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de Pablos LM, Ferreira TR, Dowle AA, Forrester S, Parry E, Newling K, Walrad PB. The mRNA-bound Proteome of Leishmania mexicana: Novel Genetic Insight into an Ancient Parasite. Mol Cell Proteomics 2019; 18:1271-1284. [PMID: 30948621 PMCID: PMC6601212 DOI: 10.1074/mcp.ra118.001307] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [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: 12/29/2018] [Revised: 02/23/2019] [Indexed: 01/08/2023] Open
Abstract
Leishmania parasite infections, termed the leishmaniases, cause significant global infectious disease burden. The lifecycle of the parasite embodies three main stages that require precise coordination of gene regulation to survive environmental shifts between sandfly and mammalian hosts. Constitutive transcription in kinetoplastid parasites means that gene regulation is overwhelmingly reliant on post-transcriptional mechanisms, yet strikingly few Leishmania trans-regulators are known. Using optimized crosslinking and deep, quantified mass spectrometry, we present a comprehensive analysis of 1400 mRNA binding proteins (mRBPs) and whole cell proteomes from the three main Leishmania lifecycle stages. Supporting the validity, although the crosslinked RBPome is magnitudes more enriched, the protein identities of the crosslinked and non-crosslinked RBPomes were nearly identical. Moreover, multiple candidate RBPs were endogenously tagged and found to associate with discrete mRNA target pools in a stage-specific manner. Results indicate that in L. mexicana parasites, mRNA levels are not a strong predictor of the whole cell expression or RNA binding potential of encoded proteins. Evidence includes a low correlation between transcript and corresponding protein expression and stage-specific variation in protein expression versus RNA binding potential. Unsurprisingly, RNA binding protein enrichment correlates strongly with relative replication efficiency of the specific lifecycle stage. Our study is the first to quantitatively define and compare the mRBPome of multiple stages in kinetoplastid parasites. It provides novel, in-depth insight into the trans-regulatory mRNA:Protein (mRNP) complexes that drive Leishmania parasite lifecycle progression.
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Affiliation(s)
| | | | - Adam A Dowle
- §Metabolomics and Proteomics Lab, Bioscience Technology Facility, and
| | | | - Ewan Parry
- From the ‡Centre for Immunology and Infection
| | - Katherine Newling
- ¶Genomics and Bioinformatics Lab, Bioscience Technology Facility, Department of Biology, University of York, UK
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Chachami G, Stankovic-Valentin N, Karagiota A, Basagianni A, Plessmann U, Urlaub H, Melchior F, Simos G. Hypoxia-induced Changes in SUMO Conjugation Affect Transcriptional Regulation Under Low Oxygen. Mol Cell Proteomics 2019; 18:1197-1209. [PMID: 30926672 PMCID: PMC6553927 DOI: 10.1074/mcp.ra119.001401] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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: 02/18/2019] [Revised: 03/14/2019] [Indexed: 12/20/2022] Open
Abstract
Hypoxia occurs in pathological conditions, such as cancer, as a result of the imbalance between oxygen supply and consumption by proliferating cells. HIFs are critical molecular mediators of the physiological response to hypoxia but also regulate multiple steps of carcinogenesis including tumor progression and metastasis. Recent data support that sumoylation, the covalent attachment of the Small Ubiquitin-related MOdifier (SUMO) to proteins, is involved in the activation of the hypoxic response and the ensuing signaling cascade. To gain insights into differences of the SUMO1 and SUMO2/3 proteome of HeLa cells under normoxia and cells grown for 48 h under hypoxic conditions, we employed endogenous SUMO-immunoprecipitation in combination with quantitative mass spectrometry (SILAC). The group of proteins whose abundance was increased both in the total proteome and in the SUMO IPs from hypoxic conditions was enriched in enzymes linked to the hypoxic response. In contrast, proteins whose SUMOylation status changed without concomitant change in abundance were predominantly transcriptions factors or transcription regulators. Particularly interesting was transcription factor TFAP2A (Activating enhancer binding Protein 2 alpha), whose sumoylation decreased on hypoxia. TFAP2A is known to interact with HIF-1 and we provide evidence that deSUMOylation of TFAP2A enhances the transcriptional activity of HIF-1 under hypoxic conditions. Overall, these results support the notion that SUMO-regulated signaling pathways contribute at many distinct levels to the cellular response to low oxygen.
