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Sechovcová H, Rudl Kulhavá L, Fliegerová K, Killer J, Kopečný J. Advantages of label free method in comparison with 2DE proteomic analysis of Butyrivibrio fibrisolvens 3071 grown on different carbon sources. ITALIAN JOURNAL OF ANIMAL SCIENCE 2022. [DOI: 10.1080/1828051x.2022.2129477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Hana Sechovcová
- Institute of Animal Physiology and Genetics, CAS, Laboratory of Anaerobic Microbiology, Prague, Czech Republic
- Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Prague, Czech Republic
| | | | - Kateřina Fliegerová
- Institute of Animal Physiology and Genetics, CAS, Laboratory of Anaerobic Microbiology, Prague, Czech Republic
| | - Jiří Killer
- Institute of Animal Physiology and Genetics, CAS, Laboratory of Anaerobic Microbiology, Prague, Czech Republic
- Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Prague, Czech Republic
| | - Jan Kopečný
- Institute of Animal Physiology and Genetics, CAS, Laboratory of Anaerobic Microbiology, Prague, Czech Republic
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52
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Escobar-Sánchez M, Carrasco-Navarro U, Juárez-Castelán C, Lozano-Aguirre Beltrán L, Pérez-Chabela ML, Ponce-Alquicira E. Probiotic Properties and Proteomic Analysis of Pediococcus pentosaceus 1101. Foods 2022; 12:foods12010046. [PMID: 36613263 PMCID: PMC9818561 DOI: 10.3390/foods12010046] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/10/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Pediococcus pentosaceus 1101 was identified by using 16S rRNA and MALDI-Biotyper. The strain was exposed to conditions that resemble the gastrointestinal tract (GT) to evaluate its probiotic properties. That included the growth kinetics, proteolytic and inhibitory activities within a pH range, survival at low pH and in the presence of bile salts, antagonistic activity, cell-adhesion properties, and antibiotic resistance. The evaluation was followed by a genomic and proteomic analysis that involved the identification of proteins obtained under control and gastrointestinal conditions. The strain showed antagonistic activity against Gram-negative and Gram-positive bacteria, high resistance to acidity (87% logarithmic survival rate, pH 2) and bile salts (99% logarithmic survival rate, 0.5% w/v), and hydrophobic binding, as well as sensitivity to penicillin, amoxicillin, and chloramphenicol. On the other hand, P. pentosaceus 1101 has a genome size of 1.76 Mbp, with 1754 coding sequences, 55 rRNAs, and 33 tRNAs. The proteomic analysis showed that 120 proteins were involved in mechanisms in which the strain senses the effects of acid and bile salts. Moreover, the strain produces at least one lytic enzyme (N-acetylmuramoyl-L-alanine amidase; 32 kDa) that may be related to the antimicrobial activity. Therefore, proteins identified might be a key factor when it comes to the adaptation of P. pentosaceus 1101 into the GT and associated with its technological and probiotic properties.
