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Sarihan M, Kasap M, Akpinar G. Streamlined Biotinylation, Enrichment and Analysis for Enhanced Plasma Membrane Protein Identification Using TurboID and TurboID-Start Biotin Ligases. J Membr Biol 2024; 257:91-105. [PMID: 38289568 DOI: 10.1007/s00232-023-00303-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 12/23/2023] [Indexed: 04/11/2024]
Abstract
Plasma membrane proteins (PMPs) play pivotal roles in various cellular events and are crucial in disease pathogenesis, making their comprehensive characterization vital for biomedical research. However, the hydrophobic nature and low expression levels of PMPs pose challenges for conventional enrichment methods, hindering their identification and functional profiling. In this study, we presented a novel TurboID-based enrichment approach for PMPs that helped overcoming some of the existing limitations. We evaluated the efficacy of TurboID and its modified form, TurboID-START, in PMP enrichment, achieving efficient and targeted labelling of PMPs without the need for stable cell line generation. This approach resulted reduction in non-specific biotinylation events, leading to improved PMP enrichment and enabled assessment of the subcellular proteome associated with the plasma membrane. Our findings paved the way for studies targeting the dynamic nature of the plasma membrane proteome and aiming to capture transient associations of proteins with the plasma membrane. The novel TurboID-based enrichment approach presented here offers promising prospects for in-depth investigations into PMPs and their roles in cellular processes.
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Affiliation(s)
- Mehmet Sarihan
- Department of Medical Biology/Proteomics Laboratory, Kocaeli University Medical School, 41001, Umuttepe, Kocaeli, Turkey
| | - Murat Kasap
- Department of Medical Biology/Proteomics Laboratory, Kocaeli University Medical School, 41001, Umuttepe, Kocaeli, Turkey.
| | - Gurler Akpinar
- Department of Medical Biology/Proteomics Laboratory, Kocaeli University Medical School, 41001, Umuttepe, Kocaeli, Turkey
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2
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Grunfeld N, Levine E, Libby E. Experimental measurement and computational prediction of bacterial Hanks-type Ser/Thr signaling system regulatory targets. Mol Microbiol 2024. [PMID: 38167835 DOI: 10.1111/mmi.15220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/15/2023] [Accepted: 12/17/2023] [Indexed: 01/05/2024]
Abstract
Bacteria possess diverse classes of signaling systems that they use to sense and respond to their environments and execute properly timed developmental transitions. One widespread and evolutionarily ancient class of signaling systems are the Hanks-type Ser/Thr kinases, also sometimes termed "eukaryotic-like" due to their homology with eukaryotic kinases. In diverse bacterial species, these signaling systems function as critical regulators of general cellular processes such as metabolism, growth and division, developmental transitions such as sporulation, biofilm formation, and virulence, as well as antibiotic tolerance. This multifaceted regulation is due to the ability of a single Hanks-type Ser/Thr kinase to post-translationally modify the activity of multiple proteins, resulting in the coordinated regulation of diverse cellular pathways. However, in part due to their deep integration with cellular physiology, to date, we have a relatively limited understanding of the timing, regulatory hierarchy, the complete list of targets of a given kinase, as well as the potential regulatory overlap between the often multiple kinases present in a single organism. In this review, we discuss experimental methods and curated datasets aimed at elucidating the targets of these signaling pathways and approaches for using these datasets to develop computational models for quantitative predictions of target motifs. We emphasize novel approaches and opportunities for collecting data suitable for the creation of new predictive computational models applicable to diverse species.
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Affiliation(s)
- Noam Grunfeld
- Department of Bioengineering, Northeastern University, Boston, Massachusetts, USA
| | - Erel Levine
- Department of Bioengineering, Northeastern University, Boston, Massachusetts, USA
- Department of Chemical Engineering, Northeastern University, Boston, Massachusetts, USA
| | - Elizabeth Libby
- Department of Bioengineering, Northeastern University, Boston, Massachusetts, USA
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3
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Sinitcyn P, Richards AL, Weatheritt RJ, Brademan DR, Marx H, Shishkova E, Meyer JG, Hebert AS, Westphall MS, Blencowe BJ, Cox J, Coon JJ. Global detection of human variants and isoforms by deep proteome sequencing. Nat Biotechnol 2023; 41:1776-1786. [PMID: 36959352 PMCID: PMC10713452 DOI: 10.1038/s41587-023-01714-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 02/15/2023] [Indexed: 03/25/2023]
Abstract
An average shotgun proteomics experiment detects approximately 10,000 human proteins from a single sample. However, individual proteins are typically identified by peptide sequences representing a small fraction of their total amino acids. Hence, an average shotgun experiment fails to distinguish different protein variants and isoforms. Deeper proteome sequencing is therefore required for the global discovery of protein isoforms. Using six different human cell lines, six proteases, deep fractionation and three tandem mass spectrometry fragmentation methods, we identify a million unique peptides from 17,717 protein groups, with a median sequence coverage of approximately 80%. Direct comparison with RNA expression data provides evidence for the translation of most nonsynonymous variants. We have also hypothesized that undetected variants likely arise from mutation-induced protein instability. We further observe comparable detection rates for exon-exon junction peptides representing constitutive and alternative splicing events. Our dataset represents a resource for proteoform discovery and provides direct evidence that most frame-preserving alternatively spliced isoforms are translated.
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Affiliation(s)
- Pavel Sinitcyn
- Computational Systems Biochemistry Research Group, Max Planck Institute of Biochemistry, Martinsried, Germany
- Morgridge Institute for Research, Madison, WI, USA
| | - Alicia L Richards
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Robert J Weatheritt
- EMBL Australia and Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Dain R Brademan
- Morgridge Institute for Research, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Harald Marx
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Evgenia Shishkova
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Jesse G Meyer
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Alexander S Hebert
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, WI, USA
| | - Michael S Westphall
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Benjamin J Blencowe
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jürgen Cox
- Computational Systems Biochemistry Research Group, Max Planck Institute of Biochemistry, Martinsried, Germany.
| | - Joshua J Coon
- Morgridge Institute for Research, Madison, WI, USA.
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
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4
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Jiang Q, Wang H, Qiao Z, Hou Y, Sui Z, Zhao B, Liang Z, Jiang B, Zhang Y, Zhang L. Metal organic layers enabled cell surface engineering coupling biomembrane fusion for dynamic membrane proteome profiling. Chem Sci 2023; 14:11727-11736. [PMID: 37920345 PMCID: PMC10619618 DOI: 10.1039/d3sc03725h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/30/2023] [Indexed: 11/04/2023] Open
Abstract
Systematically dissecting the highly dynamic and tightly communicating membrane proteome of living cells is essential for the system-level understanding of fundamental cellular processes and intricate relationship between membrane-bound organelles constructed through membrane traffic. While extensive efforts have been made to enrich membrane proteins, their comprehensive analysis with high selectivity and deep coverage remains a challenge, especially at the living cell state. To address this problem, we developed the cell surface engineering coupling biomembrane fusion method to map the whole membrane proteome from the plasma membrane to various organelle membranes taking advantage of the exquisite interaction between two-dimensional metal-organic layers and phospholipid bilayers on the membrane. This approach, which bypassed conventional biochemical fractionation and ultracentrifugation, facilitated the enrichment of membrane proteins in their native phospholipid bilayer environment, helping to map the membrane proteome with a specificity of 77% and realizing the deep coverage of the HeLa membrane proteome (5087 membrane proteins). Furthermore, membrane N-phosphoproteome was profiled by integrating the N-phosphoproteome analysis strategy, and the dynamic membrane proteome during apoptosis was deciphered in combination with quantitative proteomics. The features of membrane protein N-phosphorylation modifications and many differential proteins during apoptosis associated with mitochondrial dynamics and ER homeostasis were found. The method provided a simple and robust strategy for efficient analysis of membrane proteome, offered a reliable platform for research on membrane-related cell dynamic events and expanded the application of metal-organic layers.
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Affiliation(s)
- Qianqian Jiang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - He Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Zichun Qiao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Yutong Hou
- Dalian Medical University Dalian 116044 China
| | - Zhigang Sui
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Baofeng Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Zhen Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Bo Jiang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Yukui Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
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Sávio de Almeida Assunção A, Aparecida Martins R, Cavalcante Souza Vieira J, Campos Rocha L, Kaiser de Lima Krenchinski F, Afonso Rabelo Buzalaf M, Roberto Sartori J, de Magalhães Padilha P. Shotgun proteomics reveals changes in the pectoralis major muscle of broilers supplemented with passion fruit seed oil under cyclic heat stress conditions. Food Res Int 2023; 167:112731. [PMID: 37087218 DOI: 10.1016/j.foodres.2023.112731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 03/13/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023]
Abstract
The aim of this study was to characterize the proteins differentially expressed in the pectoralis major muscle of broilers supplemented with passion fruit seed oil (PFSO) under cyclic heat stress conditions. Ninety one-day-old male chicks were housed in cages arranged in a climatic chamber, where they were kept under cyclic heat stress for eight hours a day from the beginning to the end of the experiment. The birds were divided into two experimental groups, one group supplemented with 0.9% PFSO and a control group (CON) without PFSO supplementation. At 36 days of age, 18 birds were slaughtered to collect muscle samples. From pools of breast fillet samples from each group, proteolytic cleavage of the protein extracts was performed, and later, the peptides were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The 0.9% PFSO supplementation revealed the modulation of 57 proteins in the pectoralis major muscle of broilers exposed to cyclic heat stress. Among them, four proteins were upregulated, and 46 proteins were downregulated. In addition, seven proteins were expressed only in the CON group. These results suggest that PFSO may increase heat tolerance, with a possible reduction in oxidative stress, activation of neuroprotective mechanisms, protection against apoptosis, decrease in inflammatory responses, and regulation of energy metabolism.
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Affiliation(s)
| | - Renata Aparecida Martins
- School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | | | - Leone Campos Rocha
- School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | | | | | - José Roberto Sartori
- School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
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6
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Ahmed TI, Ali S. The enduring interdependence of shotgun and targeted proteomics in cancer research. Proteomics 2023. [DOI: 10.1016/b978-0-323-95072-5.00005-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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7
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Savić ND, Salazar Marcano DE, Parac-Vogt TN. Expanding the Scope of Polyoxometalates as Artificial Proteases towards Hydrolysis of Insoluble Proteins. Chemistry 2021; 28:e202104224. [PMID: 34860460 DOI: 10.1002/chem.202104224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Indexed: 11/08/2022]
Abstract
Despite the enormous importance of insoluble proteins in biological processes, their structural investigation remains a challenging task. The development of artificial enzyme-like catalysts would greatly facilitate the elucidation of their structure since currently used enzymes in proteomics largely lose activity in the presence of surfactants, which are necessary to solubilize insoluble proteins. In this study, the hydrolysis of a fully insoluble protein by polyoxometalate complexes as artificial proteases in surfactant solutions is reported for the first time. The hydrolysis of zein as a model protein was investigated in the presence of Zr(IV) and Hf(IV) substituted Keggin-type polyoxometalates (POMs), (Et2 NH2 )10 [M(α-PW11 O39 )2 ] (M = Zr or Hf), and different concentrations of the anionic surfactant sodium dodecyl sulfate (SDS). Selective hydrolysis of the protein upon incubation with the catalyst was observed, and the results indicate that the hydrolytic selectivity and activity of the POM catalysts strongly depends on the concentration of surfactant. The molecular interactions between the POM catalyst and zein in the presence of SDS were explored using a combination of spectroscopic techniques which indicated competitive binding between POM and SDS towards the protein. Furthermore, the formation of micellar superstructures in ternary POM/surfactant/protein solutions has been confirmed by conductivity and Dynamic Light Scattering measurements.
