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Lefa P, Samiotaki M, Farmaki T. Proteome Analysis of the ROF-FKBP Mutants Reveals Functional Relations among Heat Stress Responses, Plant Development, and Protein Quality Control during Heat Acclimation in Arabidopsis thaliana. ACS OMEGA 2024; 9:2391-2408. [PMID: 38250364 PMCID: PMC10795062 DOI: 10.1021/acsomega.3c06773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/24/2023] [Accepted: 12/07/2023] [Indexed: 01/23/2024]
Abstract
In the present study, a differential screening following heat stress acclimation was performed in Arabidopsis thaliana WT and ROF-FKBP mutated plants using mass spectrometry, and the results were used to understand and analyze the effect of the ROF PPIases during thermotolerance acquisition in plants. Our data highlight the central role of these two PPIases in heat stress and point to their direct or indirect effect on other proteins participating in cellular functions such as protein folding and quality control, cell division, photosynthesis, and other metabolic and signaling processes. Specifically, the heat stress response, protein folding, and protein ER processing pathways are enhanced following a 37 °C acclimation period independent of the mutation state. However, at 37 °C, and in the double-mutated rof1-/2- plants, a higher accumulation of proteins belonging to the above pathways is observed compared with all other conditions (WT, single mutants, control, and heat-acclimated plants). Furthermore, the proteasomal pathway, involving the common member of both the protasomal and the lysosomal degradation pathway, CDC48, is over-represented in the extracts of both the untreated and heat-stressed rof1-/2- mutants compared with the other extracts. In contrast, in the single rof1- mutation, the heat acclimation pathway is suppressed at 37 °C when compared to the WT. Protein accumulation related to the heat stress and the protein quality control pathways points to a differential but also synergistic role of the two proteins. Protein complexes of other biochemical and developmental mechanisms, such as the light-harvesting complex of the photosynthetic pathway and the phosphoinositide binding proteins involved in membrane-trafficking events during cell plate formation and cytokinesis (patellin 1, 2, and 4), are negatively regulated in the rof1-/2- mutant. Our results suggest that ROF1 and ROF2 FKBPs regulate stress response, and developmental and metabolic pathways via a complex feedback mechanism involving partners that ensure protein quality control and plant survival during heat stress.
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Affiliation(s)
- Paraskevi Lefa
- Institute
of Applied Biosciences, Center for Research and Technology—Hellas, Sixth km Charilaou-Thermi rd., 57001 Thermi Thessaloniki, Greece
| | - Martina Samiotaki
- Biomedical
Sciences Research Center “Alexander Fleming”, Institute for Bioinnovation, 16672 Vari, Greece
| | - Theodora Farmaki
- Institute
of Applied Biosciences, Center for Research and Technology—Hellas, Sixth km Charilaou-Thermi rd., 57001 Thermi Thessaloniki, Greece
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Chavarria C, Zaffalon L, Ribeiro ST, Op M, Quadroni M, Iatrou MS, Chapuis C, Martinon F. ER-trafficking triggers NRF1 ubiquitination to promote its proteolytic activation. iScience 2023; 26:107777. [PMID: 37720101 PMCID: PMC10502413 DOI: 10.1016/j.isci.2023.107777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 08/15/2023] [Accepted: 08/28/2023] [Indexed: 09/19/2023] Open
Abstract
The transcription factor NRF1 resides in the endoplasmic reticulum (ER) and is constantly transported to the cytosol for proteasomal degradation. However, when the proteasome is defective, NRF1 escapes degradation and undergoes proteolytic cleavage by the protease DDI2, generating a transcriptionally active form that restores proteostasis, including proteasome function. The mechanisms that regulate NRF1 proteolytic activation and transcriptional potential remain poorly understood. This study demonstrates that the ER is a crucial regulator of NRF1 function by orchestrating its ubiquitination through the E3 ubiquitin ligase HRD1. We show that HRD1-mediated NRF1 ubiquitination is necessary for DDI2-mediated processing in cells. Furthermore, we found that deficiency in both RAD23A and RAD23B impaired DDI2-mediated NRF1 processing, indicating that these genes are essential components of the DDI2 proteolytic machinery. Our findings highlight the intricate mechanism by which the ER activates NRF1 to coordinate the transcriptional activity of an adaptation response in cells.
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Affiliation(s)
- Claire Chavarria
- Department of Immunobiology, University of Lausanne, 155 Ch. des Boveresses, 1066 Epalinges, Switzerland
| | - LĂ©a Zaffalon
- Department of Immunobiology, University of Lausanne, 155 Ch. des Boveresses, 1066 Epalinges, Switzerland
| | - SĂ©rgio T. Ribeiro
- Department of Immunobiology, University of Lausanne, 155 Ch. des Boveresses, 1066 Epalinges, Switzerland
| | - MĂ©lanie Op
- Department of Immunobiology, University of Lausanne, 155 Ch. des Boveresses, 1066 Epalinges, Switzerland
| | - Manfredo Quadroni
- Protein Analysis Facility, Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Maria Sofia Iatrou
- Department of Immunobiology, University of Lausanne, 155 Ch. des Boveresses, 1066 Epalinges, Switzerland
| | - Chloé Chapuis
- Department of Immunobiology, University of Lausanne, 155 Ch. des Boveresses, 1066 Epalinges, Switzerland
| | - Fabio Martinon
- Department of Immunobiology, University of Lausanne, 155 Ch. des Boveresses, 1066 Epalinges, Switzerland
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Chen S, Su H, Xing H, Mao J, Sun P, Li M. Comparative Proteomics Reveals the Difference in Root Cold Resistance between Vitis. riparia Ă— V. labrusca and Cabernet Sauvignon in Response to Freezing Temperature. PLANTS (BASEL, SWITZERLAND) 2022; 11:971. [PMID: 35406951 PMCID: PMC9003149 DOI: 10.3390/plants11070971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/28/2022] [Accepted: 04/01/2022] [Indexed: 06/14/2023]
Abstract
Grapevines, bearing fruit containing large amounts of bioactive metabolites that offer health benefits, are widely cultivated around the world. However, the cold damage incurred when grown outside in extremely low temperatures during the overwintering stage limits the expansion of production. Although the morphological, biochemical, and molecular levels in different Vitis species exposed to different temperatures have been investigated, differential expression of proteins in roots is still limited. Here, the roots of cold-resistant (Vitis. riparia × V. labrusca, T1) and cold-sensitive varieties (Cabernet Sauvignon, T3) at -4 °C, and also at -15 °C for the former (T2), were measured by iTRAQ-based proteomic analysis. Expression levels of genes encoding candidate proteins were validated by qRT-PCR, and the root activities during different treatments were determined using a triphenyl tetrazolium chloride method. The results show that the root activity of the cold-resistant variety was greater than that of the cold-sensitive variety, and it declined with the decrease in temperature. A total of 25 proteins were differentially co-expressed in T2 vs. T1 and T1 vs. T3, and these proteins were involved in stress response, bio-signaling, metabolism, energy, and translation. The relative expression levels of the 13 selected genes were consistent with their fold-change values of proteins. The signature translation patterns for the roots during spatio-temporal treatments of different varieties at different temperatures provide insight into the differential mechanisms of cold resistance of grapevine.
