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Yang YY, Shan W, Yang TW, Wu CJ, Liu XC, Chen JY, Lu WJ, Li ZG, Deng W, Kuang JF. MaMYB4 is a negative regulator and a substrate of RING-type E3 ligases MaBRG2/3 in controlling banana fruit ripening. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1651-1669. [PMID: 35395128 DOI: 10.1111/tpj.15762] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/14/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Fruit ripening is a complex developmental process, which is modulated by both transcriptional and post-translational events. Control of fruit ripening is important in maintaining moderate quality traits and minimizing postharvest deterioration. In this study, we discovered that the transcription factor MaMYB4 acts as a negative regulator of fruit ripening in banana. The protein levels of MaMYB4 decreased gradually with banana fruit ripening, paralleling ethylene production, and decline in firmness. DNA affinity purification sequencing combined with RNA-sequencing analyses showed that MaMYB4 preferentially binds to the promoters of various ripening-associated genes including ethylene biosynthetic and cell wall modifying genes. Furthermore, ectopic expression of MaMYB4 in tomato delayed tomato fruit ripening, which was accompanied by downregulation of ethylene biosynthetic and cell wall modifying genes. Importantly, two RING finger E3 ligases MaBRG2/3, whose protein accumulation increased progressively with fruit ripening, were found to interact with and ubiquitinate MaMYB4, contributing to decreased accumulation of MaMYB4 during fruit ripening. Transient overexpression of MaMYB4 and MaBRG2/3 in banana fruit ripening delayed or promoted fruit ripening by inhibiting or stimulating ethylene biosynthesis, respectively. Taken together, we demonstrate that MaMYB4 negatively modulates banana fruit ripening, and that MaMYB4 abundance could be regulated by protein ubiquitination, thus providing insights into the role of MaMYB4 in controlling fruit ripening at both transcriptional and post-translational levels.
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Affiliation(s)
- Ying-Ying Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticultural Science, South China Agricultural University, Guangzhou, 510642, China
| | - Wei Shan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticultural Science, South China Agricultural University, Guangzhou, 510642, China
| | - Tian-Wei Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticultural Science, South China Agricultural University, Guangzhou, 510642, China
| | - Chao-Jie Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticultural Science, South China Agricultural University, Guangzhou, 510642, China
| | - Xun-Cheng Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Jian-Ye Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticultural Science, South China Agricultural University, Guangzhou, 510642, China
| | - Wang-Jin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticultural Science, South China Agricultural University, Guangzhou, 510642, China
| | - Zheng-Guo Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 400044, China
| | - Wei Deng
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 400044, China
| | - Jian-Fei Kuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticultural Science, South China Agricultural University, Guangzhou, 510642, China
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Rodriguez Carvajal A, Grishkovskaya I, Gomez Diaz C, Vogel A, Sonn-Segev A, Kushwah MS, Schodl K, Deszcz L, Orban-Nemeth Z, Sakamoto S, Mechtler K, Kukura P, Clausen T, Haselbach D, Ikeda F. The linear ubiquitin chain assembly complex (LUBAC) generates heterotypic ubiquitin chains. eLife 2021; 10:e60660. [PMID: 34142657 PMCID: PMC8245127 DOI: 10.7554/elife.60660] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 06/17/2021] [Indexed: 12/21/2022] Open
Abstract
The linear ubiquitin chain assembly complex (LUBAC) is the only known ubiquitin ligase for linear/Met1-linked ubiquitin chain formation. One of the LUBAC components, heme-oxidized IRP2 ubiquitin ligase 1 (HOIL-1L), was recently shown to catalyse oxyester bond formation between ubiquitin and some substrates. However, oxyester bond formation in the context of LUBAC has not been directly observed. Here, we present the first 3D reconstruction of human LUBAC obtained by electron microscopy and report its generation of heterotypic ubiquitin chains containing linear linkages with oxyester-linked branches. We found that this event depends on HOIL-1L catalytic activity. By cross-linking mass spectrometry showing proximity between the catalytic RING-in-between-RING (RBR) domains, a coordinated ubiquitin relay mechanism between the HOIL-1-interacting protein (HOIP) and HOIL-1L ligases is suggested. In mouse embryonic fibroblasts, these heterotypic chains were induced by TNF, which is reduced in cells expressing an HOIL-1L catalytic inactive mutant. In conclusion, we demonstrate that LUBAC assembles heterotypic ubiquitin chains by the concerted action of HOIP and HOIL-1L.
