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Cuesta R, Gritsenko MA, Petyuk VA, Shukla AK, Tsai CF, Liu T, McDermott JE, Holz MK. Phosphoproteome Analysis Reveals Estrogen-ER Pathway as a Modulator of mTOR Activity Via DEPTOR. Mol Cell Proteomics 2019; 18:1607-1618. [PMID: 31189691 PMCID: PMC6683011 DOI: 10.1074/mcp.ra119.001506] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 05/22/2019] [Indexed: 12/14/2022] Open
Abstract
ER-positive breast tumors represent ∼70% of all breast cancer cases. Although their treatment with endocrine therapies is effective in the adjuvant or recurrent settings, the development of resistance compromises their effectiveness. The binding of estrogen to ERα, a transcription factor, triggers the regulation of the target genes (genomic pathway). Additionally, a cytoplasmic fraction of estrogen-bound ERα activates oncogenic signaling pathways such as PI3K/AKT/mTOR (nongenomic pathway). The upregulation of the estrogenic and the PI3K/AKT/mTOR signaling pathways are frequently associated with a poor outcome. To better characterize the connection between these two pathways, we performed a phosphoproteome analysis of ER-positive MCF7 breast cancer cells treated with estrogen or estrogen and the mTORC1 inhibitor rapamycin. Many proteins were identified as estrogen-regulated mTORC1 targets and among them, DEPTOR was selected for further characterization. DEPTOR binds to mTOR and inhibits the kinase activity of both mTOR complexes mTORC1 and mTORC2, but mitogen-activated mTOR promotes phosphorylation-mediated DEPTOR degradation. Although estrogen enhances the phosphorylation of DEPTOR by mTORC1, DEPTOR levels increase in estrogen-stimulated cells. We demonstrated that DEPTOR accumulation is the result of estrogen-ERα-mediated transcriptional upregulation of DEPTOR expression. Consequently, the elevated levels of DEPTOR partially counterbalance the estrogen-induced activation of mTORC1 and mTORC2. These results underscore the critical role of estrogen-ERα as a modulator of the PI3K/AKT/mTOR signaling pathway in ER-positive breast cancer cells. Additionally, these studies provide evidence supporting the use of dual PI3K/mTOR or dual mTORC1/2 inhibitors in combination with endocrine therapies as a first-line treatment option for the patients with ER-positive advanced breast cancer.
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Affiliation(s)
- Rafael Cuesta
- Department of Cell Biology and Anatomy, New York Medical College, Valhalla NY 10595
| | - Marina A Gritsenko
- §Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA 99352
| | - Vladislav A Petyuk
- §Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA 99352
| | - Anil K Shukla
- §Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA 99352
| | - Chia-Feng Tsai
- §Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA 99352
| | - Tao Liu
- §Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA 99352
| | - Jason E McDermott
- ¶Computational Biology and Bioinformatics Group, Pacific Northwest National Laboratory, Richland WA 99352
| | - Marina K Holz
- Department of Cell Biology and Anatomy, New York Medical College, Valhalla NY 10595; ‖Albert Einstein Cancer Center, Bronx NY 10461.
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2
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Weiss-Sadan T, Itzhak G, Kaschani F, Yu Z, Mahameed M, Anaki A, Ben-Nun Y, Merquiol E, Tirosh B, Kessler B, Kaiser M, Blum G. Cathepsin L Regulates Metabolic Networks Controlling Rapid Cell Growth and Proliferation. Mol Cell Proteomics 2019; 18:1330-1344. [PMID: 31010818 PMCID: PMC6601214 DOI: 10.1074/mcp.ra119.001392] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/07/2019] [Indexed: 01/07/2023] Open
Abstract
Rapidly proliferating cells reshape their metabolism to satisfy their ever-lasting need for cellular building blocks. This phenomenon is exemplified in certain malignant conditions such as cancer but also during embryonic development when cells rely heavily on glycolytic metabolism to exploit its metabolic intermediates for biosynthetic processes. How cells reshape their metabolism is not fully understood. Here we report that loss of cathepsin L (Cts L) is associated with a fast proliferation rate and enhanced glycolytic metabolism that depend on lactate dehydrogenase A (LDHA) activity. Using mass spectrometry analysis of cells treated with a pan cathepsin inhibitor, we observed an increased abundance of proteins involved in central carbon metabolism. Further inspection of putative Cts L targets revealed an enrichment for glycolytic metabolism that was independently confirmed by metabolomic and biochemical analyses. Moreover, proteomic analysis of Cts L-knockout cells identified LDHA overexpression that was demonstrated to be a key metabolic junction in these cells. Lastly, we show that Cts L inhibition led to increased LDHA protein expression, suggesting a causal relationship between LDHA expression and function. In conclusion, we propose that Cts L regulates this metabolic circuit to keep cell division under control, suggesting the therapeutic potential of targeting this protein and its networks in cancer.