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Affiliation(s)
- Sijin Chen
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (S.C.); (H.S.); (H.X.)
| | - Hongyan Su
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (S.C.); (H.S.); (H.X.)
| | - Hua Xing
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (S.C.); (H.S.); (H.X.)
| | - Juan Mao
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China;
| | - Ping Sun
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (S.C.); (H.S.); (H.X.)
| | - Mengfei Li
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (S.C.); (H.S.); (H.X.)
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Ciardullo C, Szoltysek K, Zhou P, Pietrowska M, Marczak L, Willmore E, Enshaei A, Walaszczyk A, Ho JY, Rand V, Marshall S, Hall AG, Harrison CJ, Soundararajan M, Eswaran J. Low BACH2 Expression Predicts Adverse Outcome in Chronic Lymphocytic Leukaemia. Cancers (Basel) 2021; 14:23. [PMID: 35008187 PMCID: PMC8750551 DOI: 10.3390/cancers14010023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/14/2021] [Accepted: 12/17/2021] [Indexed: 12/31/2022] Open
Abstract
Chronic lymphocytic leukaemia (CLL) is a heterogeneous disease with a highly variable clinical outcome. There are well-established CLL prognostic biomarkers that have transformed treatment and improved the understanding of CLL biology. Here, we have studied the clinical significance of two crucial B cell regulators, BACH2 (BTB and CNC homology 1, basic leucine zipper transcription factor 2) and BCL6 (B-cell CLL/lymphoma 6), in a cohort of 102 CLL patients and determined the protein interaction networks that they participate in using MEC-1 CLL cells. We observed that CLL patients expressing low levels of BCL6 and BACH2 RNA had significantly shorter overall survival (OS) than high BCL6- and BACH2-expressing cases. Notably, their low expression specifically decreased the OS of immunoglobulin heavy chain variable region-mutated (IGHV-M) CLL patients, as well as those with 11q and 13q deletions. Similar to the RNA data, a low BACH2 protein expression was associated with a significantly shorter OS than a high expression. There was no direct interaction observed between BACH2 and BCL6 in MEC-1 CLL cells, but they shared protein networks that included fifty different proteins. Interestingly, a prognostic index (PI) model that we generated, using integrative risk score values of BACH2 RNA expression, age, and 17p deletion status, predicted patient outcomes in our cohort. Taken together, these data have shown for the first time a possible prognostic role for BACH2 in CLL and have revealed protein interaction networks shared by BCL6 and BACH2, indicating a significant role for BACH2 and BCL6 in key cellular processes, including ubiquitination mediated B-cell receptor functions, nucleic acid metabolism, protein degradation, and homeostasis in CLL biology.
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Affiliation(s)
- Carmela Ciardullo
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK; (C.C.); (M.S.)
- Translational & Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (K.S.); (E.W.); (A.E.); (A.G.H.); (C.J.H.)
| | - Katarzyna Szoltysek
- Translational & Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (K.S.); (E.W.); (A.E.); (A.G.H.); (C.J.H.)
- Maria Sklodowska-Curie Institute, Oncology Center, Gliwice Branch, 02-034 Warszawa, Poland;
| | - Peixun Zhou
- School of Health & Life Sciences, Teesside University, Middlesbrough TS1 3JN, UK; (P.Z.); (V.R.)
- National Horizons Centre, Teesside University, Darlington DL1 1HG, UK
| | - Monika Pietrowska
- Maria Sklodowska-Curie Institute, Oncology Center, Gliwice Branch, 02-034 Warszawa, Poland;
| | - Lukasz Marczak
- Department of Natural Products Biochemistry, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland;
| | - Elaine Willmore
- Translational & Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (K.S.); (E.W.); (A.E.); (A.G.H.); (C.J.H.)
| | - Amir Enshaei
- Translational & Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (K.S.); (E.W.); (A.E.); (A.G.H.); (C.J.H.)
| | - Anna Walaszczyk
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 7RU, UK;
| | - Jia Yee Ho
- Newcastle University Medicine Malaysia, EduCity Iskandar, Johor 79200, Malaysia;
| | - Vikki Rand
- School of Health & Life Sciences, Teesside University, Middlesbrough TS1 3JN, UK; (P.Z.); (V.R.)
- National Horizons Centre, Teesside University, Darlington DL1 1HG, UK
| | - Scott Marshall
- Department of Haematology, City Hospitals Sunderland NHS Trust, Sunderland SR4 7TP, UK;
| | - Andrew G. Hall
- Translational & Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (K.S.); (E.W.); (A.E.); (A.G.H.); (C.J.H.)
| | - Christine J. Harrison
- Translational & Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (K.S.); (E.W.); (A.E.); (A.G.H.); (C.J.H.)
| | - Meera Soundararajan
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK; (C.C.); (M.S.)
| | - Jeyanthy Eswaran
- Translational & Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (K.S.); (E.W.); (A.E.); (A.G.H.); (C.J.H.)