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Affiliation(s)
- Monserrat Escobar-Sánchez
- Departamento de Biotecnología, Universidad Autónoma Metropolitana Unidad Iztapalapa, Ciudad de México 09340, Mexico
| | - Ulises Carrasco-Navarro
- Departamento de Biotecnología, Universidad Autónoma Metropolitana Unidad Iztapalapa, Ciudad de México 09340, Mexico
| | - Carmen Juárez-Castelán
- Cinvestav, Departamento de Genética y Biología Molecular, Ciudad de México 07360, Mexico
| | | | - M. Lourdes Pérez-Chabela
- Departamento de Biotecnología, Universidad Autónoma Metropolitana Unidad Iztapalapa, Ciudad de México 09340, Mexico
| | - Edith Ponce-Alquicira
- Departamento de Biotecnología, Universidad Autónoma Metropolitana Unidad Iztapalapa, Ciudad de México 09340, Mexico
- Correspondence: ; Tel.: +52-55-58044600 (ext. 2676)
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53
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Välikangas T, Suomi T, Chandler CE, Scott AJ, Tran BQ, Ernst RK, Goodlett DR, Elo LL. Benchmarking tools for detecting longitudinal differential expression in proteomics data allows establishing a robust reproducibility optimization regression approach. Nat Commun 2022; 13:7877. [PMID: 36550114 PMCID: PMC9780321 DOI: 10.1038/s41467-022-35564-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
Quantitative proteomics has matured into an established tool and longitudinal proteomics experiments have begun to emerge. However, no effective, simple-to-use differential expression method for longitudinal proteomics data has been released. Typically, such data is noisy, contains missing values, and has only few time points and biological replicates. To address this need, we provide a comprehensive evaluation of several existing differential expression methods for high-throughput longitudinal omics data and introduce a Robust longitudinal Differential Expression (RolDE) approach. The methods are evaluated using over 3000 semi-simulated spike-in proteomics datasets and three large experimental datasets. In the comparisons, RolDE performs overall best; it is most tolerant to missing values, displays good reproducibility and is the top method in ranking the results in a biologically meaningful way. Furthermore, RolDE is suitable for different types of data with typically unknown patterns in longitudinal expression and can be applied by non-experienced users.
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Affiliation(s)
- Tommi Välikangas
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland
| | - Tomi Suomi
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland
| | | | - Alison J Scott
- University of Maryland - Baltimore, Baltimore, MD, 21201, USA
| | - Bao Q Tran
- US Army 20th Support Command CBRNE Analytical and Remediation Activity, Baltimore, MD, 21010-5424, USA
| | - Robert K Ernst
- University of Maryland - Baltimore, Baltimore, MD, 21201, USA
| | - David R Goodlett
- University of Victoria, Victoria, BC, V8P 3E6, Canada
- International Centre for Cancer Vaccine Science, Gdansk, Poland
| | - Laura L Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland.
- Institute of Biomedicine, University of Turku, FI-20520, Turku, Finland.
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54
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Liu M, Martyn AP, Quinn RJ. Natural product-based PROteolysis TArgeting Chimeras (PROTACs). Nat Prod Rep 2022; 39:2292-2307. [PMID: 36196977 DOI: 10.1039/d2np00038e] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covering: upto 2022Natural products have an embedded recognition of protein surfaces. They possess this property as they are produced by biosynthetic enzymes and are substrates for one or more enzymes in the biosynthetic pathway. The inherent advantages, compared to synthetic compound libraries, is this ligand-protein binding which is, in many cases, a function of the 3-dimensional properties. Protein degradation is a recent novel therapeutic approach with several compounds now in the clinic. This review highlights the potential of PROteolysis TArgeting Chimeras (PROTACs) in the area of natural products. The approach will complement existing approaches such as the direct use of a bioactive natural product or its analogues, pharmacophore development and drug-antibody conjugates. The chemical synthesis and challenges of using natural product-based PROTACs are summarised. The review also highlights methods to detect the ternary complexes necessary for PROTAC mechanism of action.
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Affiliation(s)
- Miaomiao Liu
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia.
| | - Alexander P Martyn
- Cancer and Ageing Research Program (CARP), Centre for Genomics and Personalised Health (CGPH), Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Ronald J Quinn
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia.