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Affiliation(s)
- Nada D Savić
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001, Leuven, Belgium
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8
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Araújo MJ, Sousa ML, Felpeto AB, Turkina MV, Fonseca E, Martins JC, Vasconcelos V, Campos A. Comparison of Sample Preparation Methods for Shotgun Proteomic Studies in Aquaculture Species. Proteomes 2021; 9:proteomes9040046. [PMID: 34842808 PMCID: PMC8628934 DOI: 10.3390/proteomes9040046] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 02/07/2023] Open
Abstract
Proteomics has been recently introduced in aquaculture research, and more methodological studies are needed to improve the quality of proteomics studies. Therefore, this work aims to compare three sample preparation methods for shotgun LC–MS/MS proteomics using tissues of two aquaculture species: liver of turbot Scophthalmus maximus and hepatopancreas of Mediterranean mussel Mytilus galloprovincialis. We compared the three most common sample preparation workflows for shotgun analysis: filter-aided sample preparation (FASP), suspension-trapping (S-Trap), and solid-phase-enhanced sample preparations (SP3). FASP showed the highest number of protein identifications for turbot samples, and S-Trap outperformed other methods for mussel samples. Subsequent functional analysis revealed a large number of Gene Ontology (GO) terms in turbot liver proteins (nearly 300 GO terms), while fewer GOs were found in mussel proteins (nearly 150 GO terms for FASP and S-Trap and 107 for SP3). This result may reflect the poor annotation of the genomic information in this specific group of animals. FASP was confirmed as the most consistent method for shotgun proteomic studies; however, the use of the other two methods might be important in specific experimental conditions (e.g., when samples have a very low amount of protein).
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Affiliation(s)
- Mário Jorge Araújo
- CIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; (M.J.A.); (M.L.S.); (A.B.F.); (E.F.); (J.C.M.); (V.V.)
| | - Maria Lígia Sousa
- CIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; (M.J.A.); (M.L.S.); (A.B.F.); (E.F.); (J.C.M.); (V.V.)
| | - Aldo Barreiro Felpeto
- CIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; (M.J.A.); (M.L.S.); (A.B.F.); (E.F.); (J.C.M.); (V.V.)
| | - Maria V. Turkina
- Department of Biomedical and Clinical Sciences, Faculty of Medicine and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden;
| | - Elza Fonseca
- CIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; (M.J.A.); (M.L.S.); (A.B.F.); (E.F.); (J.C.M.); (V.V.)
| | - José Carlos Martins
- CIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; (M.J.A.); (M.L.S.); (A.B.F.); (E.F.); (J.C.M.); (V.V.)
| | - Vítor Vasconcelos
- CIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; (M.J.A.); (M.L.S.); (A.B.F.); (E.F.); (J.C.M.); (V.V.)
- Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Alexandre Campos
- CIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; (M.J.A.); (M.L.S.); (A.B.F.); (E.F.); (J.C.M.); (V.V.)
- Correspondence:
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9
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Lawal RO, Richardson LT, Dong C, Donnarumma F, Solouki T, Murray KK. Deep-ultraviolet laser ablation sampling for proteomic analysis of tissue. Anal Chim Acta 2021; 1184:339021. [PMID: 34625253 DOI: 10.1016/j.aca.2021.339021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/29/2021] [Accepted: 08/30/2021] [Indexed: 01/22/2023]
Abstract
Deep-ultraviolet laser ablation with a pulsed 193 nm ArF excimer laser was used to remove localized regions from tissue sections from which proteins were extracted for spatially resolved proteomic analysis by liquid chromatography tandem mass spectrometry (LC-MS/MS). The ability to capture intact proteins by ablation at 193 nm wavelength was verified by matrix-assisted laser desorption ionization (MALDI) of the protein standard bovine serum albumin (BSA), which showed that BSA was ablated and captured without fragmentation. A Bradford assay of the ablated and captured proteins indicated 90% efficiency for transfer of the intact protein at a laser fluence of 3 kJ/m2. Rat brain tissue sections mounted on quartz microscope slides and ablated in transmission mode yielded 2 μg protein per mm2 as quantified by the Bradford assay. Tissue areas ranging from 0.06 mm2 to 1 mm2 were ablated and the ejected material was collected for proteomic analysis. Extracted proteins were digested and the resulting peptides were analyzed by LC-MS/MS. The proteins extracted from the ablated areas were identified and the average number of identified proteins ranged from 85 in the 0.06 mm2 area to 2400 in the 1 mm2 area of a 50 μm thick tissue. In comparison to infrared laser ablation of equivalent sampled areas, both the protein mass and number of proteins identified using DUV laser ablation sampling were approximately four times larger.
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Affiliation(s)
- Remilekun O Lawal
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Luke T Richardson
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76706, USA
| | - Chao Dong
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Fabrizio Donnarumma
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Touradj Solouki
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76706, USA
| | - Kermit K Murray
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA.
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10
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Carbonara K, Andonovski M, Coorssen JR. Proteomes Are of Proteoforms: Embracing the Complexity. Proteomes 2021; 9:38. [PMID: 34564541 PMCID: PMC8482110 DOI: 10.3390/proteomes9030038] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 08/24/2021] [Accepted: 08/29/2021] [Indexed: 12/17/2022] Open
Abstract
Proteomes are complex-much more so than genomes or transcriptomes. Thus, simplifying their analysis does not simplify the issue. Proteomes are of proteoforms, not canonical proteins. While having a catalogue of amino acid sequences provides invaluable information, this is the Proteome-lite. To dissect biological mechanisms and identify critical biomarkers/drug targets, we must assess the myriad of proteoforms that arise at any point before, after, and between translation and transcription (e.g., isoforms, splice variants, and post-translational modifications [PTM]), as well as newly defined species. There are numerous analytical methods currently used to address proteome depth and here we critically evaluate these in terms of the current 'state-of-the-field'. We thus discuss both pros and cons of available approaches and where improvements or refinements are needed to quantitatively characterize proteomes. To enable a next-generation approach, we suggest that advances lie in transdisciplinarity via integration of current proteomic methods to yield a unified discipline that capitalizes on the strongest qualities of each. Such a necessary (if not revolutionary) shift cannot be accomplished by a continued primary focus on proteo-genomics/-transcriptomics. We must embrace the complexity. Yes, these are the hard questions, and this will not be easy…but where is the fun in easy?
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Affiliation(s)
| | | | - Jens R. Coorssen
- Faculties of Applied Health Sciences and Mathematics & Science, Departments of Health Sciences and Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON L2S 3A1, Canada; (K.C.); (M.A.)
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11
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Navon G, Novak L, Shenkar N. Proteomic changes in the solitary ascidian Herdmania momus following exposure to the anticonvulsant medication carbamazepine. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2021; 237:105886. [PMID: 34134060 DOI: 10.1016/j.aquatox.2021.105886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 05/18/2021] [Accepted: 05/30/2021] [Indexed: 06/12/2023]
Abstract
The increasing use of pharmaceuticals in human and veterinary medicine, along with their poor removal rates at wastewater treatment facilities is resulting in the chronic release of pharmaceutically-active compounds (PhACs) into the marine environment, where they pose a threat to non-target organisms. A useful approach, as applied in the current study for assessing the effects of PhACs on non-target organisms, is the proteomic approach: the large-scale study of an organism's proteins. Using 'shotgun' proteomics, we identified differentially-expressed proteins based on peptide fragments in the solitary ascidian, Herdmania momus, following a 14-day laboratory experimental exposure to the PhAC carbamazepine (CBZ), an anticonvulsant and antidepressant medication, frequently detected in the aquatic environment. Individuals were exposed to environmentally relevant concentrations: 5 or 10 µg/L of CBZ, in addition to a control treatment. Out of 199 identified proteins, 24 were differentially expressed (12%) between the treatment groups, and thus can potentially be developed as biomarkers for CBZ contamination. Ascidians' phylogenetic position within the closest sister group to vertebrates presents an advantage in examining the pathological effects of PhACs on vertebrate-related organs and systems. Together with the world-wide distribution of some model ascidian species, and their ability to flourish in pristine and polluted sites, they provide a promising tool through which to study the extent and effects of PhAC contamination on marine organisms.
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Affiliation(s)
- Gal Navon
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Lion Novak
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel; The Steinhardt Museum of Natural History and National Research Center, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Noa Shenkar
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel; The Steinhardt Museum of Natural History and National Research Center, Tel Aviv University, Tel Aviv, 69978, Israel.
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12
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Prinsi B, Muratore C, Espen L. Biochemical and Proteomic Changes in the Roots of M4 Grapevine Rootstock in Response to Nitrate Availability. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10040792. [PMID: 33920578 PMCID: PMC8073184 DOI: 10.3390/plants10040792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 04/12/2021] [Accepted: 04/15/2021] [Indexed: 06/12/2023]
Abstract
In agricultural soils, nitrate (NO3-) is the major nitrogen (N) nutrient for plants, but few studies have analyzed molecular and biochemical responses involved in its acquisition by grapevine roots. In viticulture, considering grafting, NO3- acquisition is strictly dependent on rootstock. To improve the knowledge about N nutrition in grapevine, this study analyzed biochemical and proteomic changes induced by, NO3- availability, in a hydroponic system, in the roots of M4, a recently selected grapevine rootstock. The evaluation of biochemical parameters, such as NO3-, sugar and amino acid contents in roots, and the abundance of nitrate reductase, allowed us to define the time course of the metabolic adaptations to NO3- supply. On the basis of these results, the proteomic analysis was conducted by comparing the root profiles in N-starved plants and after 30 h of NO3- resupply. The analysis quantified 461 proteins, 26% of which differed in abundance between conditions. Overall, this approach highlighted, together with an increased N assimilatory metabolism, a concomitant rise in the oxidative pentose phosphate pathway and glycolysis, needed to fulfill the redox power and carbon skeleton demands, respectively. Moreover, a wide modulation of protein and amino acid metabolisms and changes of proteins involved in root development were observed. Finally, some results open new questions about the importance of redox-related post-translational modifications and of NO3- availability in modulating the dialog between root and rhizosphere.