- Newcastle University Medicine Malaysia, EduCity Iskandar, Johor 79200, Malaysia;
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Park JS, Ma H, Roh YS. Ubiquitin pathways regulate the pathogenesis of chronic liver disease. Biochem Pharmacol 2021; 193:114764. [PMID: 34529948 DOI: 10.1016/j.bcp.2021.114764] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/05/2021] [Accepted: 09/08/2021] [Indexed: 02/07/2023]
Abstract
Chronic liver disease (CLD) is considered the leading cause of global mortality. In westernized countries, increased consumption of alcohol and overeating foods with high fat/ high glucose promote progression of CLD such as alcoholic liver disease (ALD) and non-alcoholic liver disease (NAFLD). Accumulating evidence and research suggest that ubiquitin, a 75 amino acid protein, plays crucial role in the pathogenesis of CLD through dynamic post-translational modifications (PTMs) exerting diverse cellular outcomes such as protein degradation through ubiquitin-proteasome system (UPS) and autophagy, and regulation of signal transduction. In this review, we present the function of ubiquitination and latest findings on diverse mechanism of PTMs, UPS and autophagy which significantly contribute to the pathogenesis of alcoholic liver disease (ALD), non-alcoholic fatty liver disease (NAFLD), cirrhosis, and HCC. Despite its high prevalence, morbidity, and mortality, there are only few FDA approved drugs that could be administered to CLD patients. The goal of this review is to present a variety of pathways and therapeutic targets involving ubiquitination in the pathogenesis of CLD. Further, this review summarizes collective views of pharmaceutical inhibition or activation of recent drugs targeting UPS and autophagy system to highlight potential targets and new approaches to treat CLD.
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Affiliation(s)
- Jeong-Su Park
- College of Pharmacy and Medical Research Center, Chungbuk National University, Cheongju 28160, South Korea
| | - Hwan Ma
- College of Pharmacy and Medical Research Center, Chungbuk National University, Cheongju 28160, South Korea
| | - Yoon-Seok Roh
- College of Pharmacy and Medical Research Center, Chungbuk National University, Cheongju 28160, South Korea.
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6
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Yang Q, Nong X, Xu J, Huang F, Wang F, Wu J, Zhang C, Liu C. Unraveling the Genetic Basis of Fertility Restoration for Cytoplasmic Male Sterile Line WNJ01A Originated From Brassica juncea in Brassica napus. FRONTIERS IN PLANT SCIENCE 2021; 12:721980. [PMID: 34531887 PMCID: PMC8438535 DOI: 10.3389/fpls.2021.721980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/05/2021] [Indexed: 06/13/2023]
Abstract
Crosses that lead to heterosis have been widely used in the rapeseed (Brassica napus L.) industry. Cytoplasmic male sterility (CMS)/restorer-of-fertility (Rf) systems represent one of the most useful tools for rapeseed production. Several CMS types and their restorer lines have been identified in rapeseed, but there are few studies on the mechanisms underlying fertility restoration. Here, we performed morphological observation, map-based cloning, and transcriptomic analysis of the F2 population developed by crossing the CMS line WNJ01A with its restorer line Hui01. Paraffin-embedded sections showed that the sporogenous cell stage was the critical pollen degeneration period, with major sporogenous cells displaying loose and irregular arrangement in sterile anthers. Most mitochondrial electron transport chain (mtETC) complex genes were upregulated in fertile compared to sterile buds. Using bulked segregant analysis (BSA)-seq to analyze mixed DNA pools from sterile and fertile F2 buds, respectively, we identified a 6.25 Mb candidate interval where Rfw is located. Using map-based cloning experiments combined with bacterial artificial chromosome (BAC) clone sequencing, the candidate interval was reduced to 99.75 kb and two pentatricopeptide repeat (PPR) genes were found among 28 predicted genes in this interval. Transcriptome sequencing showed that there were 1679 DEGs (1023 upregulated and 656 downregulated) in fertile compared to sterile F2 buds. The upregulated differentially expressed genes (DEGs) were enriched in the Kyoto Encyclopedia of Genes and Genomes (KEGG) lysine degradation pathway and phenylalanine metabolism, and the downregulated DEGs were enriched in cutin, suberine, and wax biosynthesis. Furthermore, 44 DEGs were involved in pollen and anther development, such as tapetum, microspores, and pollen wall development. All of them were upregulated except a few such as POE1 genes (which encode Pollen Ole e I allergen and extensin family proteins). There were 261 specifically expressed DEGs (9 and 252 in sterile and fertile buds, respectively). Regarding the fertile bud-specific upregulated DEGs, the ubiquitin-proteasome pathway was enriched. The top four hub genes in the protein-protein interaction network (BnaA09g56400D, BnaA10g18210D, BnaA10g18220D, and BnaC09g41740D) encode RAD23d proteins, which deliver ubiquitinated substrates to the 26S proteasome. These findings provide evidence on the pathways regulated by Rfw and improve our understanding of fertility restoration.
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Fry MY, Saladi SM, Clemons WM. The STI1-domain is a flexible alpha-helical fold with a hydrophobic groove. Protein Sci 2021; 30:882-898. [PMID: 33620121 PMCID: PMC7980504 DOI: 10.1002/pro.4049] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 01/05/2023]
Abstract
STI1-domains are present in a variety of co-chaperone proteins and are required for the transfer of hydrophobic clients in various cellular processes. The domains were first identified in the yeast Sti1 protein where they were referred to as DP1 and DP2. Based on hidden Markov model searches, this domain had previously been found in other proteins including the mammalian co-chaperone SGTA, the DNA damage response protein Rad23, and the chloroplast import protein Tic40. Here, we refine the domain definition and carry out structure-based sequence alignment of STI1-domains showing conservation of five amphipathic helices. Upon examinations of these identified domains, we identify a preceding helix 0 and unifying sequence properties, determine new molecular models, and recognize that STI1-domains nearly always occur in pairs. The similarity at the sequence, structure, and molecular levels likely supports a unified functional role.
