiliated Nanhua Hospital, University of South China, 336 South of Dongfeng Road, Hengyang, 421000, China
| | - Wang Shi
- Department of Pulmonary and Critical Care Medicine, Affiliated Nanhua Hospital, University of South China, 336 South of Dongfeng Road, Hengyang, 421000, China.
| | - Ke Tian
- Department of Pulmonary and Critical Care Medicine, Affiliated Nanhua Hospital, University of South China, 336 South of Dongfeng Road, Hengyang, 421000, China
| | - Yushan Kong
- Department of Pulmonary and Critical Care Medicine, Affiliated Nanhua Hospital, University of South China, 336 South of Dongfeng Road, Hengyang, 421000, China
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15
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Araujo-Garrido JL, Baisón-Olmo F, Bernal-Bayard J, Romero F, Ramos-Morales F. Tubulin Folding Cofactor TBCB is a Target of the Salmonella Effector Protein SseK1. Int J Mol Sci 2020; 21:ijms21093193. [PMID: 32366039 PMCID: PMC7246435 DOI: 10.3390/ijms21093193] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 12/11/2022] Open
Abstract
Salmonella enterica serovar Typhimurium is a human and animal pathogen that uses type III secretion system effectors to manipulate the host cell and fulfill infection. SseK1 is a Salmonella effector with glycosyltransferase activity. We carried out a yeast two-hybrid screen and have identified tubulin-binding cofactor B (TBCB) as a new binding partner for this effector. SseK1 catalyzed the addition of N-acetylglucosamine to arginine on TBCB, and its expression promoted the stabilization of the microtubule cytoskeleton of HEK293T cells. The conserved Asp-x-Asp (DxD) motif that is essential for the activity of SseK1 was required for the binding and modification of TBCB and for the effect on the cytoskeleton. Our study has identified a novel target for SseK1 and suggests that this effector may have a role in the manipulation of the host cell microtubule network to provide a safe niche for this pathogen.
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Affiliation(s)
- Juan Luis Araujo-Garrido
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Sevilla, Spain; (J.L.A.-G.); (F.B.-O.); (J.B.-B.)
| | - Fernando Baisón-Olmo
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Sevilla, Spain; (J.L.A.-G.); (F.B.-O.); (J.B.-B.)
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago 1058, Chile
| | - Joaquín Bernal-Bayard
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Sevilla, Spain; (J.L.A.-G.); (F.B.-O.); (J.B.-B.)
| | - Francisco Romero
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, 41012 Sevilla, Spain;
| | - Francisco Ramos-Morales
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Sevilla, Spain; (J.L.A.-G.); (F.B.-O.); (J.B.-B.)
- Correspondence:
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16
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BommaReddy RR, Patel R, Smalley T, Acevedo-Duncan M. Effects of Atypical Protein Kinase C Inhibitor (DNDA) on Lung Cancer Proliferation and Migration by PKC-ι/FAK Ubiquitination Through the Cbl-b Pathway. Onco Targets Ther 2020; 13:1661-1676. [PMID: 32158232 PMCID: PMC7047975 DOI: 10.2147/ott.s224866] [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: 07/29/2019] [Accepted: 02/03/2020] [Indexed: 01/23/2023] Open
Abstract
Purpose The options for treating lung cancers are limited, as diagnosis typically occurs during the late stages of the disease. There is a dire need to develop aPKC (atypical Protein Kinase C) inhibitors due to aPKC overexpression and contributions to lung cancer malignancies. In this study, we investigate the role of atypical PKCs (aPKCs) in cell proliferation and migration in lung cancer cell lines and the effect of the novel aPKC inhibitor DNDA (3,4-amino-2,7 napthalene disulfonic acid). Methods The normal and lung cancer cells were treated with various concentrations of DNDA. We used a WST assay to determine lung cell viability, then analyzed cell apoptosis through Annexin V/PI staining and flow cytometry. Immunoprecipitation determined the proteins' associations, and Western blot allowed testing of the expression of interest proteins. We also employed the UbiTest to identify the ubiquitination of the FAK. The scratch and transwell assays measured cell migration and invasion of lung cancer cells. Results Our data from cell viability and flow cytometry showed a significant reduction in cell proliferation and induction of apoptosis with DNDA treatment in lung cancer cells, as well as no toxic effect on normal BEAS-2B lung cells. Western blot results showed that the phosphorylation of PKC-iota and phosphorylation of FAK decreased in A549 lung cancer cells upon DNDA treatment. Immunoprecipitation (IP) data revealed an association of PKC-ι with FAK and FAK with Casitas B-lineage lymphoma proto-oncogene-b (Cbl-b). UbiTest results suggest that PKC-ι regulates FAK cleavage through its ubiquitination by Cbl-b, thereby inhibiting A549 lung cancer cells' migration. This was evident from scratch, invasion, and migration assays. Conclusion Our study data suggest that DNDA inhibits cell proliferation and induces apoptosis in lung cancer cells. Moreover, DNDA inhibit A549 lung cancer cells' migration by PKC- ι/FAK ubiquitination via Cbl-b.
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Affiliation(s)
| | - Rekha Patel
- Department of Chemistry, University of South Florida, Tampa, FL 33620, USA
| | - Tracess Smalley
- Department of Chemistry, University of South Florida, Tampa, FL 33620, USA
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17
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Ahn HK, Yoon JT, Choi I, Kim S, Lee HS, Pai HS. Functional characterization of chaperonin containing T-complex polypeptide-1 and its conserved and novel substrates in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2741-2757. [PMID: 30825377 PMCID: PMC6506772 DOI: 10.1093/jxb/erz099] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 02/21/2019] [Indexed: 05/31/2023]
Abstract
Chaperonin containing T-complex polypeptide-1 (CCT) is an evolutionarily conserved chaperonin multi-subunit complex that mediates protein folding in eukaryotes. It is essential for cell growth and survival in yeast and mammals, with diverse substrate proteins. However, only a few studies on plant CCT have been reported to date, due to the essentiality of CCT subunit genes and the large size of the complex. Here, we have investigated the structure and function of the Arabidopsis CCT complex in detail. The plant CCT consisted of eight subunits that assemble to form a high-molecular-mass protein complex, shown by diverse methods. CCT-deficient cells exhibited depletion of cortical microtubules, accompanied by a reduction in cellular α- and β-tubulin levels due to protein degradation. Cycloheximide-chase assays suggested that CCT is involved in the folding of tubulins in plants. Furthermore, CCT interacted with PPX1, the catalytic subunit of protein phosphatase 4, and may participate in the folding of PPX1 as its substrate. CCT also interacted with Tap46, a regulatory subunit of PP2A family phosphatases, but Tap46 appeared to function in PPX1 stabilization, rather than as a CCT substrate. Collectively, our findings reveal the essential functions of CCT chaperonin in plants and its conserved and novel substrates.
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Affiliation(s)
- Hee-Kyung Ahn
- Department of Systems Biology, Yonsei University, Seoul, Korea
| | - Joong-Tak Yoon
- Department of Systems Biology, Yonsei University, Seoul, Korea
| | - Ilyeong Choi
- Department of Systems Biology, Yonsei University, Seoul, Korea
| | - Sumin Kim
- Department of Systems Biology, Yonsei University, Seoul, Korea
| | - Ho-Seok Lee
- Department of Systems Biology, Yonsei University, Seoul, Korea
| | - Hyun-Sook Pai
- Department of Systems Biology, Yonsei University, Seoul, Korea
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18
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Ohhara Y, Nakamura A, Kato Y, Yamakawa-Kobayashi K. Chaperonin TRiC/CCT supports mitotic exit and entry into endocycle in Drosophila. PLoS Genet 2019; 15:e1008121. [PMID: 31034473 PMCID: PMC6508744 DOI: 10.1371/journal.pgen.1008121] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 05/09/2019] [Accepted: 04/02/2019] [Indexed: 12/24/2022] Open
Abstract
Endocycle is a commonly observed cell cycle variant through which cells undergo repeated rounds of genome DNA replication without mitosis. Endocycling cells arise from mitotic cells through a switch of the cell cycle mode, called the mitotic-to-endocycle switch (MES), to initiate cell growth and terminal differentiation. However, the underlying regulatory mechanisms of MES remain unclear. Here we used the Drosophila steroidogenic organ, called the prothoracic gland (PG), to study regulatory mechanisms of MES, which is critical for the PG to upregulate biosynthesis of the steroid hormone ecdysone. We demonstrate that PG cells undergo MES through downregulation of mitotic cyclins, which is mediated by Fizzy-related (Fzr). Moreover, we performed a RNAi screen to further elucidate the regulatory mechanisms of MES, and identified the evolutionarily conserved chaperonin TCP-1 ring complex (TRiC) as a novel regulator of MES. Knockdown of TRiC subunits in the PG caused a prolonged mitotic period, probably due to impaired nuclear translocation of Fzr, which also caused loss of ecdysteroidogenic activity. These results indicate that TRiC supports proper MES and endocycle progression by regulating Fzr folding. We propose that TRiC-mediated protein quality control is a conserved mechanism supporting MES and endocycling, as well as subsequent terminal differentiation.