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Affiliation(s)
- Georgia Chachami
- From the ‡Laboratory of Biochemistry, Faculty of Medicine, University of Thessaly, 41500 Larissa, Greece;
- ‡‡Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, 69120 Heidelberg, Germany
| | - Nicolas Stankovic-Valentin
- §Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, 69120 Heidelberg, Germany
| | - Angeliki Karagiota
- From the ‡Laboratory of Biochemistry, Faculty of Medicine, University of Thessaly, 41500 Larissa, Greece
| | - Angeliki Basagianni
- From the ‡Laboratory of Biochemistry, Faculty of Medicine, University of Thessaly, 41500 Larissa, Greece
| | - Uwe Plessmann
- ¶Bioanalytical Mass Spectrometry Group Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Henning Urlaub
- ¶Bioanalytical Mass Spectrometry Group Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
- ‖Bioanalytics, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Frauke Melchior
- §Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, 69120 Heidelberg, Germany
| | - George Simos
- From the ‡Laboratory of Biochemistry, Faculty of Medicine, University of Thessaly, 41500 Larissa, Greece
- **Gerald Bronfman Department of Oncology, Faculty of Medicine, McGill University, Montreal, Canada
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Hu H, Bezabih G, Feng M, Wei Q, Zhang X, Wu F, Meng L, Fang Y, Han B, Ma C, Li J. In-depth Proteome of the Hypopharyngeal Glands of Honeybee Workers Reveals Highly Activated Protein and Energy Metabolism in Priming the Secretion of Royal Jelly. Mol Cell Proteomics 2019; 18:606-621. [PMID: 30617159 PMCID: PMC6442370 DOI: 10.1074/mcp.ra118.001257] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [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: 12/12/2018] [Indexed: 11/06/2022] Open
Abstract
Royal jelly (RJ) is a secretion of the hypopharyngeal glands (HGs) of honeybee workers. High royal jelly producing bees (RJBs), a stock of honeybees selected from Italian bees (ITBs), have developed a stronger ability to produce RJ than ITBs. However, the mechanism underpinning the high RJ-producing performance in RJBs is still poorly understood. We have comprehensively characterized and compared the proteome across the life span of worker bees between the ITBs and RJBs. Our data uncover distinct molecular landscapes that regulate the gland ontogeny and activity corresponding with age-specific tasks. Nurse bees (NBs) have a well-developed acini morphology and cytoskeleton of secretory cells in HGs to prime the gland activities of RJ secretion. In RJB NBs, pathways involved in protein synthesis and energy metabolism are functionally induced to cement the enhanced RJ secretion compared with ITBs. In behavior-manipulated RJB NBs, the strongly expressed proteins implicated in protein synthesis and energy metabolism further demonstrate their critical roles in the regulation of RJ secretion. Our findings provide a novel understanding of the mechanism consolidating the high RJ-output in RJBs.
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Affiliation(s)
- Han Hu
- From the ‡ Institute of Apicultural Research/Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Chinese Academy of Agricultural Sciences, No. 1 Beigou Xiangshan, Beijing, 100093, China
| | - Gebreamlak Bezabih
- From the ‡ Institute of Apicultural Research/Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Chinese Academy of Agricultural Sciences, No. 1 Beigou Xiangshan, Beijing, 100093, China
| | - Mao Feng
- From the ‡ Institute of Apicultural Research/Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Chinese Academy of Agricultural Sciences, No. 1 Beigou Xiangshan, Beijing, 100093, China
| | - Qiaohong Wei
- From the ‡ Institute of Apicultural Research/Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Chinese Academy of Agricultural Sciences, No. 1 Beigou Xiangshan, Beijing, 100093, China
| | - Xufeng Zhang
- From the ‡ Institute of Apicultural Research/Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Chinese Academy of Agricultural Sciences, No. 1 Beigou Xiangshan, Beijing, 100093, China
| | - Fan Wu
- From the ‡ Institute of Apicultural Research/Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Chinese Academy of Agricultural Sciences, No. 1 Beigou Xiangshan, Beijing, 100093, China
| | - Lifeng Meng
- From the ‡ Institute of Apicultural Research/Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Chinese Academy of Agricultural Sciences, No. 1 Beigou Xiangshan, Beijing, 100093, China
| | - Yu Fang
- From the ‡ Institute of Apicultural Research/Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Chinese Academy of Agricultural Sciences, No. 1 Beigou Xiangshan, Beijing, 100093, China
| | - Bin Han
- From the ‡ Institute of Apicultural Research/Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Chinese Academy of Agricultural Sciences, No. 1 Beigou Xiangshan, Beijing, 100093, China
| | - Chuan Ma
- From the ‡ Institute of Apicultural Research/Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Chinese Academy of Agricultural Sciences, No. 1 Beigou Xiangshan, Beijing, 100093, China
| | - Jianke Li
- From the ‡ Institute of Apicultural Research/Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Chinese Academy of Agricultural Sciences, No. 1 Beigou Xiangshan, Beijing, 100093, China.