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Affiliation(s)
- Michelle Y. Fry
- Division of Chemistry and Chemical EngineeringCalifornia Institute of TechnologyPasadenaCaliforniaUSA
| | - Shyam M. Saladi
- Division of Chemistry and Chemical EngineeringCalifornia Institute of TechnologyPasadenaCaliforniaUSA
| | - William M. Clemons
- Division of Chemistry and Chemical EngineeringCalifornia Institute of TechnologyPasadenaCaliforniaUSA
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Li Y, Wang WX. Protein molecular responses of field-collected oysters Crassostrea hongkongensis with greatly varying Cu and Zn body burdens. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2021; 232:105749. [PMID: 33513458 DOI: 10.1016/j.aquatox.2021.105749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/27/2020] [Accepted: 01/11/2021] [Indexed: 06/12/2023]
Abstract
The oyster Crassostrea hongkongensis is an ideal biomonitor due to its widespread distribution along the coast of Southern China and the ability to hyperaccumulate metals including Cu and Zn. In this study, we conducted the first investigation of the molecular responses to metal hyperaccumulation based on quantitative shotgun proteomics technique and genome information. Gill tissue of oysters collected from the uncontaminated environment (Site 1, 59.6 ÎĽg/g and 670 ÎĽg/g dry weight for Cu and Zn) displayed significant protein profile differentiation compared to those from a moderately contaminated (Site 2, 1,465 ÎĽg/g and 10,170 ÎĽg/g for Cu and Zn) and a severely contaminated environment (Site 3, 3,899 ÎĽg/g and 39,170 ÎĽg/g for Cu and Zn). There were 626 proteins identified to be differentially expressed at Site 3 but only 247 proteins at Site 2. Oysters from a moderately contaminated estuary (Site 2) displayed fewer effects as compared to oysters under severe contamination, with fluctuated small molecule metabolism and enhanced translation process. At Site 3, the induction of reactive oxygen species (ROS) was the main toxicity under the extremely high level of metal stress, which resulted in protein damage. Additionally, the impaired structure of cytoskeleton and modified membrane tracking process at Site 3 oysters led to the blockage or less efficient protein or macromolecule distribution within cells. Nonetheless, proteomic analysis in this study revealed that oysters could partly alleviate the adverse metal effects by boosting the translation process, enhancing the ability to recycle the misfolded proteins, and enhancing the potential to eliminate the excess ROS. Our study demonstrated an adaptive potential of oysters at the protein level to survive under conditions of metal hyper-accumulation.
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Affiliation(s)
- Yunlong Li
- Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong; School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong
| | - Wen-Xiong Wang
- School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong; Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen, 518057, China.
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Štefl M, Herbst K, Rübsam M, Benda A, Knop M. Single-Color Fluorescence Lifetime Cross-Correlation Spectroscopy In Vivo. Biophys J 2020; 119:1359-1370. [PMID: 32919495 DOI: 10.1016/j.bpj.2020.06.039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 05/29/2020] [Accepted: 06/16/2020] [Indexed: 01/18/2023] Open
Abstract
The ability to quantify protein concentrations and to measure protein interactions in vivo is key information needed for the understanding of complex processes inside cells, but the acquisition of such information from living cells is still demanding. Fluorescence-based methods like two-color fluorescence cross-correlation spectroscopy can provide this information, but measurement precision is hampered by various sources of errors caused by instrumental or optical limitations such as imperfect overlap of detection volumes or detector cross talk. Furthermore, the nature and properties of used fluorescent proteins or fluorescent dyes, such as labeling efficiency, fluorescent protein maturation, photostability, bleaching, and fluorescence brightness can have an impact. Here, we take advantage of previously published fluorescence lifetime correlation spectroscopy which relies on lifetime differences as a mean to discriminate fluorescent proteins with similar spectral properties and to use them for single-color fluorescence lifetime cross-correlation spectroscopy (sc-FLCCS). By using only one excitation and one detection wavelength, this setup avoids all sources of errors resulting from chromatic aberrations and detector cross talk. To establish sc-FLCCS, we first engineered and tested multiple green fluorescent protein (GFP)-like fluorescent proteins for their suitability. This identified a novel, to our knowledge, GFP variant termed short-lifetime monomeric GFP with the so-far shortest lifetime. Monte-Carlo simulations were employed to explore the suitability of different combinations of GFP variants. Two GFPs, Envy and short-lifetime monomeric GFP, were predicted to constitute the best performing couple for sc-FLCCS measurements. We demonstrated application of this GFP pair for measuring protein interactions between the proteasome and interacting proteins and for measuring protein interactions between three partners when combined with a red florescent protein. Together, our findings establish sc-FLCCS as a valid alternative for conventional dual-color fluorescence cross-correlation spectroscopy measurements.
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Affiliation(s)
- Martin Ĺ tefl
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), University of Heidelberg, Heidelberg, Germany; J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences, Prague, Czech Republic.
| | - Konrad Herbst
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), University of Heidelberg, Heidelberg, Germany
| | - Marc RĂĽbsam
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), University of Heidelberg, Heidelberg, Germany
| | - Aleš Benda
- IMCF at BIOCEV, Faculty of Science, Charles University, Vestec, Czech Republic
| | - Michael Knop
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), University of Heidelberg, Heidelberg, Germany; Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany.
