1
|
Kumar M, Has C, Lam-Kamath K, Ayciriex S, Dewett D, Bashir M, Poupault C, Schuhmann K, Thomas H, Knittelfelder O, Raghuraman BK, Ahrends R, Rister J, Shevchenko A. Eye proteome of Drosophila melanogaster. Proteomics 2024; 24:e2300330. [PMID: 37963819 DOI: 10.1002/pmic.202300330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 10/22/2023] [Accepted: 10/23/2023] [Indexed: 11/16/2023]
Abstract
Drosophila melanogaster is a popular model organism to elucidate the molecular mechanisms that underlie the structure and function of the eye as well as the causes of retinopathies, aging, light-induced damage, or dietary deficiencies. Large-scale screens have isolated genes whose mutation causes morphological and functional ocular defects, which led to the discovery of key components of the phototransduction cascade. However, the proteome of the Drosophila eye is poorly characterized. Here, we used GeLC-MS/MS to quantify 3516 proteins, including the absolute (molar) quantities of 43 proteins in the eye of adult male Drosophila reared on standard laboratory food. This work provides a generic and expandable resource for further genetic, pharmacological, and dietary studies.
Collapse
Affiliation(s)
- Mukesh Kumar
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Canan Has
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Khanh Lam-Kamath
- Department of Biology, University of Massachusetts Boston, Integrated Sciences Complex, Boston, Massachusetts, USA
| | - Sophie Ayciriex
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Deepshe Dewett
- Department of Biology, University of Massachusetts Boston, Integrated Sciences Complex, Boston, Massachusetts, USA
| | - Mhamed Bashir
- Department of Biology, University of Massachusetts Boston, Integrated Sciences Complex, Boston, Massachusetts, USA
| | - Clara Poupault
- Department of Biology, University of Massachusetts Boston, Integrated Sciences Complex, Boston, Massachusetts, USA
| | - Kai Schuhmann
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Henrik Thomas
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Oskar Knittelfelder
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Robert Ahrends
- Department of Analytical Chemistry, University of Vienna, Vienna, Austria
| | - Jens Rister
- Department of Biology, University of Massachusetts Boston, Integrated Sciences Complex, Boston, Massachusetts, USA
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| |
Collapse
|
2
|
Kumar M, Has C, Lam-Kamath K, Ayciriex S, Dewett D, Bashir M, Poupault C, Schuhmann K, Knittelfelder O, Raghuraman BK, Ahrends R, Rister J, Shevchenko A. Eye proteome of Drosophila melanogaster. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.04.531088. [PMID: 36945598 PMCID: PMC10028839 DOI: 10.1101/2023.03.04.531088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
The Drosophila melanogaster eye is a popular model to elucidate the molecular mechanisms that underlie the structure and function of the eye as well as the causes of retinopathies. For instance, the Drosophila eye has been used to investigate the impacts of ageing and environmental stresses such as light-induced damage or dietary deficiencies. Moreover, large-scale screens have isolated genes whose mutation causes morphological and functional ocular defects, which includes key components of the phototransduction cascade. However, the proteome of the Drosophila eye is poorly characterized. Here, we used GeLC-MS/MS to quantify 3516 proteins he adult Drosophila melanogaster eye and provide a generic and expandable resource for further genetic, pharmacological, and dietary studies.
Collapse
|
3
|
Zhang Z, Wang Q, Yao J, Zhou X, Zhao J, Zhang X, Dong J, Liao L. Chemokine Receptor 5, a Double-Edged Sword in Metabolic Syndrome and Cardiovascular Disease. Front Pharmacol 2020; 11:146. [PMID: 32194402 PMCID: PMC7063056 DOI: 10.3389/fphar.2020.00146] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 02/04/2020] [Indexed: 01/01/2023] Open
Abstract
The key characteristic of cardiovascular disease (CVD) is endothelial dysfunction, which is likely the consequence of inflammation. It is well demonstrated that chemokines and their receptors play a crucial role in regulating inflammatory responses, and recently, much attention has been paid to chemokine receptor 5 (CCR5) and its ligands. For example, CCR5 aggravates the inflammatory response in adipose tissue by regulating macrophage recruitment and M1/M2 phenotype switch, thus causing insulin resistance and obesity. Inhibition of CCR5 expression reduces the aggregation of pro-atherogenic cytokines to the site of arterial injury. However, targeting CCR5 is not always effective, and emerging evidence has shown that CCR5 facilitates progenitor cell recruitment and promotes vascular endothelial cell repair. In this paper, we provide recent insights into the role of CCR5 and its ligands in metabolic syndrome as related to cardiovascular disease and the opportunities and roadblocks in targeting CCR5 and its ligands.
Collapse
Affiliation(s)
- Zhongwen Zhang
- Department of Endocrinology, Shandong Provincial Qianfoshan Hospital, the First Hospital Affiliated with Shandong First Medical University, Jinan, China.,Division of Endocrinology, Department of Internal Medicine, Shandong Provincial QianFoShan Hospital, Shandong University, Jinan, China
| | - Qiannan Wang
- Department of Endocrinology, Shandong Provincial Qianfoshan Hospital, the First Hospital Affiliated with Shandong First Medical University, Jinan, China.,Division of Endocrinology, Department of Internal Medicine, Shandong Provincial QianFoShan Hospital, Shandong University, Jinan, China
| | - Jinming Yao
- Department of Endocrinology, Shandong Provincial Qianfoshan Hospital, the First Hospital Affiliated with Shandong First Medical University, Jinan, China.,Division of Endocrinology, Department of Internal Medicine, Shandong Provincial QianFoShan Hospital, Shandong University, Jinan, China
| | - Xiaojun Zhou
- Department of Endocrinology, Shandong Provincial Qianfoshan Hospital, the First Hospital Affiliated with Shandong First Medical University, Jinan, China.,Division of Endocrinology, Department of Internal Medicine, Shandong Provincial QianFoShan Hospital, Shandong University, Jinan, China
| | - Junyu Zhao
- Department of Endocrinology, Shandong Provincial Qianfoshan Hospital, the First Hospital Affiliated with Shandong First Medical University, Jinan, China.,Division of Endocrinology, Department of Internal Medicine, Shandong Provincial QianFoShan Hospital, Shandong University, Jinan, China
| | - Xiaoqian Zhang
- Department of Endocrinology, Shandong Provincial Qianfoshan Hospital, the First Hospital Affiliated with Shandong First Medical University, Jinan, China.,Division of Endocrinology, Department of Internal Medicine, Shandong Provincial QianFoShan Hospital, Shandong University, Jinan, China
| | - Jianjun Dong
- Division of Endocrinology, Department of Internal Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Lin Liao
- Department of Endocrinology, Shandong Provincial Qianfoshan Hospital, the First Hospital Affiliated with Shandong First Medical University, Jinan, China.,Division of Endocrinology, Department of Internal Medicine, Shandong Provincial QianFoShan Hospital, Shandong University, Jinan, China
| |
Collapse
|
4
|
Pontiggia D, Spinelli F, Fabbri C, Licursi V, Negri R, De Lorenzo G, Mattei B. Changes in the microsomal proteome of tomato fruit during ripening. Sci Rep 2019; 9:14350. [PMID: 31586085 PMCID: PMC6778153 DOI: 10.1038/s41598-019-50575-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 08/23/2019] [Indexed: 11/09/2022] Open
Abstract
The variations in the membrane proteome of tomato fruit pericarp during ripening have been investigated by mass spectrometry-based label-free proteomics. Mature green (MG30) and red ripe (R45) stages were chosen because they are pivotal in the ripening process: MG30 corresponds to the end of cellular expansion, when fruit growth has stopped and fruit starts ripening, whereas R45 corresponds to the mature fruit. Protein patterns were markedly different: among the 1315 proteins identified with at least two unique peptides, 145 significantly varied in abundance in the process of fruit ripening. The subcellular and biochemical fractionation resulted in GO term enrichment for organelle proteins in our dataset, and allowed the detection of low-abundance proteins that were not detected in previous proteomic studies on tomato fruits. Functional annotation showed that the largest proportion of identified proteins were involved in cell wall metabolism, vesicle-mediated transport, hormone biosynthesis, secondary metabolism, lipid metabolism, protein synthesis and degradation, carbohydrate metabolic processes, signalling and response to stress.
Collapse
Affiliation(s)
- Daniela Pontiggia
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Francesco Spinelli
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Claudia Fabbri
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Valerio Licursi
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy.,Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Rodolfo Negri
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy.,Foundation Cenci Bolognetti-Institut Pasteur, Rome, Italy
| | - Giulia De Lorenzo
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy. .,Foundation Cenci Bolognetti-Institut Pasteur, Rome, Italy.
| | - Benedetta Mattei
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| |
Collapse
|
5
|
Sauls K, Greco TM, Wang L, Zou M, Villasmil M, Qian L, Cristea IM, Conlon FL. Initiating Events in Direct Cardiomyocyte Reprogramming. Cell Rep 2019; 22:1913-1922. [PMID: 29444441 DOI: 10.1016/j.celrep.2018.01.047] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 11/30/2017] [Accepted: 01/17/2018] [Indexed: 01/14/2023] Open
Abstract
Direct reprogramming of fibroblasts into cardiomyocyte-like cells (iCM) holds great potential for heart regeneration and disease modeling and may lead to future therapeutic applications. Currently, application of this technology is limited by our lack of understanding of the molecular mechanisms that drive direct iCM reprogramming. Using a quantitative mass spectrometry-based proteomic approach, we identified the temporal global changes in protein abundance that occur during initial phases of iCM reprogramming. Collectively, our results show systematic and temporally distinct alterations in levels of specific functional classes of proteins during the initiating steps of reprogramming including extracellular matrix proteins, translation factors, and chromatin-binding proteins. We have constructed protein relational networks associated with the initial transition of a fibroblast into an iCM. These findings demonstrate the presence of an orchestrated series of temporal steps associated with dynamic changes in protein abundance in a defined group of protein pathways during the initiating events of direct reprogramming.