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Affiliation(s)
- Yuya Ohhara
- School of Food and Nutritional Sciences, University of Shizuoka, Shizuoka, Japan
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, Shizuoka, Japan
- * E-mail:
| | - Aki Nakamura
- School of Food and Nutritional Sciences, University of Shizuoka, Shizuoka, Japan
| | - Yuki Kato
- School of Food and Nutritional Sciences, University of Shizuoka, Shizuoka, Japan
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, Shizuoka, Japan
| | - Kimiko Yamakawa-Kobayashi
- School of Food and Nutritional Sciences, University of Shizuoka, Shizuoka, Japan
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, Shizuoka, Japan
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19
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Denarier E, Brousse C, Sissoko A, Andrieux A, Boscheron C. A neurodevelopmental TUBB2B β-tubulin mutation impairs Bim1 (yeast EB1)-dependent spindle positioning. Biol Open 2019; 8:bio.038620. [PMID: 30674462 PMCID: PMC6361202 DOI: 10.1242/bio.038620] [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: 01/06/2023] Open
Abstract
Malformations of the human cerebral cortex can be caused by mutations in tubulins that associate to compose microtubules. Cerebral cortical folding relies on neuronal migration and on progenitor proliferation partly dictated by microtubule-dependent mitotic spindle positioning. A single amino acid change, F265L, in the conserved TUBB2B β-tubulin gene has been identified in patients with abnormal cortex formation. A caveat for studying this mutation in mammalian cells is that nine genes encode β-tubulin in human. Here, we generate a yeast strain expressing F265L tubulin mutant as the sole source of β-tubulin. The F265L mutation does not preclude expression of a stable β-tubulin protein which is incorporated into microtubules. However, impaired cell growth was observed at high temperatures along with altered microtubule dynamics and stability. In addition, F265L mutation produces a highly specific mitotic spindle positioning defect related to Bim1 (yeast EB1) dysfunction. Indeed, F265L cells display an abnormal Bim1 recruitment profile at microtubule plus-ends. These results indicate that the F265L β-tubulin mutation affects microtubule plus-end complexes known to be important for microtubule dynamics and for microtubule function during mitotic spindle positioning.
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Affiliation(s)
- Eric Denarier
- Univ. Grenoble Alpes, Grenoble Institut des Neurosciences, GIN, F-38000, Grenoble, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U1216, F-38000, Grenoble, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Biosciences and Biotechnology Institute of Grenoble, Grenoble, France
| | - Carine Brousse
- Institut National de la Transfusion Sanguine (INTS), F-75015 Paris, France
| | | | - Annie Andrieux
- Univ. Grenoble Alpes, Grenoble Institut des Neurosciences, GIN, F-38000, Grenoble, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U1216, F-38000, Grenoble, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Biosciences and Biotechnology Institute of Grenoble, Grenoble, France
| | - Cécile Boscheron
- Univ. Grenoble Alpes, Grenoble Institut des Neurosciences, GIN, F-38000, Grenoble, France .,Institut National de la Santé et de la Recherche Médicale (INSERM), U1216, F-38000, Grenoble, France.,Institut de Biologie Structurale (IBS) , F-38000 Grenoble, France
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20
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Kooistra RL, David R, Ruiz AC, Powers SW, Haselton KJ, Kiernan K, Blagborough AM, Solamen L, Olsen KW, Putonti C, Kanzok SM. Characterization of a protozoan Phosducin-like protein-3 (PhLP-3) reveals conserved redox activity. PLoS One 2019; 13:e0209699. [PMID: 30596727 PMCID: PMC6312279 DOI: 10.1371/journal.pone.0209699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 12/09/2018] [Indexed: 11/18/2022] Open
Abstract
We recently identified three novel thioredoxin-like genes in the genome of the protozoan parasite Plasmodium that belong to the Phosducin-like family of proteins (PhLP). PhLPs are small cytosolic proteins hypothesized to function in G-protein signaling and protein folding. Although PhLPs are highly conserved in eukaryotes from yeast to mammals, only a few representatives have been experimentally characterized to date. In addition, while PhLPs contain a thioredoxin domain, they lack a CXXC motif, a strong indicator for redox activity, and it is unclear whether members of the PhLP family are enzymatically active. Here, we describe PbPhLP-3 as the first phosducin-like protein of a protozoan organism, Plasmodium berghei. Initial transcription analysis revealed continuous low-level expression of pbphlp-3 throughout the complex Plasmodium life cycle. Attempts to knockout pbphlp-3 in P. berghei did not yield live parasites, suggesting an essential role for the gene in Plasmodium. We cloned, expressed and purified PbPhLP-3 and determined that the recombinant protein is redox active in vitro in a thioredoxin-coupled redox assay. It also has the capacity to reduce the organic compound tert-Butyl hydroperoxide (TBHP) in vitro, albeit at low efficiency. Sequence analysis, structural modeling, and site-directed mutagenesis revealed a conserved cysteine in the thioredoxin domain to be the redox active residue. Lastly, we provide evidence that recombinant human PhLP-3 exhibits redox activity similar to that of PbPhLP-3 and suggest that redox activity may be conserved in PhLP-3 homologs of other species. Our data provide new insight into the function of PhLP-3, which is hypothesized to act as co-chaperones in the folding and regulation of cytoskeletal proteins. We discuss the potential implications of PhLP-3 as a thioredoxin-target protein and possible links between the cellular redox network and the eukaryotic protein folding machinery.
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Affiliation(s)
- Rachel L. Kooistra
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America
| | - Robin David
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America
| | - Ana C. Ruiz
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America
| | - Sean W. Powers
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America
| | - Kyle J. Haselton
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America
| | - Kaitlyn Kiernan
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America
| | - Andrew M. Blagborough
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, United Kingdom
| | - Ligin Solamen
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, United States of America
| | - Kenneth W. Olsen
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States of America
| | - Catherine Putonti
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, United States of America
- Department of Computer Science, Loyola University Chicago, Chicago, IL, United States of America
| | - Stefan M. Kanzok
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, United States of America
- * E-mail:
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21
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Son HG, Seo K, Seo M, Park S, Ham S, An SWA, Choi ES, Lee Y, Baek H, Kim E, Ryu Y, Ha CM, Hsu AL, Roh TY, Jang SK, Lee SJV. Prefoldin 6 mediates longevity response from heat shock factor 1 to FOXO in C. elegans. Genes Dev 2018; 32:1562-1575. [PMID: 30478249 PMCID: PMC6295163 DOI: 10.1101/gad.317362.118] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 10/02/2018] [Indexed: 12/31/2022]
Abstract
Heat shock factor 1 (HSF-1) and forkhead box O (FOXO) are key transcription factors that protect cells from various stresses. In Caenorhabditis elegans, HSF-1 and FOXO together promote a long life span when insulin/IGF-1 signaling (IIS) is reduced. However, it remains poorly understood how HSF-1 and FOXO cooperate to confer IIS-mediated longevity. Here, we show that prefoldin 6 (PFD-6), a component of the molecular chaperone prefoldin-like complex, relays longevity response from HSF-1 to FOXO under reduced IIS. We found that PFD-6 was specifically required for reduced IIS-mediated longevity by acting in the intestine and hypodermis. We showed that HSF-1 increased the levels of PFD-6 proteins, which in turn directly bound FOXO and enhanced its transcriptional activity. Our work suggests that the prefoldin-like chaperone complex mediates longevity response from HSF-1 to FOXO to increase the life span in animals with reduced IIS.
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Affiliation(s)
- Heehwa G Son
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Keunhee Seo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Mihwa Seo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea.,School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea.,Center for plant Aging Research, Institute for Basic Science, Daegu Gyeongbuk Institute of Science and Technology, Daegu 42988, South Korea.,Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu 42988, South Korea
| | - Sangsoon Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Seokjin Ham
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Seon Woo A An
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Eun-Seok Choi
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Yujin Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Haeshim Baek
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Eunju Kim
- Department of Internal Medicine, Division of Geriatric and Palliative Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Youngjae Ryu
- Research Division, Korea Brain Research Institute, Daegu 41068, South Korea
| | - Chang Man Ha
- Research Division, Korea Brain Research Institute, Daegu 41068, South Korea
| | - Ao-Lin Hsu
- Department of Internal Medicine, Division of Geriatric and Palliative Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA.,Research Center for Healthy Aging, China Medical University, Taichung 404, Taiwan.,Institute of New Drug Development, China Medical University, Taichung 404, Taiwan
| | - Tae-Young Roh
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea.,Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Sung Key Jang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Seung-Jae V Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea.,School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
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22
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McNally FJ, Roll-Mecak A. Microtubule-severing enzymes: From cellular functions to molecular mechanism. J Cell Biol 2018; 217:4057-4069. [PMID: 30373906 PMCID: PMC6279391 DOI: 10.1083/jcb.201612104] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 08/13/2018] [Accepted: 10/04/2018] [Indexed: 12/24/2022] Open
Abstract
McNally and Roll-Mecak review the molecular mechanism of microtubule-severing enzymes and their diverse roles in processes ranging from cell division to ciliogensis and morphogenesis. Microtubule-severing enzymes generate internal breaks in microtubules. They are conserved in eukaryotes from ciliates to mammals, and their function is important in diverse cellular processes ranging from cilia biogenesis to cell division, phototropism, and neurogenesis. Their mutation leads to neurodegenerative and neurodevelopmental disorders in humans. All three known microtubule-severing enzymes, katanin, spastin, and fidgetin, are members of the meiotic subfamily of AAA ATPases that also includes VPS4, which disassembles ESCRTIII polymers. Despite their conservation and importance to cell physiology, the cellular and molecular mechanisms of action of microtubule-severing enzymes are not well understood. Here we review a subset of cellular processes that require microtubule-severing enzymes as well as recent advances in understanding their structure, biophysical mechanism, and regulation.