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Urizar-Arenaza I, Osinalde N, Akimov V, Puglia M, Candenas L, Pinto FM, Muñoa-Hoyos I, Gianzo M, Matorras R, Irazusta J, Blagoev B, Subiran N, Kratchmarova I. Phosphoproteomic and Functional Analyses Reveal Sperm-specific Protein Changes Downstream of Kappa Opioid Receptor in Human Spermatozoa. Mol Cell Proteomics 2019; 18:S118-S131. [PMID: 30622161 PMCID: PMC6427232 DOI: 10.1074/mcp.ra118.001133] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 12/27/2018] [Indexed: 12/11/2022] Open
Abstract
G-protein coupled receptors (GPCRs) belong to the seven transmembrane receptor superfamily that transduce signals via G proteins in response to external stimuli to initiate different intracellular signaling pathways which culminate in specific cellular responses. The expression of diverse GPCRs at the plasma membrane of human spermatozoa suggests their involvement in the regulation of sperm fertility. However, the signaling events downstream of many GPCRs in spermatozoa remain uncharacterized. Here, we selected the kappa-opioid receptor (KOR) as a study model and applied phosphoproteomic approach based on TMT labeling and LC-MS/MS analyses. Quantitative coverage of more than 5000 proteins with over 3500 phosphorylation sites revealed changes in the phosphorylation levels of sperm-specific proteins involved in the regulation of the sperm fertility in response to a specific agonist of KOR, U50488H. Further functional studies indicate that KOR could be involved in the regulation of sperm fertile capacity by modulation of calcium channels. Our findings suggest that human spermatozoa possess unique features in the molecular mechanisms downstream of GPCRs which could be key regulators of sperm fertility and improved knowledge of these specific processes may contribute to the development of useful biochemical tools for diagnosis and treatment of male infertility.
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Affiliation(s)
- Itziar Urizar-Arenaza
- From the ‡Department of Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Leioa, Bizkaia, Spain, 49840;; Biocruces Bizkaia Health Research Institute, Barakaldo, Bizkaia, Spain, 48903
| | - Nerea Osinalde
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Araba, Spain, 01006
| | - Vyacheslav Akimov
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark, 5320
| | - Michele Puglia
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark, 5320
| | - Luz Candenas
- Instituto de Investigaciones Químicas, CSIC, Sevilla, Spain, 41092
| | | | - Iraia Muñoa-Hoyos
- From the ‡Department of Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Leioa, Bizkaia, Spain, 49840;; Biocruces Bizkaia Health Research Institute, Barakaldo, Bizkaia, Spain, 48903
| | - Marta Gianzo
- From the ‡Department of Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Leioa, Bizkaia, Spain, 49840;; Biocruces Bizkaia Health Research Institute, Barakaldo, Bizkaia, Spain, 48903
| | - Roberto Matorras
- Biocruces Bizkaia Health Research Institute, Barakaldo, Bizkaia, Spain, 48903
| | - Jon Irazusta
- From the ‡Department of Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Leioa, Bizkaia, Spain, 49840
| | - Blagoy Blagoev
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark, 5320
| | - Nerea Subiran
- From the ‡Department of Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Leioa, Bizkaia, Spain, 49840;; Biocruces Bizkaia Health Research Institute, Barakaldo, Bizkaia, Spain, 48903;.
| | - Irina Kratchmarova
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark, 5320;.
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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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