Collapse
Affiliation(s)
- Kimberly Sauls
- University of North Carolina McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, UNC-Chapel Hill, Chapel Hill, NC 27599 USA
| | - Todd M Greco
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Li Wang
- University of North Carolina McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA; Pathology and Laboratory Medicine, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Meng Zou
- University of North Carolina McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, UNC-Chapel Hill, Chapel Hill, NC 27599 USA
| | - Michelle Villasmil
- University of North Carolina McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, UNC-Chapel Hill, Chapel Hill, NC 27599 USA; Lineberger Comprehensive Cancer Center, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Li Qian
- University of North Carolina McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA; Pathology and Laboratory Medicine, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Frank L Conlon
- University of North Carolina McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, UNC-Chapel Hill, Chapel Hill, NC 27599 USA; Lineberger Comprehensive Cancer Center, UNC-Chapel Hill, Chapel Hill, NC 27599, USA; Integrative Program for Biological and Genome Sciences, UNC-Chapel Hill, Chapel Hill, NC 27599, USA.
| |
Collapse
|
6
|
Moritz CP, Mühlhaus T, Tenzer S, Schulenborg T, Friauf E. Poor transcript-protein correlation in the brain: negatively correlating gene products reveal neuronal polarity as a potential cause. J Neurochem 2019; 149:582-604. [PMID: 30664243 DOI: 10.1111/jnc.14664] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 12/15/2018] [Accepted: 01/02/2019] [Indexed: 01/02/2023]
Abstract
Transcription, translation, and turnover of transcripts and proteins are essential for cellular function. The contribution of those factors to protein levels is under debate, as transcript levels and cognate protein levels do not necessarily correlate due to regulation of translation and protein turnover. Here we propose neuronal polarity as a third factor that is particularly evident in the CNS, leading to considerable distances between somata and axon terminals. Consequently, transcript levels may negatively correlate with cognate protein levels in CNS regions, i.e., transcript and protein levels behave reciprocally. To test this hypothesis, we performed an integrative inter-omics study and analyzed three interconnected rat auditory brainstem regions (cochlear nuclear complex, CN; superior olivary complex, SOC; inferior colliculus, IC) and the rest of the brain as a reference. We obtained transcript and protein sets in these regions of interest (ROIs) by DNA microarrays and label-free mass spectrometry, and performed principal component and correlation analyses. We found 508 transcript|protein pairs and detected poor to moderate transcript|protein correlation in all ROIs, as evidenced by coefficients of determination from 0.34 to 0.54. We identified 57-80 negatively correlating gene products in the ROIs and intensively analyzed four of them for which the correlation was poorest. Three cognate proteins (Slc6a11, Syngr1, Tppp) were synaptic and hence candidates for a negative correlation because of protein transport into axon terminals. Thus, we systematically analyzed the negatively correlating gene products. Gene ontology analyses revealed overrepresented transport/synapse-related proteins, supporting our hypothesis. We present 30 synapse/transport-related proteins with poor transcript|protein correlation. In conclusion, our analyses support that protein transport in polar cells is a third factor that influences the protein level and, thereby, the transcript|protein correlation. OPEN SCIENCE BADGES: This article has received a badge for *Open Materials* and *Open Data* because it provided all relevant information to reproduce the study in the manuscript and because it made the data publicly available. The data can be accessed at https://osf.io/ha28n/. The complete Open Science Disclosure form for this article can be found at the end of the article. More information about the Open Practices badges can be found at https://cos.io/our-services/open-science-badges/.
Collapse
Affiliation(s)
- Christian P Moritz
- Animal Physiology Group, Department of Biology, University of Kaiserslautern, Kaiserslautern, Germany.,Synaptopathies and Autoantibodies, Institut NeuroMyoGène INSERM U1217/ CNRS, UMR 5310, Faculty of Medicine, University Jean Monnet, Saint-Étienne, France
| | - Timo Mühlhaus
- Computational Systems Biology, Department of Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Stefan Tenzer
- Institute of Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Thomas Schulenborg
- Animal Physiology Group, Department of Biology, University of Kaiserslautern, Kaiserslautern, Germany.,Division of Allergology, Paul-Ehrlich-Institut, Langen, Germany
| | - Eckhard Friauf
- Animal Physiology Group, Department of Biology, University of Kaiserslautern, Kaiserslautern, Germany
| |
Collapse
|
7
|
Dorr KM, Conlon FL. Proteomic-based approaches to cardiac development and disease. Curr Opin Chem Biol 2019; 48:150-157. [PMID: 30711722 DOI: 10.1016/j.cbpa.2019.01.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 01/02/2019] [Accepted: 01/03/2019] [Indexed: 01/14/2023]
Abstract
Congenital malformations, or structural birth defects, are now the leading cause of infant mortality in the United States and Europe (Dolk et al., 2010; Heron et al., 2009). Of the congenital malformations, congenital heart disease (CHD) is the most common (Dolk et al., 2010; Heron et al., 2009). Thus, a molecular understanding of heart development is an essential goal for improving clinical approaches to CHD. However, CHDs are commonly a result of genetic defects that manifest themselves in a spatial and temporal manner during the early stages of embryogenesis, leaving them mostly intractable to mass spectrometry-based analysis. Here, we describe the technologies and advancements in the field of mass spectrometry over the past few years that have begun to provide insights into the molecular and cellular basis of CHD and prospects for these types of approaches in the future.
Collapse
Affiliation(s)
- Kerry M Dorr
- Department of Biology and Genetics, McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Frank L Conlon
- Department of Biology and Genetics, McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA.
| |
Collapse
|
8
|
Yang X, Zhang Y, Lai W, Xiang Z, Tu B, Li D, Nan X, Chen C, Hu Z, Fang Q. Proteomic profiling of RAW264.7 macrophage cells exposed to graphene oxide: insights into acute cellular responses. Nanotoxicology 2019; 13:35-49. [DOI: 10.1080/17435390.2018.1530389] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Xiaoliang Yang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China
- Beijing Key Laboratory of Ambient Particles Health Effects and Prevention Techniques, National Center for Nanoscience and Technology, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Zhang
- Central laboratory, Beijing Luhe Hospital, Capital Medical University, Beijing, China
| | - Wenjia Lai
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China
- Beijing Key Laboratory of Ambient Particles Health Effects and Prevention Techniques, National Center for Nanoscience and Technology, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhichu Xiang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China
- Beijing Key Laboratory of Ambient Particles Health Effects and Prevention Techniques, National Center for Nanoscience and Technology, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Sino-Danish Center for Education and Research, Beijing, China
| | - Bin Tu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China
- Beijing Key Laboratory of Ambient Particles Health Effects and Prevention Techniques, National Center for Nanoscience and Technology, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dan Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China
- Beijing Key Laboratory of Ambient Particles Health Effects and Prevention Techniques, National Center for Nanoscience and Technology, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaohui Nan
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China
- Beijing Key Laboratory of Ambient Particles Health Effects and Prevention Techniques, National Center for Nanoscience and Technology, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chunying Chen
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China
- Beijing Key Laboratory of Ambient Particles Health Effects and Prevention Techniques, National Center for Nanoscience and Technology, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Sino-Danish Center for Education and Research, Beijing, China
| | - Zhiyuan Hu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China
- Beijing Key Laboratory of Ambient Particles Health Effects and Prevention Techniques, National Center for Nanoscience and Technology, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Sino-Danish Center for Education and Research, Beijing, China
| | - Qiaojun Fang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China
- Beijing Key Laboratory of Ambient Particles Health Effects and Prevention Techniques, National Center for Nanoscience and Technology, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Sino-Danish Center for Education and Research, Beijing, China
| |
Collapse
|
9
|
Zhai Y, Fan X, Yin Z, Yue X, Men X, Zheng L, Zhang W. Identification and Functional Analysis of Chitin Synthase A in Oriental Armyworm, Mythimna separata. Proteomics 2017; 17. [PMID: 28941069 DOI: 10.1002/pmic.201700165] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 09/01/2017] [Indexed: 11/09/2022]
Abstract
Chitin synthases are very important enzymes for chitin synthesis in various species, which makes them a specific target of insecticides. In the present study, the function of the chitin synthase A (CHSA) gene isolated from Mythimna separate is investigated. The majority of dsMysCHSA treated larvae (89.50%) exhibit lethal phenotypes, including three phenotypes with severe cuticle deformations. The dsMysCHSA treatment in adult females affects oogenesis, and significantly reduce the ovary size and the oviposition number compared with controls. To determine how MysCHSA affects female fecundity, combined analyses of RNA-sequencing (RNA-Seq) transcriptome and TMT proteome (tandem mass tags) data in M. separata after treatment with MysCHSA-RNAi is performed. The differentially expressed proteins and genes affect fecundity-related proteins, energy metabolism, fatty acid metabolism, amino sugars, and nucleotide sugar metabolism pathways. Taken together, these results suggest that MysCHSA acts on M. separata ecdysis and fecundity, and has the potential as a target gene for pest control.
Collapse
Affiliation(s)
- Yifan Zhai
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, P. R. China.,State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
| | - Xiaobin Fan
- State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
| | - Zhenjuan Yin
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
| | - Xiangzhao Yue
- State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
| | - Xingyuan Men
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
| | - Li Zheng
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
| | - Wenqing Zhang
- State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
| |
Collapse
|
10
|
Zhai Y, Zhang Z, Gao H, Chen H, Sun M, Zhang W, Yu Y, Zheng L. Hormone Signaling Regulates Nymphal Diapause in Laodelphax striatellus (Hemiptera: Delphacidae). Sci Rep 2017; 7:13370. [PMID: 29042683 PMCID: PMC5645394 DOI: 10.1038/s41598-017-13879-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 10/03/2017] [Indexed: 01/09/2023] Open
Abstract
Diapause is a physiological adaptation that allows an organism to survive adverse environmental conditions. Diapause occurs at a specific developmental stage in each species. There are few reports regarding the molecular regulatory mechanism of nymphal diapause in Laodelphax striatellus, which is an important graminaceous crop pest. Our previous studies identified the conditions for nymphal diapause in this species. Here, we combined RNA sequencing transcriptomics and quantitative proteomic analyses to identify nymphal diapause-related genes and proteins. The analysis of differentially regulated genes identified four gene/protein pairs that were synchronously up-regulated, and six gene/protein pairs that were synchronously down-regulated, suggesting that these genes may regulate nymphal diapause. The up-regulated gene juvenile hormone acid methyl transferase (JHAMT) and the down-regulated gene cytochrome P450 monooxygenase (CYP314A1, Shd) were chosen for further functional studies. After knocking-down of LsJHAMT and LsShd in vivo by RNA interference, the titer of JH III and 20E decreased significantly, and the duration of the nymphal development period was severely altered. Thus LsJHAMT and LsShd regulated JH III and 20E titers in the hemolymph to control the nymphal diapause status. This study may lead to new information on the regulation nymphal diapause of this important agricultural insect pest.