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55
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Study on spoilage potential and its molecular basis of Shewanella putrefaciens in response to cold conditions by Label-free quantitative proteomic analysis. World J Microbiol Biotechnol 2022; 39:40. [PMID: 36512125 DOI: 10.1007/s11274-022-03479-y] [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: 05/31/2022] [Accepted: 11/18/2022] [Indexed: 12/15/2022]
Abstract
To elucidate how Shewanella putrefaciens survives and produces spoilage products in response to cold conditions, the metabolic and protease activity of S. putrefaciens DSM6067 cultured at three different temperatures (30 °C, 10 °C, and 4 °C) was studied by determining the bacterial growth, total volatile basic nitrogen (TVB-N), biogenic amines, extracellular protease activity, as well as the differential expressed proteins via Label-free quantitative proteomics analysis. The lag phase of the strain cultured at 10 °C and 4 °C was about 20 h and 120 h longer than at 30 °C, respectively. The TVB-N increased to 89.23 mg N/100 g within 28 h at 30 °C, and it needed at least 72 h and 224 h at 10 °C and 4 °C, respectively. Cold temperatures (10 °C and 4 °C) also inhibited the yield factors and the extracellular protease activity per cell at the lag phase. However, the protease activity per cell and the yield factors of the sample cultivated at 10 °C and 4 °C well recovered, especially at the mid and latter stages of the log phase. The further quantitative proteomic analysis displayed a complex biological network to tackle cold stress: cold stress responses, nutrient uptake, and energy conservation strategy. It was observed that the protease and peptidase were upregulated, so as to the degradation pathways of serine, arginine, and aspartate, which might lead to the accumulation of spoilage products. This study highlighted the spoilage potential of S. putrefaciens still should be concerned even at low temperatures.
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56
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Ashrafmansouri M, Amiri-Dashatan N, Ahmadi N. Identification of protein profile in metacyclic and amastigote-like stages of Leishmania tropica: a proteomic approach. AMB Express 2022; 12:142. [PMID: 36370199 PMCID: PMC9653527 DOI: 10.1186/s13568-022-01481-z] [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: 05/22/2022] [Accepted: 10/23/2022] [Indexed: 11/13/2022] Open
Abstract
Leishmaniasis is a tropical disease that leads to various clinical phenotypes. This study aimed to investigate protein expression changes in metacyclic and amastigote-like stages of L. tropica isolated from Iranian cutaneous leishmaniasis patients. Isolated samples were cultured and species type identified using PCR-RFLP technique. The promastigotes were grown in RPMI1640 media and differentiated to metacyclic and amastigote-like forms, followed by the extracted proteins of both successive stages carried out for proteomics and bioinformatics analysis. Using SWATH-MS quantitative proteomics technique, a total 176 and 155 distinct proteins were identified in metacyclic and axenic amastigote stages, respectively. Of these, 65 proteins were altered significantly (p-value < 0.05 and fold change ≥ 2) between studied stages. Several gene ontology (GO) categories were enriched for biological process during conversion of metacyclic promastigotes into amastigote-like, which "metabolic process" (GO: 0044281, P-Value: 6.52e-5), and "translation" (GO: 0006412, p-value: 5.01e-14) were disclosed as the top category in up and down-regulated proteins, respectively. Also, the KEGG pathway analysis indicated "metabolic pathways" and "ribosome" term as the most important pathways in up and down-regulated proteins, respectively. According to protein interaction network analysis, enolase (ENOL) has been detected as main hub proteins during differentiation, followed by Putative NADH-dependent fumarate reductase (LmjF.35.1180) and 40S ribosomal protein S2 (LmjF.32.0450). Overall, protein changes possibly play important roles in L. tropica biology. Anabolic pathways were down-regulated, whereas catabolic pathways were up-regulated during L. tropica differentiation. These protein expression changes could provide parasite survival in host macrophages, and could use as novel potential drug and vaccine targets for leishmaniasis.