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Affiliation(s)
- Francis J McNally
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA
| | - Antonina Roll-Mecak
- Cell Biology and Biophysics Unit, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, Bethesda, MD .,Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD
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23
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Mücke N, Kämmerer L, Winheim S, Kirmse R, Krieger J, Mildenberger M, Baßler J, Hurt E, Goldmann WH, Aebi U, Toth K, Langowski J, Herrmann H. Assembly Kinetics of Vimentin Tetramers to Unit-Length Filaments: A Stopped-Flow Study. Biophys J 2018; 114:2408-2418. [PMID: 29754715 DOI: 10.1016/j.bpj.2018.04.032] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 03/20/2018] [Accepted: 04/19/2018] [Indexed: 01/01/2023] Open
Abstract
Intermediate filaments (IFs) are principal components of the cytoskeleton, a dynamic integrated system of structural proteins that provides the functional architecture of metazoan cells. They are major contributors to the elasticity of cells and tissues due to their high mechanical stability and intrinsic flexibility. The basic building block for the assembly of IFs is a rod-like, 60-nm-long tetrameric complex made from two antiparallel, half-staggered coiled coils. In low ionic strength, tetramers form stable complexes that rapidly assemble into filaments upon raising the ionic strength. The first assembly products, "frozen" by instantaneous chemical fixation and viewed by electron microscopy, are 60-nm-long "unit-length" filaments (ULFs) that apparently form by lateral in-register association of tetramers. ULFs are the active elements of IF growth, undergoing longitudinal end-to-end annealing with one another and with growing filaments. Originally, we have employed quantitative time-lapse atomic force and electron microscopy to analyze the kinetics of vimentin-filament assembly starting from a few seconds to several hours. To obtain detailed quantitative insight into the productive reactions that drive ULF formation, we now introduce a "stopped-flow" approach in combination with static light-scattering measurements. Thereby, we determine the basic rate constants for lateral assembly of tetramers to ULFs. Processing of the recorded data by a global fitting procedure enables us to describe the hierarchical steps of IF formation. Specifically, we propose that tetramers are consumed within milliseconds to yield octamers that are obligatory intermediates toward ULF formation. Although the interaction of tetramers is diffusion controlled, it is strongly driven by their geometry to mediate effective subunit targeting. Importantly, our model conclusively reflects the previously described occurrence of polymorphic ULF and mature filaments in terms of their number of tetramers per cross section.
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Affiliation(s)
- Norbert Mücke
- Division Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, Germany
| | - Lara Kämmerer
- Division Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, Germany
| | - Stefan Winheim
- Division Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, Germany
| | - Robert Kirmse
- Division Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, Germany
| | - Jan Krieger
- Division Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, Germany
| | - Maria Mildenberger
- Division Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, Germany
| | - Jochen Baßler
- Biochemistry Center of Heidelberg University, Heidelberg, Germany
| | - Ed Hurt
- Biochemistry Center of Heidelberg University, Heidelberg, Germany
| | - Wolfgang H Goldmann
- Department of Physics, Biophysics group, Friedrich-Alexander-University of Erlangen-Nuremberg, Erlangen, Germany
| | - Ueli Aebi
- Biozentrum, University of Basel, Basel, Switzerland
| | - Katalin Toth
- Division Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, Germany
| | - Jörg Langowski
- Division Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, Germany
| | - Harald Herrmann
- Institute of Neuropathology, University Hospital Erlangen, Erlangen, Germany; Division of Molecular Genetics, German Cancer Research Center, Heidelberg, Germany.
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24
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Gemechu JM, Sharma A, Yu D, Xie Y, Merkel OM, Moszczynska A. Characterization of Dopaminergic System in the Striatum of Young Adult Park2 -/- Knockout Rats. Sci Rep 2018; 8:1517. [PMID: 29367643 PMCID: PMC5784013 DOI: 10.1038/s41598-017-18526-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 11/20/2017] [Indexed: 12/13/2022] Open
Abstract
Mutations in parkin gene (Park2) are linked to early-onset autosomal recessive Parkinson's disease (PD) and young-onset sporadic PD. Park2 knockout (PKO) rodents; however, do not display neurodegeneration of the nigrostriatal pathway, suggesting age-dependent compensatory changes. Our goal was to examine dopaminergic (DAergic) system in the striatum of 2 month-old PKO rats in order to characterize compensatory mechanisms that may have occurred within the system. The striata form wild type (WT) and PKO Long Evans male rats were assessed for the levels of DAergic markers, for monoamine oxidase (MAO) A and B activities and levels, and for the levels of their respective preferred substrates, serotonin (5-HT) and ß-phenylethylamine (ß-PEA). The PKO rats displayed lower activities of MAOs and higher levels of ß-PEA in the striatum than their WT counterparts. Decreased levels of ß-PEA receptor, trace amine-associated receptor 1 (TAAR-1), and postsynaptic DA D2 (D2L) receptor accompanied these alterations. Drug-naive PKO rats displayed normal locomotor activity; however, they displayed decreased locomotor response to a low dose of psychostimulant methamphetamine, suggesting altered DAergic neurotransmission in the striatum when challenged with an indirect agonist. Altogether, our findings suggest that 2 month-old PKO male rats have altered DAergic and trace aminergic signaling.
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Affiliation(s)
- Jickssa M Gemechu
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, MI, USA
- Department of Biomedical Sciences, OUWB School of Medicine, Rochester, MI, USA
| | - Akhil Sharma
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, MI, USA
| | - Dongyue Yu
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, MI, USA
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, USA
| | - Yuran Xie
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, MI, USA
- Boston Biomedical Inc., Allston, MA, USA
| | - Olivia M Merkel
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, MI, USA
- Department of Pharmacy, Ludwig-Maximilians University of Munich, Munich, Germany
| | - Anna Moszczynska
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, MI, USA.
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25
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Melkani GC, Bhide S, Han A, Vyas J, Livelo C, Bodmer R, Bernstein SI. TRiC/CCT chaperonins are essential for maintaining myofibril organization, cardiac physiological rhythm, and lifespan. FEBS Lett 2017; 591:3447-3458. [PMID: 28963798 PMCID: PMC5683924 DOI: 10.1002/1873-3468.12860] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 09/08/2017] [Accepted: 09/19/2017] [Indexed: 01/12/2023]
Abstract
We recently reported that CCT chaperonin subunits are upregulated in a cardiac-specific manner under time-restricted feeding (TRF) [Gill S et al. (2015) Science 347, 1265-1269], suggesting that TRiC/CCT has a heart-specific function. To understand the CCT chaperonin function in cardiomyocytes, we performed its cardiac-specific knock-down in the Drosophila melanogaster model. This resulted in disorganization of cardiac actin- and myosin-containing myofibrils and severe physiological dysfunction, including restricted heart diameters, elevated cardiac dysrhythmia and compromised cardiac performance. We also noted that cardiac-specific knock-down of CCT chaperonin significantly shortens lifespans. Additionally, disruption of circadian rhythm yields further deterioration of cardiac function of hypomorphic CCT mutants. Our analysis reveals that both the orchestration of protein folding and circadian rhythms mediated by CCT chaperonin are critical for maintaining heart contractility.
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Affiliation(s)
- Girish C. Melkani
- Department of Biology, Molecular Biology and Heart Institutes, San Diego State University San Diego, CA 92182, USA
| | - Shruti Bhide
- Department of Biology, Molecular Biology and Heart Institutes, San Diego State University San Diego, CA 92182, USA
| | - Andrew Han
- Department of Biology, Molecular Biology and Heart Institutes, San Diego State University San Diego, CA 92182, USA
| | - Jay Vyas
- Department of Biology, Molecular Biology and Heart Institutes, San Diego State University San Diego, CA 92182, USA
| | - Catherine Livelo
- Department of Biology, Molecular Biology and Heart Institutes, San Diego State University San Diego, CA 92182, USA
| | - Rolf Bodmer
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Sanford I. Bernstein
- Department of Biology, Molecular Biology and Heart Institutes, San Diego State University San Diego, CA 92182, USA
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26
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Abstract
Txndc9 (thioredoxin domain containing protein 9) has been shown to be involved in mammalian mitosis; however, its function in mammalian oocyte meiosis remains unclear. In this study, we initially found that Txndc9 is expressed during meiotic maturation of mouse oocytes and higher expression of Txndc9 mRNA and protein occurred in germinal vesicle (GV) stage. By using confocal scanning, we observed that Txndc9 localized at both nucleus and cytoplasm, especially at spindle microtubules. Specific depletion of Txndc9 by siRNA in mouse oocyte resulted in decreasing the rate of first polar body extrusion and increasing abnormal spindle assemble. Moreover, knockdown of Txndc9 in germinal vesicle (GV) stage oocytes led to higher level of reactive oxygen species (ROS) and lower level of antioxidant glutathione (GSH) as compared with control oocytes, which indicated that Txndc9 may be involved in mediating the redox balance. In summary, our results demonstrated that Txndc9 is crucial for mouse oocyte maturation by regulating spindle assembly, polar body extrusion, and redox status.
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27
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Abstract
The human chaperonin TRiC consists of eight non-identical subunits, and its protein-folding activity is critical for cellular health. Misfolded proteins are associated with many human diseases, such as amyloid diseases, cancer, and neuropathies, making TRiC a potential therapeutic target. A detailed structural understanding of its ATP-dependent folding mechanism and substrate recognition is therefore of great importance. Of particular health-related interest is the mutation Histidine 147 to Arginine (H147R) in human TRiC subunit 5 (CCT5), which has been associated with hereditary sensory neuropathy. In this paper, we describe the crystal structures of CCT5 and the CCT5-H147R mutant, which provide important structural information for this vital protein-folding machine in humans. This first X-ray crystallographic study of a single human CCT subunit in the context of a hexadecameric complex can be expanded in the future to the other 7 subunits that form the TRiC complex.