Collapse
Affiliation(s)
- Yifan Zhai
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
| | - Zhiming Zhang
- Collage of Forestry, Henan Agricultural University, Zhengzhou, 450001, China
| | - Huanhuan Gao
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Hao Chen
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Meng Sun
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Wenqing Zhang
- State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yi Yu
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Li Zheng
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
| |
Collapse
|
11
|
Casas-Vila N, Bluhm A, Sayols S, Dinges N, Dejung M, Altenhein T, Kappei D, Altenhein B, Roignant JY, Butter F. The developmental proteome of Drosophila melanogaster. Genome Res 2017; 27:1273-1285. [PMID: 28381612 PMCID: PMC5495078 DOI: 10.1101/gr.213694.116] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 03/30/2017] [Indexed: 01/12/2023]
Abstract
Drosophila melanogaster is a widely used genetic model organism in developmental biology. While this model organism has been intensively studied at the RNA level, a comprehensive proteomic study covering the complete life cycle is still missing. Here, we apply label-free quantitative proteomics to explore proteome remodeling across Drosophila’s life cycle, resulting in 7952 proteins, and provide a high temporal-resolved embryogenesis proteome of 5458 proteins. Our proteome data enabled us to monitor isoform-specific expression of 34 genes during development, to identify the pseudogene Cyp9f3Ψ as a protein-coding gene, and to obtain evidence of 268 small proteins. Moreover, the comparison with available transcriptomic data uncovered examples of poor correlation between mRNA and protein, underscoring the importance of proteomics to study developmental progression. Data integration of our embryogenesis proteome with tissue-specific data revealed spatial and temporal information for further functional studies of yet uncharacterized proteins. Overall, our high resolution proteomes provide a powerful resource and can be explored in detail in our interactive web interface.
Collapse
Affiliation(s)
- Nuria Casas-Vila
- Quantitative Proteomics, Institute of Molecular Biology, 55128 Mainz, Germany
| | - Alina Bluhm
- Quantitative Proteomics, Institute of Molecular Biology, 55128 Mainz, Germany
| | - Sergi Sayols
- Bioinformatics Core Facility, Institute of Molecular Biology, 55128 Mainz, Germany
| | - Nadja Dinges
- RNA Epigenetics, Institute of Molecular Biology, 55128 Mainz, Germany
| | - Mario Dejung
- Proteomics Core Facility, Institute of Molecular Biology, 55128 Mainz, Germany
| | - Tina Altenhein
- Institute of Genetics, Johannes Gutenberg University, 55128 Mainz, Germany
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599
| | - Benjamin Altenhein
- Institute of Genetics, Johannes Gutenberg University, 55128 Mainz, Germany.,Institute of Zoology, University of Cologne, 50674 Cologne, Germany
| | | | - Falk Butter
- Quantitative Proteomics, Institute of Molecular Biology, 55128 Mainz, Germany
| |
Collapse
|
12
|
Pang R, Qiu J, Li T, Yang P, Yue L, Pan Y, Zhang W. The regulation of lipid metabolism by a hypothetical P-loop NTPase and its impact on fecundity of the brown planthopper. Biochim Biophys Acta Gen Subj 2017; 1861:1750-1758. [PMID: 28315769 DOI: 10.1016/j.bbagen.2017.03.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 02/25/2017] [Accepted: 03/14/2017] [Indexed: 01/02/2023]
Abstract
BACKGROUND Insect fecundity can be regulated by multiple genes in several important signaling pathways which form an extremely complicated regulatory network. However, there are still many genes that have significant impact on insect fecundity but their action mode are still unknown. METHODS Quantitative real-time PCR (qRT-PCR), immunofluorescence and western blot were used to study the expression profile of Nl23867 in the brown planthopper, Nilaparvata lugens. RNA interference (RNAi), RNA-seq and isobaric tags for relative and absolute quantification (iTRAQ) were performed to investigate the action mode of Nl23867 in the regulation of fecundity. High performance liquid chromatography (HPLC) analysis was performed to detect the fatty acid contents. RESULTS We show that knockdown of Nl23867, a gene encoding a hypothetical P-loop NTPase, significantly decreased fecundity of N. lugens. Underdeveloped ovaries, fewer eggs laid and reduction in vitellogenin (Vg) protein expression were observed after RNAi knockdown of Nl23867, and most of the affected genes and pathways are fatty acid metabolism-related. We further determined that Nl23867 directly impacts the palmitic acid biosynthesis by regulating the expression of palmitoyl-protein thioesterase (PPT), subsequently affecting the content of total lipids in N. lugens. CONCLUSIONS Nl23867 regulates the fecundity of N. lugens by modulating the biosynthetic pathway of palmitic acid and affecting lipid metabolism during vitellogenesis and oocyte development. GENERAL SIGNIFICANCE The presented study pioneers the exploration into how a function-unknown gene takes part in the regulation of fecundity in an insect, and will contribute to the construction of gene regulatory network for insect fecundity.
Collapse
Affiliation(s)
- Rui Pang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Jieqi Qiu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Tengchao Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Pan Yang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Lei Yue
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yixin Pan
- ZhiXin High School, Guangzhou, 510080, China
| | - Wenqing Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
| |
Collapse
|
13
|
Batista M, Kugeratski FG, de Paula Lima CV, Probst CM, Kessler RL, de Godoy LM, Krieger MA, Marchini FK. The MAP kinase MAPKLK1 is essential to Trypanosoma brucei proliferation and regulates proteins involved in mRNA metabolism. J Proteomics 2016; 154:118-127. [PMID: 28039027 DOI: 10.1016/j.jprot.2016.12.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 11/23/2016] [Accepted: 12/21/2016] [Indexed: 10/20/2022]
Abstract
Protein phosphorylation and dephosphorylation events regulate many cellular processes. The identification of all phosphorylation sites and their association to a respective protein kinase or phosphatase is a challenging and crucial step to have a deeper understanding of the effects of signaling networks on cells. Pathogenic trypanosomatids have a large number of protein kinases and phosphatases in comparison to other organisms, which reinforces the relevance of the phosphorylation process in these early eukaryotes, nevertheless little is known about protein phosphorylation in these protozoa. In this context, the role of a MAP kinase-like kinase (MAPKLK1), observed to be essential to proliferation of procyclic Trypanosoma brucei, was studied. After silencing MAPKLK1 expression by RNAi, the cells were evaluated by SILAC MS-based proteomics and RNA-Seq. We identified 1756 phosphorylation sites of which 384 were not previously described in T. brucei. Despite being essential, few modulations were observed at the phosphorylation patterns and gene expression levels of MAPKLK1 knockdown. These indirect targets and potential substrates of MAPKLK1 are related to key cellular processes enriched to mRNA processing and stability control. SIGNIFICANCE The field of cell signaling is a promising topic of study for trypanosomatids, since little is known about this topic and the gene expression regulation occurs at post-transcriptional level. In this sense, the present work increases the knowledge on protein phosphorylation process in Trypanosoma brucei. We depleted one MAP kinase (MAPKLK1) of T. brucei and evaluated the effects on the cell. We showed that MAPKLK1 is essential to the cell, while few modulations on phosphoproteome, proteome and transcriptome are observed with its depletion. Although in low number, the changes in phosphoproteome were significant, presenting possible substrate candidates of MAPKLK1 and indirect targets related to mRNA processing and stability control, metabolic pathways, among others. This result provides insights in the phosphorylation network of T. brucei, a model organism that impacts human and animal health.
Collapse
Affiliation(s)
- Michel Batista
- Functional Genomics Laboratory, Carlos Chagas Institute, Fiocruz, Curitiba, Parana, Brazil; Mass Spectrometry Facility RPT02H, Carlos Chagas Institute, Fiocruz, Parana, Brazil
| | - Fernanda G Kugeratski
- Functional Genomics Laboratory, Carlos Chagas Institute, Fiocruz, Curitiba, Parana, Brazil
| | - Carla V de Paula Lima
- Functional Genomics Laboratory, Carlos Chagas Institute, Fiocruz, Curitiba, Parana, Brazil
| | - Christian M Probst
- Functional Genomics Laboratory, Carlos Chagas Institute, Fiocruz, Curitiba, Parana, Brazil
| | - Rafael L Kessler
- Functional Genomics Laboratory, Carlos Chagas Institute, Fiocruz, Curitiba, Parana, Brazil
| | - Lyris M de Godoy
- Functional Genomics Laboratory, Carlos Chagas Institute, Fiocruz, Curitiba, Parana, Brazil
| | - Marco A Krieger
- Functional Genomics Laboratory, Carlos Chagas Institute, Fiocruz, Curitiba, Parana, Brazil
| | - Fabricio K Marchini
- Functional Genomics Laboratory, Carlos Chagas Institute, Fiocruz, Curitiba, Parana, Brazil; Mass Spectrometry Facility RPT02H, Carlos Chagas Institute, Fiocruz, Parana, Brazil.
| |
Collapse
|
14
|
Qiu J, He Y, Zhang J, Kang K, Li T, Zhang W. Discovery and functional identification of fecundity-related genes in the brown planthopper by large-scale RNA interference. INSECT MOLECULAR BIOLOGY 2016; 25:724-733. [PMID: 27472833 DOI: 10.1111/imb.12257] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Recently, transcriptome and proteome data have increasingly been used to identify potential novel genes related to insect phenotypes. However, there are few studies reporting the large-scale functional identification of such genes in insects. To identify novel genes related to fecundity in the brown planthopper (BPH), Nilaparvata lugens, 115 genes were selected from the transcriptomic and proteomic data previously obtained from high- and low-fecundity populations in our laboratory. The results of RNA interference (RNAi) feeding experiments showed that 91.21% of the genes were involved in the regulation of vitellogenin (Vg) expression and may influence BPH fecundity. After RNAi injection experiments, 12 annotated genes were confirmed as fecundity-related genes and three novel genes were identified in the BPH. Finally, C-terminal binding protein (CtBP) was shown to play an important role in BPH fecundity. Knockdown of CtBP not only led to lower survival, underdeveloped ovaries and fewer eggs laid but also resulted in a reduction in Vg protein expression. The novel gene resources gained from this study will be useful for constructing a Vg regulation network and may provide potential target genes for RNAi-based pest control.