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Affiliation(s)
- Marzieh Ashrafmansouri
- Department of Medical Laboratory Sciences, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nasrin Amiri-Dashatan
- Zanjan Metabolic Diseases Research Center, Zanjan University of Medical Sciences, Zanjan, Iran
- Proteomics Research Center, Department of Medical Lab Sciences, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Nayebali Ahmadi
- Proteomics Research Center, Department of Medical Lab Sciences, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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57
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Phillips AL, Scafaro AP, Atwell BJ. Photosynthetic traits of Australian wild rice (Oryza australiensis) confer tolerance to extreme daytime temperatures. PLANT MOLECULAR BIOLOGY 2022; 110:347-363. [PMID: 34997897 PMCID: PMC9646608 DOI: 10.1007/s11103-021-01210-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 10/27/2021] [Indexed: 05/08/2023]
Abstract
A wild relative of rice from the Australian savannah was compared with cultivated rice, revealing thermotolerance in growth and photosynthetic processes and a more robust carbon economy in extreme heat. Above ~ 32 °C, impaired photosynthesis compromises the productivity of rice. We compared leaf tissues from heat-tolerant wild rice (Oryza australiensis) with temperate-adapted O. sativa after sustained exposure to heat, as well as diurnal heat shock. Leaf elongation and shoot biomass in O. australiensis were unimpaired at 45 °C, and soluble sugar concentrations trebled during 10 h of a 45 °C shock treatment. By contrast, 45 °C slowed growth strongly in O. sativa. Chloroplastic CO2 concentrations eliminated CO2 supply to chloroplasts as the basis of differential heat tolerance. This directed our attention to carboxylation and the abundance of the heat-sensitive chaperone Rubisco activase (Rca) in each species. Surprisingly, O. australiensis leaves at 45 °C had 50% less Rca per unit Rubisco, even though CO2 assimilation was faster than at 30 °C. By contrast, Rca per unit Rubisco doubled in O. sativa at 45 °C while CO2 assimilation was slower, reflecting its inferior Rca thermostability. Plants grown at 45 °C were simultaneously exposed to 700 ppm CO2 to enhance the CO2 supply to Rubisco. Growth at 45 °C responded to CO2 enrichment in O. australiensis but not O. sativa, reflecting more robust carboxylation capacity and thermal tolerance in the wild rice relative.
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Affiliation(s)
- Aaron L Phillips
- Waite Research Institute and School of Agriculture, Food, and Wine, University of Adelaide, Adelaide, SA, Australia
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
- ARC Centre of Excellence in Plant Energy Biology, School of Agriculture, Food, and Wine, The University of Adelaide, Adelaide, SA, Australia
| | - Andrew P Scafaro
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Brian J Atwell
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia.
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58
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Cupp-Sutton KA, Fang M, Wu S. Separation methods in single-cell proteomics: RPLC or CE? INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2022; 481:116920. [PMID: 36211475 PMCID: PMC9542495 DOI: 10.1016/j.ijms.2022.116920] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Cellular heterogeneity is commonly investigated using single-cell genomics and transcriptomics to investigate biological questions such as disease mechanism, therapeutic screening, and genomic and transcriptomic diversity between cellular populations and subpopulations at the cellular level. Single-cell mass spectrometry (MS)-based proteomics enables the high-throughput examination of protein expression at the single-cell level with wide applicability, and with spatial and temporal resolution, applicable to the study of cellular development, disease, effect of treatment, etc. The study of single-cell proteomics has lagged behind genomics and transcriptomics largely because proteins from single-cell samples cannot be amplified as DNA and RNA can using well established techniques such as PCR. Therefore, analytical methods must be robust, reproducible, and sensitive enough to detect the very small amount of protein within a single cell. To this end, nearly every step of the proteomics process has been extensively altered and improved to facilitate the proteomics analysis of single cells including cell counting and sorting, lysis, protein digestion, sample cleanup, separation, MS data acquisition, and data analysis. Here, we have reviewed recent advances in single-cell protein separation using nano reversed phase liquid chromatography (nRPLC) and capillary electrophoresis (CE) to inform application driven selection of separation techniques in the laboratory setting.