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28
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Melkani GC, Panda S. Time-restricted feeding for prevention and treatment of cardiometabolic disorders. J Physiol 2017; 595:3691-3700. [PMID: 28295377 PMCID: PMC5471414 DOI: 10.1113/jp273094] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 02/01/2017] [Indexed: 12/11/2022] Open
Abstract
The soaring prevalence of obesity and diabetes is associated with an increase in comorbidities, including elevated risk for cardiovascular diseases (CVDs). CVDs continue to be among the leading causes of death and disability in the United States. While increased nutritional intake from an energy-dense diet is known to disrupt metabolic homeostasis and contributes to the disease risk, circadian rhythm disruption is emerging as a new risk factor for CVD. Circadian rhythms coordinate cardiovascular health via temporal control of organismal metabolism and physiology. Thus, interventions that improve circadian rhythms are prospective entry points to mitigate cardiometabolic disease risk. Although light is a strong modulator of the neural circadian clock, time of food intake is emerging as a dominant agent that affects circadian clocks in metabolic organs. We discovered that imposing a time-restricted feeding (TRF) regimen in which all caloric intakes occur consistently within ≤ 12 h every day exerts many cardiometabolic benefits. TRF prevents excessive body weight gain, improves sleep, and attenuates age- and diet-induced deterioration in cardiac performance. Using an integrative approach that combines Drosophila melanogaster (fruit fly) genetics with transcriptome analyses it was found that the beneficial effects of TRF are mediated by circadian clock, ATP-dependent TCP/TRiC/CCT chaperonin and mitochondrial electron transport chain components. Parallel studies in rodents have shown TRF reduces metabolic disease risks by maintaining metabolic homeostasis. As modern humans continue to live under extended periods of wakefulness and ingestion events, daily eating pattern offers a new potential target for lifestyle intervention to reduce CVD risk.
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Affiliation(s)
- Girish C. Melkani
- Department of Biology, Molecular Biology and Heart InstitutesSan Diego State University San DiegoCA92182USA
| | - Satchidananda Panda
- Regulatory Biology LaboratorySalk Institute for Biological StudiesLa JollaCA92037USA
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29
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McMurray MA. Coupling de novo protein folding with subunit exchange into pre-formed oligomeric protein complexes: the 'heritable template' hypothesis. Biomol Concepts 2017; 7:271-281. [PMID: 27875316 DOI: 10.1515/bmc-2016-0023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 10/11/2016] [Indexed: 11/15/2022] Open
Abstract
Despite remarkable advances in synthetic biology, the fact remains that it takes a living cell to make a new living cell. The information encoded in the genome is necessary to direct assembly of all cellular components, but it may not be sufficient. Some components (e.g. mitochondria) cannot be synthesized de novo, and instead require pre-existing templates, creating a fundamental continuity of life: if the template information is ever lost, the genomic code cannot suffice to ensure proper biogenesis. One type of information only incompletely encoded in the genome is the structures of macromolecular assemblies, which emerge from the conformations of the constituent molecules coupled with the ways in which these molecules interact. For many, if not most proteins, gene sequence is not the sole determinant of native conformation, particularly in the crowded cellular milieu. A partial solution to this problem lies in the functions of molecular chaperones, encoded by nearly all cellular genomes. Chaperones effectively restrict the ensemble of conformations sampled by polypeptides, promoting the acquisition of native, functional forms, but multiple proteins have evolved ways to achieve chaperone independence, perhaps by coupling folding with higher-order assembly. Here, I propose the existence of another solution: a novel mechanism of de novo folding in which the folding of specific proteins is templated by pre-folded molecules of a partner protein whose own folding also required similar templating. This hypothesis challenges prevailing paradigms by predicting that, in order to achieve a functional fold, some non-prion proteins require a seed passed down through generations.
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30
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A Genetic Screen for Fission Yeast Gene Deletion Mutants Exhibiting Hypersensitivity to Latrunculin A. G3-GENES GENOMES GENETICS 2016; 6:3399-3408. [PMID: 27466272 PMCID: PMC5068959 DOI: 10.1534/g3.116.032664] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Fission yeast cells treated with low doses of the actin depolymerizing drug, latrunculin A (LatA), delay entry into mitosis via a mechanism that is dependent on both the Clp1p and Rad24p proteins. During this delay, cells remain in a cytokinesis-competent state that is characterized by continuous repair and/or reestablishment of the actomyosin ring. In this manner, cells ensure the faithful completion of the preceding cytokinesis in response to perturbation of the cell division machinery. To uncover other genes with a role in this response, or simply genes with roles in adapting to LatA-induced stress, we carried out a genome-wide screen and identified a group of 38 gene deletion mutants that are hyper-sensitive to the drug. As expected, we found genes affecting cytokinesis and/or the actin cytoskeleton within this set (ain1, acp2, imp2). We also identified genes with roles in histone modification (tra1, ngg1), intracellular transport (apl5, aps3), and glucose-mediated signaling (git3, git5, git11, pka1, cgs2). Importantly, while the identified gene deletion mutants are prone to cytokinesis failure in the presence of LatA, they are nevertheless fully capable of cell division in the absence of the drug. These results indicate that fission yeast cells make use of a diverse set of regulatory modules to counter abnormal cytoskeletal perturbations, and furthermore, that these modules act redundantly to ensure cell survival and proliferation.
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31
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Common variants on 17q25 and gene-gene interactions conferring risk of schizophrenia in Han Chinese population and regulating gene expressions in human brain. Mol Psychiatry 2016; 21:1244-50. [PMID: 26728569 DOI: 10.1038/mp.2015.204] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 10/11/2015] [Accepted: 11/05/2015] [Indexed: 11/09/2022]
Abstract
Recently, two genome-wide association studies (GWASs) of schizophrenia (SCZ) in Han Chinese identified several susceptibility loci. Replication efforts aiming to validate the GWAS findings were made and focused on the top hits. We conducted a more extensive follow-up study in an independent sample of 1471 cases and 1528 matched controls to verify 26 genetic variants by including nine top single-nucleotide polymorphisms (SNPs) that reached genome-wide significance and 17 promising SNPs nominated in the initial discovery phase. rs8073471 in an intron of tubulin-folding cofactor D (TBCD) obtained nominal significance (P<0.01) in single SNP analysis. Logistic regression identified significant interaction between rs3744165 (5'-untranslated region variant of exon 2 of zinc finger protein 750 (ZNF750), and in an intron of TBCD) and rs8073471 (Deviance test P-value=2.77 × 10(-34)). Both SNPs are located at 17q25, an interesting region that has been implicated in SCZ. By using the Genotype-Tissue Expression (GTEx) data set, we implemented an expression quantitative trait loci epistasis analysis to explore the association between the genotype combinations of the two SNPs and gene expression levels in 13 areas of human central nervous system. We observed that rs3744165 × rs8073471 interaction modulated the expression profile of TEAD3 (P=1.87 × 10(-8)), SH3TC2 (P=2.00 × 10(-8)), KCNK9 (P=5.20 × 10(-7)) and PPDPF (P=1.13 × 10(-6)) in postmortem cortex tissue; EFNA1 (P=7.26 × 10(-9)), RNU4ATAC (P=2.32 × 10(-8)) and NUPL2 (P=6.79 × 10(-8)) in cerebellum tissue. To the best of our knowledge, our study is the first one that links TBCD and ZNF750 mutations to SCZ susceptibility and to the transcript levels in human brain tissues. Further efforts are needed to understand the role of those variants in the pathogenesis of SCZ.
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32
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Ansseau E, Eidahl JO, Lancelot C, Tassin A, Matteotti C, Yip C, Liu J, Leroy B, Hubeau C, Gerbaux C, Cloet S, Wauters A, Zorbo S, Meyer P, Pirson I, Laoudj-Chenivesse D, Wattiez R, Harper SQ, Belayew A, Coppée F. Homologous Transcription Factors DUX4 and DUX4c Associate with Cytoplasmic Proteins during Muscle Differentiation. PLoS One 2016; 11:e0146893. [PMID: 26816005 PMCID: PMC4729438 DOI: 10.1371/journal.pone.0146893] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 12/24/2015] [Indexed: 12/26/2022] Open
Abstract
Hundreds of double homeobox (DUX) genes map within 3.3-kb repeated elements dispersed in the human genome and encode DNA-binding proteins. Among these, we identified DUX4, a potent transcription factor that causes facioscapulohumeral muscular dystrophy (FSHD). In the present study, we performed yeast two-hybrid screens and protein co-purifications with HaloTag-DUX fusions or GST-DUX4 pull-down to identify protein partners of DUX4, DUX4c (which is identical to DUX4 except for the end of the carboxyl terminal domain) and DUX1 (which is limited to the double homeodomain). Unexpectedly, we identified and validated (by co-immunoprecipitation, GST pull-down, co-immunofluorescence and in situ Proximal Ligation Assay) the interaction of DUX4, DUX4c and DUX1 with type III intermediate filament protein desmin in the cytoplasm and at the nuclear periphery. Desmin filaments link adjacent sarcomere at the Z-discs, connect them to sarcolemma proteins and interact with mitochondria. These intermediate filament also contact the nuclear lamina and contribute to positioning of the nuclei. Another Z-disc protein, LMCD1 that contains a LIM domain was also validated as a DUX4 partner. The functionality of DUX4 or DUX4c interactions with cytoplasmic proteins is underscored by the cytoplasmic detection of DUX4/DUX4c upon myoblast fusion. In addition, we identified and validated (by co-immunoprecipitation, co-immunofluorescence and in situ Proximal Ligation Assay) as DUX4/4c partners several RNA-binding proteins such as C1QBP, SRSF9, RBM3, FUS/TLS and SFPQ that are involved in mRNA splicing and translation. FUS and SFPQ are nuclear proteins, however their cytoplasmic translocation was reported in neuronal cells where they associated with ribonucleoparticles (RNPs). Several other validated or identified DUX4/DUX4c partners are also contained in mRNP granules, and the co-localizations with cytoplasmic DAPI-positive spots is in keeping with such an association. Large muscle RNPs were recently shown to exit the nucleus via a novel mechanism of nuclear envelope budding. Following DUX4 or DUX4c overexpression in muscle cell cultures, we observed their association with similar nuclear buds. In conclusion, our study demonstrated unexpected interactions of DUX4/4c with cytoplasmic proteins playing major roles during muscle differentiation. Further investigations are on-going to evaluate whether these interactions play roles during muscle regeneration as previously suggested for DUX4c.