Collapse
Affiliation(s)
- J Qiu
- State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Y He
- State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - J Zhang
- State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - K Kang
- State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - T Li
- State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - W Zhang
- State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| |
Collapse
|
15
|
Ghosh S, Narula K, Sinha A, Ghosh R, Jawa P, Chakraborty N, Chakraborty S. Proteometabolomic Study of Compatible Interaction in Tomato Fruit Challenged with Sclerotinia rolfsii Illustrates Novel Protein Network during Disease Progression. FRONTIERS IN PLANT SCIENCE 2016; 7:1034. [PMID: 27507973 PMCID: PMC4960257 DOI: 10.3389/fpls.2016.01034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 06/30/2016] [Indexed: 05/27/2023]
Abstract
Fruit is an assimilator of metabolites, nutrients, and signaling molecules, thus considered as potential target for pathogen attack. In response to patho-stress, such as fungal invasion, plants reorganize their proteome, and reconfigure their physiology in the infected organ. This remodeling is coordinated by a poorly understood signal transduction network, hormonal cascades, and metabolite reallocation. The aim of the study was to explore organ-based proteomic alterations in the susceptibility of heterotrophic fruit to necrotrophic fungal attack. We conducted time-series protein profiling of Sclerotinia rolfsii invaded tomato (Solanum lycopersicum) fruit. The differential display of proteome revealed 216 patho-stress responsive proteins (PSRPs) that change their abundance by more than 2.5-fold. Mass spectrometric analyses led to the identification of 56 PSRPs presumably involved in disease progression; regulating diverse functions viz. metabolism, signaling, redox homeostasis, transport, stress-response, protein folding, modification and degradation, development. Metabolome study indicated differential regulation of organic acid, amino acids, and carbohydrates paralleling with the proteomics analysis. Further, we interrogated the proteome data using network analysis that identified two significant functional protein hubs centered around malate dehydrogenase, T-complex protein 1 subunit gamma, and ATP synthase beta. This study reports, for the first-time, kinetically controlled patho-stress responsive protein network during post-harvest storage in a sink tissue, particularly fruit and constitute the basis toward understanding the onset and context of disease signaling and metabolic pathway alterations. The network representation may facilitate the prioritization of candidate proteins for quality improvement in storage organ.
Collapse
|
16
|
Brewer-Jensen P, Wilson CB, Abernethy J, Mollison L, Card S, Searles LL. Suppressor of sable [Su(s)] and Wdr82 down-regulate RNA from heat-shock-inducible repetitive elements by a mechanism that involves transcription termination. RNA (NEW YORK, N.Y.) 2016; 22:139-54. [PMID: 26577379 PMCID: PMC4691828 DOI: 10.1261/rna.048819.114] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 10/23/2015] [Indexed: 05/26/2023]
Abstract
Although RNA polymerase II (Pol II) productively transcribes very long genes in vivo, transcription through extragenic sequences often terminates in the promoter-proximal region and the nascent RNA is degraded. Mechanisms that induce early termination and RNA degradation are not well understood in multicellular organisms. Here, we present evidence that the suppressor of sable [su(s)] regulatory pathway of Drosophila melanogaster plays a role in this process. We previously showed that Su(s) promotes exosome-mediated degradation of transcripts from endogenous repeated elements at an Hsp70 locus (Hsp70-αβ elements). In this report, we identify Wdr82 as a component of this process and show that it works with Su(s) to inhibit Pol II elongation through Hsp70-αβ elements. Furthermore, we show that the unstable transcripts produced during this process are polyadenylated at heterogeneous sites that lack canonical polyadenylation signals. We define two distinct regions that mediate this regulation. These results indicate that the Su(s) pathway promotes RNA degradation and transcription termination through a novel mechanism.
Collapse
Affiliation(s)
- Paul Brewer-Jensen
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3280, USA
| | - Carrie B Wilson
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3280, USA
| | - John Abernethy
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3280, USA
| | - Lonna Mollison
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3280, USA
| | - Samantha Card
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3280, USA
| | - Lillie L Searles
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3280, USA Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3280, USA
| |
Collapse
|
17
|
Chen X, Wei S, Ji Y, Guo X, Yang F. Quantitative proteomics using SILAC: Principles, applications, and developments. Proteomics 2015; 15:3175-92. [DOI: 10.1002/pmic.201500108] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 04/24/2015] [Accepted: 06/08/2015] [Indexed: 12/21/2022]
Affiliation(s)
- Xiulan Chen
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
| | - Shasha Wei
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
| | - Yanlong Ji
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
- University of Chinese Academy of Sciences; Beijing P. R. China
| | - Xiaojing Guo
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
| | - Fuquan Yang
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
| |
Collapse
|
18
|
Le Bihan MC, Barrio-Hernandez I, Mortensen TP, Henningsen J, Jensen SS, Bigot A, Blagoev B, Butler-Browne G, Kratchmarova I. Cellular Proteome Dynamics during Differentiation of Human Primary Myoblasts. J Proteome Res 2015; 14:3348-61. [DOI: 10.1021/acs.jproteome.5b00397] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Marie-Catherine Le Bihan
- Department
of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Inigo Barrio-Hernandez
- Department
of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Tenna Pavia Mortensen
- Department
of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Jeanette Henningsen
- Department
of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Søren Skov Jensen
- Department
of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Anne Bigot
- Center
for Research in Myology, Sorbonne Universités, UPMC Univ Paris 06, INSERM UMRS975, CNRS FRE3617, 75013 Paris, France
| | - Blagoy Blagoev
- Department
of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Gillian Butler-Browne
- Center
for Research in Myology, Sorbonne Universités, UPMC Univ Paris 06, INSERM UMRS975, CNRS FRE3617, 75013 Paris, France
| | - Irina Kratchmarova
- Department
of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| |
Collapse
|
19
|
Zhai Y, Sun Z, Zhang J, Kang K, Chen J, Zhang W. Activation of the TOR Signalling Pathway by Glutamine Regulates Insect Fecundity. Sci Rep 2015; 5:10694. [PMID: 26024507 PMCID: PMC4448656 DOI: 10.1038/srep10694] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 04/27/2015] [Indexed: 12/18/2022] Open
Abstract
The target of rapamycin (TOR) positively controls cell growth in response to nutrients such as amino acids. However, research on the specific nutrients sensed by TOR is limited. Glutamine (Gln), a particularly important amino acid involved in metabolism in organisms, is synthesised and catalysed exclusively by glutamine synthetase (GS), and our previous studies have shown that Gln may regulate fecundity in vivo levels of the brown planthopper (BPH) Nilaparvata lugens. Until now, it has remained unclear whether Gln activates or inhibits the TOR signalling pathway. Here, we performed the combined analyses of iTRAQ (isobaric tags for relative and absolute quantification) and DGE (tag-based digital gene expression) data in N. lugens at the protein and transcript levels after GS RNAi, and we found that 52 pathways overlap, including the TOR pathway. We further experimentally demonstrate that Gln activates the TOR pathway by promoting the serine/threonine protein kinase AKT and inhibiting the 5'AMP-activated protein kinase AMPK phosphorylation activity in the pest. Furthermore, TOR regulates the fecundity of N. lugens probably by mediating vitellogenin (Vg) expression. This work is the first report that Gln activates the TOR pathway in vivo.
Collapse
Affiliation(s)
- Yifan Zhai
- 1] State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China [2] Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Zhongxiang Sun
- State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jianqing Zhang
- State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Kui Kang
- State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jie Chen
- State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Wenqing Zhang
- State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| |
Collapse
|
20
|
Liang R, Shen XL, Zhang B, Li Y, Xu W, Zhao C, Luo Y, Huang K. Apoptosis signal-regulating kinase 1 promotes Ochratoxin A-induced renal cytotoxicity. Sci Rep 2015; 5:8078. [PMID: 25627963 PMCID: PMC5389036 DOI: 10.1038/srep08078] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 01/05/2015] [Indexed: 01/04/2023] Open
Abstract
Oxidative stress and apoptosis are involved in Ochratoxin A (OTA)-induced renal cytotoxicity. Apoptosis signal-regulating kinase 1 (ASK1) is a Mitogen-Activated Protein Kinase Kinase Kinase (MAPKKK, MAP3K) family member that plays an important role in oxidative stress-induced cell apoptosis. In this study, we performed RNA interference of ASK1 in HEK293 cells and employed an iTRAQ-based quantitative proteomics approach to globally investigate the regulatory mechanism of ASK1 in OTA-induced renal cytotoxicity. Our results showed that ASK1 knockdown alleviated OTA-induced ROS generation and Δψm loss and thus desensitized the cells to OTA-induced apoptosis. We identified 33 and 24 differentially expressed proteins upon OTA treatment in scrambled and ASK1 knockdown cells, respectively. Pathway classification and analysis revealed that ASK1 participated in OTA-induced inhibition of mRNA splicing, nucleotide metabolism, the cell cycle, DNA repair, and the activation of lipid metabolism. We concluded that ASK1 plays an essential role in promoting OTA-induced renal cytotoxicity.
Collapse
Affiliation(s)
- Rui Liang
- Laboratory of food safety and molecular biology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, P.R. China
| | - Xiao Li Shen
- 1] Laboratory of food safety and molecular biology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, P.R. China [2] School of Public Health, Zunyi Medical University, Zunyi, Guizhou 563003, P.R. China
| | - Boyang Zhang
- Laboratory of food safety and molecular biology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, P.R. China
| | - Yuzhe Li
- Laboratory of food safety and molecular biology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, P.R. China
| | - Wentao Xu
- Laboratory of food safety and molecular biology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, P.R. China
| | - Changhui Zhao
- Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA
| | - YunBo Luo
- Laboratory of food safety and molecular biology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, P.R. China
| | - Kunlun Huang
- Laboratory of food safety and molecular biology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, P.R. China
| |
Collapse
|
21
|
A genetic screen and transcript profiling reveal a shared regulatory program for Drosophila linker histone H1 and chromatin remodeler CHD1. G3-GENES GENOMES GENETICS 2015; 5:677-87. [PMID: 25628309 PMCID: PMC4390582 DOI: 10.1534/g3.115.016709] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Chromatin structure and activity can be modified through ATP-dependent repositioning of nucleosomes and posttranslational modifications of core histone tails within nucleosome core particles and by deposition of linker histones into the oligonucleosome fiber. The linker histone H1 is essential in metazoans. It has a profound effect on organization of chromatin into higher-order structures and on recruitment of histone-modifying enzymes to chromatin. Here, we describe a genetic screen for modifiers of the lethal phenotype caused by depletion of H1 in Drosophila melanogaster. We identify 41 mis-expression alleles that enhance and 20 that suppress the effect of His1 depletion in vivo. Most of them are important for chromosome organization, transcriptional regulation, and cell signaling. Specifically, the reduced viability of H1-depleted animals is strongly suppressed by ubiquitous mis-expression of the ATP-dependent chromatin remodeling enzyme CHD1. Comparison of transcript profiles in H1-depleted and Chd1 null mutant larvae revealed that H1 and CHD1 have common transcriptional regulatory programs in vivo. H1 and CHD1 share roles in repression of numerous developmentally regulated and extracellular stimulus-responsive transcripts, including immunity-related and stress response-related genes. Thus, linker histone H1 participates in various regulatory programs in chromatin to alter gene expression.