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Affiliation(s)
- Tommy Weiss-Sadan
- From the ‡Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University, Jerusalem, Israel, 9112001
| | - Gal Itzhak
- From the ‡Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University, Jerusalem, Israel, 9112001
| | - Farnusch Kaschani
- §Department of Chemical Biology, University of Duisburg-Essen, Center for Medical Biotechnology, Faculty of Biology, Essen, Germany
| | - Zhanru Yu
- ¶Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mohamed Mahameed
- From the ‡Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University, Jerusalem, Israel, 9112001
| | - Adi Anaki
- From the ‡Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University, Jerusalem, Israel, 9112001
| | - Yael Ben-Nun
- From the ‡Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University, Jerusalem, Israel, 9112001
| | - Emmanuelle Merquiol
- From the ‡Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University, Jerusalem, Israel, 9112001
| | - Boaz Tirosh
- From the ‡Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University, Jerusalem, Israel, 9112001
| | - Benedikt Kessler
- ¶Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Markus Kaiser
- §Department of Chemical Biology, University of Duisburg-Essen, Center for Medical Biotechnology, Faculty of Biology, Essen, Germany
| | - Galia Blum
- From the ‡Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University, Jerusalem, Israel, 9112001;.
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Zhang G, Li J, Zhang J, Liang X, Zhang X, Wang T, Yin S. Integrated Analysis of Transcriptomic, miRNA and Proteomic Changes of a Novel Hybrid Yellow Catfish Uncovers Key Roles for miRNAs in Heterosis. Mol Cell Proteomics 2019; 18:1437-1453. [PMID: 31092672 PMCID: PMC6601203 DOI: 10.1074/mcp.ra118.001297] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 04/09/2019] [Indexed: 01/14/2023] Open
Abstract
Heterosis is a complex biological phenomenon in which hybridization produces offspring that exhibit superior phenotypic characteristics compared with the parents. Heterosis is widely utilized in agriculture, for example in fish farming; however, its underlying molecular basis remains elusive. To gain a comprehensive and unbiased molecular understanding of fish heterosis, we analyzed the mRNA, miRNA, and proteomes of the livers of three catfish species, Pelteobagrus fulvidraco, P. vachelli, and their hybrid, the hybrid yellow catfish "Huangyou-1" (P. fulvidraco ♀ × P. vachelli ♂). Using next-generation sequencing and mass spectrometry, we show that the nonadditive, homoeolog expression bias and expression level dominance pattern were readily identified at the transcriptional, post-transcriptional, or protein levels, providing the evidence for the widespread presence of dominant models during hybridization. A number of predicted miRNA-mRNA-protein pairs were found and validated by qRT-PCR and PRM assays. Furthermore, several diverse key pathways were identified, including immune defense, metabolism, digestion and absorption, and cell proliferation and development, suggesting the vital mechanisms involved in the generation of the heterosis phenotype in progenies. We propose that the high parental expression of genes/proteins (growth, nutrition, feeding, and disease resistance) coupled with low parental miRNAs of the offspring, are inherited from the mother or father, thus indicating that the offspring were enriched with the advantages of the father or mother. We provide new and important information about the molecular mechanisms of heterosis, which represents a significant step toward a more complete elucidation of this phenomenon.
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Affiliation(s)
- Guosong Zhang
- From the ‡College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China;; §Key Laboratory for Physiology Biochemistry and Application, School of Agriculture and Bioengineering, Heze University, Heze, Shandong 274015, China
| | - Jie Li
- From the ‡College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China;; ¶Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang, 222005, China
| | - Jiajia Zhang
- From the ‡College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China;; ¶Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang, 222005, China
| | - Xia Liang
- §Key Laboratory for Physiology Biochemistry and Application, School of Agriculture and Bioengineering, Heze University, Heze, Shandong 274015, China
| | - Xinyu Zhang
- From the ‡College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China;; ¶Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang, 222005, China
| | - Tao Wang
- From the ‡College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China;; ¶Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang, 222005, China
| | - Shaowu Yin
- From the ‡College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China;; ¶Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang, 222005, China.