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Di Mauro G, Carbonell A, Escudero-Ferruz P, AzorĂn F. The zinc-finger proteins WOC and ROW play distinct functions within the HP1c transcription complex. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194492. [PMID: 32006714 DOI: 10.1016/j.bbagrm.2020.194492] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 01/28/2020] [Accepted: 01/29/2020] [Indexed: 11/20/2022]
Abstract
In Drosophila, the Heterochromatin Protein 1c (HP1c) forms a transcriptional complex with the zinc-finger proteins WOC and ROW, and the extraproteasomal ubiquitin receptor Dsk2. This complex localizes at promoters of active genes and it is required for transcription. The functions played by the different components of the HP1c complex are not fully understood. In this study we show that WOC and ROW are required for chromatin binding of both Dsk2 and HP1c. However, while impairing chromatin binding strongly destabilizes HP1c, it does not affect Dsk2 stability. We also show that WOC, but not ROW, is required for nuclear localization of Dsk2. Moreover, WOC and Dsk2 co-immunoprecitate upon ROW depletion. These results suggest that WOC and Dsk2 interact to form a subcomplex that mediates nuclear translocation of Dsk2. We also show that ROW mediates chromatin binding of the WOC/Dsk2 subcomplex, as well as of HP1c. Altogether these observations favor a model by which the interaction with WOC recruits Dsk2 to the HP1c complex that, in its turn, binds chromatin in a ROW-dependent manner.
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Affiliation(s)
- Gianmarco Di Mauro
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 10-12, 08028 Barcelona, Spain; Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute for Science and Technology, Baldiri Reixac, 10-12, 08028 Barcelona, Spain
| | - Albert Carbonell
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 10-12, 08028 Barcelona, Spain; Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute for Science and Technology, Baldiri Reixac, 10-12, 08028 Barcelona, Spain
| | - Paula Escudero-Ferruz
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 10-12, 08028 Barcelona, Spain; Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute for Science and Technology, Baldiri Reixac, 10-12, 08028 Barcelona, Spain
| | - Fernando AzorĂn
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 10-12, 08028 Barcelona, Spain; Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute for Science and Technology, Baldiri Reixac, 10-12, 08028 Barcelona, Spain.
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11
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West S, Kumar S, Batra SK, Ali H, Ghersi D. Uncovering and characterizing splice variants associated with survival in lung cancer patients. PLoS Comput Biol 2019; 15:e1007469. [PMID: 31652257 PMCID: PMC6834284 DOI: 10.1371/journal.pcbi.1007469] [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: 05/03/2019] [Revised: 11/06/2019] [Accepted: 10/08/2019] [Indexed: 12/16/2022] Open
Abstract
Splice variants have been shown to play an important role in tumor initiation and progression and can serve as novel cancer biomarkers. However, the clinical importance of individual splice variants and the mechanisms by which they can perturb cellular functions are still poorly understood. To address these issues, we developed an efficient and robust computational method to: (1) identify splice variants that are associated with patient survival in a statistically significant manner; and (2) predict rewired protein-protein interactions that may result from altered patterns of expression of such variants. We applied our method to the lung adenocarcinoma dataset from TCGA and identified splice variants that are significantly associated with patient survival and can alter protein-protein interactions. Among these variants, several are implicated in DNA repair through homologous recombination. To computationally validate our findings, we characterized the mutational signatures in patients, grouped by low and high expression of a splice variant associated with patient survival and involved in DNA repair. The results of the mutational signature analysis are in agreement with the molecular mechanism suggested by our method. To the best of our knowledge, this is the first attempt to build a computational approach to systematically identify splice variants associated with patient survival that can also generate experimentally testable, mechanistic hypotheses. Code for identifying survival-significant splice variants using the Null Empirically Estimated P-value method can be found at https://github.com/thecodingdoc/neep. Code for construction of Multi-Granularity Graphs to discover potential rewired protein interactions can be found at https://github.com/scwest/SINBAD.
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Affiliation(s)
- Sean West
- College of Information Science & Technology, University of Nebraska at Omaha, Omaha, Nebraska, United States of America
| | - Sushil Kumar
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Surinder K. Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Hesham Ali
- College of Information Science & Technology, University of Nebraska at Omaha, Omaha, Nebraska, United States of America
| | - Dario Ghersi
- College of Information Science & Technology, University of Nebraska at Omaha, Omaha, Nebraska, United States of America
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12
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Oner M, Lin E, Chen MC, Hsu FN, Shazzad Hossain Prince GM, Chiu KY, Teng CLJ, Yang TY, Wang HY, Yue CH, Yu CH, Lai CH, Hsieh JT, Lin H. Future Aspects of CDK5 in Prostate Cancer: From Pathogenesis to Therapeutic Implications. Int J Mol Sci 2019; 20:ijms20163881. [PMID: 31395805 PMCID: PMC6720211 DOI: 10.3390/ijms20163881] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 08/06/2019] [Accepted: 08/07/2019] [Indexed: 01/03/2023] Open
Abstract
Cyclin-dependent kinase 5 (CDK5) is a unique member of the cyclin-dependent kinase family. CDK5 is activated by binding with its regulatory proteins, mainly p35, and its activation is essential in the development of the central nervous system (CNS) and neurodegeneration. Recently, it has been reported that CDK5 plays important roles in regulating various biological and pathological processes, including cancer progression. Concerning prostate cancer, the androgen receptor (AR) is majorly involved in tumorigenesis, while CDK5 can phosphorylate AR and promotes the proliferation of prostate cancer cells. Clinical evidence has also shown that the level of CDK5 is associated with the progression of prostate cancer. Interestingly, inhibition of CDK5 prevents prostate cancer cell growth, while drug-triggered CDK5 hyperactivation leads to apoptosis. The blocking of CDK5 activity by its small interfering RNAs (siRNA) or Roscovitine, a pan-CDK inhibitor, reduces the cellular AR protein level and triggers the death of prostate cancer cells. Thus, CDK5 plays a crucial role in the growth of prostate cancer cells, and AR regulation is one of the important pathways. In this review paper, we summarize the significant studies on CDK5-mediated regulation of prostate cancer cells. We propose that the CDK5–p35 complex might be an outstanding candidate as a diagnostic marker and potential target for prostate cancer treatment in the near future.