Collapse
|
22
|
Sap KA, Bezstarosti K, Dekkers DHW, van den Hout M, van Ijcken W, Rijkers E, Demmers JAA. Global quantitative proteomics reveals novel factors in the ecdysone signaling pathway in Drosophila melanogaster. Proteomics 2015; 15:725-38. [PMID: 25403936 DOI: 10.1002/pmic.201400308] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 09/19/2014] [Accepted: 11/12/2014] [Indexed: 01/06/2023]
Abstract
The ecdysone signaling pathway plays a major role in various developmental transitions in insects. Recent advances in the understanding of ecdysone action have relied to a large extent on the application of molecular genetic tools in Drosophila. Here, we used a comprehensive quantitative SILAC MS-based approach to study the global, dynamic proteome of a Drosophila cell line to investigate how hormonal signals are transduced into specific cellular responses. Global proteome data after ecdysone treatment after various time points were then integrated with transcriptome data. We observed a substantial overlap in terms of affected targets between the dynamic proteome and transcriptome, although there were some clear differences in timing effects. Also, downregulation of several specific mRNAs did not always correlate with downregulation of their corresponding protein counterparts, and in some cases there was no correlation between transcriptome and proteome dynamics whatsoever. In addition, we performed a comprehensive interactome analysis of EcR, the major target of ecdysone. Proteins copurified with EcR include factors involved in transcription, chromatin remodeling, ecdysone signaling, ecdysone biosynthesis, and other signaling pathways. Novel ecdysone-responsive proteins identified in this study might link previously unknown proteins to the ecdysone signaling pathway and might be novel targets for developmental studies. To our knowledge, this is the first time that ecdysone signaling is studied by global quantitative proteomics. All MS data have been deposited in the ProteomeXchange with identifier PXD001455 (http://proteomecentral.proteomexchange.org/dataset/PXD001455).
Collapse
Affiliation(s)
- Karen A Sap
- Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands; Netherlands Proteomics Center, Rotterdam, The Netherlands
| | | | | | | | | | | | | |
Collapse
|
23
|
Borner GHH, Hein MY, Hirst J, Edgar JR, Mann M, Robinson MS. Fractionation profiling: a fast and versatile approach for mapping vesicle proteomes and protein-protein interactions. Mol Biol Cell 2014; 25:3178-94. [PMID: 25165137 PMCID: PMC4196868 DOI: 10.1091/mbc.e14-07-1198] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 08/06/2014] [Accepted: 08/07/2014] [Indexed: 01/06/2023] Open
Abstract
We developed "fractionation profiling," a method for rapid proteomic analysis of membrane vesicles and protein particles. The approach combines quantitative proteomics with subcellular fractionation to generate signature protein abundance distribution profiles. Functionally associated groups of proteins are revealed through cluster analysis. To validate the method, we first profiled >3500 proteins from HeLa cells and identified known clathrin-coated vesicle proteins with >90% accuracy. We then profiled >2400 proteins from Drosophila S2 cells, and we report the first comprehensive insect clathrin-coated vesicle proteome. Of importance, the cluster analysis extends to all profiled proteins and thus identifies a diverse range of known and novel cytosolic and membrane-associated protein complexes. We show that it also allows the detailed compositional characterization of complexes, including the delineation of subcomplexes and subunit stoichiometry. Our predictions are presented in an interactive database. Fractionation profiling is a universal method for defining the clathrin-coated vesicle proteome and may be adapted for the analysis of other types of vesicles and particles. In addition, it provides a versatile tool for the rapid generation of large-scale protein interaction maps.
Collapse
Affiliation(s)
- Georg H H Borner
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Marco Y Hein
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Jennifer Hirst
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - James R Edgar
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Margaret S Robinson
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| |
Collapse
|
24
|
Nolte H, Konzer A, Ruhs A, Jungblut B, Braun T, Krüger M. Global Protein Expression Profiling of Zebrafish Organs Based on in Vivo Incorporation of Stable Isotopes. J Proteome Res 2014; 13:2162-74. [DOI: 10.1021/pr5000335] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Hendrik Nolte
- Max Planck Institute for
Heart and Lung Research, Parkstr. 1, 61231 Bad Nauheim, Germany
| | - Anne Konzer
- Max Planck Institute for
Heart and Lung Research, Parkstr. 1, 61231 Bad Nauheim, Germany
| | - Aaron Ruhs
- Max Planck Institute for
Heart and Lung Research, Parkstr. 1, 61231 Bad Nauheim, Germany
| | - Benno Jungblut
- Max Planck Institute for
Heart and Lung Research, Parkstr. 1, 61231 Bad Nauheim, Germany
| | - Thomas Braun
- Max Planck Institute for
Heart and Lung Research, Parkstr. 1, 61231 Bad Nauheim, Germany
| | - Marcus Krüger
- Max Planck Institute for
Heart and Lung Research, Parkstr. 1, 61231 Bad Nauheim, Germany
| |
Collapse
|
25
|
Xing X, Zhang C, Li N, Zhai L, Zhu Y, Yang X, Xu P. Qualitative and quantitative analysis of the adult Drosophila melanogaster proteome. Proteomics 2014; 14:286-290. [PMID: 24259522 DOI: 10.1002/pmic.201300121] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 10/17/2013] [Accepted: 11/11/2013] [Indexed: 01/22/2024]
Abstract
Drosophila melanogaster is one of the most widely used model organisms in life sciences. Mapping its proteome is of great significance for understanding the biological characteristics and tissue functions of this species. However, the comprehensive coverage of its proteome remains a challenge. Here, we describe a high-coverage analysis of whole fly through a 1D gel electrophoresis and LC-MS/MS approach. By combining the datasets of two types of SDS-PAGE and two kinds of tagmata, the high-coverage analysis resulted in the identification of 5262 genes, which correspond to 38.23% of the entire coding genes. Moreover, we found that the fly head and body have different molecular weight distributions of their proteomes when the proteins were resolved with SDS-PAGE and image analysis of the stained gel. This phenomenon was further confirmed by both label-free and isobaric tags for relative and absolute quantitation-based quantitative approaches. The consistent results of the two different quantitation methods also demonstrated the stability and accuracy of the LC-MS/MS platform. The MS proteomics data have been deposited to the ProteomeXchange with identifiers PXD000454 and PXD000455 (http://proteomecentral.proteomexchange.org/dataset/PXD000454; (http://proteomecentral.proteomexchange.org/dataset/PXD000455).
Collapse
Affiliation(s)
- Xiaohua Xing
- State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing, P. R. China; College of Life Science and Bioengineering, Beijing University of Technology, Beijing, P. R. China
| | | | | | | | | | | | | |
Collapse
|
26
|
Proteomics meets genetics: SILAC labeling of Drosophila melanogaster larvae and cells for in vivo functional studies. Methods Mol Biol 2014; 1188:293-311. [PMID: 25059620 DOI: 10.1007/978-1-4939-1142-4_21] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Stable isotope labeling by amino acids in cell culture (SILAC) is an established and potent method for quantitative proteomics. When combined with high-resolution mass spectrometry (MS) and efficient algorithms for the analysis of quantitative MS data, SILAC has proven to be the strategy of choice for the in-depth characterization of functional states at the protein level. The fruit fly Drosophila melanogaster is one of the most widely used model systems for studies of genetics and developmental biology. Despite this, a global proteomic approach in Drosophila is rarely considered. Here, we describe an adaptation of SILAC for functional investigation of fruit flies by proteomics: We illustrate how to perform efficient SILAC labeling of cells in culture and whole fly larvae. The combination of SILAC, a highly accurate global protein quantification method, and of the fruit fly, the prime genetics and developmental model, represents a unique opportunity for quantitative proteomic studies in vivo.
Collapse
|
27
|
Sury MD, Chen JX, Selbach M. In vivo stable isotope labeling by amino acids in Drosophila melanogaster. Methods Mol Biol 2014; 1188:85-93. [PMID: 25059606 DOI: 10.1007/978-1-4939-1142-4_7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The fruit fly Drosophila melanogaster is one of the most widely used and well-studied model organisms in biology and therefore a promising tool for quantitative proteomics. Here, we describe a method to label D. melanogaster with stable isotope labeled amino acids in vivo. Feeding flies with heavy lysine labeled yeast cells leads to virtually complete heavy labeling already in the first filial generation. The approach is simple, fast, and cost-effective, which makes SILAC flies an attractive model system for the emerging field of in vivo quantitative proteomics.
Collapse
Affiliation(s)
- Matthias D Sury
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, Berlin, D-13092, Germany
| | | | | |
Collapse
|
28
|
SILAC Proteomics of Planarians Identifies Ncoa5 as a Conserved Component of Pluripotent Stem Cells. Cell Rep 2013; 5:1142-55. [DOI: 10.1016/j.celrep.2013.10.035] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 08/09/2013] [Accepted: 10/21/2013] [Indexed: 12/19/2022] Open
|
29
|
Syred HM, Welburn J, Rappsilber J, Ohkura H. Cell cycle regulation of microtubule interactomes: multi-layered regulation is critical for the interphase/mitosis transition. Mol Cell Proteomics 2013; 12:3135-47. [PMID: 23893837 PMCID: PMC3820929 DOI: 10.1074/mcp.m113.028563] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 07/25/2013] [Indexed: 12/17/2022] Open
Abstract
Microtubules dramatically change their dynamics and organization at the entry into mitosis. Although this change is mediated by microtubule-associated proteins (MAPs), how MAPs themselves are regulated is not well understood. Here we used an integrated multi-level approach to establish the framework and biological significance of MAP regulation critical for the interphase/mitosis transition. Firstly, we applied quantitative proteomics to determine global cell cycle changes in the profiles of MAPs in human and Drosophila cells. This uncovered a wide range of cell cycle regulations of MAPs previously unidentified. Secondly, systematic studies of human kinesins highlighted an overlooked aspect of kinesins: most mitotic kinesins suppress their affinity to microtubules or reduce their protein levels in interphase in combination with nuclear localization. Thirdly, in-depth analysis of a novel Drosophila MAP (Mink) revealed that the suppression of the microtubule affinity of this mitotic MAP in combination with nuclear localization is essential for microtubule organization in interphase, and phosphorylation of Mink is needed for kinetochore-microtubule attachment in mitosis. Thus, this first comprehensive analysis of MAP regulation for the interphase/mitosis transition advances our understanding of kinesin biology and reveals the prevalence and importance of multi-layered MAP regulation.