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Degner EC, Ahmed-Braimah YH, Borziak K, Wolfner MF, Harrington LC, Dorus S. Proteins, Transcripts, and Genetic Architecture of Seminal Fluid and Sperm in the Mosquito Aedes aegypti. Mol Cell Proteomics 2019; 18:S6-S22. [PMID: 30552291 PMCID: PMC6427228 DOI: 10.1074/mcp.ra118.001067] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 11/29/2018] [Indexed: 11/06/2022] Open
Abstract
The yellow fever mosquito, Aedes aegypti,, transmits several viruses causative of serious diseases, including dengue, Zika, and chikungunya. Some proposed efforts to control this vector involve manipulating reproduction to suppress wild populations or to replace them with disease-resistant mosquitoes. The design of such strategies requires an intimate knowledge of reproductive processes, yet our basic understanding of reproductive genetics in this vector remains largely incomplete. To accelerate future investigations, we have comprehensively catalogued sperm and seminal fluid proteins (SFPs) transferred to females in the ejaculate using tandem mass spectrometry. By excluding female-derived proteins using an isotopic labeling approach, we identified 870 sperm proteins and 280 SFPs. Functional composition analysis revealed parallels with known aspects of sperm biology and SFP function in other insects. To corroborate our proteome characterization, we also generated transcriptomes for testes and the male accessory glands-the primary contributors to Ae. aegypti, sperm and seminal fluid, respectively. Differential gene expression of accessory glands from virgin and mated males suggests that transcripts encoding proteins involved in protein translation are upregulated post-mating. Several SFP transcripts were also modulated after mating, but >90% remained unchanged. Finally, a significant enrichment of SFPs was observed on chromosome 1, which harbors the male sex determining locus in this species. Our study provides a comprehensive proteomic and transcriptomic characterization of ejaculate production and composition and thus provides a foundation for future investigations of Ae. aegypti, reproductive biology, from functional analysis of individual proteins to broader examination of reproductive processes.
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Affiliation(s)
- Ethan C Degner
- From the ‡Department of Entomology, Cornell University, Ithaca, New York
| | | | - Kirill Borziak
- Center for Reproductive Evolution, Syracuse University, Syracuse, New York
| | - Mariana F Wolfner
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York;.
| | - Laura C Harrington
- From the ‡Department of Entomology, Cornell University, Ithaca, New York;.
| | - Steve Dorus
- Center for Reproductive Evolution, Syracuse University, Syracuse, New York.
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5
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Myers SA, Rhoads A, Cocco AR, Peckner R, Haber AL, Schweitzer LD, Krug K, Mani DR, Clauser KR, Rozenblatt-Rosen O, Hacohen N, Regev A, Carr SA. Streamlined Protocol for Deep Proteomic Profiling of FAC-sorted Cells and Its Application to Freshly Isolated Murine Immune Cells. Mol Cell Proteomics 2019; 18:995-1009. [PMID: 30792265 DOI: 10.1074/mcp.ra118.001259] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/15/2019] [Indexed: 12/27/2022] Open
Abstract
Proteomic profiling describes the molecular landscape of proteins in cells immediately available to sense, transduce, and enact the appropriate responses to extracellular queues. Transcriptional profiling has proven invaluable to our understanding of cellular responses; however, insights may be lost as mounting evidence suggests transcript levels only moderately correlate with protein levels in steady state cells. Mass spectrometry-based quantitative proteomics is a well-suited and widely used analytical tool for studying global protein abundances. Typical proteomic workflows are often limited by the amount of sample input that is required for deep and quantitative proteome profiling. This is especially true if the cells of interest need to be purified by fluorescence-activated cell sorting (FACS) and one wants to avoid ex vivo culturing. To address this need, we developed an easy to implement, streamlined workflow that enables quantitative proteome profiling from roughly 2 μg of protein input per experimental condition. Utilizing a combination of facile cell collection from cell sorting, solid-state isobaric labeling and multiplexing of peptides, and small-scale fractionation, we profiled the proteomes of 12 freshly isolated, primary murine immune cell types. Analyzing half of the 3e5 cells collected per cell type, we quantified over 7000 proteins across 12 key immune cell populations directly from their resident tissues. We show that low input proteomics is precise, and the data generated accurately reflects many aspects of known immunology, while expanding the list of cell-type specific proteins across the cell types profiled. The low input proteomics methods we developed are readily adaptable and broadly applicable to any cell or sample types and should enable proteome profiling in systems previously unattainable.