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Affiliation(s)
- Eugénie Ansseau
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Jocelyn O. Eidahl
- Center for Gene Therapy, Research Institute at Nationwide Children's Hospital, Columbus, OH, United States of America
| | - Céline Lancelot
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Alexandra Tassin
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Christel Matteotti
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Cassandre Yip
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Jian Liu
- Center for Gene Therapy, Research Institute at Nationwide Children's Hospital, Columbus, OH, United States of America
| | - Baptiste Leroy
- Laboratory of Proteomic and Microbiology, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Céline Hubeau
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Cécile Gerbaux
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Samuel Cloet
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Armelle Wauters
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Sabrina Zorbo
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Pierre Meyer
- Pediatric Department, CHRU Montpellier, Montpellier, France
| | - Isabelle Pirson
- I.R.I.B.H.M., Free University of Brussels, Brussels, Belgium
| | | | - Ruddy Wattiez
- Laboratory of Proteomic and Microbiology, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Scott Q. Harper
- Center for Gene Therapy, Research Institute at Nationwide Children's Hospital, Columbus, OH, United States of America
- Department of Pediatrics, Ohio State University College of Medicine, Columbus, OH, United States of America
| | - Alexandra Belayew
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Frédérique Coppée
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
- * E-mail:
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33
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Abstract
Biogenesis of the Gram-negative outer membrane involves the chaperone seventeen kilodalton protein (Skp). A Skp trimer is currently thought to bind its unfolded outer membrane protein (uOMP) substrates. Using sedimentation equilibrium, we discovered that Skp is not an obligate trimer under physiological conditions and that Na(+), Cl(-), Mg(2+), and PO4(3-) ions are not linked to Skp trimerization. These findings suggest that electrostatics play a negligible role in Skp assembly. Our results demonstrate that Skp monomers are populated at biologically relevant concentrations, which raises the idea that kinetic formation of Skp-uOMP complexes likely involves Skp monomer assembly around its substrate. In addition, van't Hoff analysis of Skp self-association does not support a previously proposed coupled folding and trimerization of Skp.
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Affiliation(s)
- Clifford W. Sandlin
- T.C. Jenkins Department of Biophysics, The Johns Hopkins University, Baltimore MD 21218
| | - Nathan R. Zaccai
- T.C. Jenkins Department of Biophysics, The Johns Hopkins University, Baltimore MD 21218
| | - Karen G. Fleming
- T.C. Jenkins Department of Biophysics, The Johns Hopkins University, Baltimore MD 21218
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Wang P, Zhao J, Yang X, Guan S, Feng H, Han D, Lu J, Ou B, Jin R, Sun J, Zong Y, Feng B, Ma J, Lu A, Zheng M. PFDN1, an indicator for colorectal cancer prognosis, enhances tumor cell proliferation and motility through cytoskeletal reorganization. Med Oncol 2015; 32:264. [PMID: 26553318 DOI: 10.1007/s12032-015-0710-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 10/31/2015] [Indexed: 11/24/2022]
Abstract
Prefoldin (PFDN) subunits have been reported upregulated in various tumor types, while the expression and functions of PFDN1 (PFDN subunit 1) in colorectal cancer (CRC) are not well elucidated. The aim of this study was to investigate the use of PFDN1 as a poor prognosis indicator for CRC and explore the functions of PFDN1 in CRC. The relationship between PFDN1 expression and CRC clinical-pathological statistics was detected on the tissue microarray containing 145 cases of CRC. ShRNA was used to silence PFDN1 expression in SW480 and RKO CRC cells, and these transfected cells were analyzed for changes in proliferation, colony formation, cell cycle, migration, and invasion. Immunofluorescence and immunoblot were used to determine the remodeling of the F-actin and α-tubulin. Finally, tumor growth on nude mice was observed and measured. In this study, we found PFDN1 was upregulated in CRC tissues compared with adjacent normal tissues. Also, PFDN1 expression positively correlated with tumor size and tumor invasion. Moreover, after silencing PFDN1 in SW480 and RKO cells, the proliferation and motility of CRC cells were significantly suppressed. The inhibitory effect of PFDN1 on tumor cell growth and motility was partially due to G2/M cell cycle blockage and cytoskeletal deficiency. Finally, in vivo assay showed that downregulation of PFDN1 inhibited tumor growth on nude mice and PFDN1 expression correlated with higher levels of Ki-67 staining. These findings indicate that PFDN1 was involved in the progression of CRC, and provide new insights into PFDN1 as a potential therapeutic target for CRC treatment.
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Affiliation(s)
- Puxiongzhi Wang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China. .,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai, China.
| | - Jingkun Zhao
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai, China
| | - Xiao Yang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai, China
| | - Shaopei Guan
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai, China
| | - Hao Feng
- School of Medicine, University of Munich, Munich, Germany
| | - Dingpei Han
- Department of Thoracic Surgery, Ruijin Hospital, Shanghai, China
| | - Jun Lu
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Baochi Ou
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Runsen Jin
- Department of Thoracic Surgery, Ruijin Hospital, Shanghai, China
| | - Jing Sun
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai, China
| | - Yaping Zong
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai, China
| | - Bo Feng
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Junjun Ma
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Aiguo Lu
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China. .,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai, China.
| | - Minhua Zheng
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai, China
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35
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Olshina MA, Baumann H, Willison KR, Baum J. Plasmodium actin is incompletely folded by heterologous protein-folding machinery and likely requires the native Plasmodium chaperonin complex to enter a mature functional state. FASEB J 2015; 30:405-16. [PMID: 26443825 PMCID: PMC5423778 DOI: 10.1096/fj.15-276618] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 09/14/2015] [Indexed: 12/18/2022]
Abstract
Actin filament turnover underpins several processes in the life cycle of the malaria parasite, Plasmodium falciparum. Polymerization and depolymerization are especially important for gliding motility, a substrate-dependent form of cell movement that underpins the protozoan parasite’s ability to disseminate and invade host cells. To date, given difficulties in extraction of native actins directly from parasites, much of our biochemical understanding of malarial actin has instead relied on recombinant protein extracted and purified from heterologous protein expression systems. Here, using in vitro transcription-translation methodologies and quantitative protein-binding assays, we explored the folding state of heterologously expressed P. falciparum actin 1 (PfACTI) with the aim of assessing the reliability of current recombinant-protein-based data. We demonstrate that PfACTI, when expressed in non-native systems, is capable of binding to and release from bacterial, yeast, and mammalian chaperonin complexes but appears to be incompletely folded. Characterization of the native Plasmodium folding machinery in silico, the chaperonin containing t-complex protein-1 complex, highlights key divergences between the different chaperonin systems that likely underpins this incomplete folded state. These results highlight the importance of characterizing actin’s folded state and raise concerns about the interpretation of actin polymerization kinetics based solely on protein derived from heterologous expression systems.—Olshina, M. A., Baumann, H., Willison, K. R., Baum, J. Plasmodium actin is incompletely folded by heterologous protein-folding machinery and likely requires the native Plasmodium chaperonin complex to enter a mature functional state.