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Affiliation(s)
- Muhammet Oner
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan
| | - Eugene Lin
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan
- Department of Urology, Chang Bing Show Chwan Memorial Hospital, Changhua 505, Taiwan
| | - Mei-Chih Chen
- Translational Cell Therapy Center, Department of Medical Research, China Medical University Hospital, Taichung 40447, Taiwan
| | - Fu-Ning Hsu
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan
| | | | - Kun-Yuan Chiu
- Division of Urology, Department of Surgery, Taichung Veterans General Hospital, Taichung 40705, Taiwan
| | - Chieh-Lin Jerry Teng
- Division of Hematology/Medical Oncology, Department of Internal, Medicine, Taichung Veterans General Hospital, Taichung 40705, Taiwan
| | - Tsung-Ying Yang
- Division of Chest Medicine, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung 40705, Taiwan
| | - Hsin-Yi Wang
- Department of Nuclear Medicine, Taichung Veterans General Hospital, Taichung 40705, Taiwan
| | - Chia-Herng Yue
- Department of Surgery, Tung's Taichung Metro Harbor Hospital, Taichung 435, Taiwan
| | - Ching-Han Yu
- Department of Physiology, School of Medicine, Chung Shan Medical University, Taichung 40201, Taiwan
| | - Chih-Ho Lai
- Department of Microbiology and Immunology, Chang Gung Medical University, Taoyuan 33302, Taiwan
| | - Jer-Tsong Hsieh
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ho Lin
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan.
- Program in Translational Medicine and Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung 40227, Taiwan.
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13
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Verma S, Shakya VPS, Idnurm A. The dual function gene RAD23 contributes to Cryptococcus neoformans virulence independently of its role in nucleotide excision DNA repair. Gene 2019; 717:144043. [PMID: 31400407 DOI: 10.1016/j.gene.2019.144043] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 08/05/2019] [Accepted: 08/06/2019] [Indexed: 11/18/2022]
Abstract
Genes involved in the repair of DNA damage are emerging as playing important roles during the disease processes caused by pathogenic fungi. However, there are potentially hundreds of genes involved in DNA repair in a fungus and some of those genes can play additional roles within the cell. One such gene is RAD23, required for virulence of the human pathogenic fungus Cryptococcus neoformans, that encodes a protein involved in the nucleotide excision repair (NER) pathway. However, Rad23 is a dual function protein, with a role in either repair of damaged DNA or protein turn over by directing proteins to the proteasome. Here, these two functions of Rad23 were tested by the creation of a series of domain deletion alleles of RAD23 and the assessment of the strains for DNA repair, proteasome functions, and virulence properties. Deletion of the different domains was able to uncouple the two functions of Rad23, and the phenotypes of strains carrying such forms indicated that the role of RAD23 in virulence is due to its function in proteasomal-mediated protein degradation rather than NER.
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Affiliation(s)
- Surbhi Verma
- Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO, USA; Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Viplendra P S Shakya
- Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO, USA; Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Alexander Idnurm
- Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO, USA; School of BioSciences, University of Melbourne, Parkville, VIC, Australia.
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14
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Butler RM, McKenzie RC, Jones CL, Flanagan CE, Woollard WJ, Demontis M, Ferreira S, Tosi I, John S, Whittaker SJ, Mitchell TJ. Contribution of STAT3 and RAD23B in Primary SĂ©zary Cells to Histone Deacetylase Inhibitor FK228 Resistance. J Invest Dermatol 2019; 139:1975-1984.e2. [PMID: 30910759 DOI: 10.1016/j.jid.2019.03.1130] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 02/23/2019] [Accepted: 03/06/2019] [Indexed: 01/12/2023]
Abstract
FK228 (romidepsin) and suberoylanilide hydroxamic acid (vorinostat) are histone deacetylase inhibitors (HDACi) approved by the US Food and Drug Administration for cutaneous T-cell lymphoma (CTCL), including the leukemic subtype Sézary syndrome. This study investigates RAD23B and STAT3 gene perturbations in a large cohort of primary Sézary cells and the effect of FK228 treatment on tyrosine phosphorylation of STAT3 (pYSTAT3) and RAD23B expression. We report RAD23B copy number variation in 10% (12/119, P ≤ 0.01) of SS patients, associated with reduced mRNA expression (P = 0.04). RAD23B knockdown in a CTCL cell line led to a reduction in FK228-induced apoptosis. Histone deacetylase inhibitor treatment significantly reduced pYSTAT3 in primary Sézary cells and was partially mediated by RAD23B. A distinct pattern of RAD23B-pYSTAT3 co-expression in primary Sézary cells was detected. Critically, Sézary cells harboring the common STAT3 Y640F variant were less sensitive to FK228-induced apoptosis and exogenous expression of STAT3 Y640F, and D661Y conferred partial resistance to STAT3 transcriptional inhibition by FK228 (P ≤ 0.0024). These findings suggest that RAD23B and STAT3 gene perturbations could reduce sensitivity to histone deacetylase inhibitors in SS patients.
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Affiliation(s)
- Rosie M Butler
- St. John's Institute of Dermatology, King's College London, Guy's Hospital, London, UK
| | - Robert C McKenzie
- St. John's Institute of Dermatology, King's College London, Guy's Hospital, London, UK
| | - Christine L Jones
- St. John's Institute of Dermatology, King's College London, Guy's Hospital, London, UK
| | - Charlotte E Flanagan
- St. John's Institute of Dermatology, King's College London, Guy's Hospital, London, UK
| | - Wesley J Woollard
- St. John's Institute of Dermatology, King's College London, Guy's Hospital, London, UK
| | - Maria Demontis
- St. John's Institute of Dermatology, King's College London, Guy's Hospital, London, UK
| | - Silvia Ferreira
- St. John's Institute of Dermatology, King's College London, Guy's Hospital, London, UK
| | - Isabella Tosi
- St. John's Institute of Dermatology, King's College London, Guy's Hospital, London, UK
| | - Susan John
- Department of Immunology, Infection and Inflammatory Disease, King's College London, Guy's Hospital, London, UK
| | - Sean J Whittaker
- St. John's Institute of Dermatology, King's College London, Guy's Hospital, London, UK
| | - Tracey J Mitchell
- St. John's Institute of Dermatology, King's College London, Guy's Hospital, London, UK.