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Affiliation(s)
- Alan Rodriguez Carvajal
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC)ViennaAustria
| | - Irina Grishkovskaya
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
| | - Carlos Gomez Diaz
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC)ViennaAustria
| | - Antonia Vogel
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
| | - Adar Sonn-Segev
- Department of Chemistry, University of Oxford, Chemistry Research LaboratoryOxfordUnited Kingdom
| | - Manish S Kushwah
- Department of Chemistry, University of Oxford, Chemistry Research LaboratoryOxfordUnited Kingdom
| | - Katrin Schodl
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC)ViennaAustria
| | - Luiza Deszcz
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC)ViennaAustria
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
| | | | | | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
| | - Philipp Kukura
- Department of Chemistry, University of Oxford, Chemistry Research LaboratoryOxfordUnited Kingdom
| | - Tim Clausen
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
| | - David Haselbach
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
| | - Fumiyo Ikeda
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC)ViennaAustria
- Medical Institute of Bioregulation (MIB), Kyushu UniversityFukuokaJapan
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Zhang P, Wang J, Zhang X, Wang X, Jiang L, Gu X. Identification of AIDS-Associated Kaposi Sarcoma: A Functional Genomics Approach. Front Genet 2020; 10:1376. [PMID: 32038721 PMCID: PMC6992650 DOI: 10.3389/fgene.2019.01376] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 12/17/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Kaposi sarcoma-associated herpes virus (KSHV) is one of the most common causal agents of Kaposi Sarcoma (KS) in individuals with HIV-infections. The virus has gained attention over the past few decades due to its remarkable pathogenic mechanisms. A group of genes, ORF71, ORF72, and ORF73, are expressed as polycistronic mRNAs and the functions of ORF71 and ORF72 in KSHV are already reported in the literature. However, the function of ORF73 has remained a mystery. The aim of this study is to conduct comprehensive exploratory experiments to clarify the role of ORF73 in KSHV pathology and discover markers of AIDS-associated KSHV-induced KS by bioinformatic approaches. METHODS AND RESULTS We searched for homologues of ORF-73 and attempted to predict protein-protein interactions (PPI) based on GeneCards and UniProtKB, utilizing Position-Specific Iterated BLAST (PSI-BLAST). We applied Gene Ontology (GO) and KEGG pathway analyses to identify highly conserved regions between ORF-73 and p53to help us identify potential markers with predominant hits and interactions in the KEGG pathway associated with host apoptosis and cell arrest. The protein p53 is selected because it is an important tumor suppressor antigen. To identify the potential roles of the candidate markers at the molecular level, we used PSIPRED keeping the conserved domains as the major parameters to predict secondary structures. We based the FUGE interpretation consolidations of the sequence-structure comparisons on distance homology, where the score for the amino acids matching the insertion/deletion (indels) detected were based on structures compared to the FUGE database of structural profiles. We also calculated the compatibility scores of sequence alignments accordingly. Based on the PSI-BLAST homologues, we checked the disordered structures predicted using PSI-Pred and DISO-Pred for developing a hidden Markov model (HMM). We further applied these HMMs models based on the alignment of constructed 3D models between the known structure and the HMM of our sequence. Moreover, stable homology and structurally conserved domains confirmed that ORF-73 maybe an important prognostic marker for AIDS-associated KS. CONCLUSION Collectively, similar variants of ORF-73 markers involved in the immune response may interact with targeted host proteins as predicted by our computational analysis. This work also suggests the existence of potential conformational changes that need to be further explored to help elucidate the role of immune signaling during KS towards the development of therapeutic applications.