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Affiliation(s)
| | - Mulin Fang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019
| | - Si Wu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019
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59
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Kumar A, Nonnis S, Castellano I, AbdElgawad H, Beemster GTS, Buia MC, Maffioli E, Tedeschi G, Palumbo A. Molecular response of Sargassum vulgare to acidification at volcanic CO 2 vents: Insights from proteomic and metabolite analyses. Mol Ecol 2022; 31:3844-3858. [PMID: 35635253 DOI: 10.1111/mec.16553] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 05/16/2022] [Accepted: 05/20/2022] [Indexed: 11/30/2022]
Abstract
Ocean acidification is impacting marine life all over the world. Understanding how species can cope with the changes in seawater carbonate chemistry represents a challenging issue. We addressed this topic using underwater CO2 vents that naturally acidify some marine areas off the island of Ischia. In the most acidified area of the vents, having a mean pH value of 6.7, comparable to far-future predicted acidification scenarios (by 2300), the biomass is dominated by the brown alga Sargassum vulgare. The novelty of the present study is the characterization of the S. vulgare proteome together with metabolite analyses to identify the key proteins, metabolites, and pathways affected by ocean acidification. A total of 367 and 387 proteins were identified in populations grown at pH that approximates the current global average (8.1) and acidified sites, respectively. Analysis of their relative abundance revealed that 304 proteins are present in samples from both sites: 111 proteins are either higher or exclusively present under acidified conditions, whereas 120 proteins are either lower or present only under control conditions. Functionally, under acidification, a decrease in proteins related to translation and post-translational processes and an increase of proteins involved in photosynthesis, glycolysis, oxidation-reduction processes, and protein folding were observed. In addition, small-molecule metabolism was affected, leading to a decrease of some fatty acids and antioxidant compounds under acidification. Overall, the results obtained by proteins and metabolites analyses, integrated with previous transcriptomic, physiological, and biochemical studies, allowed us to delineate the molecular strategies adopted by S. vulgare to grow in future acidified environments, including an increase of proteins involved in energetic metabolism, oxidation-reduction processes, and protein folding at the expense of proteins involved in translation and post-translational processes.
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Affiliation(s)
- Amit Kumar
- Stazione Zoologica Anton Dohrn, Department of Integrative Marine Ecology, Marine Research Center, Naples, Italy
- Centre for Climate Change Studies, Sathyabama Institute of Science and Technology, Chennai, India
| | - Simona Nonnis
- Department of Veterinary Medicine and Animal Science (DIVAS), Università degli Studi di Milano, Milan, Italy
- CRC "Innovation for well-being and environment" (I-WE), Università degli Studi di Milano, Milan, Italy
| | - Immacolata Castellano
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
- Stazione Zoologica Anton Dohrn, Department of Biology and Evolution of Marine Organisms, Naples, Italy
| | - Hamada AbdElgawad
- Department of Botany, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
- Integrated Molecular Plant Physiology Research Group (IMPRES), Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Gerrit T S Beemster
- Integrated Molecular Plant Physiology Research Group (IMPRES), Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Maria Cristina Buia
- Stazione Zoologica Anton Dohrn, Department of Integrative Marine Ecology, Marine Research Center, Naples, Italy
| | - Elisa Maffioli
- Department of Veterinary Medicine and Animal Science (DIVAS), Università degli Studi di Milano, Milan, Italy
| | - Gabriella Tedeschi
- Department of Veterinary Medicine and Animal Science (DIVAS), Università degli Studi di Milano, Milan, Italy
- CRC "Innovation for well-being and environment" (I-WE), Università degli Studi di Milano, Milan, Italy
| | - Anna Palumbo
- Stazione Zoologica Anton Dohrn, Department of Biology and Evolution of Marine Organisms, Naples, Italy
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Gawor A, Ruszczyńska A, Konopka A, Wryk G, Czauderna M, Bulska E. Label-Free Mass Spectrometry-Based Proteomic Analysis in Lamb Tissues after Fish Oil, Carnosic Acid, and Inorganic Selenium Supplementation. Animals (Basel) 2022; 12:ani12111428. [PMID: 35681892 PMCID: PMC9179315 DOI: 10.3390/ani12111428] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/23/2022] [Accepted: 05/30/2022] [Indexed: 02/05/2023] Open
Abstract