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Affiliation(s)
| | | | - Luca Espen
- Correspondence: ; Tel.: +39-02-503-16610
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Liu J, Dong W, Wong TY, Qiu C, Wu J, Zhao J, Xia J, Xie S, Song X. Proteome-wide analysis of protein alterations in response to aristolochic acids in rat kidney and liver tissues. Mol Omics 2021; 17:405-412. [PMID: 34008672 DOI: 10.1039/d1mo00015b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Aristolochic acids (AAs), nephrotoxic components of herbs, have been previously demonstrated to cause DNA damage by forming DNA-AA adducts. However, the changes of tissue proteome profiles revealing AA toxicity need to be further studied. We conducted a proteomic study on the kidney and liver tissues of AA treated rats by a shotgun proteomics approach coupled with LC-MS/MS technology. A total of 1543 and 1641 proteins were identified and quantified in the kidneys and liver. Due to AA dosage, 10 and 4 proteins significantly changed in kidneys and the liver after multiple testing correction. Pathway enrichment analysis results were variant in kidneys and the liver. The enrichment analysis of metabolic pathways showed that gene expression and protein biosynthesis disorders were the common causes of AA toxicity to organs. Biological processes that positively responded to AAs in the liver probably have a detoxification function. SEC14-like protein 2 and synaptic vesicle membrane protein VAT-1 homolog were the mostly downregulated proteins in the liver and kidneys respectively.
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Affiliation(s)
- Jingjing Liu
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China.
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Iacobucci I, Monaco V, Cozzolino F, Monti M. From classical to new generation approaches: An excursus of -omics methods for investigation of protein-protein interaction networks. J Proteomics 2020; 230:103990. [PMID: 32961344 DOI: 10.1016/j.jprot.2020.103990] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/11/2020] [Accepted: 08/31/2020] [Indexed: 01/24/2023]
Abstract
Functional Proteomics aims to the identification of in vivo protein-protein interaction (PPI) in order to piece together protein complexes, and therefore, cell pathways involved in biological processes of interest. Over the years, proteomic approaches used for protein-protein interaction investigation have relied on classical biochemical protocols adapted to a global overview of protein-protein interactions, within so-called "interactomics" investigation. In particular, their coupling with advanced mass spectrometry instruments and innovative analytical methods led to make great strides in the PPIs investigation in proteomics. In this review, an overview of protein complexes purification strategies, from affinity purification approaches, including proximity-dependent labeling techniques and cross-linking strategy for the identification of transient interactions, to Blue Native Gel Electrophoresis (BN-PAGE) and Size Exclusion Chromatography (SEC) employed in the "complexome profiling", has been reported, giving a look to their developments, strengths and weakness and providing to readers several recent applications of each strategy. Moreover, a section dedicated to bioinformatic databases and platforms employed for protein networks analyses was also included.
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Affiliation(s)
- Ilaria Iacobucci
- Department of Chemical Sciences, University Federico II of Naples, Strada Comunale Cinthia, 26, 80126 Naples, Italy; CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy
| | - Vittoria Monaco
- CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy
| | - Flora Cozzolino
- Department of Chemical Sciences, University Federico II of Naples, Strada Comunale Cinthia, 26, 80126 Naples, Italy; CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy.
| | - Maria Monti
- Department of Chemical Sciences, University Federico II of Naples, Strada Comunale Cinthia, 26, 80126 Naples, Italy; CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy.
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15
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Quanten T, Savić ND, Parac-Vogt TN. Hydrolysis of Peptide Bonds in Protein Micelles Promoted by a Zirconium(IV)-Substituted Polyoxometalate as an Artificial Protease. Chemistry 2020; 26:11170-11179. [PMID: 32515831 DOI: 10.1002/chem.202001920] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Indexed: 12/22/2022]
Abstract
The development of artificial proteases is challenging, but important for many applications in modern proteomics and biotechnology. The hydrolysis of hydrophobic or unstructured proteins is particularly difficult due to their poor solubility, which often requires the presence of surfactants. Herein, it is shown that a zirconium(IV)-substituted Keggin polyoxometalate (POM), (Et2 NH2 )10 [Zr(α-PW11 O39 )2 ] (1), is able to selectively hydrolyze β-casein, which is an intrinsically unstructured protein at pH 7.4 and 60 °C. Four surfactants (sodium dodecyl sulfate (SDS), N-dodecyl-N,N-dimethyl-3-ammonio-1-propanesulfonate (ZW3-12), 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS), and polyethylene glycol tert-octylphenyl ether (TX-100)), which differ in the nature of their polar groups, were investigated for their role in influencing the selectivity and efficiency of protein hydrolysis. Under experimental conditions, β-casein forms micellar structures in which the hydrophilic part of the protein is water accessible and able to interact with 1. Identical fragmentation patterns of β-casein in the presence of 1 were observed through SDS poly(acrylamide) gel electrophoresis both in the presence and absence of surfactants, but the rate of hydrolysis varied, depending on the nature of surfactant. Whereas TX-100 surfactant, which has a neutral polar head, caused only a slight decrease in the hydrolysis rate, stronger inhibition was observed in the presence surfactants with charges in their polar heads (CHAPS, ZW3-12, SDS). These results were consistent with those of tryptophan fluorescencequenching studies, which showed that the binding between β-casein and 1 decreased with increasing repulsion between the POM and the polar heads of the surfactants. In all cases, the micellar structure of β-casein was not significantly affected by the presence of POM or surfactants, as indicated by circular dichroism spectroscopy.
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Affiliation(s)
- Thomas Quanten
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Box 2404, 3001, Leuven, Belgium
| | - Nada D Savić
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Box 2404, 3001, Leuven, Belgium
| | - Tatjana N Parac-Vogt
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Box 2404, 3001, Leuven, Belgium
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Gou MJ, Nys G, Cobraiville G, Demelenne A, Servais AC, Fillet M. Hyphenation of capillary zone electrophoresis with mass spectrometry for proteomic analysis: Optimization and comparison of two coupling interfaces. J Chromatogr A 2020; 1618:460873. [DOI: 10.1016/j.chroma.2020.460873] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 01/08/2020] [Accepted: 01/09/2020] [Indexed: 11/30/2022]
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17
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Prinsi B, Failla O, Scienza A, Espen L. Root Proteomic Analysis of Two Grapevine Rootstock Genotypes Showing Different Susceptibility to Salt Stress. Int J Mol Sci 2020; 21:ijms21031076. [PMID: 32041176 PMCID: PMC7037071 DOI: 10.3390/ijms21031076] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 01/30/2020] [Accepted: 02/04/2020] [Indexed: 11/23/2022] Open
Abstract
Salinity represents a very limiting factor that affects the fertility of agricultural soils. Although grapevine is moderately susceptible to salinity, both natural causes and agricultural practices could worsen the impact of this abiotic stress. A promising possibility to reduce this problem in vineyards is the use of appropriate graft combinations. The responses of grapevine rootstocks to this abiotic stress at the root level still remain poorly investigated. In order to obtain further information on the multifaceted responses induced by salt stress at the biochemical level, in the present work we analyzed the changes that occurred under control and salt conditions in the root proteomes of two grapevine rootstock genotypes, M4 and 101.14. Moreover, we compared the results considering that M4 and 101.14 were previously described to have lower and higher susceptibility to salt stress, respectively. This study highlighted the greater capability of M4 to maintain and adapt energy metabolism (i.e., synthesis of ATP and NAD(P)H) and to sustain the activation of salt-protective mechanisms (i.e., Na sequestration into the vacuole and synthesis of osmoprotectant compounds). Comparitively, in 101.14 the energy metabolism was deeply affected and there was an evident induction of the enzymatic antioxidant system that occurred, pointing to a metabolic scenario typical of a suffering tissue. Overall, this study describes for the first time in grapevine roots some of the more crucial events that characterize positive (M4) or negative (101.14) responses evoked by salt stress conditions.
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Affiliation(s)
| | | | | | - Luca Espen
- Correspondence: ; Tel.: +39-02-503-16610
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Mechanisms of Sugar Beet Response to Biotic and Abiotic Stresses. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1241:167-194. [PMID: 32383121 DOI: 10.1007/978-3-030-41283-8_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Sugar beet is used not only in the sugar production, but also in a wide range of industries including the production of bioethanol as a source of renewable energy, extraction of pectin and production of molasses. The red beetroot has attracted much attention as health-promoting and disease-preventing functional food. The negative effects of environmental stresses, including abiotic and biotic ones, significantly decrease the cash crop sugar beet productivity. In this paper, we outline the mechanisms of sugar beet response to biotic and abiotic stresses at the levels of physiological change, the genes' functions, transcription and translation. Regarding the physiological changes, most research has been carried out on salt and drought stress. The functions of genes from sugar beet in response to salt, cold and heavy metal stresses were mainly investigated by transgenic technologies. At the transcriptional level, the transcriptome analysis of sugar beet in response to salt, cold and biotic stresses were conducted by RNA-Seq or SSH methods. At the translational level, more than 800 differentially expressed proteins in response to salt, K+/Na+ ratio, iron deficiency and resupply and heavy metal (zinc) stress were identified by quantitative proteomics techniques. Understanding how sugar beet respond and tolerate biotic and abiotic stresses is important for boosting sugar beet productivity under these challenging conditions. In order to minimize the negative impact of these stresses, studying how the sugar beet has evolved stress coping mechanisms will provide new insights and lead to novel strategies for improving the breeding of stress-resistant sugar beet and other crops.
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Liu J, Hao C, Wu L, Madej D, Chan W, Lam H. Proteomic analysis of thioproline misincorporation in Escherichia coli. J Proteomics 2020; 210:103541. [DOI: 10.1016/j.jprot.2019.103541] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 09/27/2019] [Accepted: 10/07/2019] [Indexed: 01/01/2023]
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da Silva-Gomes RN, Gabriel Kuniyoshi ML, Oliveira da Silva Duran B, Thomazini Zanella BT, Paccielli Freire P, Gutierrez de Paula T, de Almeida Fantinatti BE, Simões Salomão RA, Carvalho RF, Delazari Santos L, Dal-Pai-Silva M. Prolonged fasting followed by refeeding modifies proteome profile and parvalbumin expression in the fast-twitch muscle of pacu (Piaractus mesopotamicus). PLoS One 2019; 14:e0225864. [PMID: 31856193 PMCID: PMC6922423 DOI: 10.1371/journal.pone.0225864] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 11/13/2019] [Indexed: 01/01/2023] Open
Abstract
Here, we analyzed the fast-twitch muscle of juvenile Piaractus mesopotamicus (pacu) submitted to prolonged fasting (30d) and refeeding (6h, 24h, 48h and 30d). We measured the relative rate of weight and length increase (RRIlength and RRIweight), performed shotgun proteomic analysis and did Western blotting for PVALB after 30d of fasting and 30d of refeeding. We assessed the gene expression of igf-1, mafbx and pvalb after 30d of fasting and after 6h, 24h, 48h and 30d of refeeding. We performed a bioinformatic analysis to predict miRNAs that possibly control parvalbumin expression. After fasting, RRIlength, RRIweight and igf-1 expression decreased, while the mafbx expression increased, which suggest that prolonged fasting caused muscle atrophy. After 6h and 24h of refeeding, mafbx was not changed and igf-1 was downregulated, while after 48h of refeeding mafbx was downregulated and igf-1 was not changed. After 30d of refeeding, RRIlength and RRIweight were increased and igf-1 and mafbx expression were not changed. Proteomic analysis identified 99 proteins after 30d of fasting and 71 proteins after 30d of refeeding, of which 23 and 17, respectively, were differentially expressed. Most of these differentially expressed proteins were related to cytoskeleton, muscle contraction, and metabolism. Among these, parvalbumin (PVALB) was selected for further validation. The analysis showed that pvalb mRNA was downregulated after 6h and 24h of refeeding, but was not changed after 30d of fasting or 48h and 30d of refeeding. The Western blotting confirmed that PVALB protein was downregulated after 30d of fasting and 30d of refeeding. The downregulation of the protein and the unchanged expression of the mRNA after 30d of fasting and 30d of refeeding suggest a post-transcriptional regulation of PVALB. Our miRNA analysis predicted 444 unique miRNAs that may target pvalb. In conclusion, muscle atrophy and partial compensatory growth caused by prolonged fasting followed by refeeding affected the muscle proteome and PVALB expression.