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Affiliation(s)
- Peng Zhang
- School of Clinical Medicine, Shanghai University of Medicine & Health Sciences, Shanghai, China
- Department of Public Health, Shanghai General Practice Medical Education and Research Center, Shanghai, China
| | - Jiafeng Wang
- Stem Cell Research and Cellular Therapy Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Xiao Zhang
- Department of Implant Dentistry, Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiaolan Wang
- College of Nursing and Health Management, Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Liying Jiang
- Shanghai Key Laboratory of Molecular Imaging, Collaborative Research Center, Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Xuefeng Gu
- Shanghai Key Laboratory of Molecular Imaging, Collaborative Research Center, Shanghai University of Medicine & Health Sciences, Shanghai, China
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PRKCSH contributes to tumorigenesis by selective boosting of IRE1 signaling pathway. Nat Commun 2019; 10:3185. [PMID: 31320625 PMCID: PMC6639383 DOI: 10.1038/s41467-019-11019-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 06/12/2019] [Indexed: 02/06/2023] Open
Abstract
Unfolded protein response (UPR) is an adaptive mechanism that aims at restoring ER homeostasis under severe environmental stress. Malignant cells are resistant to environmental stress, which is largely due to an activated UPR. However, the molecular mechanisms by which different UPR branches are selectively controlled in tumor cells are not clearly understood. Here, we provide evidence that PRKCSH, previously known as glucosidase II beta subunit, functions as a regulator for selective activation of the IRE1α branch of UPR. PRKCSH boosts ER stress–mediated autophosphorylation and oligomerization of IRE1α through mutual interaction. PRKCSH contributes to the induction of tumor-promoting factors and to tumor resistance to ER stress. Increased levels of PRKCSH in various tumor tissues are positively correlated with the expression of XBP1-target genes. Taken together, our data provide a molecular rationale for selective activation of the IRE1α branch in tumors and adaptation of tumor cells to severe environmental stress. Cancer cells utilise the unfolded protein response (UPR) to adapt to environmental and ER stress. Here, the authors show that the glycosidase II beta subunit, PRKSCH, protects cancer cells from ER stress, by interacting with IRE1α and activating the IRE1α-XBP1 branch of the UPR.
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Zhang Y, Huang Y, Srivathsan A, Lim TK, Lin Q, He CY. The unusual flagellar-targeting mechanism and functions of the trypanosome ortholog of the ciliary GTPase Arl13b. J Cell Sci 2018; 131:jcs.219071. [PMID: 30097558 PMCID: PMC6140319 DOI: 10.1242/jcs.219071] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 07/28/2018] [Indexed: 12/11/2022] Open
Abstract
The small GTPase Arl13b is one of the most conserved and ancient ciliary proteins. In human and animals, Arl13b is primarily associated with the ciliary membrane, where it acts as a guanine-nucleotide-exchange factor (GEF) for Arl3 and is implicated in a variety of ciliary and cellular functions. We have identified and characterized Trypanosoma brucei (Tb)Arl13, the sole Arl13b homolog in this evolutionarily divergent, protozoan parasite. TbArl13 has conserved flagellar functions and exhibits catalytic activity towards two different TbArl3 homologs. However, TbArl13 is distinctly associated with the axoneme through a dimerization/docking (D/D) domain. Replacing the D/D domain with a sequence encoding a flagellar membrane protein created a viable alternative to the wild-type TbArl13 in our RNA interference (RNAi)-based rescue assay. Therefore, flagellar enrichment is crucial for TbArl13, but mechanisms to achieve this could be flexible. Our findings thus extend the understanding of the roles of Arl13b and Arl13b–Arl3 pathway in a divergent flagellate of medical importance. This article has an associated First Person interview with the first author of the paper. Highlighted Article: All roads lead to cilia – how the essential flagellar enrichment of Arl13 is achieved in trypanosome cells using a fundamentally different strategy compared with that of animal cells.