Collapse
Affiliation(s)
- Heather M. Syred
- From the ‡Wellcome Trust Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
| | - Julie Welburn
- From the ‡Wellcome Trust Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
| | - Juri Rappsilber
- From the ‡Wellcome Trust Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
| | - Hiroyuki Ohkura
- From the ‡Wellcome Trust Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
| |
Collapse
|
30
|
Li M, Durbin KR, Sweet SMM, Tipton JD, Zheng Y, Kelleher NL. Oncogene-induced cellular senescence elicits an anti-Warburg effect. Proteomics 2013; 13:2585-96. [PMID: 23798001 DOI: 10.1002/pmic.201200298] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 05/04/2013] [Accepted: 06/12/2013] [Indexed: 11/06/2022]
Abstract
Cellular senescence, an irreversible cell cycle arrest induced by a diversity of stimuli, has been considered as an innate tumor suppressing mechanism with implications and applications in cancer therapy. Using a targeted proteomics approach, we show that fibroblasts induced into senescence by expression of oncogenic Ras exhibit a decrease of global acetylation on all core histones, consistent with formation of senescence-associated heterochromatic foci. We also detected clear increases in repressive markers (e.g. >50% elevation of H3K27me2/3) along with decreases in histone marks associated with increased transcriptional expression/elongation (e.g. H3K36me2/3). Despite the increases in repressive marks of chromatin, 179 loci (of 2206 total) were found to be upregulated by global quantitative proteomics. The changes in the cytosolic proteome indicated an upregulation of mitochondrial proteins and downregulation of proteins involved in glycolysis. These alterations in primary metabolism are opposite to the well-known Warburg effect observed in cancer cells. This study significantly improves our understanding of stress-induced senescence and provides a potential application for triggering it in antiproliferative strategies that target the primary metabolism in cancer cells.
Collapse
Affiliation(s)
- Mingxi Li
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | | | | | | | | | | |
Collapse
|
31
|
Sergeeva AM, Pinzón Restrepo N, Seitz H. Quantitative aspects of RNA silencing in metazoans. BIOCHEMISTRY. BIOKHIMIIA 2013; 78:613-626. [PMID: 23980888 DOI: 10.1134/s0006297913060072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Small regulatory RNAs (microRNAs, siRNAs, and piRNAs) exhibit several unique features that clearly distinguish them from other known gene regulators. Their genomic organization, mode of action, and proposed biological functions raise specific questions. In this review, we focus on the quantitative aspect of small regulatory RNA biology. The original nature of these small RNAs accelerated the development of novel detection techniques and improved statistical methods and promoted new concepts that may unexpectedly generalize to other gene regulators. Quantification of natural phenomena is at the core of scientific practice, and the unique challenges raised by small regulatory RNAs have prompted many creative innovations by the scientific community.
Collapse
Affiliation(s)
- A M Sergeeva
- IGH du CNRS UPR 1142, 34396 Montpellier, France.
| | | | | |
Collapse
|
32
|
Chang YC, Tang HW, Liang SY, Pu TH, Meng TC, Khoo KH, Chen GC. Evaluation of Drosophila Metabolic Labeling Strategies for in Vivo Quantitative Proteomic Analyses with Applications to Early Pupa Formation and Amino Acid Starvation. J Proteome Res 2013; 12:2138-50. [DOI: 10.1021/pr301168x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Ying-Che Chang
- Institute
of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical
Sciences, National Taiwan University, Taipei,
Taiwan
- Clinical Proteomics
Center, Chang Gung Memorial Hospital, Taoyuan,
Taiwan
| | - Hong-Wen Tang
- Institute
of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical
Sciences, National Taiwan University, Taipei,
Taiwan
| | - Suh-Yuen Liang
- NRPB
Core Facilities for Protein
Structural Analysis, Academia Sinica, Taipei,
Taiwan
| | - Tsung-Hsien Pu
- NRPB
Core Facilities for Protein
Structural Analysis, Academia Sinica, Taipei,
Taiwan
| | - Tzu-Ching Meng
- Institute
of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical
Sciences, National Taiwan University, Taipei,
Taiwan
| | - Kay-Hooi Khoo
- Institute
of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical
Sciences, National Taiwan University, Taipei,
Taiwan
| | - Guang-Chao Chen
- Institute
of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical
Sciences, National Taiwan University, Taipei,
Taiwan
| |
Collapse
|
33
|
Krahmer N, Hilger M, Kory N, Wilfling F, Stoehr G, Mann M, Farese RV, Walther TC. Protein correlation profiles identify lipid droplet proteins with high confidence. Mol Cell Proteomics 2013; 12:1115-26. [PMID: 23319140 DOI: 10.1074/mcp.m112.020230] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Lipid droplets (LDs) are important organelles in energy metabolism and lipid storage. Their cores are composed of neutral lipids that form a hydrophobic phase and are surrounded by a phospholipid monolayer that harbors specific proteins. Most well-established LD proteins perform important functions, particularly in cellular lipid metabolism. Morphological studies show LDs in close proximity to and interacting with membrane-bound cellular organelles, including the endoplasmic reticulum, mitochondria, peroxisomes, and endosomes. Because of these close associations, it is difficult to purify LDs to homogeneity. Consequently, the confident identification of bona fide LD proteins via proteomics has been challenging. Here, we report a methodology for LD protein identification based on mass spectrometry and protein correlation profiles. Using LD purification and quantitative, high-resolution mass spectrometry, we identified LD proteins by correlating their purification profiles to those of known LD proteins. Application of the protein correlation profile strategy to LDs isolated from Drosophila S2 cells led to the identification of 111 LD proteins in a cellular LD fraction in which 1481 proteins were detected. LD localization was confirmed in a subset of identified proteins via microscopy of the expressed proteins, thereby validating the approach. Among the identified LD proteins were both well-characterized LD proteins and proteins not previously known to be localized to LDs. Our method provides a high-confidence LD proteome of Drosophila cells and a novel approach that can be applied to identify LD proteins of other cell types and tissues.
Collapse
Affiliation(s)
- Natalie Krahmer
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | | | | | | | | | | | | | | |
Collapse
|
34
|
Veraksa A. Regulation of developmental processes: insights from mass spectrometry-based proteomics. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2012; 2:723-34. [PMID: 24014456 DOI: 10.1002/wdev.102] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Mass spectrometry (MS)-based proteomics has become an indispensable tool for protein identification and quantification. In this paper, common MS workflows are described, with an emphasis on applications of MS-based proteomics in developmental biology. Progress has been made in the analysis of proteome changes during tissue differentiation and in various genetic perturbations. MS-based proteomics has been particularly useful for identifying novel protein interactions by affinity purification-mass spectrometry (AP-MS), many of which have been subsequently functionally validated and led to the discovery of previously unknown modes of developmental regulation. Quantitative proteomics approaches can be used to study posttranslational modifications (PTMs) of proteins such as phosphorylation, to reveal the dynamics of intracellular signal transduction. Integrative approaches combine quantitative MS-based proteomics with other high-throughput methods, with the promise of a systems level understanding of developmental regulation.
Collapse
Affiliation(s)
- Alexey Veraksa
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA.
| |
Collapse
|
35
|
Cox J, Mann M. 1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data. BMC Bioinformatics 2012; 13 Suppl 16:S12. [PMID: 23176165 PMCID: PMC3489530 DOI: 10.1186/1471-2105-13-s16-s12] [Citation(s) in RCA: 445] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Quantitative proteomics now provides abundance ratios for thousands of proteins upon perturbations. These need to be functionally interpreted and correlated to other types of quantitative genome-wide data such as the corresponding transcriptome changes. We describe a new method, 2D annotation enrichment, which compares quantitative data from any two 'omics' types in the context of categorical annotation of the proteins or genes. Suitable genome-wide categories are membership of proteins in biochemical pathways, their annotation with gene ontology terms, sub-cellular localization, the presence of protein domains or the membership in protein complexes. 2D annotation enrichment detects annotation terms whose members show consistent behavior in one or both of the data dimensions. This consistent behavior can be a correlation between the two data types, such as simultaneous up- or down-regulation in both data dimensions, or a lack thereof, such as regulation in one dimension but no change in the other. For the statistical formulation of the test we introduce a two-dimensional generalization of the nonparametric two-sample test. The false discovery rate is stringently controlled by correcting for multiple hypothesis testing. We also describe one-dimensional annotation enrichment, which can be applied to single omics data. The 1D and 2D annotation enrichment algorithms are freely available as part of the Perseus software.
Collapse
Affiliation(s)
- Juergen Cox
- Department for Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany.
| | | |
Collapse
|
36
|
Dunham WH, Mullin M, Gingras AC. Affinity-purification coupled to mass spectrometry: basic principles and strategies. Proteomics 2012; 12:1576-90. [PMID: 22611051 DOI: 10.1002/pmic.201100523] [Citation(s) in RCA: 230] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Identifying the interactions established by a protein of interest can be a critical step in understanding its function. This is especially true when an unknown protein of interest is demonstrated to physically interact with proteins of known function. While many techniques have been developed to characterize protein-protein interactions, one strategy that has gained considerable momentum over the past decade for identification and quantification of protein-protein interactions, is affinity-purification followed by mass spectrometry (AP-MS). Here, we briefly review the basic principles used in affinity-purification coupled to mass spectrometry, with an emphasis on tools (both biochemical and computational), which enable the discovery and reporting of high quality protein-protein interactions.
Collapse
Affiliation(s)
- Wade H Dunham
- Samuel Lunenfeld Research Institute at Mount Sinai Hospital, Toronto, ON, Canada
| | | | | |
Collapse
|
37
|
Hsieh SI, Castruita M, Malasarn D, Urzica E, Erde J, Page MD, Yamasaki H, Casero D, Pellegrini M, Merchant SS, Loo JA. The proteome of copper, iron, zinc, and manganese micronutrient deficiency in Chlamydomonas reinhardtii. Mol Cell Proteomics 2012; 12:65-86. [PMID: 23065468 DOI: 10.1074/mcp.m112.021840] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Trace metals such as copper, iron, zinc, and manganese play important roles in several biochemical processes, including respiration and photosynthesis. Using a label-free, quantitative proteomics strategy (MS(E)), we examined the effect of deficiencies in these micronutrients on the soluble proteome of Chlamydomonas reinhardtii. We quantified >10(3) proteins with abundances within a dynamic range of 3 to 4 orders of magnitude and demonstrated statistically significant changes in ~200 proteins in each metal-deficient growth condition relative to nutrient-replete media. Through analysis of Pearson's coefficient, we also examined the correlation between protein abundance and transcript abundance (as determined via RNA-Seq analysis) and found moderate correlations under all nutritional states. Interestingly, in a subset of transcripts known to significantly change in abundance in metal-replete and metal-deficient conditions, the correlation to protein abundance is much stronger. Examples of new discoveries highlighted in this work include the accumulation of O(2) labile, anaerobiosis-related enzymes (Hyd1, Pfr1, and Hcp2) in copper-deficient cells; co-variation of Cgl78/Ycf54 and coprogen oxidase; the loss of various stromal and lumenal photosynthesis-related proteins, including plastocyanin, in iron-limited cells; a large accumulation (from undetectable amounts to over 1,000 zmol/cell) of two COG0523 domain-containing proteins in zinc-deficient cells; and the preservation of photosynthesis proteins in manganese-deficient cells despite known losses in photosynthetic function in this condition.