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15
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Wang J, Wang J, Lu Y, Fang Y, Gao X, Wang Z, Zheng W, Xu S. The heat responsive wheat TaRAD23 rescues developmental and thermotolerant defects of the rad23b mutant in Arabidopsis thaliana. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 274:23-31. [PMID: 30080608 DOI: 10.1016/j.plantsci.2018.04.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 03/30/2018] [Accepted: 04/30/2018] [Indexed: 05/24/2023]
Abstract
High temperature severely damage the growth and development of crops with climate change. To effectively screen heat responsive proteins in wheat (Triticum aestivum L.), the isobaric tandem mass tag (TMT)-labeled quantitative proteomic analysis and quantitative real-time PCR (qRT-PCR) were performed. Here, we found that a wheat RADIATION SENSITIVE 23 protein, TaRAD23, was up-regulated at both protein and RNA levels by exposing to heat stress. Sequence homology analysis indicated that the TaRAD23 is a conserved protein, which is closely related to the Arabidopsis thaliana proteins AtRAD23B and AtRAD23A. Genetic knockout of AtRAD23B, but not AtRAD23A, shows multiple developmental defects, as well as sensitivity to heat stress. Meanwhile, we observed that constitutive overexpression of TaRAD23 in rad23b fully rescued developmental and thermotolerant defects of the mutant. Furthermore, qRT-PCR analysis of heat responsive genes in rad23b and its complementary lines suggested that suppression of the heat shock transcription factor AtHSFA2 and heat responsive genes (HSP70, HSP90, HSP17.6 and HSA32) may be the cause of the weaker thermotolerance in rad23b. Taken together, the data suggest that the heat responsive TaRAD23 is a functionally highly conserved protein that plays an important role in development, as well as the regulation in heat stress response network.
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Affiliation(s)
- Jun Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China.
| | - Junzhe Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China.
| | - Yunze Lu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China.
| | - Yan Fang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, China.
| | - Xin Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China.
| | - Zhonghua Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China.
| | - Weijun Zheng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China.
| | - Shengbao Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China.
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16
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dDsk2 regulates H2Bub1 and RNA polymerase II pausing at dHP1c complex target genes. Nat Commun 2015; 6:7049. [PMID: 25916810 DOI: 10.1038/ncomms8049] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Accepted: 03/26/2015] [Indexed: 12/13/2022] Open
Abstract
dDsk2 is a conserved extraproteasomal ubiquitin receptor that targets ubiquitylated proteins for degradation. Here we report that dDsk2 plays a nonproteolytic function in transcription regulation. dDsk2 interacts with the dHP1c complex, localizes at promoters of developmental genes and is required for transcription. Through the ubiquitin-binding domain, dDsk2 interacts with H2Bub1, a modification that occurs at dHP1c complex-binding sites. H2Bub1 is not required for binding of the complex; however, dDsk2 depletion strongly reduces H2Bub1. Co-depletion of the H2Bub1 deubiquitylase dUbp8/Nonstop suppresses this reduction and rescues expression of target genes. RNA polymerase II is strongly paused at promoters of dHP1c complex target genes and dDsk2 depletion disrupts pausing. Altogether, these results suggest that dDsk2 prevents dUbp8/Nonstop-dependent H2Bub1 deubiquitylation at promoters of dHP1c complex target genes and regulates RNA polymerase II pausing. These results expand the catalogue of nonproteolytic functions of ubiquitin receptors to the epigenetic regulation of chromatin modifications.
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17
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Gueugneau M, Coudy-Gandilhon C, Gourbeyre O, Chambon C, Combaret L, Polge C, Taillandier D, Attaix D, Friguet B, Maier AB, Butler-Browne G, BĂ©chet D. Proteomics of muscle chronological ageing in post-menopausal women. BMC Genomics 2014; 15:1165. [PMID: 25532418 PMCID: PMC4523020 DOI: 10.1186/1471-2164-15-1165] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 12/16/2014] [Indexed: 12/18/2022] Open
Abstract
Background Muscle ageing contributes to both loss of functional autonomy and increased morbidity. Muscle atrophy accelerates after 50 years of age, but the mechanisms involved are complex and likely result from the alteration of a variety of interrelated functions. In order to better understand the molecular mechanisms underlying muscle chronological ageing in human, we have undertaken a top-down differential proteomic approach to identify novel biomarkers after the fifth decade of age. Results Muscle samples were compared between adult (56 years) and old (78 years) post-menopausal women. In addition to total muscle extracts, low-ionic strength extracts were investigated to remove high abundance myofibrillar proteins and improve the detection of low abundance proteins. Two-dimensional gel electrophoreses with overlapping IPGs were used to improve the separation of muscle proteins. Overall, 1919 protein spots were matched between all individuals, 95 were differentially expressed and identified by mass spectrometry, and they corresponded to 67 different proteins. Our results suggested important modifications in cytosolic, mitochondrial and lipid energy metabolism, which may relate to dysfunctions in old muscle force generation. A fraction of the differentially expressed proteins were linked to the sarcomere and cytoskeleton (myosin light-chains, troponin T, ankyrin repeat domain-containing protein-2, vinculin, four and a half LIM domain protein-3), which may account for alterations in contractile properties. In line with muscle contraction, we also identified proteins related to calcium signal transduction (calsequestrin-1, sarcalumenin, myozenin-1, annexins). Muscle ageing was further characterized by the differential regulation of several proteins implicated in cytoprotection (catalase, peroxiredoxins), ion homeostasis (carbonic anhydrases, selenium-binding protein 1) and detoxification (aldo-keto reductases, aldehyde dehydrogenases). Notably, many of the differentially expressed proteins were central for proteostasis, including heat shock proteins and proteins involved in proteolysis (valosin-containing protein, proteasome subunit beta type-4, mitochondrial elongation factor-Tu). Conclusions This study describes the most extensive proteomic analysis of muscle ageing in humans, and identified 34 new potential biomarkers. None of them were previously recognized as differentially expressed in old muscles, and each may represent a novel starting point to elucidate the mechanisms of muscle chronological ageing in humans.