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Affiliation(s)
- Yiliu Zhang
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | - Yameng Huang
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | - Amrita Srivathsan
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | - Teck Kwang Lim
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | - Qingsong Lin
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | - Cynthia Y He
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 14 Science Drive 4, Singapore 117543
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Yang Z, Hou Y, Hao T, Rho HS, Wan J, Luan Y, Gao X, Yao J, Pan A, Xie Z, Qian J, Liao W, Zhu H, Zhou X. A Human Proteome Array Approach to Identifying Key Host Proteins Targeted by Toxoplasma Kinase ROP18. Mol Cell Proteomics 2017; 16:469-484. [PMID: 28087594 DOI: 10.1074/mcp.m116.063602] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Revised: 12/20/2016] [Indexed: 12/18/2022] Open
Abstract
Toxoplasma kinase ROP18 is a key molecule responsible for the virulence of Toxoplasma gondii; however, the mechanisms by which ROP18 exerts parasite virulence via interaction with host proteins remain limited to a small number of identified substrates. To identify a broader array of ROP18 substrates, we successfully purified bioactive mature ROP18 and used it to probe a human proteome array. Sixty eight new putative host targets were identified. Functional annotation analysis suggested that these proteins have a variety of functions, including metabolic process, kinase activity and phosphorylation, cell growth, apoptosis and cell death, and immunity, indicating a pleiotropic role of ROP18 kinase. Among these proteins, four candidates, p53, p38, UBE2N, and Smad1, were further validated. We demonstrated that ROP18 targets p53, p38, UBE2N, and Smad1 for degradation. Importantly, we demonstrated that ROP18 phosphorylates Smad1 Ser-187 to trigger its proteasome-dependent degradation. Further functional characterization of the substrates of ROP18 may enhance understanding of the pathogenesis of Toxoplasma infection and provide new therapeutic targets. Similar strategies could be used to identify novel host targets for other microbial kinases functioning at the pathogen-host interface.
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Affiliation(s)
- Zhaoshou Yang
- From the ‡Department of Biochemistry and Molecular Biology, Sun Yat-Sen University Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Yongheng Hou
- From the ‡Department of Biochemistry and Molecular Biology, Sun Yat-Sen University Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Taofang Hao
- From the ‡Department of Biochemistry and Molecular Biology, Sun Yat-Sen University Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Hee-Sool Rho
- the §Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Jun Wan
- the ¶Department of Ophthalmology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21287
| | - Yizhao Luan
- the ‖State Key Lab of Ophthalmology, Guangdong Provincial Key Lab of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, China.,the **School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xin Gao
- ‡‡The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510630, China; and
| | - Jianping Yao
- §§The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Aihua Pan
- From the ‡Department of Biochemistry and Molecular Biology, Sun Yat-Sen University Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Zhi Xie
- the ‖State Key Lab of Ophthalmology, Guangdong Provincial Key Lab of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, China
| | - Jiang Qian
- the ¶Department of Ophthalmology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21287
| | - Wanqin Liao
- From the ‡Department of Biochemistry and Molecular Biology, Sun Yat-Sen University Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China;
| | - Heng Zhu
- the §Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205;
| | - Xingwang Zhou
- From the ‡Department of Biochemistry and Molecular Biology, Sun Yat-Sen University Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China;
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Immunoprecipitation of native botulinum neurotoxin complexes from Clostridium botulinum subtype A strains. Appl Environ Microbiol 2014; 81:481-91. [PMID: 25362065 DOI: 10.1128/aem.02817-14] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Botulinum neurotoxins (BoNTs) naturally exist as components of protein complexes containing nontoxic proteins. The nontoxic proteins impart stability of BoNTs in the gastrointestinal tract and during purification and handling. The two primary neurotoxin complexes (TCs) are (i) TC1, consisting of BoNT, nontoxin-nonhemagglutinin (NTNH), and hemagglutinins (HAs), and (ii) TC2, consisting of BoNT and NTNH (and possibly OrfX proteins). In this study, BoNT/A subtypes A1, A2, A3, and A5 were examined for the compositions of their TCs in culture extracts using immunoprecipitation (IP). IP analyses showed that BoNT/A1 and BoNT/A5 form TC1s, while BoNT/A2 and BoNT/A3 form TC2s. A Clostridium botulinum host strain expressing recombinant BoNT/A4 (normally present as a TC2) from an extrachromosomal plasmid formed a TC1 with complexing proteins from the host strain, indicating that the HAs and NTNH encoded on the chromosome associated with the plasmid-encoded BoNT/A4. Strain NCTC 2916 (A1/silent B1), which carries both an ha silent bont/b cluster and an orfX bont/a1 cluster, was also examined. IP analysis revealed that NCTC 2916 formed only a TC2 containing BoNT/A1 and its associated NTNH. No association between BoNT/A1 and the nontoxic proteins from the silent bont/b cluster was detected, although the HAs were expressed as determined by Western blotting analysis. Additionally, NTNH and HAs from the silent bont/b cluster did not form a complex in NCTC 2916. The stabilities of the two types of TC differed at various pHs and with addition of KCl and NaCl. TC1 complexes were more stable than TC2 complexes. Mouse serum stabilized TC2, while TC1 was unaffected.