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Affiliation(s)
- Maya A Olshina
- *Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia; Department of Life Sciences and Department of Chemistry, Imperial College London, South Kensington, London, United Kingdom
| | - Hella Baumann
- *Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia; Department of Life Sciences and Department of Chemistry, Imperial College London, South Kensington, London, United Kingdom
| | - Keith R Willison
- *Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia; Department of Life Sciences and Department of Chemistry, Imperial College London, South Kensington, London, United Kingdom
| | - Jake Baum
- *Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia; Department of Life Sciences and Department of Chemistry, Imperial College London, South Kensington, London, United Kingdom
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Nithianantham S, Le S, Seto E, Jia W, Leary J, Corbett KD, Moore JK, Al-Bassam J. Tubulin cofactors and Arl2 are cage-like chaperones that regulate the soluble αβ-tubulin pool for microtubule dynamics. eLife 2015. [PMID: 26208336 PMCID: PMC4574351 DOI: 10.7554/elife.08811] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Microtubule dynamics and polarity stem from the polymerization of
αβ-tubulin heterodimers. Five conserved tubulin cofactors/chaperones
and the Arl2 GTPase regulate α- and β-tubulin assembly into
heterodimers and maintain the soluble tubulin pool in the cytoplasm, but their
physical mechanisms are unknown. Here, we reconstitute a core tubulin chaperone
consisting of tubulin cofactors TBCD, TBCE, and Arl2, and reveal a cage-like
structure for regulating αβ-tubulin. Biochemical assays and electron
microscopy structures of multiple intermediates show the sequential binding of
αβ-tubulin dimer followed by tubulin cofactor TBCC onto this chaperone,
forming a ternary complex in which Arl2 GTP hydrolysis is activated to alter
αβ-tubulin conformation. A GTP-state locked Arl2 mutant inhibits
ternary complex dissociation in vitro and causes severe defects in microtubule
dynamics in vivo. Our studies suggest a revised paradigm for tubulin cofactors and
Arl2 functions as a catalytic chaperone that regulates soluble
αβ-tubulin assembly and maintenance to support microtubule
dynamics. DOI:http://dx.doi.org/10.7554/eLife.08811.001 Cells contain a network of protein filaments called microtubules. These filaments are
involved in many biological processes; for example, they help cells keep the right
shape, and they help to transport proteins and other materials inside cells. Two proteins called α-tubulin and β-tubulin are the building blocks of
microtubules. The filaments are very dynamic structures that can rapidly change
length as individual tubulin units are either added or removed to the filament ends.
Several proteins known as tubulin cofactors and an enzyme called Arl2 help to build a
vast pool of tubulin units that are able attach to the microtubules. These
units—called αβ-tubulin—are formed by α-tubulin
and β-tubulin binding to each other, but it not clear exactly what roles the
tubulin cofactors and Arl2 play in this process. Nithianantham et al. used a combination of microscopy and biochemical techniques to
study how the tubulin cofactors and Arl2 are organised, and their role in the
assembly of microtubules in yeast. The experiments show that Arl2 and two tubulin
cofactors associate with each other to form a stable ‘complex’ that has
a cage-like structure. A molecule of αβ-tubulin binds to the complex,
followed by another cofactor called TBCC. This activates the enzyme activity of Arl2,
which releases the energy needed to alter the shape of the αβ-tubulin.
Nithianantham et al. also found that yeast cells with a mutant form of Arl2 that
lacked enzyme activity had problems forming microtubules. Together, these findings show that the tubulin cofactors and Arl2 form a complex that
regulates the assembly and maintenance of αβ-tubulin. The next
challenge is to understand how this regulation influences the way that microtubules
grow and shrink inside cells. DOI:http://dx.doi.org/10.7554/eLife.08811.002
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Affiliation(s)
- Stanley Nithianantham
- Department of Molecular Cellular Biology, University of California, Davis, Davis, United States
| | - Sinh Le
- Department of Molecular Cellular Biology, University of California, Davis, Davis, United States
| | - Elbert Seto
- Department of Molecular Cellular Biology, University of California, Davis, Davis, United States
| | - Weitao Jia
- Department of Molecular Cellular Biology, University of California, Davis, Davis, United States
| | - Julie Leary
- Department of Molecular Cellular Biology, University of California, Davis, Davis, United States
| | - Kevin D Corbett
- Ludwig Institute for Cancer Research, University of California, San Diego, San Diego, United States
| | - Jeffrey K Moore
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, United States
| | - Jawdat Al-Bassam
- Department of Molecular Cellular Biology, University of California, Davis, Davis, United States
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37
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Barrack KL, Fyfe PK, Finney AJ, Hunter WN. Crystal structure of the C-terminal domain of tubulin-binding cofactor C from Leishmania major. Mol Biochem Parasitol 2015; 201:26-30. [PMID: 25982270 PMCID: PMC4539340 DOI: 10.1016/j.molbiopara.2015.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 05/01/2015] [Accepted: 05/08/2015] [Indexed: 01/23/2023]
Abstract
Tubulin-binding cofactor C stimulates GTPase activity and contributes to the release of the heterodimeric α/β-tubulin from a super-complex of tubulin monomers and two ancillary cofactors. We have determined the 2.2 Å resolution crystal structure of the C-terminal domain of tubulin-binding cofactor C from Leishmania major based on single wavelength anomalous dispersion measurements targeting a selenomethionine derivative. Although previously predicted to consist of two domains the structure is best described as a single domain dominated by a right-handed β-helix of five turns that form a triangular prism. One face of the prism is covered by the C-terminal residues leaving another face solvent exposed. Comparisons with an orthologous human GTPase activating protein match key residues involved in binding nucleotide and identify the face of the β-helix fold likely involved in interacting with the β-tubulin:GTP complex.
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Affiliation(s)
- Keri L Barrack
- Division of Biological Chemistry & Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Paul K Fyfe
- Division of Biological Chemistry & Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Alex J Finney
- Division of Biological Chemistry & Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - William N Hunter
- Division of Biological Chemistry & Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK.
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38
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Kodavanti PRS, Royland JE, Osorio C, Winnik WM, Ortiz P, Lei L, Ramabhadran R, Alzate O. Developmental exposure to a commercial PBDE mixture: effects on protein networks in the cerebellum and hippocampus of rats. ENVIRONMENTAL HEALTH PERSPECTIVES 2015; 123:428-36. [PMID: 25616259 PMCID: PMC4421769 DOI: 10.1289/ehp.1408504] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 12/17/2014] [Indexed: 05/03/2023]
Abstract
BACKGROUND Polybrominated diphenyl ethers (PBDEs) are structurally similar to polychlorinated biphenyls (PCBs) and have both central (learning and memory deficits) and peripheral (motor dysfunction) neurotoxic effects at concentrations/doses similar to those of PCBs. The cellular and molecular mechanisms for these neurotoxic effects are not fully understood; however, several studies have shown that PBDEs affect thyroid hormones, cause oxidative stress, and disrupt Ca2+-mediated signal transduction. Changes in these signal transduction pathways can lead to differential gene regulation with subsequent changes in protein expression, which can affect the development and function of the nervous system. OBJECTIVE In this study, we examined the protein expression profiles in the rat cerebellum and hippocampus following developmental exposure to a commercial PBDE mixture, DE-71. METHODS Pregnant Long-Evans rats were dosed perinatally with 0 or 30.6 mg/kg/day of DE-71 from gestation day 6 through sampling on postnatal day 14. Proteins from the cerebellum and hippocampus were extracted, expression differences were detected by two-dimensional difference gel electrophoresis, and proteins were identified by tandem mass spectrometry. Protein network interaction analysis was performed using Ingenuity® Pathway Analysis, and the proteins of interest were validated by Western blotting. RESULTS Four proteins were significantly differentially expressed in the cerebellum following DE-71 exposure, whereas 70 proteins were significantly differentially expressed in the hippocampus. Of these proteins, 4 from the cerebellum and 47 from the hippocampus, identifiable by mass spectrometry, were found to have roles in mitochondrial energy metabolism, oxidative stress, apoptosis, calcium signaling, and growth of the nervous system. CONCLUSIONS Results suggest that changes in energy metabolism and processes related to neuroplasticity and growth may be involved in the developmental neurotoxicity of PBDEs.
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Affiliation(s)
- Prasada Rao S Kodavanti
- Neurotoxicology Branch, and 2Genetic and Cellular Toxicology Branch, Office of Research and Development (ORD), U.S. Environmental Protection Agency (EPA), Research Triangle Park, North Carolina, USA
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39
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Barrack KL, Fyfe PK, Hunter WN. The structure of tubulin-binding cofactor A from Leishmania major infers a mode of association during the early stages of microtubule assembly. Acta Crystallogr F Struct Biol Commun 2015; 71:539-46. [PMID: 25945706 PMCID: PMC4427162 DOI: 10.1107/s2053230x15000990] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 01/16/2015] [Indexed: 11/13/2022] Open
Abstract
Tubulin-binding cofactor A (TBCA) participates in microtubule formation, a key process in eukaryotic biology to create the cytoskeleton. There is little information on how TBCA might interact with β-tubulin en route to microtubule biogenesis. To address this, the protozoan Leishmania major was targeted as a model system. The crystal structure of TBCA and comparisons with three orthologous proteins are presented. The presence of conserved features infers that electrostatic interactions that are likely to involve the C-terminal tail of β-tubulin are key to association. This study provides a reagent and template to support further work in this area.
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Affiliation(s)
- Keri L. Barrack
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
| | - Paul K. Fyfe
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
| | - William N. Hunter
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
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40
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Serna M, Carranza G, Martín-Benito J, Janowski R, Canals A, Coll M, Zabala JC, Valpuesta JM. The structure of the complex between α-tubulin, TBCE and TBCB reveals a tubulin dimer dissociation mechanism. J Cell Sci 2015; 128:1824-34. [PMID: 25908846 DOI: 10.1242/jcs.167387] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 03/16/2015] [Indexed: 11/20/2022] Open
Abstract
Tubulin proteostasis is regulated by a group of molecular chaperones termed tubulin cofactors (TBC). Whereas tubulin heterodimer formation is well-characterized biochemically, its dissociation pathway is not clearly understood. Here, we carried out biochemical assays to dissect the role of the human TBCE and TBCB chaperones in α-tubulin-β-tubulin dissociation. We used electron microscopy and image processing to determine the three-dimensional structure of the human TBCE, TBCB and α-tubulin (αEB) complex, which is formed upon α-tubulin-β-tubulin heterodimer dissociation by the two chaperones. Docking the atomic structures of domains of these proteins, including the TBCE UBL domain, as we determined by X-ray crystallography, allowed description of the molecular architecture of the αEB complex. We found that heterodimer dissociation is an energy-independent process that takes place through a disruption of the α-tubulin-β-tubulin interface that is caused by a steric interaction between β-tubulin and the TBCE cytoskeleton-associated protein glycine-rich (CAP-Gly) and leucine-rich repeat (LRR) domains. The protruding arrangement of chaperone ubiquitin-like (UBL) domains in the αEB complex suggests that there is a direct interaction of this complex with the proteasome, thus mediating α-tubulin degradation.