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Affiliation(s)
- Marine Gueugneau
- INRA, UMR 1019, Centre de Recherche en Nutrition Humaine, Université d'Auvergne, F-63122, Saint Genès Champanelle, France. .,Clermont Université, Université d'Auvergne, F-63000, Clermont-Ferrand, France. .,Pôle Endocrinologie, Diabétologie et Nutrition, Institut de Recherches Expérimentales et Cliniques, Université Catholique de Louvain, B-1200, Brussels, Belgium.
| | - CĂ©cile Coudy-Gandilhon
- INRA, UMR 1019, Centre de Recherche en Nutrition Humaine, Université d'Auvergne, F-63122, Saint Genès Champanelle, France. .,Clermont Université, Université d'Auvergne, F-63000, Clermont-Ferrand, France.
| | - Ophélie Gourbeyre
- INRA, UMR 1019, Centre de Recherche en Nutrition Humaine, Université d'Auvergne, F-63122, Saint Genès Champanelle, France. .,Clermont Université, Université d'Auvergne, F-63000, Clermont-Ferrand, France.
| | - Christophe Chambon
- INRA, Plateforme d'Exploration du Métabolisme, Composante Protéique, F-63122, Saint Genès Champanelle, France.
| | - Lydie Combaret
- INRA, UMR 1019, Centre de Recherche en Nutrition Humaine, Université d'Auvergne, F-63122, Saint Genès Champanelle, France. .,Clermont Université, Université d'Auvergne, F-63000, Clermont-Ferrand, France.
| | - CĂ©cile Polge
- INRA, UMR 1019, Centre de Recherche en Nutrition Humaine, Université d'Auvergne, F-63122, Saint Genès Champanelle, France. .,Clermont Université, Université d'Auvergne, F-63000, Clermont-Ferrand, France.
| | - Daniel Taillandier
- INRA, UMR 1019, Centre de Recherche en Nutrition Humaine, Université d'Auvergne, F-63122, Saint Genès Champanelle, France. .,Clermont Université, Université d'Auvergne, F-63000, Clermont-Ferrand, France.
| | - Didier Attaix
- INRA, UMR 1019, Centre de Recherche en Nutrition Humaine, Université d'Auvergne, F-63122, Saint Genès Champanelle, France. .,Clermont Université, Université d'Auvergne, F-63000, Clermont-Ferrand, France.
| | - Bertrand Friguet
- UPMC Université Paris 06, UMR 8256, Biological Adaptation and Ageing - IBPS, CNRS-UMR 8256, INSERM U1164, Sorbonne Universités, F-75005, Paris, France.
| | - Andrea B Maier
- Department of Internal Medicine, Section of Gerontology and Geriatrics, VU University Medical Center, Amsterdam, The Netherlands.
| | - Gillian Butler-Browne
- Institut de Myologie, Centre de Recherches en Myologie UMR 974 76, INSERM U974, CNRS FRE 3617, Sorbonne Universités, UPMC Université Paris 06, F-75013, Paris, France.
| | - Daniel BĂ©chet
- INRA, UMR 1019, Centre de Recherche en Nutrition Humaine, Université d'Auvergne, F-63122, Saint Genès Champanelle, France. .,Clermont Université, Université d'Auvergne, F-63000, Clermont-Ferrand, France.
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18
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Verma N, Pink M, Rettenmeier AW, Schmitz-Spanke S. Benzo[a]pyrene-mediated toxicity in primary pig bladder epithelial cells: A proteomic approach. J Proteomics 2013; 85:53-64. [DOI: 10.1016/j.jprot.2013.04.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 03/21/2013] [Accepted: 04/09/2013] [Indexed: 02/03/2023]
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19
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Fong YW, Cattoglio C, Yamaguchi T, Tjian R. Transcriptional regulation by coactivators in embryonic stem cells. Trends Cell Biol 2012; 22:292-8. [PMID: 22572610 DOI: 10.1016/j.tcb.2012.04.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Revised: 04/03/2012] [Accepted: 04/03/2012] [Indexed: 11/24/2022]
Abstract
Embryonic stem (ES) cells, like all cell types, are defined by their unique transcriptional signatures. The ability of ES cells to self-renew or exit the pluripotent state and enter differentiation requires extensive changes in their transcriptome and epigenome. Remarkably, transcriptional programs governing each cell fate must remain sufficiently malleable so that expression of only a handful of transcriptional activators can override the pre-existing state by collaborating with an unexpectedly elaborate collection of coactivators to specify, restrict and stabilize the new state. Here, we discuss recent advances in our understanding of how the same coactivator can interpret multiple lines of information encoded by different activators and integrate signals from diverse regulators into stem cell-specific transcriptional outputs.
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Affiliation(s)
- Yick W Fong
- Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
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20
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Fushman D, Wilkinson KD. Structure and recognition of polyubiquitin chains of different lengths and linkage. F1000 BIOLOGY REPORTS 2011; 3:26. [PMID: 22162729 PMCID: PMC3229271 DOI: 10.3410/b3-26] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The polyubiquitin signal is post-translationally attached to a large number of proteins, often directing formation of macromolecular complexes resulting in the translocation, assembly or degradation of the attached protein. Recent structural and functional studies reveal general mechanisms by which different architectures and length of the signal are distinguished.
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Affiliation(s)
- David Fushman
- Department of Chemistry and Biochemistry, University of MarylandCollege Park, MD 20742USA
| | - Keith D. Wilkinson
- Department of Biochemistry, Emory University School of MedicineAtlanta, GA 30322USA
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