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Panico K, Forti FL. Proteomic, cellular, and network analyses reveal new DUSP3 interactions with nucleolar proteins in HeLa cells. J Proteome Res 2013; 12:5851-66. [PMID: 24245651 DOI: 10.1021/pr400867j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
DUSP3 (or Vaccinia virus phosphatase VH1-related; VHR) is a small dual-specificity phosphatase known to dephosphorylate c-Jun N-terminal kinases and extracellular signal-regulated kinases. In human cervical cancer cells, DUSP3 is overexpressed, localizes preferentially to the nucleus, and plays a key role in cellular proliferation and senescence triggering. Other DUSP3 functions are still unknown, as illustrated by recent and unpublished results from our group showing that this enzyme mediates DNA damage response or repair processes. In this study, we sought to identify new interactions between DUSP3 and proteins directly or indirectly involved in or correlated with its biological roles in HeLa cells exposed to gamma or UV radiation. By using GST-DUSP as bait, we pulled down interacting proteins and identified them by LC-MS/MS. Of the 46 proteins obtained, six hits were extensively validated by immune techniques; the proteins Nucleophosmin, HnRNP C1/C2, and Nucleolin were the most promising targets found to directly interact with DUSP3. We then analyzed the DUSP3 interactomes using physical protein-protein interaction networks using our hits as the seed list. The validated hits as well as unvalidated hits fluctuated on the DUSP3 interactomes of HeLa cells, independent of the time post radiation, which confirmed our proteomic and experimental data and clearly showed the proximity of DUSP3 to proteins involved in processes intimately related to DNA repair and senescence, such as Ku70 and Tert, via interactions with nucleolar proteins, which were identified in this study, that regulate DNA/RNA structure and functions.
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Affiliation(s)
- Karine Panico
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC , Rua Santa Adélia, 166, Bairro Bangu, Santo Andre-SP 09210-170, Brazil
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Zhang C, Omran AG, He F, Deng X, Wu L, Peng J, Yin F. Screening and identification of dynamin-1 interacting proteins in rat brain synaptosomes. Brain Res 2013; 1543:17-27. [PMID: 24211660 DOI: 10.1016/j.brainres.2013.10.053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2013] [Revised: 10/23/2013] [Accepted: 10/28/2013] [Indexed: 01/27/2023]
Abstract
Dynamin-1 is a multi-domain GTPase that is crucial for the fission stage of synaptic vesicle recycling and vesicle trafficking. In this study, we constructed prokaryotic expression plasmids for the four functional domains of dynamin-1, which are pGEX-4T-2-PH, pGEX-4T-2-PRD, pGEX-4T-2-GED and pGEX-4T-2-GTPase. Glutathione S-transferase pull-down, co-immunoprecipitation (co-IP), and liquid chromatography/mass spectrometry were used to screen and identify dynamin-1 interacting proteins in rat brain synaptosomes. We identified a set of 63 candidate protein interactions, including 36 proteins interacting with dynamin-1 C-terminal proline-rich domain (PRD), 14 with pleckstrin-homology domain (PH), 7 with GTPase effector domain (GED) and 6 with GTPase domain, consisting of synaptic vesicle-associated proteins, cytoskeletal proteins, metabolic enzymes and other proteins. We selected three previously unreported dynamin-1 interacting proteins to verify their interaction with dynamin-1 under native conditions. Using co-IP, we found that Rab GDP-dissociation inhibitor (Rab GDI) and chloride channel 3 (ClC-3) do interact with dynamin-1, but not with TUC-4b (the TOAD-64/Ulip/CRMP (TUC) family member). Those novel interactions detected in our study offer valuable insight into the protein-protein interacting network that could enhance our understanding of dynamin-1 mediated synaptic vesicle recycling.