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Affiliation(s)
- Rafaela Nunes da Silva-Gomes
- Department of Morphology, Institute of Bioscience of Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Maria Laura Gabriel Kuniyoshi
- Department of Morphology, Institute of Bioscience of Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Bruno Oliveira da Silva Duran
- Department of Morphology, Institute of Bioscience of Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Bruna Tereza Thomazini Zanella
- Department of Morphology, Institute of Bioscience of Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Paula Paccielli Freire
- Department of Morphology, Institute of Bioscience of Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Tassiana Gutierrez de Paula
- Department of Morphology, Institute of Bioscience of Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | | | | | - Robson Francisco Carvalho
- Department of Morphology, Institute of Bioscience of Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Lucilene Delazari Santos
- Center for the Studies of Venoms and Venomous Animals (CEVAP)/ Graduate Program in Tropical Diseases (FMB), São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Maeli Dal-Pai-Silva
- Department of Morphology, Institute of Bioscience of Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
- * E-mail:
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Yoneten KK, Kasap M, Akpinar G, Kanli A, Karaoz E. Comparative Proteomics Analysis of Four Commonly Used Methods for Identification of Novel Plasma Membrane Proteins. J Membr Biol 2019; 252:587-608. [PMID: 31346646 DOI: 10.1007/s00232-019-00084-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/17/2019] [Indexed: 11/25/2022]
Abstract
Plasma membrane proteins perform a variety of important tasks in the cells. These tasks can be diverse as carrying nutrients across the plasma membrane, receiving chemical signals from outside the cell, translating them into intracellular action, and anchoring the cell in a particular location. When these crucial roles of plasma membrane proteins are considered, the need for their characterization becomes inevitable. Certain characteristics of plasma membrane proteins such as hydrophobicity, low solubility, and low abundance limit their detection by proteomic analyses. Here, we presented a comparative proteomics study in which the most commonly used plasma membrane protein enrichment methods were evaluated. The methods that were utilized include biotinylation, selective CyDye labeling, temperature-dependent phase partition, and density-gradient ultracentrifugation. Western blot analysis was performed to assess the level of plasma membrane protein enrichment using plasma membrane and cytoplasmic protein markers. Quantitative evaluation of the level of enrichment was performed by two-dimensional electrophoresis (2-DE) and benzyldimethyl-n-hexadecylammonium chloride/sodium dodecyl sulfate polyacrylamide gel electrophoresis (16-BAC/SDS-PAGE) from which the protein spots were cut and identified. Results from this study demonstrated that density-gradient ultracentrifugation method was superior when coupled with 16-BAC/SDS-PAGE. This work presents a valuable contribution and provides a future direction to the membrane sub-proteome research by evaluating commonly used methods for plasma membrane protein enrichment.
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Affiliation(s)
| | - Murat Kasap
- Department of Medical Biology, School of Medicine, Kocaeli University, 41380, Kocaeli, Turkey.
| | - Gurler Akpinar
- Department of Medical Biology, School of Medicine, Kocaeli University, 41380, Kocaeli, Turkey
| | - Aylin Kanli
- Department of Medical Biology, School of Medicine, Kocaeli University, 41380, Kocaeli, Turkey
| | - Erdal Karaoz
- Department of Histology and Embryology, School of Medicine, Istinye University, 34010, Istanbul, Turkey
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22
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Gupta S. Using X-ray Footprinting and Mass Spectrometry to Study the Structure and Function of Membrane Proteins. Protein Pept Lett 2019; 26:44-54. [PMID: 30484402 DOI: 10.2174/0929866526666181128142401] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 10/22/2018] [Accepted: 11/06/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND Membrane proteins are crucial for cellular sensory cascades and metabolite transport, and hence are key pharmacological targets. Structural studies by traditional highresolution techniques are limited by the requirements for high purity and stability when handled in high concentration and nonnative buffers. Hence, there is a growing requirement for the use of alternate methods in a complementary but orthogonal approach to study the dynamic and functional aspects of membrane proteins in physiologically relevant conditions. In recent years, significant progress has been made in the field of X-ray radiolytic labeling in combination with mass spectroscopy, commonly known as X-ray Footprinting and Mass Spectrometry (XFMS), which provide residue-specific information on the solvent accessibility of proteins. In combination with both lowresolution biophysical methods and high-resolution structural data, XFMS is capable of providing valuable insights into structure and dynamics of membrane proteins, which have been difficult to obtain by standalone high-resolution structural techniques. The XFMS method has also demonstrated a unique capability for identification of structural waters and their dynamics in protein cavities at both a high degree of spatial and temporal resolution, and thus capable of identifying conformational hot-spots in transmembrane proteins. CONCLUSION We provide a perspective on the place of XFMS amongst other structural biology methods and showcase some of the latest developments in its usage for studying conformational changes in membrane proteins.
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Affiliation(s)
- Sayan Gupta
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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Battchikova N, Muth-Pawlak D, Aro EM. Proteomics of cyanobacteria: current horizons. Curr Opin Biotechnol 2018; 54:65-71. [DOI: 10.1016/j.copbio.2018.02.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 01/31/2018] [Accepted: 02/13/2018] [Indexed: 12/01/2022]
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Mata CI, Fabre B, Parsons HT, Hertog MLATM, Van Raemdonck G, Baggerman G, Van de Poel B, Lilley KS, Nicolaï BM. Ethylene Receptors, CTRs and EIN2 Target Protein Identification and Quantification Through Parallel Reaction Monitoring During Tomato Fruit Ripening. FRONTIERS IN PLANT SCIENCE 2018; 9:1626. [PMID: 30467512 PMCID: PMC6235968 DOI: 10.3389/fpls.2018.01626] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 10/18/2018] [Indexed: 05/18/2023]
Abstract
Ethylene, the plant ripening hormone of climacteric fruit, is perceived by ethylene receptors which is the first step in the complex ethylene signal transduction pathway. Much progress has been made in elucidating the mechanism of this pathway, but there is still a lot to be done in the proteomic quantification of the main proteins involved, particularly during fruit ripening. This work focuses on the mass spectrometry based identification and quantification of the ethylene receptors (ETRs) and the downstream components of the pathway, CTR-like proteins (CTRs) and ETHYLENE INSENSITIVE 2 (EIN2). We used tomato as a model fruit to study changes in protein abundance involved in the ethylene signal transduction during fruit ripening. In order to detect and quantify these low abundant proteins located in the membrane of the endoplasmic reticulum, we developed a workflow comprising sample fractionation and MS analysis using parallel reaction monitoring. This work shows the feasibility of the identification and absolute quantification of all seven ethylene receptors, three out of four CTRs and EIN2 in four ripening stages of tomato. In parallel, gene expression was analyzed through real-time qPCR. Correlation between transcriptomic and proteomic profiles during ripening was only observed for three of the studied proteins, suggesting that the other signaling proteins are likely post-transcriptionally regulated. Based on our quantification results we were able to show that the protein levels of SlETR3 and SlETR4 increased during ripening, probably to control ethylene sensitivity. The other receptors and CTRs showed either stable levels that could sustain, or decreasing levels that could promote fruit ripening.
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Affiliation(s)
- Clara I. Mata
- Postharvest Group, Division of Mechatronics, Biostatistics and Sensors, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Bertrand Fabre
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - Harriet T. Parsons
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - Maarten L. A. T. M. Hertog
- Postharvest Group, Division of Mechatronics, Biostatistics and Sensors, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Geert Van Raemdonck
- Centre for Proteomics and Mass Spectrometry, University of Antwerp, Antwerp, Belgium
| | - Geert Baggerman
- Centre for Proteomics and Mass Spectrometry, University of Antwerp, Antwerp, Belgium
- Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Bram Van de Poel
- Molecular Plant Hormone Physiology, Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Kathryn S. Lilley
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - Bart M. Nicolaï
- Postharvest Group, Division of Mechatronics, Biostatistics and Sensors, Department of Biosystems, KU Leuven, Leuven, Belgium
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Prinsi B, Espen L. Time-Course of Metabolic and Proteomic Responses to Different Nitrate/Ammonium Availabilities in Roots and Leaves of Maize. Int J Mol Sci 2018; 19:ijms19082202. [PMID: 30060519 PMCID: PMC6121299 DOI: 10.3390/ijms19082202] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 07/24/2018] [Accepted: 07/25/2018] [Indexed: 12/16/2022] Open
Abstract
The availability of nitrate and ammonium significantly affects plant growth. Co-provision of both nutrients is generally the best nutritional condition, due to metabolic interactions not yet fully elucidated. In this study, maize grown in hydroponics was exposed to different nitrogen (N) availabilities, consisting of nitrate, ammonium and co-provision. Roots and leaves were analyzed after 6, 30, and 54 h by biochemical evaluations and proteomics. The ammonium-fed plants showed the lowest biomass accumulation and the lowest ratio of inorganic to organic N content, suggesting a metabolic need to assimilate ammonium that was not evident in plants grown in co-provision. The N sources differently affected the root proteome, inducing changes in abundance of proteins involved in N and carbon (C) metabolisms, cell water homeostasis, and cell wall metabolism. Notable among these changes was that some root enzymes, such as asparagine synthetase, phosphoenolpyruvate (PEP) carboxylase, and formate dehydrogenase showed a relevant upsurge only under the sole ammonium nutrition. However, the leaf proteome appeared mainly influenced by total N availability, showing changes in the abundance of several proteins involved in photosynthesis and in energy metabolism. Overall, the study provides novel information about the biochemical determinants involved in plant adaptation to different N mineral forms.