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Affiliation(s)
- Marina Serna
- Departamento de Estructura de Macromoléculas, Centro Nacional de Biotecnología (CNB-CSIC), Madrid 28049, Spain
| | - Gerardo Carranza
- Departamento de Biología Molecular, Facultad de Medicina, IDIVAL-Universidad de Cantabria, Santander 39011, Spain
| | - Jaime Martín-Benito
- Departamento de Estructura de Macromoléculas, Centro Nacional de Biotecnología (CNB-CSIC), Madrid 28049, Spain
| | - Robert Janowski
- Departamento de Biología Estructural y Computacional, Institute for Research in Biomedicine (IRB-Barcelona), Barcelona 08028, Spain Departamento de Biología Estructural, Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Barcelona 08028, Spain
| | - Albert Canals
- Departamento de Biología Estructural y Computacional, Institute for Research in Biomedicine (IRB-Barcelona), Barcelona 08028, Spain Departamento de Biología Estructural, Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Barcelona 08028, Spain
| | - Miquel Coll
- Departamento de Biología Estructural y Computacional, Institute for Research in Biomedicine (IRB-Barcelona), Barcelona 08028, Spain Departamento de Biología Estructural, Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Barcelona 08028, Spain
| | - Juan Carlos Zabala
- Departamento de Biología Molecular, Facultad de Medicina, IDIVAL-Universidad de Cantabria, Santander 39011, Spain
| | - José María Valpuesta
- Departamento de Estructura de Macromoléculas, Centro Nacional de Biotecnología (CNB-CSIC), Madrid 28049, Spain
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41
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Johnson CR, Weems AD, Brewer JM, Thorner J, McMurray MA. Cytosolic chaperones mediate quality control of higher-order septin assembly in budding yeast. Mol Biol Cell 2015; 26:1323-44. [PMID: 25673805 PMCID: PMC4454179 DOI: 10.1091/mbc.e14-11-1531] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Septin hetero-oligomers polymerize into cytoskeletal filaments with essential functions in many eukaryotic cell types. Mutations within the oligomerization interface that encompasses the GTP-binding pocket of a septin (its "G interface") cause thermoinstability of yeast septin hetero-oligomer assembly, and human disease. When coexpressed with its wild-type counterpart, a G interface mutant is excluded from septin filaments, even at moderate temperatures. We show that this quality control mechanism is specific to G interface mutants, operates during de novo septin hetero-oligomer assembly, and requires specific cytosolic chaperones. Chaperone overexpression lowers the temperature permissive for proliferation of cells expressing a G interface mutant as the sole source of a given septin. Mutations that perturb the septin G interface retard release from these chaperones, imposing a kinetic delay on the availability of nascent septin molecules for higher-order assembly. Un-expectedly, the disaggregase Hsp104 contributes to this delay in a manner that does not require its "unfoldase" activity, indicating a latent "holdase" activity toward mutant septins. These findings provide new roles for chaperone-mediated kinetic partitioning of non-native proteins and may help explain the etiology of septin-linked human diseases.
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Affiliation(s)
- Courtney R Johnson
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Andrew D Weems
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Jennifer M Brewer
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Jeremy Thorner
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Michael A McMurray
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
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42
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Abstract
Microtubules (MTs) are highly conserved polar polymers that are key elements of the eukaryotic cytoskeleton and are essential for various cell functions. αβ-tubulin, a heterodimer containing one structural GTP and one hydrolysable and exchangeable GTP, is the building block of MTs and is formed by the sequential action of several molecular chaperones. GTP hydrolysis in the MT lattice is mechanistically coupled with MT growth, thus giving MTs a metastable and dynamic nature. MTs adopt several distinct higher-order organizations that function in cell division and cell morphogenesis. Small molecular weight compounds that bind tubulin are used as herbicides and as research tools to investigate MT functions in plant cells. The de novo formation of MTs in cells requires conserved γ-tubulin-containing complexes and targeting/activating regulatory proteins that contribute to the geometry of MT arrays. Various MT regulators and tubulin modifications control the dynamics and organization of MTs throughout the cell cycle and in response to developmental and environmental cues. Signaling pathways that converge on the regulation of versatile MT functions are being characterized.
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Affiliation(s)
- Takashi Hashimoto
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara 630-0192, Japan
- Address correspondence to
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43
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Khowal S, Mustufa MMA, Chaudhary NK, Naqvi SH, Parvez S, Jain SK, Wajid S. Assessment of the therapeutic potential of hesperidin and proteomic resolution of diabetes-mediated neuronal fluctuations expediting Alzheimer’s disease. RSC Adv 2015. [DOI: 10.1039/c5ra01977j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Alzheimer’s disease (AD) has been proposed as type III diabetes mellitus. Prognosis and early stage diagnosis of AD is essentially required in diabetes to avoid extensive irreversible neuronal damage.
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Affiliation(s)
- Sapna Khowal
- Department of Biotechnology
- Faculty of Science
- Hamdard University (Jamia Hamdard)
- India
| | - Malik M. A. Mustufa
- Department of Biotechnology
- Faculty of Science
- Hamdard University (Jamia Hamdard)
- India
| | - Naveen K. Chaudhary
- Department of Biotechnology
- Faculty of Science
- Hamdard University (Jamia Hamdard)
- India
| | | | - Suhel Parvez
- Department of Medical Elementology and Toxicology
- Faculty of Science
- Hamdard University (Jamia Hamdard)
- India
| | - Swatantra K. Jain
- Department of Biochemistry
- Hamdard Institute of Medical Sciences and Research
- Hamdard University (Jamia Hamdard)
- India
| | - Saima Wajid
- Department of Biotechnology
- Faculty of Science
- Hamdard University (Jamia Hamdard)
- India
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Jordán-Pla A, Gupta I, de Miguel-Jiménez L, Steinmetz LM, Chávez S, Pelechano V, Pérez-Ortín JE. Chromatin-dependent regulation of RNA polymerases II and III activity throughout the transcription cycle. Nucleic Acids Res 2014; 43:787-802. [PMID: 25550430 PMCID: PMC4333398 DOI: 10.1093/nar/gku1349] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The particular behaviour of eukaryotic RNA polymerases along different gene regions and amongst distinct gene functional groups is not totally understood. To cast light onto the alternative active or backtracking states of RNA polymerase II, we have quantitatively mapped active RNA polymerases at a high resolution following a new biotin-based genomic run-on (BioGRO) technique. Compared with conventional profiling with chromatin immunoprecipitation, the analysis of the BioGRO profiles in Saccharomyces cerevisiae shows that RNA polymerase II has unique activity profiles at both gene ends, which are highly dependent on positioned nucleosomes. This is the first demonstration of the in vivo influence of positioned nucleosomes on transcription elongation. The particular features at the 5' end and around the polyadenylation site indicate that this polymerase undergoes extensive specific-activity regulation in the initial and final transcription elongation phases. The genes encoding for ribosomal proteins show distinctive features at both ends. BioGRO also provides the first nascentome analysis for RNA polymerase III, which indicates that transcription of tRNA genes is poorly regulated at the individual copy level. The present study provides a novel perspective of the transcription cycle that incorporates inactivation/reactivation as an important aspect of RNA polymerase dynamics.
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Affiliation(s)
- Antonio Jordán-Pla
- Departamento de Bioquímica y Biología Molecular and ERI Biotecmed, Facultad de Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain
| | - Ishaan Gupta
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Lola de Miguel-Jiménez
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, 41013 Seville, Spain
| | - Lars M Steinmetz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany Stanford University School of Medicine, Department of Genetics, Stanford, CA 94305, USA Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA
| | - Sebastián Chávez
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, 41013 Seville, Spain
| | - Vicent Pelechano
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - José E Pérez-Ortín
- Departamento de Bioquímica y Biología Molecular and ERI Biotecmed, Facultad de Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain
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S-Nitrosylation in neurogenesis and neuronal development. Biochim Biophys Acta Gen Subj 2014; 1850:1588-93. [PMID: 25527866 DOI: 10.1016/j.bbagen.2014.12.013] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 12/03/2014] [Accepted: 12/10/2014] [Indexed: 12/27/2022]
Abstract
BACKGROUND Nitric oxide (NO) is a pleiotropic messenger molecule. The multidimensional actions of NO species are, in part, mediated by their redox nature. Oxidative posttranslational modification of cysteine residues to regulate protein function, termed S-nitrosylation, constitutes a major form of redox-based signaling by NO. SCOPE OF REVIEW S-Nitrosylation directly modifies a number of cytoplasmic and nuclear proteins in neurons. S-Nitrosylation modulates neuronal development by reaction with specific proteins, including the transcription factor MEF2. This review focuses on the impact of S-nitrosylation on neurogenesis and neuronal development. MAJOR CONCLUSIONS Functional characterization of S-nitrosylated proteins that regulate neuronal development represents a rapidly emerging field. Recent studies reveal that S-nitrosylation-mediated redox signaling plays an important role in several biological processes essential for neuronal differentiation and maturation. GENERAL SIGNIFICANCE Investigation of S-nitrosylation in the nervous system has elucidated new molecular and cellular mechanisms for neuronal development. S-Nitrosylated proteins in signaling networks modulate key events in brain development. Dysregulation of this redox-signaling pathway may contribute to neurodevelopmental disabilities such as autism spectrum disorder (ASD). Thus, further elucidation of the involvement of S-nitrosylation in brain development may offer potential therapeutic avenues for neurodevelopmental disorders. This article is part of a Special Issue entitled Redox regulation of differentiation and de-differentiation.