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Affiliation(s)
- Ciliu Zhang
- Department of Pediatrics, Xiangya Hospital, Central South University, 87 Xiangya Road, Hunan 410008, PR China.
| | - Ahmed Galal Omran
- Department of Pediatrics, Xiangya Hospital, Central South University, 87 Xiangya Road, Hunan 410008, PR China.
| | - Fang He
- Department of Pediatrics, Xiangya Hospital, Central South University, 87 Xiangya Road, Hunan 410008, PR China.
| | - Xiaolu Deng
- Department of Pediatrics, Xiangya Hospital, Central South University, 87 Xiangya Road, Hunan 410008, PR China.
| | - Lei Wu
- Department of Pediatrics, Xiangya Hospital, Central South University, 87 Xiangya Road, Hunan 410008, PR China.
| | - Jing Peng
- Department of Pediatrics, Xiangya Hospital, Central South University, 87 Xiangya Road, Hunan 410008, PR China.
| | - Fei Yin
- Department of Pediatrics, Xiangya Hospital, Central South University, 87 Xiangya Road, Hunan 410008, PR China.
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Ethanol promotes clathrin adaptor-mediated endocytosis via the intracellular domain of δ-containing GABAA receptors. J Neurosci 2013; 32:17874-81. [PMID: 23223306 DOI: 10.1523/jneurosci.2535-12.2012] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Pharmacological and genetic evidence reveals that GABA(A) receptor (GABA(A)-R) expression and localization are modulated in response to acute and chronic ethanol (EtOH) exposure. To determine molecular mechanisms of GABA(A)-R plasticity in response to in vivo acute EtOH, we measured early time changes in GABA(A)-R subunit localization. Single doses of EtOH (3 g/kg via i.p. injection in rats) produced decreases in surface levels of GABA(A)-R α4 and δ subunits at 5-15 min post-EtOH in hippocampus CA1 and dentate gyrus, verifying our earlier report (Liang et al., 2007). Here we also examined the β3 subunit and its phosphorylation state during internalization. β3 also was internalized during 5-15 min after EtOH exposure, while phosphorylation of β3 was increased, then decreased at later times, ruling out β3 dephosphorylation-dependent endocytosis. As early as 5 min post-EtOH, there is an initial increase in association between the δ subunits with clathrin adaptor proteins AP2-μ2 revealed by coimmunoprecipitation, followed by a decrease in association 15 min post-EtOH. In vitro studies using glutathione S-transferase fused to the δ subunit intracellular domain (ICD) show that two regions, one containing a classical YxxΦ motif and the other an atypical R/K-rich motif, directly and differentially bind to AP2-μ2, with the former YRSV exhibiting higher affinity. Mutating both regions in the δ-ICD abolishes μ2 binding, providing a possible mechanism that can explain the rapid downregulation of extrasynaptic α4βδ-GABA(A)-R following in vivo EtOH administration, in which the δ-ICD increases in affinity for clathrin AP2-μ2 leading to endocytosis.