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Affiliation(s)
- Bhakti Prinsi
- Department of Agricultural and Environmental Sciences-Production, Landscape, Agroenergy (DiSAA), Università degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy.
| | - Luca Espen
- Department of Agricultural and Environmental Sciences-Production, Landscape, Agroenergy (DiSAA), Università degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy.
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Fechter P. Mapping Changes in Cell Surface Protein Expression Through Selective Labeling of Live Cells. Methods Mol Biol 2018; 1737:119-127. [PMID: 29484591 DOI: 10.1007/978-1-4939-7634-8_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
ncRNAs are key players in the adaptation of bacteria to new environments, by modulating the composition of the membrane upon changes in the environment. Nevertheless, monitoring the changes in surface protein expression is still a challenge, since these proteins are present in low abundance, and are difficult to extract. Here is described a method to easily, reproducibly, and specifically enrich total protein extracts in surface proteins. This method comprises a direct labeling of surface proteins on living cells using fluorescent dyes, followed by total protein extraction and subsequent separation of these extracts by 2D gel electrophoresis.
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Affiliation(s)
- Pierre Fechter
- UMR7242 Biotechnologie et Signalisation Cellulaire, CNRS, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg, Université de Strasbourg, Illkirch-Graffenstaden, France.
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Junková P, Daněk M, Kocourková D, Brouzdová J, Kroumanová K, Zelazny E, Janda M, Hynek R, Martinec J, Valentová O. Mapping of Plasma Membrane Proteins Interacting With Arabidopsis thaliana Flotillin 2. FRONTIERS IN PLANT SCIENCE 2018; 9:991. [PMID: 30050548 PMCID: PMC6052134 DOI: 10.3389/fpls.2018.00991] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 06/19/2018] [Indexed: 05/08/2023]
Abstract
Arabidopsis flotillin 2 (At5g25260) belongs to the group of plant flotillins, which are not well characterized. In contrast, metazoan flotillins are well known as plasma membrane proteins associated with membrane microdomains that act as a signaling hub. The similarity of plant and metazoan flotillins, whose functions most likely consist of affecting other proteins via protein-protein interactions, determines the necessity of detecting their interacting partners in plants. Nevertheless, identifying the proteins that form complexes on the plasma membrane is a challenging task due to their low abundance and hydrophobic character. Here we present an approach for mapping Arabidopsis thaliana flotillin 2 plasma membrane interactors, based on the immunoaffinity purification of crosslinked and enriched plasma membrane proteins with mass spectrometry detection. Using this approach, 61 proteins were enriched in the AtFlot-GFP plasma membrane fraction, and 19 of them were proposed to be flotillin 2 interaction partners. Among our proposed partners of Flot2, proteins playing a role in the plant response to various biotic and abiotic stresses were detected. Additionally, the use of the split-ubiquitin yeast system helped us to confirm that plasma-membrane ATPase 1, early-responsive to dehydration stress protein 4, syntaxin-71, harpin-induced protein-like 3, hypersensitive-induced response protein 2 and two aquaporin isoforms interact with flotillin 2 directly. Based on the results of our study and the reported properties of Flot2 interactors, we propose that Flot2 complexes may be involved in plant-pathogen interactions, water transport and intracellular trafficking.
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Affiliation(s)
- Petra Junková
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Prague, Czechia
- *Correspondence: Petra Junková, ;
| | - Michal Daněk
- Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czechia
| | - Daniela Kocourková
- Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Jitka Brouzdová
- Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Kristýna Kroumanová
- Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Enric Zelazny
- Institut de Biologie Intégrative de la Cellule (I2BC), CNRS–CEA–Université Paris Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Martin Janda
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Prague, Czechia
- Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Radovan Hynek
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Prague, Czechia
| | - Jan Martinec
- Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Olga Valentová
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Prague, Czechia
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28
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Membrane Proteomics in Gram-Positive Bacteria: Two Complementary Approaches to Target the Hydrophobic Species of Proteins. Methods Mol Biol 2018; 1841:21-33. [PMID: 30259477 DOI: 10.1007/978-1-4939-8695-8_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
This protocol represents a detailed instruction how to prepare protein samples in order to raise mass spectrometry-based identification and quantification rates with respect to the challenging class of membrane proteins. This will increase comprehensiveness of global proteome studies on the one hand but could also be of interest for researchers targeting specific membrane proteins or membrane protein sequences on the other hand. The protocol is a composite of two parts, one focusing on the identification of protein sequences exterior to a cellular membrane (loops of integral membrane proteins, peripheral membrane proteins), and the other part targeting primarily protein domains spanning the lipid bilayer. The feasibility of the protocol, as it is described here, was originally shown for the gram-positive pathogenic bacterium Staphylococcus aureus but should be applicable to any kind of membrane protein.
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29
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Bührmann M, Hardick J, Weisner J, Quambusch L, Rauh D. Kovalente Liganden zur Adressierung einer lipophilen Bindetasche in der MAPK p38 α. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Mike Bührmann
- Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
| | - Julia Hardick
- Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
| | - Jörn Weisner
- Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
| | - Lena Quambusch
- Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
| | - Daniel Rauh
- Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
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30
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Bührmann M, Hardick J, Weisner J, Quambusch L, Rauh D. Covalent Lipid Pocket Ligands Targeting p38α MAPK Mutants. Angew Chem Int Ed Engl 2017; 56:13232-13236. [DOI: 10.1002/anie.201706345] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Mike Bührmann
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Julia Hardick
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Jörn Weisner
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Lena Quambusch
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Daniel Rauh
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
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31
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Wöhlbrand L, Rabus R, Blasius B, Feenders C. Influence of NanoLC Column and Gradient Length as well as MS/MS Frequency and Sample Complexity on Shotgun Protein Identification of Marine Bacteria. J Mol Microbiol Biotechnol 2017; 27:199-212. [PMID: 28850952 DOI: 10.1159/000478907] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 06/22/2017] [Indexed: 11/19/2022] Open
Abstract
Protein identification by shotgun proteomics, i.e., nano-liquid chromatography (nanoLC) peptide separation online coupled to electrospray ionization (ESI) mass spectrometry (MS)/MS, is the most widely used gel-free approach in proteome research. While the mass spectrometer accounts for mass accuracy and MS/MS frequency, the nanoLC setup and gradient time influence the number of peptides available for MS analysis, which ultimately determine the number of proteins identifiable. Here, we report on the influence of (i) analytical column length (15, 25, or 50 cm) coupled to (ii) the applied gradient length (120, 240, 360, 480, or 600 min), as well as (iii) MS/MS frequency on peptide/protein identification by shotgun proteomics of (iv) 2 marine bacteria. Longer gradients increased the number of peptides/proteins identified as well as the reproducibility of identification. Furthermore, longer analytical columns strictly enlarge the covered proteome complement. Notably, the proteome complement identified with a short column and applying a long gradient is also covered when using longer columns with shorter gradients. Coverage of the proteome complement further increases with higher MS/MS frequency. Compilation of peptide lists of replicate analyses (same gradient length) improves protein identification, while compilation of analyses with different gradient lengths yields a similar or even higher number of proteins using comparable or even less total analysis time.
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Affiliation(s)
- Lars Wöhlbrand
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
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32
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Yan L, Fan G, Deng M, Zhao Z, Dong Y, Li Y. Comparative proteomic analysis of autotetraploid and diploid Paulownia tomentosa reveals proteins associated with superior photosynthetic characteristics and stress adaptability in autotetraploid Paulownia. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2017; 23:605-617. [PMID: 28878499 PMCID: PMC5567708 DOI: 10.1007/s12298-017-0447-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 04/13/2017] [Accepted: 05/12/2017] [Indexed: 05/09/2023]
Abstract
To enlarge the germplasm resource of Paulownia plants, we used colchicine to induce autotetraploid Paulownia tomentosa, as reported previously. Compared with its diploid progenitor, autotetraploid P. tomentosa exhibits better photosynthetic characteristics and higher stress resistance. However, the underlying mechanism for its predominant characteristics has not been determined at the proteome level. In this study, isobaric tag for relative and absolute quantitation coupled with liquid chromatography-tandem mass spectrometry was employed to compare proteomic changes between autotetraploid and diploid P. tomentosa. A total of 1427 proteins were identified in our study, of which 130 proteins were differentially expressed between autotetraploid and diploid P. tomentosa. Functional analysis of differentially expressed proteins revealed that photosynthesis-related proteins and stress-responsive proteins were significantly enriched among the differentially expressed proteins, suggesting they may be responsible for the photosynthetic characteristics and stress adaptability of autotetraploid P. tomentosa. The correlation analysis between transcriptome and proteome data revealed that only 15 (11.5%) of the differentially expressed proteins had corresponding differentially expressed unigenes between diploid and autotetraploid P. tomentosa. These results indicated that there was a limited correlation between the differentially expressed proteins and the previously reported differentially expressed unigenes. This work provides new clues to better understand the superior traits in autotetraploid P. tomentosa and lays a theoretical foundation for developing Paulownia breeding strategies in the future.
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Affiliation(s)
- Lijun Yan
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, 450002 Henan People’s Republic of China
- College of Forestry, Henan Agricultural University, Zhengzhou, 450002 Henan People’s Republic of China
| | - Guoqiang Fan
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, 450002 Henan People’s Republic of China
- College of Forestry, Henan Agricultural University, Zhengzhou, 450002 Henan People’s Republic of China
| | - Minjie Deng
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, 450002 Henan People’s Republic of China
- College of Forestry, Henan Agricultural University, Zhengzhou, 450002 Henan People’s Republic of China
| | - Zhenli Zhao
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, 450002 Henan People’s Republic of China
- College of Forestry, Henan Agricultural University, Zhengzhou, 450002 Henan People’s Republic of China
| | - Yanpeng Dong
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, 450002 Henan People’s Republic of China
- College of Forestry, Henan Agricultural University, Zhengzhou, 450002 Henan People’s Republic of China
| | - Yongsheng Li
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, 450002 Henan People’s Republic of China
- College of Forestry, Henan Agricultural University, Zhengzhou, 450002 Henan People’s Republic of China
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33
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Kessler RL, Contreras VT, Marliére NP, Aparecida Guarneri A, Villamizar Silva LH, Mazzarotto GACA, Batista M, Soccol VT, Krieger MA, Probst CM. Recently differentiated epimastigotes fromTrypanosoma cruziare infective to the mammalian host. Mol Microbiol 2017; 104:712-736. [DOI: 10.1111/mmi.13653] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2017] [Indexed: 12/31/2022]
Affiliation(s)
| | - Víctor Tulio Contreras
- Laboratorio de Protozoología, Centro de Biología Molecular de Parásitos, Facultad Ciencias de la Salud; Universidad de Carabobo; Valencia Venezuela
| | - Newmar Pinto Marliére
- Vector Behavior and Pathogen Interaction Group; Centro de Pesquisas René Rachou, Fiocruz; Belo Horizonte Minas Gerais Brazil
| | - Alessandra Aparecida Guarneri
- Vector Behavior and Pathogen Interaction Group; Centro de Pesquisas René Rachou, Fiocruz; Belo Horizonte Minas Gerais Brazil
| | | | | | | | - Vanete Thomaz Soccol
- Programa de Pós-Graduação em Processos Biotecnológicos e Biotecnologia, Centro Politécnico; Universidade Federal do Paraná; Curitiba PR Brazil
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34
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Muthusamy S, Lundin D, Mamede Branca RM, Baltar F, González JM, Lehtiö J, Pinhassi J. Comparative proteomics reveals signature metabolisms of exponentially growing and stationary phase marine bacteria. Environ Microbiol 2017; 19:2301-2319. [PMID: 28371138 DOI: 10.1111/1462-2920.13725] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 03/05/2017] [Indexed: 11/30/2022]
Abstract
Much of the phenotype of a microorganism consists of its repertoire of metabolisms and how and when its proteins are deployed under different growth conditions. Hence, analyses of protein expression could provide important understanding of how bacteria adapt to different environmental settings. To characterize the flexibility of proteomes of marine bacteria, we investigated protein profiles of three important marine bacterial lineages - Oceanospirillaceae (Neptuniibacter caesariensis strain MED92), Roseobacter (Phaeobacter sp. MED193) and Flavobacteria (Dokdonia sp. MED134) - during transition from exponential to stationary phase. As much as 59-80% of each species' total proteome was expressed. Moreover, all three bacteria profoundly altered their expressed proteomes during growth phase transition, from a dominance of proteins involved in translation to more diverse proteomes, with a striking appearance of enzymes involved in different nutrient-scavenging metabolisms. Whereas the three bacteria shared several overarching metabolic strategies, they differed in important details, including distinct expression patterns of membrane transporters and proteins in carbon and phosphorous metabolism and storage compounds. These differences can be seen as signature metabolisms - metabolisms specific for lineages. These findings suggest that quantitative proteomics can inform about the divergent ecological strategies of marine bacteria in adapting to changes in environmental conditions.