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Affiliation(s)
- Samuel A Myers
- From the ‡The Broad Institute or MIT and Harvard, Cambridge, Massachusetts 02142;; §Klarman Cell Observatory, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142;.
| | - Andrew Rhoads
- ¶Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, and Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts
| | - Alexandra R Cocco
- From the ‡The Broad Institute or MIT and Harvard, Cambridge, Massachusetts 02142
| | - Ryan Peckner
- From the ‡The Broad Institute or MIT and Harvard, Cambridge, Massachusetts 02142
| | - Adam L Haber
- From the ‡The Broad Institute or MIT and Harvard, Cambridge, Massachusetts 02142;; §Klarman Cell Observatory, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | | | - Karsten Krug
- From the ‡The Broad Institute or MIT and Harvard, Cambridge, Massachusetts 02142
| | - D R Mani
- From the ‡The Broad Institute or MIT and Harvard, Cambridge, Massachusetts 02142
| | - Karl R Clauser
- From the ‡The Broad Institute or MIT and Harvard, Cambridge, Massachusetts 02142
| | - Orit Rozenblatt-Rosen
- From the ‡The Broad Institute or MIT and Harvard, Cambridge, Massachusetts 02142;; §Klarman Cell Observatory, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Nir Hacohen
- From the ‡The Broad Institute or MIT and Harvard, Cambridge, Massachusetts 02142;; ‖Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215;; **Center for Cancer Immunology, Massachusetts General Hospital, Boston, Massachusetts 02114
| | - Aviv Regev
- From the ‡The Broad Institute or MIT and Harvard, Cambridge, Massachusetts 02142;; §Klarman Cell Observatory, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142;; ‡‡Howard Hughes Medical Institute and Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02140
| | - Steven A Carr
- From the ‡The Broad Institute or MIT and Harvard, Cambridge, Massachusetts 02142;.
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6
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Delcourt V, Brunelle M, Roy AV, Jacques JF, Salzet M, Fournier I, Roucou X. The Protein Coded by a Short Open Reading Frame, Not by the Annotated Coding Sequence, Is the Main Gene Product of the Dual-Coding Gene MIEF1. Mol Cell Proteomics 2018; 17:2402-2411. [PMID: 30181344 PMCID: PMC6283296 DOI: 10.1074/mcp.ra118.000593] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 07/19/2018] [Indexed: 12/18/2022] Open
Abstract
Proteogenomics and ribosome profiling concurrently show that genes may code for both a large and one or more small proteins translated from annotated coding sequences (CDSs) and unannotated alternative open reading frames (named alternative ORFs or altORFs), respectively, but the stoichiometry between large and small proteins translated from a same gene is unknown. MIEF1, a gene recently identified as a dual-coding gene, harbors a CDS and a newly annotated and actively translated altORF located in the 5′UTR. Here, we use absolute quantification with stable isotope-labeled peptides and parallel reaction monitoring to determine levels of both proteins in two human cells lines and in human colon. We report that the main MIEF1 translational product is not the canonical 463 amino acid MiD51 protein but the small 70 amino acid alternative MiD51 protein (altMiD51). These results demonstrate the inadequacy of the single CDS concept and provide a strong argument for incorporating altORFs and small proteins in functional annotations.
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Affiliation(s)
- Vivian Delcourt
- Département de Biochimie, Université de Sherbrooke, Québec, Canada; Univ. Lille, INSERM U1192, Laboratoire Protéomique, Réponse Inflammatoire and Spectrométrie de Masse (PRISM) F-59000 Lille, France; PROTEO, Québec Network for Research on Protein Function, Structure, and Engineering, Québec, Canada
| | - Mylène Brunelle
- Département de Biochimie, Université de Sherbrooke, Québec, Canada; PROTEO, Québec Network for Research on Protein Function, Structure, and Engineering, Québec, Canada
| | - Annie V Roy
- Département de Biochimie, Université de Sherbrooke, Québec, Canada; PROTEO, Québec Network for Research on Protein Function, Structure, and Engineering, Québec, Canada
| | - Jean-François Jacques
- Département de Biochimie, Université de Sherbrooke, Québec, Canada; PROTEO, Québec Network for Research on Protein Function, Structure, and Engineering, Québec, Canada
| | - Michel Salzet
- Univ. Lille, INSERM U1192, Laboratoire Protéomique, Réponse Inflammatoire and Spectrométrie de Masse (PRISM) F-59000 Lille, France
| | - Isabelle Fournier
- Univ. Lille, INSERM U1192, Laboratoire Protéomique, Réponse Inflammatoire and Spectrométrie de Masse (PRISM) F-59000 Lille, France
| | - Xavier Roucou
- Département de Biochimie, Université de Sherbrooke, Québec, Canada; PROTEO, Québec Network for Research on Protein Function, Structure, and Engineering, Québec, Canada.