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Hertel P, Daniel J, Stegehake D, Vaupel H, Kailayangiri S, Gruel C, Woltersdorf C, Liebau E. The ubiquitin-fold modifier 1 (Ufm1) cascade of Caenorhabditis elegans. J Biol Chem 2013; 288:10661-71. [PMID: 23449979 DOI: 10.1074/jbc.m113.458000] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Ufm1 (ubiquitin-fold modifier 1) is the most recently identified member of the ubiquitin-like protein family. We characterized the Ufm1 cascade of the model organism Caenorhabditis elegans in terms of function and analyzed interactions of the involved proteins in vitro and in vivo. Furthermore, we investigated the phenotypes of the deletion mutants uba5(ok3364) (activating enzyme of Ufm1) and ufc1(tm4888) (conjugating enzyme of Ufm1). The viable deletion mutants showed a decrease in reproduction, development, life span, and a reduced survival under heavy metal stress. However, an increased survival rate under pathogenic, oxidative, heat, and endoplasmic reticulum stress was observed. We propose that the Ufm1 cascade negatively regulates the IRE1-mediated unfolded protein response.
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Affiliation(s)
- Patrick Hertel
- Department of Molecular Physiology, Institute for Animal Physiology, University of Muenster, Schlossplatz 8, 48143 Muenster, Germany
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Trinkle-Mulcahy L. Resolving protein interactions and complexes by affinity purification followed by label-based quantitative mass spectrometry. Proteomics 2012; 12:1623-38. [PMID: 22610586 DOI: 10.1002/pmic.201100438] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Label-based quantitative mass spectrometry analysis of affinity purified complexes, with its built-in negative controls and relative ease of use, is an increasingly popular choice for defining protein-protein interactions and multiprotein complexes. This approach, which differentially labels proteins/peptides from two or more populations and combines them prior to analysis, permits direct comparison of a protein pulldown (e.g. affinity purified tagged protein) to that of a control pulldown (e.g. affinity purified tag alone) in a single mass spectrometry (MS) run, thus avoiding the variability inherent in separate runs. The use of quantitative techniques has been driven in large part by significant improvements in the resolution and sensitivity of high-end mass spectrometers. Importantly, the availability of commercial reagents and open source identification/quantification software has made these powerful techniques accessible to nonspecialists. Benefits and drawbacks of the most popular labeling-based approaches are discussed here, and key steps/strategies for the use of labeling in quantitative immunoprecipitation experiments detailed.
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Affiliation(s)
- Laura Trinkle-Mulcahy
- Department of Cellular & Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.
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Sorokina EM, Feinstein SI, Zhou S, Fisher AB. Intracellular targeting of peroxiredoxin 6 to lysosomal organelles requires MAPK activity and binding to 14-3-3ε. Am J Physiol Cell Physiol 2011; 300:C1430-41. [PMID: 21346153 DOI: 10.1152/ajpcell.00285.2010] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Peroxiredoxin 6 (Prdx6), a bifunctional protein with GSH peroxidase and lysosomal-type phospholipase A(2) activities, has been localized to both cytosolic and acidic compartments (lamellar bodies and lysosomes) in lung alveolar epithelium. We postulate that Prdx6 subcellular localization affects the balance between the two activities. Immunostaining localized Prdx6 to lysosome-related organelles in the MLE12 and A549 alveolar epithelial cell lines. Inhibition of trafficking by brefeldin A indicated processing of the protein through the vesicular pathway. Trafficking of Prdx6 was decreased by inhibitors of PKC, ERK, and p38 MAPK. Immunocytochemistry, immunoprecipitation, and an in situ proximity ligation assay (Duolink) showed that binding of the lysosomal targeting sequence of Prdx6 (amino acids 31-40) to 14-3-3ε was dependent on activity of PKC, ERK, and p38 MAPK. Knockdown of 14-3-3ε with siRNA inhibited the lysosomal targeting of Prdx6. In vitro study with recombinant proteins by pull-down assay and surface plasmon resonance confirmed the interaction of Prdx6 and 14-3-3ε. These findings suggest that ERK and p38 MAPK regulate subcellular localization of Prdx6 by activation of 14-3-3ε as a chaperone protein, resulting in its translocation to acidic organelles.