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Affiliation(s)
- Saraladevi Muthusamy
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, SE-39182, Sweden
| | - Daniel Lundin
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, SE-39182, Sweden
| | - Rui Miguel Mamede Branca
- Department of Oncology-Pathology, Science for Life Laboratory and Karolinska Institute, Clinical Proteomics Mass Spectrometry, Stockholm, Sweden
| | - Federico Baltar
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, SE-39182, Sweden.,Department of Marine Science, University of Otago, Dunedin, New Zealand
| | - José M González
- Department of Microbiology, University of La Laguna, La Laguna, ES-38200, Spain
| | - Janne Lehtiö
- Department of Oncology-Pathology, Science for Life Laboratory and Karolinska Institute, Clinical Proteomics Mass Spectrometry, Stockholm, Sweden
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, SE-39182, Sweden
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35
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Quantitative Proteomics of Sleep-Deprived Mouse Brains Reveals Global Changes in Mitochondrial Proteins. PLoS One 2016; 11:e0163500. [PMID: 27684481 PMCID: PMC5042483 DOI: 10.1371/journal.pone.0163500] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 09/09/2016] [Indexed: 12/13/2022] Open
Abstract
Sleep is a ubiquitous, tightly regulated, and evolutionarily conserved behavior observed in almost all animals. Prolonged sleep deprivation can be fatal, indicating that sleep is a physiological necessity. However, little is known about its core function. To gain insight into this mystery, we used advanced quantitative proteomics technology to survey the global changes in brain protein abundance. Aiming to gain a comprehensive profile, our proteomics workflow included filter-aided sample preparation (FASP), which increased the coverage of membrane proteins; tandem mass tag (TMT) labeling, for relative quantitation; and high resolution, high mass accuracy, high throughput mass spectrometry (MS). In total, we obtained the relative abundance ratios of 9888 proteins encoded by 6070 genes. Interestingly, we observed significant enrichment for mitochondrial proteins among the differentially expressed proteins. This finding suggests that sleep deprivation strongly affects signaling pathways that govern either energy metabolism or responses to mitochondrial stress. Additionally, the differentially-expressed proteins are enriched in pathways implicated in age-dependent neurodegenerative diseases, including Parkinson’s, Huntington’s, and Alzheimer’s, hinting at possible connections between sleep loss, mitochondrial stress, and neurodegeneration.
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36
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Piovesana S, Capriotti AL, Colapicchioni V, Ferraris F, La Barbera G, Ventura S. Membrane proteome functional characterization of breast cancer-initiating cells subjected to bone morphogenetic protein signaling inhibition by dorsomorphin. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1657-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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37
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Shen S, Jiang X, Li J, Straubinger RM, Suarez M, Tu C, Duan X, Thompson AC, Qu J. Large-Scale, Ion-Current-Based Proteomic Investigation of the Rat Striatal Proteome in a Model of Short- and Long-Term Cocaine Withdrawal. J Proteome Res 2016; 15:1702-16. [PMID: 27018876 DOI: 10.1021/acs.jproteome.6b00137] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Given the tremendous detriments of cocaine dependence, effective diagnosis and patient stratification are critical for successful intervention yet difficult to achieve due to the largely unknown molecular mechanisms involved. To obtain new insights into cocaine dependence and withdrawal, we employed a reproducible, reliable, and large-scale proteomics approach to investigate the striatal proteomes of rats (n = 40, 10 per group) subjected to chronic cocaine exposure, followed by either short- (WD1) or long- (WD22) term withdrawal. By implementing a surfactant-aided precipitation/on-pellet digestion procedure, a reproducible and sensitive nanoLC-Orbitrap MS analysis, and an optimized ion-current-based MS1 quantification pipeline, >2000 nonredundant proteins were quantified confidently without missing data in any replicate. Although cocaine was cleared from the body, 129/37 altered proteins were observed in WD1/WD22 that are implicated in several biological processes related closely to drug-induced neuroplasticity. Although many of these changes recapitulate the findings from independent studies reported over the last two decades, some novel insights were obtained and further validated by immunoassays. For example, significantly elevated striatal protein kinase C activity persisted over the 22 day cocaine withdrawal. Cofilin-1 activity was up-regulated in WD1 and down-regulated in WD22. These discoveries suggest potentially distinct structural plasticity after short- and long-term cocaine withdrawal. In addition, this study provides compelling evidence that blood vessel narrowing, a long-known effect of cocaine use, occurred after long-term but not short-term withdrawal. In summary, this work developed a well-optimized paradigm for ion-current-based quantitative proteomics in brain tissues and obtained novel insights into molecular alterations in the striatum following cocaine exposure and withdrawal.
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Affiliation(s)
- Shichen Shen
- New York State Center of Excellence in Bioinformatics & Life Sciences , Buffalo, New York 14203, United States.,Department of Biochemistry, School of Medicine and Biomedical Sciences, SUNY at Buffalo , Buffalo, New York 14214, United States
| | - Xiaosheng Jiang
- Department of Pharmaceutical Sciences, SUNY at Buffalo , Buffalo, New York 14214, United States.,New York State Center of Excellence in Bioinformatics & Life Sciences , Buffalo, New York 14203, United States
| | - Jun Li
- Department of Pharmaceutical Sciences, SUNY at Buffalo , Buffalo, New York 14214, United States.,New York State Center of Excellence in Bioinformatics & Life Sciences , Buffalo, New York 14203, United States
| | - Robert M Straubinger
- Department of Pharmaceutical Sciences, SUNY at Buffalo , Buffalo, New York 14214, United States
| | - Mauricio Suarez
- Department of Psychology, SUNY at Buffalo , Buffalo, New York 14260, United States.,Research Institute on Addictions, SUNY at Buffalo , Buffalo, New York 14203, United States
| | - Chengjian Tu
- New York State Center of Excellence in Bioinformatics & Life Sciences , Buffalo, New York 14203, United States.,Department of Biochemistry, School of Medicine and Biomedical Sciences, SUNY at Buffalo , Buffalo, New York 14214, United States
| | - Xiaotao Duan
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology , Beijing 100850, China
| | - Alexis C Thompson
- Department of Psychology, SUNY at Buffalo , Buffalo, New York 14260, United States.,Research Institute on Addictions, SUNY at Buffalo , Buffalo, New York 14203, United States
| | - Jun Qu
- Department of Pharmaceutical Sciences, SUNY at Buffalo , Buffalo, New York 14214, United States.,New York State Center of Excellence in Bioinformatics & Life Sciences , Buffalo, New York 14203, United States
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38
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Wessels HJCT, de Almeida NM, Kartal B, Keltjens JT. Bacterial Electron Transfer Chains Primed by Proteomics. Adv Microb Physiol 2016; 68:219-352. [PMID: 27134025 DOI: 10.1016/bs.ampbs.2016.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Electron transport phosphorylation is the central mechanism for most prokaryotic species to harvest energy released in the respiration of their substrates as ATP. Microorganisms have evolved incredible variations on this principle, most of these we perhaps do not know, considering that only a fraction of the microbial richness is known. Besides these variations, microbial species may show substantial versatility in using respiratory systems. In connection herewith, regulatory mechanisms control the expression of these respiratory enzyme systems and their assembly at the translational and posttranslational levels, to optimally accommodate changes in the supply of their energy substrates. Here, we present an overview of methods and techniques from the field of proteomics to explore bacterial electron transfer chains and their regulation at levels ranging from the whole organism down to the Ångstrom scales of protein structures. From the survey of the literature on this subject, it is concluded that proteomics, indeed, has substantially contributed to our comprehending of bacterial respiratory mechanisms, often in elegant combinations with genetic and biochemical approaches. However, we also note that advanced proteomics offers a wealth of opportunities, which have not been exploited at all, or at best underexploited in hypothesis-driving and hypothesis-driven research on bacterial bioenergetics. Examples obtained from the related area of mitochondrial oxidative phosphorylation research, where the application of advanced proteomics is more common, may illustrate these opportunities.
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Affiliation(s)
- H J C T Wessels
- Nijmegen Center for Mitochondrial Disorders, Radboud Proteomics Centre, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, The Netherlands
| | - N M de Almeida
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - B Kartal
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands; Laboratory of Microbiology, Ghent University, Ghent, Belgium
| | - J T Keltjens
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands.