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Lomate PR, Dewangan V, Mahajan NS, Kumar Y, Kulkarni A, Wang L, Saxena S, Gupta VS, Giri AP. Integrated Transcriptomic and Proteomic Analyses Suggest the Participation of Endogenous Protease Inhibitors in the Regulation of Protease Gene Expression in Helicoverpa armigera. Mol Cell Proteomics 2018; 17:1324-1336. [PMID: 29661852 DOI: 10.1074/mcp.ra117.000533] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 03/16/2018] [Indexed: 11/06/2022] Open
Abstract
Insects adapt to plant protease inhibitors (PIs) present in their diet by differentially regulating multiple digestive proteases. However, mechanisms regulating protease gene expression in insects are largely enigmatic. Ingestion of multi-domain recombinant Capsicum annuum protease inhibitor-7 (CanPI-7) arrests growth and development of Helicoverpa armigera (Lepidoptera: Noctuidae). Using de novo RNA sequencing and proteomic analysis, we examined the response of H. armigera larvae fed on recombinant CanPI-7 at different time intervals. Here, we present evidence supporting a dynamic transition in H. armigera protease expression on CanPI-7 feeding with general down-regulation of protease genes at early time points (0.5 to 6 h) and significant up-regulation of specific trypsin, chymotrypsin and aminopeptidase genes at later time points (12 to 48 h). Further, coexpression of H. armigera endogenous PIs with several digestive protease genes were apparent. In addition to the differential expression of endogenous H. armigera PIs, we also observed a distinct novel isoform of endogenous PI in CanPI-7 fed H. armigera larvae. Based on present and earlier studies, we propose potential mechanism of protease regulation in H. armigera and subsequent adaptation strategy to cope with anti-nutritional components of plants.
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Affiliation(s)
- Purushottam R Lomate
- From the ‡Plant Molecular Biology Unit, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, MS, India
| | - Veena Dewangan
- From the ‡Plant Molecular Biology Unit, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, MS, India
| | - Neha S Mahajan
- From the ‡Plant Molecular Biology Unit, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, MS, India
| | - Yashwant Kumar
- From the ‡Plant Molecular Biology Unit, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, MS, India
| | - Abhijeet Kulkarni
- §Bioinformatics Centre, Savitribai Phule Pune University, Pune 411007, MS, India
| | - Li Wang
- ¶Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames 50011, IA
| | - Smita Saxena
- §Bioinformatics Centre, Savitribai Phule Pune University, Pune 411007, MS, India
| | - Vidya S Gupta
- From the ‡Plant Molecular Biology Unit, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, MS, India
| | - Ashok P Giri
- From the ‡Plant Molecular Biology Unit, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, MS, India;
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8
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Crozier TWM, Tinti M, Wheeler RJ, Ly T, Ferguson MAJ, Lamond AI. Proteomic Analysis of the Cell Cycle of Procylic Form Trypanosoma brucei. Mol Cell Proteomics 2018; 17:1184-1195. [PMID: 29555687 PMCID: PMC5986242 DOI: 10.1074/mcp.ra118.000650] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 03/01/2018] [Indexed: 12/24/2022] Open
Abstract
We describe a single-step centrifugal elutriation method to produce synchronous Gap1 (G1)-phase procyclic trypanosomes at a scale amenable for proteomic analysis of the cell cycle. Using ten-plex tandem mass tag (TMT) labeling and mass spectrometry (MS)-based proteomics technology, the expression levels of 5325 proteins were quantified across the cell cycle in this parasite. Of these, 384 proteins were classified as cell-cycle regulated and subdivided into nine clusters with distinct temporal regulation. These groups included many known cell cycle regulators in trypanosomes, which validates the approach. In addition, we identify 40 novel cell cycle regulated proteins that are essential for trypanosome survival and thus represent potential future drug targets for the prevention of trypanosomiasis. Through cross-comparison to the TrypTag endogenous tagging microscopy database, we were able to validate the cell-cycle regulated patterns of expression for many of the proteins of unknown function detected in our proteomic analysis. A convenient interface to access and interrogate these data is also presented, providing a useful resource for the scientific community. Data are available via ProteomeXchange with identifier PXD008741 (https://www.ebi.ac.uk/pride/archive/).
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Affiliation(s)
- Thomas W M Crozier
- From the ‡Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.,§Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Michele Tinti
- From the ‡Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Richard J Wheeler
- ‖Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Tony Ly
- §Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Michael A J Ferguson
- From the ‡Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK;
| | - Angus I Lamond
- §Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK;
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