Collapse
Affiliation(s)
- Scott I Hsieh
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Xu P, Tan H, Duong DM, Yang Y, Kupsco J, Moberg KH, Li H, Jin P, Peng J. Stable isotope labeling with amino acids in Drosophila for quantifying proteins and modifications. J Proteome Res 2012; 11:4403-12. [PMID: 22830426 DOI: 10.1021/pr300613c] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Drosophila melanogaster is a common animal model for genetics studies, and quantitative proteomics studies of the fly are emerging. Here, we present in detail the development of a procedure to incorporate stable isotope-labeled amino acids into the fly proteome. In the method of stable isotope labeling with amino acids in Drosophila melanogaster (SILAC fly), flies were fed with SILAC-labeled yeast grown with modified media, enabling near complete labeling in a single generation. Biological variation in the proteome among individual flies was evaluated in a series of null experiments. We further applied the SILAC fly method to profile proteins from a model of fragile X syndrome, the most common cause of inherited mental retardation in human. The analysis identified a number of altered proteins in the disease model, including actin-binding protein profilin and microtubulin-associated protein futsch. The change of both proteins was validated by immunoblotting analysis. Moreover, we extended the SILAC fly strategy to study the dynamics of protein ubiquitination during the fly life span (from day 1 to day 30), by measuring the level of ubiquitin along with two major polyubiquitin chains (K48 and K63 linkages). The results show that the abundance of protein ubiquitination and the two major linkages do not change significantly within the measured age range. Together, the data demonstrate the application of the SILAC principle in D. melanogaster, facilitating the integration of powerful fly genomics with emerging proteomics.
Collapse
Affiliation(s)
- Ping Xu
- Department of Human Genetics, Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Abstract
Omics, including genomics, proteomics, and metabolomics, enable us to explain symbioses in terms of the underlying molecules and their interactions. The central task is to transform molecular catalogs of genes, metabolites, etc., into a dynamic understanding of symbiosis function. We review four exemplars of omics studies that achieve this goal, through defined biological questions relating to metabolic integration and regulation of animal-microbial symbioses, the genetic autonomy of bacterial symbionts, and symbiotic protection of animal hosts from pathogens. As omic datasets become increasingly complex, computationally sophisticated downstream analyses are essential to reveal interactions not evident from visual inspection of the data. We discuss two approaches, phylogenomics and transcriptional clustering, that can divide the primary output of omics studies-long lists of factors-into manageable subsets, and we describe how they have been applied to analyze large datasets and generate testable hypotheses.
Collapse
Affiliation(s)
- J Chaston
- Department of Entomology, Comstock Hall, Cornell University, Ithaca, New York 14853, USA
| | | |
Collapse
|
40
|
Analysing signalling networks by mass spectrometry. Amino Acids 2012; 43:1061-74. [PMID: 22821269 DOI: 10.1007/s00726-012-1293-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Accepted: 04/03/2012] [Indexed: 12/31/2022]
Abstract
Sequence analysis of the human genome and the association of genetic aberrations with diseases have provided a rough framework whereby the impact of individual genotypes can be assessed. To fully understand the effect of individual and co-occurring genetic aberrations, as well as their individual and collected contribution to the development of diseases, it is critical to analyse the matching proteome and to determine how the organisation, expression level and function of protein networks are affected. Sensitive mass spectrometric platforms in combination with innovative workflows allow qualitative and quantitative analyses of the cellular as well as the extracellular proteome. Importantly, in addition to specifically identifying the content of the proteome, several aspects of the proteomic organisation can be analysed including protein complexes, protein modifications, enzymatic activities and subcellular/organelle localisation. Together, these measurements will provide novel insight into the biological effect of disease-causing mutations ultimately coupling genotype and phenotype.
Collapse
|
41
|
Vasilj A, Gentzel M, Ueberham E, Gebhardt R, Shevchenko A. Tissue proteomics by one-dimensional gel electrophoresis combined with label-free protein quantification. J Proteome Res 2012; 11:3680-9. [PMID: 22671763 DOI: 10.1021/pr300147z] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Label-free methods streamline quantitative proteomics of tissues by alleviating the need for metabolic labeling of proteins with stable isotopes. Here we detail and implement solutions to common problems in label-free data processing geared toward tissue proteomics by one-dimensional gel electrophoresis followed by liquid chromatography tandem mass spectrometry (geLC MS/MS). Our quantification pipeline showed high levels of performance in terms of duplicate reproducibility, linear dynamic range, and number of proteins identified and quantified. When applied to the liver of an adenomatous polyposis coli (APC) knockout mouse, we demonstrated an 8-fold increase in the number of statistically significant changing proteins compared to alternative approaches, including many more previously unidentified hydrophobic proteins. Better proteome coverage and quantification accuracy revealed molecular details of the perturbed energy metabolism.
Collapse
Affiliation(s)
- Andrej Vasilj
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | | | | | | | | |
Collapse
|
42
|
Identification of differentially expressed proteins in the spinal cord of neuropathic pain models with PKCgamma silence by proteomic analysis. Brain Res 2012; 1440:34-46. [PMID: 22284620 DOI: 10.1016/j.brainres.2011.12.046] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2011] [Revised: 12/21/2011] [Accepted: 12/22/2011] [Indexed: 12/29/2022]
Abstract
In order to elucidate the mechanisms that PKCγ regulates neuropathic pain (NP), and detect proteins that are associated with the function of PKCγ in NP, we exploited a chronic constriction injury (CCI)-induced neuropathic pain rat (CCI-NP rat) model in which PKCγ knockdown in the spinal cord was successfully carried out with stable RNA interference (RNAi). The spinal cords (L4-L5) were surgically obtained from CCI-NP rats with and without PKCγ knockdown, for comparative proteomic analysis. The total proteins from the spinal cords (L4-L5) were extracted and were separated with two-dimensional gel electrophoresis (2DGE). 2D gel images were analyzed with PDQuest software. Nineteen differential gel-spots were identified with spot-volume increased and 17 spots with spot-volume decreased. Among them, eighteen differentially expressed proteins (DEPs) were identified with matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) between CCI-NP rats with and without PKCγ knockout. Those DEPs are involved in transmission and modulation of noxious information; cellular homeostasis and metabolism; antioxidant proteins, heat shock proteins and chaperones; membrane receptor trafficking; and cytoskeleton. Three DEPs (SNAP-25, TERA and AR) were validated with Western blot analysis, and confirmed the DEP data. Further study showed that AR-selective inhibitor epalrestat totally turned over the upregulated expression of AR in CCI-NP rats. Those DEP data are extensively associated with the function of PKCγ that regulates NP, and would contribute to the clarification of the mechanisms of PKCγ in NP.
Collapse
|
43
|
Kirchner M, Selbach M. In vivo quantitative proteome profiling: planning and evaluation of SILAC experiments. Methods Mol Biol 2012; 893:175-199. [PMID: 22665302 DOI: 10.1007/978-1-61779-885-6_13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Mass spectrometry-based quantitative proteomics can identify and quantify thousands of proteins in complex biological samples. Improved instrumentation, quantification strategies and data analysis tools now enable protein analysis on a genome-wide scale. Particularly, quantification based on stable isotope labeling with amino acids (SILAC) has emerged as a robust, reliable and simple method for accurate large-scale protein quantification. The spectrum of applications ranges from bacteria and eukaryotic cell culture systems to multicellular organisms. Here, we provide a step-by-step protocol on how to plan and perform large-scale quantitative proteome analysis using SILAC, from sample preparation to final data analysis.
Collapse
Affiliation(s)
- Marieluise Kirchner
- Cell Signalling and Mass Spectrometry Group, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | | |
Collapse
|
44
|
Piechura H, Oeljeklaus S, Warscheid B. SILAC for the study of mammalian cell lines and yeast protein complexes. Methods Mol Biol 2012; 893:201-221. [PMID: 22665303 DOI: 10.1007/978-1-61779-885-6_14] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Through crucial advancements in quantitative mass spectrometry (MS), proteomics has evolved from taking mere "snapshots" of proteomes to thoroughly studying dynamic changes in entire proteomes and characterizing intricate protein-protein interaction or signaling networks. Thus, quantitative MS-based proteomics offers the unique potential to place proteins into their functional context and, moreover, to improve our understanding of the molecular processes involved in the development, survival, or pathology of cells and organisms. Among the vast variety of techniques developed for the accurate quantification of proteins via MS, stable isotope labeling by amino acids in cell culture (SILAC) arguably represents the most elegant method. In this chapter, we provide a detailed protocol for the establishment of SILAC for mammalian cell culture systems. In addition, to exemplify the high versatility of SILAC for addressing different biological questions, we describe the successful "pairing" of SILAC with conventional affinity purification (AP)-MS approaches allowing for accurately characterizing protein complexes.
Collapse
Affiliation(s)
- Heike Piechura
- Faculty of Biology and BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | | | | |
Collapse
|
45
|
Cambridge SB, Gnad F, Nguyen C, Bermejo JL, Krüger M, Mann M. Systems-wide proteomic analysis in mammalian cells reveals conserved, functional protein turnover. J Proteome Res 2011; 10:5275-84. [PMID: 22050367 DOI: 10.1021/pr101183k] [Citation(s) in RCA: 193] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The turnover of each protein in the mammalian proteome is a functionally important characteristic. Here, we employed high-resolution mass spectrometry to quantify protein dynamics in nondividing mammalian cells. The ratio of externally supplied versus endogenous amino acids to de novo protein synthesis was about 17:1. Using subsaturating SILAC labeling, we obtained accurate turnover rates of 4106 proteins in HeLa and 3528 proteins in C2C12 cells. Comparison of these human and mouse cell lines revealed a highly significant turnover correlation of protein orthologs and thus high species conservation. Functionally, we observed statistically significant trends for the turnover of phosphoproteins and gene ontology categories that showed extensive covariation between mouse and human. Likewise, the members of some protein complexes, such as the proteasome, have highly similar turnover rates. The high species conservation and the low complex variances thus imply great regulatory fine-tuning of protein turnover.