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39
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Shen S, Li J, Hilchey S, Shen X, Tu C, Qiu X, Ng A, Ghaemmaghami S, Wu H, Zand MS, Qu J. Ion-Current-Based Temporal Proteomic Profiling of Influenza-A-Virus-Infected Mouse Lungs Revealed Underlying Mechanisms of Altered Integrity of the Lung Microvascular Barrier. J Proteome Res 2016; 15:540-53. [PMID: 26650791 DOI: 10.1021/acs.jproteome.5b00927] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Investigation of influenza-A-virus (IAV)-infected lung proteomes will greatly promote our understanding on the virus-host crosstalk. Using a detergent-cocktail extraction and digestion procedure and a reproducible ion-current-based method, we performed the first comprehensive temporal analysis of mouse IAV infection. Mouse lung tissues at three time points post-inoculation were compared with controls (n = 4/group), and >1600 proteins were quantified without missing value in any animal. Significantly changed proteins were identified at 4 days (n = 144), 7 days (n = 695), and 10 days (n = 396) after infection, with low false altered protein rates (1.73-8.39%). Functional annotation revealed several key biological processes involved in the systemic host responses. Intriguingly, decreased levels of several cell junction proteins as well as increased levels of tissue metalloproteinase MMP9 were observed, reflecting the IAV-induced structural breakdown of lung epithelial barrier. Supporting evidence of MMP9 activation came from immunoassays examining the abundance and phosphorylation states of all MAPKs and several relevant molecules. Importantly, IAV-induced MMP gelatinase expression was suggested to be specific to MMP9, and p38 MAPK may contribute predominantly to MMP9 elevation. These findings help to resolve the long-lasting debate regarding the signaling pathways of IAV-induced MMP9 expression and shed light on the molecular mechanisms underlying pulmonary capillary-alveolar leak syndrome that can occur during influenza infection.
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Affiliation(s)
- Shichen Shen
- New York State Center of Excellence in Bioinformatics & Life Sciences , 701 Ellicott Street, Buffalo, New York 14203, United States.,Jacobs School of Medicine and Biomedical Sciences, SUNY at Buffalo , South Campus, Buffalo, New York 14214, United States
| | - Jun Li
- Department of Pharmaceutical Sciences, SUNY at Buffalo , South Campus, Buffalo, New York 14214, United States.,New York State Center of Excellence in Bioinformatics & Life Sciences , 701 Ellicott Street, Buffalo, New York 14203, United States
| | - Shannon Hilchey
- Division of Nephrology, University of Rochester Medical Center , 601 Elmwood Avenue, Rochester, New York 14642, United States
| | - Xiaomeng Shen
- New York State Center of Excellence in Bioinformatics & Life Sciences , 701 Ellicott Street, Buffalo, New York 14203, United States.,Jacobs School of Medicine and Biomedical Sciences, SUNY at Buffalo , South Campus, Buffalo, New York 14214, United States
| | - Chengjian Tu
- Department of Pharmaceutical Sciences, SUNY at Buffalo , South Campus, Buffalo, New York 14214, United States.,New York State Center of Excellence in Bioinformatics & Life Sciences , 701 Ellicott Street, Buffalo, New York 14203, United States
| | - Xing Qiu
- Department of Biostatistics and Computational Biology, University of Rochester , 265 Crittenden Boulevard, Rochester, New York 14642, United States
| | - Andrew Ng
- Jacobs School of Medicine and Biomedical Sciences, SUNY at Buffalo , South Campus, Buffalo, New York 14214, United States
| | - Sina Ghaemmaghami
- Department of Biology, University of Rochester , 402 Hutchison Hall, Rochester, New York 14627, United States
| | - Hulin Wu
- Department of Biostatistics, School of Public Health, University of Texas Health Science Center at Houston , 1200 Pressler Street, Houston, Texas 77030, United States
| | - Martin S Zand
- Division of Nephrology, University of Rochester Medical Center , 601 Elmwood Avenue, Rochester, New York 14642, United States
| | - Jun Qu
- Department of Pharmaceutical Sciences, SUNY at Buffalo , South Campus, Buffalo, New York 14214, United States.,New York State Center of Excellence in Bioinformatics & Life Sciences , 701 Ellicott Street, Buffalo, New York 14203, United States
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40
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Vuorijoki L, Isojärvi J, Kallio P, Kouvonen P, Aro EM, Corthals GL, Jones PR, Muth-Pawlak D. Development of a Quantitative SRM-Based Proteomics Method to Study Iron Metabolism of Synechocystis sp. PCC 6803. J Proteome Res 2015; 15:266-79. [DOI: 10.1021/acs.jproteome.5b00800] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Linda Vuorijoki
- Molecular
Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
| | - Janne Isojärvi
- Molecular
Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
| | - Pauli Kallio
- Molecular
Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
| | - Petri Kouvonen
- Turku
Proteomics Facility, Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20014 Turku, Finland
| | - Eva-Mari Aro
- Molecular
Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
| | - Garry L. Corthals
- Turku
Proteomics Facility, Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20014 Turku, Finland
- Van’t
Hoff Institute for Molecular Sciences, University of Amsterdam, 1018 WV Amsterdam, The Netherlands
| | - Patrik R. Jones
- Department
of Life Sciences, Imperial College London, Sir Alexander Fleming Building, London SW7 2AZ, United Kingdom
| | - Dorota Muth-Pawlak
- Molecular
Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
- Turku
Proteomics Facility, Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20014 Turku, Finland
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41
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Battchikova N, Angeleri M, Aro EM. Proteomic approaches in research of cyanobacterial photosynthesis. PHOTOSYNTHESIS RESEARCH 2015; 126:47-70. [PMID: 25359503 DOI: 10.1007/s11120-014-0050-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 10/18/2014] [Indexed: 05/03/2023]
Abstract
Oxygenic photosynthesis in cyanobacteria, algae, and plants is carried out by a fabulous pigment-protein machinery that is amazingly complicated in structure and function. Many different approaches have been undertaken to characterize the most important aspects of photosynthesis, and proteomics has become the essential component in this research. Here we describe various methods which have been used in proteomic research of cyanobacteria, and demonstrate how proteomics is implemented into on-going studies of photosynthesis in cyanobacterial cells.
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Affiliation(s)
- Natalia Battchikova
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, 20014, Turku, Finland.
| | - Martina Angeleri
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, 20014, Turku, Finland
| | - Eva-Mari Aro
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, 20014, Turku, Finland
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Quan Q, Szeto SSW, Law HCH, Zhang Z, Wang Y, Chu IK. Fully Automated Multidimensional Reversed-Phase Liquid Chromatography with Tandem Anion/Cation Exchange Columns for Simultaneous Global Endogenous Tyrosine Nitration Detection, Integral Membrane Protein Characterization, and Quantitative Proteomics Mapping in Cerebral Infarcts. Anal Chem 2015; 87:10015-24. [DOI: 10.1021/acs.analchem.5b02619] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Quan Quan
- Department
of Chemistry, The University of Hong Kong, Hong Kong 999077, China
| | - Samuel S. W. Szeto
- Department
of Chemistry, The University of Hong Kong, Hong Kong 999077, China
| | - Henry C. H. Law
- Department
of Chemistry, The University of Hong Kong, Hong Kong 999077, China
| | - Zaijun Zhang
- Institute
of New Drug Research and Guangdong Province Key Laboratory of Pharmacodynamic
Constituents of Traditional Chinese Medicine, College of Pharmacy, Jinan University, Guangzhou, Guangdong 510632, China
| | - Yuqiang Wang
- Institute
of New Drug Research and Guangdong Province Key Laboratory of Pharmacodynamic
Constituents of Traditional Chinese Medicine, College of Pharmacy, Jinan University, Guangzhou, Guangdong 510632, China
| | - Ivan K. Chu
- Department
of Chemistry, The University of Hong Kong, Hong Kong 999077, China
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43
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iTRAQ-based quantitative proteomic analysis of esophageal squamous cell carcinoma. Tumour Biol 2015; 37:1909-18. [DOI: 10.1007/s13277-015-3840-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 07/24/2015] [Indexed: 01/09/2023] Open
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Surfaceome and exoproteome of a clinical sequence type 398 methicillin resistant Staphylococcus aureus strain. Biochem Biophys Rep 2015; 3:7-13. [PMID: 29124163 PMCID: PMC5668672 DOI: 10.1016/j.bbrep.2015.07.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 07/01/2015] [Accepted: 07/07/2015] [Indexed: 11/23/2022] Open
Abstract
For many years Staphylococcus aureus has been recognized as an important human pathogen. In this study, the surfacome and exoproteome of a clinical sample of MRSA was analyzed. The C2355 strain, previously typed as ST398 and spa-t011 and showing a phenotype of multiresistance to antibiotics, has several resistance genes. Using shotgun proteomics and bioinformatics tools, 236 proteins were identified in the surfaceome and 99 proteins in the exoproteome. Although many of these proteins are related to basic cell functions, some are related to virulence and pathogenicity like catalase and isdA, main actors in S. aureus infection, and others are related to antibiotic action or eventually resistance like penicillin binding protein, a cell-wall protein. Studying the proteomes of different subcellular compartments should improve our understanding of this pathogen, a microorganism with several mechanisms of resistance and pathogenicity, and provide valuable data for bioinformatics databases. We examine the surface proteome and exoproteome of multiresistant strains. We identify bacterial infection proteins in the extracellular proteome. Confirmation that moonlighting proteins will extend the localization data.
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Neves LX, Sanson AL, Wilson RA, Castro-Borges W. What's in SWAP? Abundance of the principal constituents in a soluble extract of Schistosoma mansoni revealed by shotgun proteomics. Parasit Vectors 2015; 8:337. [PMID: 26088647 PMCID: PMC4484702 DOI: 10.1186/s13071-015-0943-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 06/08/2015] [Indexed: 12/27/2022] Open
Abstract
Background The soluble antigen preparation of adult schistosomes (SWAP) has often been used to probe host responses against these blood-dwelling parasites. Despite its long-established use there is limited knowledge about its composition. The information we provide here on the molecular composition of SWAP may contribute as a guide for a rational selection of antigenic targets. Methods Label-free quantitative shotgun proteomics was employed to determine the composition and abundance of SWAP constituents. Briefly, paired adult Schistosoma mansoni worms were sonicated in PBS pH 7.2 and ultracentrifuged for recovery of the soluble supernatant. An aliquot was subjected to trypsin digestion. Resulting peptides were separated under ultra-high performance liquid chromatography and analysed using an orbitrap mass spectrometer. Spectral data were interrogated using SequestHT against an in-house S. mansoni database. Proteins were quantified by recording the mean area under curve obtained for up to three most intense detected peptides. Proteins within the 90th percentile of the total SWAP mass were categorized according to their sub-cellular/tissue location. Results In this work we expanded significantly the list of known SWAP constituents. Through application of stringent criteria, a total of 633 proteins were quantitatively identified. Only 18 proteins account to 50 % of the total SWAP mass as revealed by their cumulative abundance. Among them, none is predicted as a secreted molecule reinforcing the point that SWAP is dominated by cytosolic and cytoskeletal proteins. In contrast, only 3 % of the mass comprised proteins proposed to function at the host-parasite interfaces (tegument and gut), which could conceivably represent vulnerable targets of a protective immune response. Paradoxically, at least 11 SWAP proteins, comprising ~25 % of its mass, have been tested as vaccine candidates. Conclusions Our data suggest that use of SWAP to probe host responses has greatest value for diagnostic purposes or assessing intensity of infection. However, the preparation is of limited utility as an antigen source for investigating host responses to proteins expressed at or secreted from worm-host interfaces. The data also pose the question as to why vaccination with SWAP, containing so many proposed vaccine candidates, has no additive or even synergistic effects on the induction of protection. Electronic supplementary material The online version of this article (doi:10.1186/s13071-015-0943-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Leandro Xavier Neves
- Laboratório de Enzimologia e Proteômica, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil.
| | - Ananda Lima Sanson
- Laboratório de Enzimologia e Proteômica, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil.
| | - R Alan Wilson
- Centre for Immunology & Infection, Department of Biology, University of York, PO Box 373, York, YO10 5YW, UK.
| | - William Castro-Borges
- Laboratório de Enzimologia e Proteômica, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil.