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Affiliation(s)
- Elena M Sorokina
- Institute for Environmental Medicine, University of Pennsylvania, 3620 Hamilton Walk, Philadelphia, PA 19104, USA
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Abstract
A wide variety of plasmid vectors are commercially available for the production of fusion proteins in bacterial cells. Most are also designed to incorporate a tag that allows affinity purification of the expressed fusion protein from bacterial cell extracts. The most commonly used are vectors that incorporate a portion of the glutathione-S-transferase (GST) enzyme that is able to bind to immobilized glutathione and vectors that use a polyhistidine tag which binds immobilized nickel ions with high affinity. This protocol describes preparation of a soluble GST fusion protein, isolated using glutathione agarose beads.
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Abstract
A wide variety of plasmid vectors are commercially available for the production of fusion proteins in bacterial cells. Most are also designed to incorporate a tag that allows affinity purification of the expressed fusion protein from bacterial cell extracts. The most commonly used are vectors that incorporate a portion of the glutathione-S-transferase (GST) enzyme that is able to bind to immobilized glutathione and vectors that use a polyhistidine tag which binds immobilized nickel ions with high affinity. This protocol describes preparation of an insoluble GST fusion protein, isolated using glutathione agarose beads.
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Yang Y, Yang F, Xiong Z, Yan Y, Wang X, Nishino M, Mirkovic D, Nguyen J, Wang H, Yang XF. An N-terminal region of translationally controlled tumor protein is required for its antiapoptotic activity. Oncogene 2005; 24:4778-88. [PMID: 15870695 PMCID: PMC3901995 DOI: 10.1038/sj.onc.1208666] [Citation(s) in RCA: 150] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bcl-xL plays a critical role in maintaining cell survival. However, the relationship between the potential interaction of Bcl-xL with other cytosolic proteins and the regulation of cell survival remains incompletely defined. We have identified translationally controlled tumor protein (TCTP), a multifunctional protein, as a novel antiapoptotic Bcl-xL-interacting protein. TCTP interacted in vivo and in vitro with Bcl-xL, and their sites have been mapped to an N-terminal region of TCTP and the Bcl-2 homology domain 3 of Bcl-xL. Consistent with a role in maintaining T-cell survival during activation, TCTP was significantly upregulated in murine T cells activated by T-cell antigen receptor (TCR) ligation and CD28 costimulation, which was correlated with the upregulation of Bcl-xL in activated T cells. Moreover, downregulation of TCTP expression by antisense technology in T cells results in the increase of T-cell apoptosis. Furthermore, the N-terminal region of TCTP was required for its ability to inhibit apoptosis. In conclusion, this study has demonstrated that an N-terminal region of a cytosolic protein, TCTP, is required for its binding to Bcl-xL and for its antiapoptotic activity.
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Affiliation(s)
- Yu Yang
- Department of Medicine, Laboratory of Immunopathology, Biology of Inflammation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fan Yang
- Department of Medicine, Laboratory of Immunopathology, Biology of Inflammation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zeyu Xiong
- Department of Medicine, Laboratory of Immunopathology, Biology of Inflammation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yan Yan
- Department of Medicine, Laboratory of Immunopathology, Biology of Inflammation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xinmen Wang
- Department of Surgery, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michiya Nishino
- Department of Medicine, Laboratory of Immunopathology, Biology of Inflammation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dragan Mirkovic
- Department of Computer Science, University of Houston, Houston, TX 77204, USA
| | - Justin Nguyen
- Department of Medicine, Laboratory of Immunopathology, Biology of Inflammation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hong Wang
- Department of Medicine, Laboratory of Immunopathology, Biology of Inflammation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xiao-Feng Yang
- Department of Medicine, Laboratory of Immunopathology, Biology of Inflammation Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Correspondence: X-F Yang, Section of Immunology Allergy and Rheumatology, Department of Medicine, Baylor College of Medicine, One Baylor Plaza, BCM 285, Suite 672E, Houston, TX 77030-3411, USA;
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