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Taipale M, Tucker G, Peng J, Krykbaeva I, Lin ZY, Larsen B, Choi H, Berger B, Gingras AC, Lindquist S. A quantitative chaperone interaction network reveals the architecture of cellular protein homeostasis pathways. Cell 2014; 158:434-448. [PMID: 25036637 DOI: 10.1016/j.cell.2014.05.039] [Citation(s) in RCA: 295] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 03/08/2014] [Accepted: 05/16/2014] [Indexed: 12/27/2022]
Abstract
Chaperones are abundant cellular proteins that promote the folding and function of their substrate proteins (clients). In vivo, chaperones also associate with a large and diverse set of cofactors (cochaperones) that regulate their specificity and function. However, how these cochaperones regulate protein folding and whether they have chaperone-independent biological functions is largely unknown. We combined mass spectrometry and quantitative high-throughput LUMIER assays to systematically characterize the chaperone-cochaperone-client interaction network in human cells. We uncover hundreds of chaperone clients, delineate their participation in specific cochaperone complexes, and establish a surprisingly distinct network of protein-protein interactions for cochaperones. As a salient example of the power of such analysis, we establish that NUDC family cochaperones specifically associate with structurally related but evolutionarily distinct β-propeller folds. We provide a framework for deciphering the proteostasis network and its regulation in development and disease and expand the use of chaperones as sensors for drug-target engagement.
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Affiliation(s)
- Mikko Taipale
- Whitehead Institute for Biomedical Research, Cambridge, MA 02114, USA
| | - George Tucker
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jian Peng
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Irina Krykbaeva
- Whitehead Institute for Biomedical Research, Cambridge, MA 02114, USA
| | - Zhen-Yuan Lin
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1X5, Canada
| | - Brett Larsen
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1X5, Canada
| | - Hyungwon Choi
- National University of Singapore and National University Health System, Singapore 117597, Singapore
| | - Bonnie Berger
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Anne-Claude Gingras
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, MA 02114, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA.
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Sergeeva OA, Tran MT, Haase-Pettingell C, King JA. Biochemical characterization of mutants in chaperonin proteins CCT4 and CCT5 associated with hereditary sensory neuropathy. J Biol Chem 2014; 289:27470-80. [PMID: 25124038 DOI: 10.1074/jbc.m114.576033] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Hereditary sensory neuropathies are a class of disorders marked by degeneration of the nerve fibers in the sensory periphery neurons. Recently, two mutations were identified in the subunits of the eukaryotic cytosolic chaperonin TRiC, a protein machine responsible for folding actin and tubulin in the cell. C450Y CCT4 was identified in a stock of Sprague-Dawley rats, whereas H147R CCT5 was found in a human Moroccan family. As with many genetically identified mutations associated with neuropathies, the underlying molecular basis of the mutants was not defined. We investigated the biochemical properties of these mutants using an expression system in Escherichia coli that produces homo-oligomeric rings of CCT4 and CCT5. Full-length versions of both mutant protein chains were expressed in E. coli at levels approaching that of the WT chains. Sucrose gradient centrifugation revealed chaperonin-sized complexes of both WT and mutant chaperonins, but with reduced recovery of C450Y CCT4 soluble subunits. Electron microscopy of negatively stained samples of C450Y CCT4 revealed few ring-shaped species, whereas WT CCT4, H147R CCT5, and WT CCT5 revealed similar ring structures. CCT5 complexes were assayed for their ability to suppress aggregation of and refold the model substrate γd-crystallin, suppress aggregation of mutant huntingtin, and refold the physiological substrate β-actin in vitro. H147R CCT5 was not as efficient in chaperoning these substrates as WT CCT5. The subtle effects of these mutations are consistent with the homozygous disease phenotype, in which most functions are carried out during development and adulthood, but some selective function is lost or reduced.
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Affiliation(s)
- Oksana A Sergeeva
- From the Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Meme T Tran
- From the Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Cameron Haase-Pettingell
- From the Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Jonathan A King
- From the Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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Phelps DS, Umstead TM, Floros J. Sex differences in the acute in vivo effects of different human SP-A variants on the mouse alveolar macrophage proteome. J Proteomics 2014; 108:427-44. [PMID: 24954098 DOI: 10.1016/j.jprot.2014.06.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 05/28/2014] [Accepted: 06/10/2014] [Indexed: 01/06/2023]
Abstract
UNLABELLED Surfactant protein A (SP-A) is involved in lung innate immunity. Humans have two SP-A genes, SFTPA1 and SFTPA2, each with several variants. We examined the in vivo effects of treatment with specific SP-A variants on the alveolar macrophage (AM) proteome from SP-A knockout (KO) mice. KO mice received either SP-A1, SP-A2, or both. AM were collected and their proteomes examined with 2D-DIGE. We identified 90 proteins and categorized them as related to actin/cytoskeleton, oxidative stress, protease balance/chaperones, regulation of inflammation, and regulatory/developmental processes. SP-A1 and SP-A2 had different effects on the AM proteome and these effects differed between sexes. In males more changes occurred in the oxidative stress, protease/chaperones, and inflammation groups with SP-A2 treatment than with SP-A1. In females most SP-A1-induced changes were in the actin/cytoskeletal and oxidative stress groups. We conclude that after acute SP-A1 and SP-A2 treatment, sex-specific differences were observed in the AM proteomes from KO mice, and that these sex differences differ in response to SP-A1 and SP-A2. Females are more responsive to SP-A1, whereas the gene-specific differences in males were minimal. These observations not only demonstrate the therapeutic potential of exogenous SP-A, but also illustrate sex- and gene-specific differences in the response to it. BIOLOGICAL SIGNIFICANCE This study shows that changes occur in the alveolar macrophage proteome in response to a single in vivo treatment with exogenous SP-A1 and/or SP-A2. We demonstrate that SP-A1 and SP-A2 have different effects on the AM proteome and that sex differences exist in the response to each SP-A1 and SP-A2 gene product. This study illustrates the potential of exogenous SP-A1 and SP-A2 treatment for the manipulation of macrophage function and indicates that the specific SP-A variant used for treatment may vary with sex and with the cellular functions being modified. The observed changes may contribute to sex differences in the incidence of some lung diseases.
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Affiliation(s)
- David S Phelps
- The Center for Host Defense, Inflammation, and Lung Disease (CHILD) Research, Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Todd M Umstead
- The Center for Host Defense, Inflammation, and Lung Disease (CHILD) Research, Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Joanna Floros
- The Center for Host Defense, Inflammation, and Lung Disease (CHILD) Research, Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, PA, USA; Department of Obstetrics and Gynecology, The Pennsylvania State University College of Medicine, Hershey, PA, USA.
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Poulton CJ, Schot R, Seufert K, Lequin MH, Accogli A, Annunzio GD, Villard L, Philip N, de Coo R, Catsman-Berrevoets C, Grasshoff U, Kattentidt-Mouravieva A, Calf H, de Vreugt-Gronloh E, van Unen L, Verheijen FW, Galjart N, Morris-Rosendahl DJ, Mancini GMS. Severe presentation ofWDR62mutation: Is there a role for modifying genetic factors? Am J Med Genet A 2014; 164A:2161-71. [DOI: 10.1002/ajmg.a.36611] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 04/06/2014] [Indexed: 11/09/2022]
Affiliation(s)
- Cathryn J. Poulton
- Department of Clinical Genetics; Erasmus Medical Center; Rotterdam Germany
| | - Rachel Schot
- Department of Clinical Genetics; Erasmus Medical Center; Rotterdam Germany
| | - Katja Seufert
- Institute of Human Genetics; Albert-Ludwigs University Medical Centre Freiburg; Freiburg Germany
| | | | - Andrea Accogli
- Department of Pediatrics; Gaslini Institute; Genova Italy
| | | | | | - Nicole Philip
- Inserm U910; Aix Marseille University; Marseille France
| | - René de Coo
- Department of Child Neurology; Erasmus Medical Center; Rotterdam Germany
| | | | - Ute Grasshoff
- Institute of Medical Genetics and Applied Genomics; University Hospital Tuebingen; Tuebingen Germany
| | | | - Hans Calf
- ASVZ Zuid West; Rotterdam the Netherlands
| | | | - Leontine van Unen
- Department of Clinical Genetics; Erasmus Medical Center; Rotterdam Germany
| | - Frans W. Verheijen
- Department of Clinical Genetics; Erasmus Medical Center; Rotterdam Germany
| | - Niels Galjart
- Department of Cell Biology; Erasmus Medical Center; Rotterdam the Netherlands
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Choi YN, Lee SK, Seo TW, Lee JS, Yoo SJ. C-terminus of Hsc70-interacting protein regulates profilin1 and breast cancer cell migration. Biochem Biophys Res Commun 2014; 446:1060-6. [DOI: 10.1016/j.bbrc.2014.03.061] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 03/15/2014] [Indexed: 10/25/2022]
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