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Khemiri A, Jouenne T, Cosette P. Proteomics dedicated to biofilmology: What have we learned from a decade of research? Med Microbiol Immunol 2015; 205:1-19. [PMID: 26068406 DOI: 10.1007/s00430-015-0423-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 06/03/2015] [Indexed: 12/31/2022]
Abstract
Advances in proteomics techniques over the past decade, closely integrated with genomic and physicochemical approach, have played a great role in developing knowledge of the biofilm lifestyle of bacteria. Despite bacterial proteome versatility, many studies have demonstrated the ability of proteomics approaches to elucidating the biofilm phenotype. Though these investigations have been largely used for biofilm studies in the last decades, they represent, however, a very low percentage of proteomics works performed up to now. Such approaches have offered new targets for combating microbial biofilms by providing a comprehensive quantitative and qualitative overview of their protein cell content. Herein, we summarized the state of the art in knowledge about biofilm physiology after one decade of proteomic analysis. In a second part, we highlighted missing research tracks for the next decade, emphasizing the emergence of posttranslational modifications in proteomic studies stemming from recent advances in mass spectrometry-based proteomics.
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Affiliation(s)
- Arbia Khemiri
- CNRS, UMR 6270, Laboratory "Polymères, Biopolymères, Surfaces", 76820, Mont-Saint-Aignan, France.
- University of Normandy, UR, Mont-Saint-Aignan, France.
- PISSARO Proteomic Facility, IRIB, 76820, Mont-Saint-Aignan, France.
| | - Thierry Jouenne
- CNRS, UMR 6270, Laboratory "Polymères, Biopolymères, Surfaces", 76820, Mont-Saint-Aignan, France
- University of Normandy, UR, Mont-Saint-Aignan, France
- PISSARO Proteomic Facility, IRIB, 76820, Mont-Saint-Aignan, France
| | - Pascal Cosette
- CNRS, UMR 6270, Laboratory "Polymères, Biopolymères, Surfaces", 76820, Mont-Saint-Aignan, France
- University of Normandy, UR, Mont-Saint-Aignan, France
- PISSARO Proteomic Facility, IRIB, 76820, Mont-Saint-Aignan, France
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Li H, Pan Y, Zhang Y, Wu C, Ma C, Yu B, Zhu N, Koh J, Chen S. Salt stress response of membrane proteome of sugar beet monosomic addition line M14. J Proteomics 2015; 127:18-33. [PMID: 25845583 DOI: 10.1016/j.jprot.2015.03.025] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/11/2015] [Accepted: 03/27/2015] [Indexed: 11/18/2022]
Abstract
UNLABELLED Understanding how plants respond to and tolerate salt stress is important for engineering and breeding effort to boost plant productivity and bioenergy in an ever challenging environment. Sugar beet M14 line is a unique germplasm that contains genetic materials from Beta vulgaris L. and Beta corolliflora Zoss, and it exhibits tolerance to salt stress. Here we report the changes in membrane proteome of the M14 plants in response to salt stress (0, 200, 400mM NaCl) using an iTRAQ two-dimensional LC-MS/MS technology for quantitative proteomic analysis. In total, 274 proteins, mostly membrane proteins, were identified, and 50 proteins exhibited differential protein level changes, with 40 proteins increased and 10 decreased. The proteins were mainly involved in transport, metabolism, protein synthesis, photosynthesis, protein folding and degradation, signal transduction, stress and defense, energy, and cell structure. These results have revealed interesting mechanisms underlying the M14 response and tolerance to salt stress. BIOLOGICAL SIGNIFICANCE Sugar beet monosomic addition line M14 is a special variety with salt stress tolerance. Analysis of the M14 membrane proteome under salt stress may provide useful information regarding specific adaptive mechanisms underlying salt stress tolerance. Membrane proteins are known to play critical roles in salt stress signaling and adaptation. The purpose of this study was to identify significantly changed membrane proteins and determine their possible relevance to salt tolerance. The proteomic analysis of the M14 line revealed important molecular mechanisms that can be potentially applied to improving crop salt tolerance. This article is part of a Special Issue entitled: Proteomics in India.
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Affiliation(s)
- Haiying Li
- Key Laboratory of Molecular Biology of Heilongjiang Province, College of Life Sciences, Heilongjiang University, Harbin 150080, China; Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150080, China.
| | - Yu Pan
- Key Laboratory of Molecular Biology of Heilongjiang Province, College of Life Sciences, Heilongjiang University, Harbin 150080, China; Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150080, China
| | - Yongxue Zhang
- Key Laboratory of Molecular Biology of Heilongjiang Province, College of Life Sciences, Heilongjiang University, Harbin 150080, China; Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150080, China
| | - Chuan Wu
- Key Laboratory of Molecular Biology of Heilongjiang Province, College of Life Sciences, Heilongjiang University, Harbin 150080, China; Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150080, China
| | - Chunquan Ma
- Key Laboratory of Molecular Biology of Heilongjiang Province, College of Life Sciences, Heilongjiang University, Harbin 150080, China; Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150080, China
| | - Bing Yu
- Key Laboratory of Molecular Biology of Heilongjiang Province, College of Life Sciences, Heilongjiang University, Harbin 150080, China; Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150080, China
| | - Ning Zhu
- Department of Biology, Genetics Institute, Plant Molecular and Cellular Biology Program, University of FL, Gainesville, FL 32610, USA
| | - Jin Koh
- Department of Biology, Genetics Institute, Plant Molecular and Cellular Biology Program, University of FL, Gainesville, FL 32610, USA
| | - Sixue Chen
- Key Laboratory of Molecular Biology of Heilongjiang Province, College of Life Sciences, Heilongjiang University, Harbin 150080, China; Department of Biology, Genetics Institute, Plant Molecular and Cellular Biology Program, University of FL, Gainesville, FL 32610, USA.
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Golizeh M, Schneider C, Ohlund LB, Sleno L. Multidimensional LC–MS/MS analysis of liver proteins in rat, mouse and human microsomal and S9 fractions. EUPA OPEN PROTEOMICS 2015. [DOI: 10.1016/j.euprot.2015.01.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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49
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Wang W, Lv Y, Fang F, Hong S, Guo Q, Hu S, Zou F, Shi L, Lei Z, Ma K, Zhou D, Zhang D, Sun Y, Ma L, Shen B, Zhu C. Identification of proteins associated with pyrethroid resistance by iTRAQ-based quantitative proteomic analysis in Culex pipiens pallens. Parasit Vectors 2015; 8:95. [PMID: 25880395 PMCID: PMC4337324 DOI: 10.1186/s13071-015-0709-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 01/31/2015] [Indexed: 12/30/2022] Open
Abstract
Background Mosquito control based on chemical insecticides is considered as an important element in the current global strategies for the control of mosquito-borne diseases. Unfortunately, the development of pyrethroid resistance in important vector mosquito species jeopardizes the effectiveness of insecticide-based mosquito control. To date, the mechanisms of pyrethroid resistance are still unclear. Recent advances in proteomic techniques can facilitate to identify pyrethroid resistance-associated proteins at a large-scale for improving our understanding of resistance mechanisms, and more importantly, for seeking some genetic markers used for monitoring and predicting the development of resistance. Methods We performed a quantitative proteomic analysis between a deltamethrin-susceptible strain and a deltamethrin-resistant strain of laboratory population of Culex pipiens pallens using isobaric tags for relative and absolute quantitation (iTRAQ) analysis. Gene Ontology (GO) analysis was used to find the relative processes that these differentially expressed proteins were involved in. One differentially expressed protein was chosen to confirm by Western blot in the laboratory and field populations of Cx. pipiens pallens. Results We identified 30 differentially expressed proteins assigned into 10 different categories, including oxidoreductase activity, transporter activity, catalytic activity, structural constituent of cuticle and hypothetical proteins. GO analysis revealed that 25 proteins were sub-categorized into 35 hierarchically-structured GO classifications. Western blot results showed that CYP6AA9 as one of the up-regulated proteins was confirmed to be overexpressed in the deltamethrin-resistant strains compared with the deltamethrin-susceptible strains both in the laboratory and field populations. Conclusions This is the first study to use modern proteomic tools for identifying pyrethroid resistance-related proteins in Cx. pipiens. The present study brought to light many proteins that were not previously thought to be associated with pyrethroid resistance, which further expands our understanding of pyrethroid resistance mechanisms. CYP6AA9 was overexpressed in the deltamethrin-resistant strains, indicating that CYP6AA9 may be involved in pyrethroid resistance and may be used as a potential genetic marker to monitor and predict the pyrethroid resistance level of field populations. Electronic supplementary material The online version of this article (doi:10.1186/s13071-015-0709-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Weijie Wang
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, China. .,Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing Medical University, Nanjing, China. .,Department of Pathogen Biology, Hebei Medical University, Shijiazhuang, China.
| | - Yuan Lv
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, China. .,Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing Medical University, Nanjing, China.
| | - Fujin Fang
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, China. .,Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing Medical University, Nanjing, China.
| | - Shanchao Hong
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, China. .,Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing Medical University, Nanjing, China.
| | - Qin Guo
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, China. .,Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing Medical University, Nanjing, China.
| | - Shengli Hu
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, China. .,Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing Medical University, Nanjing, China.
| | - Feifei Zou
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, China. .,Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing Medical University, Nanjing, China.
| | - Linna Shi
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, China. .,Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing Medical University, Nanjing, China.
| | - Zhentao Lei
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, China. .,Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing Medical University, Nanjing, China.
| | - Kai Ma
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, China. .,Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing Medical University, Nanjing, China.
| | - Dan Zhou
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, China. .,Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing Medical University, Nanjing, China.
| | - Donghui Zhang
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, China. .,Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing Medical University, Nanjing, China.
| | - Yan Sun
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, China. .,Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing Medical University, Nanjing, China.
| | - Lei Ma
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, China. .,Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing Medical University, Nanjing, China.
| | - Bo Shen
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, China. .,Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing Medical University, Nanjing, China.
| | - Changliang Zhu
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, China. .,Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing Medical University, Nanjing, China.
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50
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Trötschel C, Poetsch A. Current approaches and challenges in targeted absolute quantification of membrane proteins. Proteomics 2015; 15:915-29. [DOI: 10.1002/pmic.201400427] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 11/05/2014] [Accepted: 12/05/2014] [Indexed: 01/08/2023]
Affiliation(s)
| | - Ansgar Poetsch
- Department of Plant Biochemistry; Ruhr-University Bochum; Bochum Germany
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