Collapse
Affiliation(s)
- Sidney B Cambridge
- Max-Planck-Institute for Biochemistry, Am Klopferspitz 18, 82152 Munich-Martinsried, Germany
| | | | | | | | | | | |
Collapse
|
46
|
Liao H, Liu XJ, Blank JL, Bouck DC, Bernard H, Garcia K, Lightcap ES. Quantitative proteomic analysis of cellular protein modulation upon inhibition of the NEDD8-activating enzyme by MLN4924. Mol Cell Proteomics 2011; 10:M111.009183. [PMID: 21873567 PMCID: PMC3226404 DOI: 10.1074/mcp.m111.009183] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 07/11/2011] [Indexed: 01/03/2023] Open
Abstract
Cullin-RING ubiquitin ligases (CRLs) are responsible for the ubiquitination of many cellular proteins, thereby targeting them for proteasomal degradation. In most cases the substrates of the CRLs have not been identified, although many of those that are known have cancer relevance. MLN4924, an investigational small molecule that is a potent and selective inhibitor of the Nedd8-activating enzyme (NAE), is currently being explored in Phase I clinical trials. Inhibition of Nedd8-activating enzyme by MLN4924 prevents the conjugation of cullin proteins with NEDD8, resulting in inactivation of the entire family of CRLs. We have performed stable isotope labeling with amino acids in cell culture analysis of A375 melanoma cells treated with MLN4924 to identify new CRL substrates, confidently identifying and quantitating 5122-6012 proteins per time point. Proteins such as MLX, EID1, KLF5, ORC6L, MAGEA6, MORF4L2, MRFAP1, MORF4L1, and TAX1BP1 are rapidly stabilized by MLN4924, suggesting that they are novel CRL substrates. Proteins up-regulated at later times were also identified and siRNA against their corresponding genes were used to evaluate their influence on MLN4924-induced cell death. Thirty-eight proteins were identified as being particularly important for the cytotoxicity of MLN4924. Strikingly, these proteins had roles in cell cycle, DNA damage repair, and ubiquitin transfer. Therefore, the combination of RNAi with stable isotope labeling with amino acids in cell culture provides a paradigm for understanding the mechanism of action of novel agents affecting the ubiquitin proteasome system and a path to identifying mechanistic biomarkers.
Collapse
Affiliation(s)
- Hua Liao
- ‡From the Discovery, Millennium Pharmaceuticals, Inc., 40 Landsdowne St., Cambridge, MA 02139
| | - Xiaozhen J. Liu
- ‡From the Discovery, Millennium Pharmaceuticals, Inc., 40 Landsdowne St., Cambridge, MA 02139
| | - Jonathan L. Blank
- ‡From the Discovery, Millennium Pharmaceuticals, Inc., 40 Landsdowne St., Cambridge, MA 02139
| | - David C. Bouck
- ‡From the Discovery, Millennium Pharmaceuticals, Inc., 40 Landsdowne St., Cambridge, MA 02139
| | - Hugues Bernard
- ‡From the Discovery, Millennium Pharmaceuticals, Inc., 40 Landsdowne St., Cambridge, MA 02139
| | - Khristofer Garcia
- ‡From the Discovery, Millennium Pharmaceuticals, Inc., 40 Landsdowne St., Cambridge, MA 02139
| | - Eric S. Lightcap
- ‡From the Discovery, Millennium Pharmaceuticals, Inc., 40 Landsdowne St., Cambridge, MA 02139
| |
Collapse
|
47
|
Böhmer M, Schroeder JI. Quantitative transcriptomic analysis of abscisic acid-induced and reactive oxygen species-dependent expression changes and proteomic profiling in Arabidopsis suspension cells. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 67:105-18. [PMID: 21426425 PMCID: PMC3125488 DOI: 10.1111/j.1365-313x.2011.04579.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Early rapid changes in response to the phytohormone abscisic acid (ABA) have been observed at the transcript level, but little is known how these transcript changes translate to changes in protein abundance under the same conditions. Here we have performed a global quantitative analysis of transcript and protein changes in Arabidopsis suspension cells in response to ABA using microarrays and quantitative proteomics. In summary, 3494 transcripts and 50 proteins were significantly regulated by ABA over a treatment period of 20-24 h. Abscisic acid also caused a rapid and strong increase in production of extracellular reactive oxygen species (ROS) with an average half-rise time of 33 sec. A subset of ABA-regulated transcripts were differentially regulated in the presence of the ROS scavenger dimethylthiourea (DMTU) as compared with ABA alone, suggesting a role for ROS in the regulation of these ABA-induced genes. Transcript changes showed an overall poor correlation to protein changes (r = 0.66). Only a subset of genes was regulated at the transcript and protein level, including known ABA marker genes. We furthermore identified ABA regulation of proteins that function in a branch of glucosinolate catabolism previously not associated with ABA signaling. The discovery of genes that were differentially regulated at the transcript and at the protein level emphasizes the strength of our combined approach. In summary, our dataset not only expands previous studies on gene and protein regulation in response to ABA, but rather uncovers unique aspects of the ABA regulon and gives rise to additional mechanisms regulated by ABA.
Collapse
Affiliation(s)
- Maik Böhmer
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0116, USA.
| | | |
Collapse
|
48
|
Abstract
Drosophila melanogaster has a long history as a model organism with several unique features that make it an ideal research tool for the study of the relationship between genotype and phenotype. Importantly fundamental genetic principles as well as key human disease genes have been uncovered through the use of Drosophila. The contribution of the fruit fly to science and medicine continues in the postgenomic era as cell-based Drosophila RNAi screens are a cost-effective and scalable enabling technology that can be used to quantify the contribution of different genes to diverse cellular processes. Drosophila high-throughput screens can also be used as integral part of systems-level approaches to describe the architecture and dynamics of cellular networks.
Collapse
Affiliation(s)
- Chris Bakal
- Dynamical Cell Systems Laboratory, Division of Cancer Biology, The Institute of Cancer Research, London, UK.
| |
Collapse
|
49
|
Vicent GP, Nacht AS, Font-Mateu J, Castellano G, Gaveglia L, Ballaré C, Beato M. Four enzymes cooperate to displace histone H1 during the first minute of hormonal gene activation. Genes Dev 2011; 25:845-62. [PMID: 21447625 DOI: 10.1101/gad.621811] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Gene regulation by external signals requires access of transcription factors to DNA sequences of target genes, which is limited by the compaction of DNA in chromatin. Although we have gained insight into how core histones and their modifications influence this process, the role of linker histones remains unclear. Here we show that, within the first minute of progesterone action, a complex cooperation between different enzymes acting on chromatin mediates histone H1 displacement as a requisite for gene induction and cell proliferation. First, activated progesterone receptor (PR) recruits the chromatin remodeling complexes NURF and ASCOM (ASC-2 [activating signal cointegrator-2] complex) to hormone target genes. The trimethylation of histone H3 at Lys 4 by the MLL2/MLL3 subunits of ASCOM, enhanced by the hormone-induced displacement of the H3K4 demethylase KDM5B, stabilizes NURF binding. NURF facilitates the PR-mediated recruitment of Cdk2/CyclinA, which is required for histone H1 displacement. Cooperation of ATP-dependent remodeling, histone methylation, and kinase activation, followed by H1 displacement, is a prerequisite for the subsequent displacement of histone H2A/H2B catalyzed by PCAF and BAF. Chromatin immunoprecipitation (ChIP) and sequencing (ChIP-seq) and expression arrays show that H1 displacement is required for hormone induction of most hormone target genes, some of which are involved in cell proliferation.
Collapse
Affiliation(s)
- Guillermo Pablo Vicent
- Centre de Regulació Genòmica (CRG), Universitat Pompeu Fabra (UPF), E-08003 Barcelona, Spain
| | | | | | | | | | | | | |
Collapse
|
50
|
Yang W, Chung YG, Kim Y, Kim TK, Keay SK, Zhang CO, Ji M, Hwang D, Kim KP, Steen H, Freeman MR, Kim J. Quantitative proteomics identifies a beta-catenin network as an element of the signaling response to Frizzled-8 protein-related antiproliferative factor. Mol Cell Proteomics 2011; 10:M110.007492. [PMID: 21422242 DOI: 10.1074/mcp.m110.007492] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Antiproliferative factor (APF), a Frizzled-8 protein-related sialoglycopeptide involved in the pathogenesis of interstitial cystitis, potently inhibits proliferation of normal urothelial cells as well as certain cancer cells. To elucidate the molecular mechanisms of the growth-inhibitory effect of APF, we performed stable isotope labeling by amino acids in cell culture analysis of T24 bladder cancer cells treated with and without APF. Among over 2000 proteins identified, 54 were significantly up-regulated and 48 were down-regulated by APF treatment. Bioinformatic analysis revealed that a protein network involved in cell adhesion was substantially altered by APF and that β-catenin was a prominent node in this network. Functional assays demonstrated that APF down-regulated β-catenin, at least in part, via proteasomal and lysosomal degradation. Moreover, silencing of β-catenin mimicked the antiproliferative effect of APF whereas ectopic expression of nondegradable β-catenin rescued growth inhibition in response to APF, confirming that β-catenin is a key mediator of APF signaling. Notably, the key role of β-catenin in APF signaling is not restricted to T24 cells, but was also observed in an hTERT-immortalized human bladder epithelial cell line, TRT-HU1. In addition, the network model suggested that β-catenin is linked to cyclooxygenase-2 (COX-2), implying a potential connection between APF and inflammation. Functional assays verified that APF increased the production of prostaglandin E(2) and that down-modulation of β-catenin elevated COX-2 expression, whereas forced expression of nondegradable β-catenin inhibited APF-induced up-regulation of COX-2. Furthermore, we confirmed that β-catenin was down-regulated whereas COX-2 was up-regulated in epithelial cells explanted from IC bladder biopsies compared with control tissues. In summary, our quantitative proteomics study describes the first provisional APF-regulated protein network, within which β-catenin is a key node, and provides new insight that targeting the β-catenin signaling pathway may be a rational approach toward treating interstitial cystitis.
Collapse
Affiliation(s)
- Wei Yang
- Urological Diseases Research Center, Children's Hospital Boston, Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|