Simple Summary Advances in proteomics and bioinformatics analysis offer the potential to investigate nutrients’ influence on protein expression profiles, and consequently on biological processes, molecular functions, and cellular components. However, knowledge in this area, particular about the exact way selenium modulates protein expression, remains limited. Therefore, in this project, global differential proteomic experiments were carried out in order to identify changes in the expression of proteins in animal tissues obtained from lambs on a specific diet involving the addition of a combination of different supplements, namely, inorganic selenium compounds, fish oil, and carnosic acid. Following inorganic selenium supplementation, a protein-protein interaction network analysis of forty differentially-expressed proteins indicated two significant clusters. Abstract Selenium is an essential nutrient, building twenty five identified selenoproteins in humans known to perform several important biological functions. The small amount of selenium in the earth’s crust in certain regions along with the risk of deficiency in organisms have resulted in increasingly popular dietary supplementation in animals, implemented via, e.g., inorganic selenium compounds. Even though selenium is included in selenoproteins in the form of selenocysteine, the dietary effect of selenium may result in the expression of other proteins or genes. Very little is known about the expression effects modulated by selenium. The present study aimed to examine the significance of protein expression in lamb tissues obtained after dietary supplementation with selenium (sodium selenate) and two other feed additives, fish oil and carnosic acid. Label-free mass spectrometry-based proteomic analysis was successfully applied to examine the animal tissues. Protein-protein interaction network analysis of forty differently-expressed proteins following inorganic selenium supplementation indicated two significant clusters which are involved in cell adhesion, heart development, actin filament-based movement, plasma membrane repair, and establishment of organelle localization.
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Affiliation(s)
- Andrzej Gawor
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland; (A.G.); (A.R.); (A.K.); (G.W.)
| | - Anna Ruszczyńska
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland; (A.G.); (A.R.); (A.K.); (G.W.)
| | - Anna Konopka
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland; (A.G.); (A.R.); (A.K.); (G.W.)
| | - Grzegorz Wryk
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland; (A.G.); (A.R.); (A.K.); (G.W.)
| | - Marian Czauderna
- The Kielanowski Institute of Animal Physiology and Nutrition, Polish Academy of Sciences, Instytucka 3, 05-110 Jabłonna, Poland;
| | - Ewa Bulska
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland; (A.G.); (A.R.); (A.K.); (G.W.)
- Correspondence:
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61
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Toldrá F, Mora L. Peptidomics as a useful tool in the follow-up of food bioactive peptides. ADVANCES IN FOOD AND NUTRITION RESEARCH 2022; 100:1-47. [PMID: 35659349 DOI: 10.1016/bs.afnr.2022.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
There is an intense research activity on bioactive peptides derived from food proteins in view of their health benefits for consumers. However, their identification is quite challenging as a consequence of their small size and low abundance in complex matrices such as foods or hydrolyzates. Recent advances in peptidomics and bioinformatics are getting improved sensitivity and accuracy and therefore such tools are contributing to the development of sophisticated methodologies for the identification and quantification of peptides. These developments are very useful for the follow-up of peptides released through proteolysis either in the food itself through the action of endogenous peptidases during processing stages like fermentation, drying or ripening, or from food proteins hydrolyzed by commercial peptidases or microorganisms with proteolytic activity. This chapter is presenting the latest advances in peptidomics and its use for the identification and quantification of peptides, and as a useful tool for controlling the proteolysis phenomena in foods and protein hydrolyzates.
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Affiliation(s)
- Fidel Toldrá
- Instituto de Agroquímica y Tecnología de Alimentos (CSIC), Paterna, Spain.
| | - Leticia Mora
- Instituto de Agroquímica y Tecnología de Alimentos (CSIC), Paterna, Spain
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62
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Murari A, Goparaju NSV, Rhooms SK, Hossain KFB, Liang FG, Garcia CJ, Osei C, Liu T, Li H, Kitsis RN, Patel R, Owusu-Ansah E. IDH2-mediated regulation of the biogenesis of the oxidative phosphorylation system. SCIENCE ADVANCES 2022; 8:eabl8716. [PMID: 35544578 PMCID: PMC9094667 DOI: 10.1126/sciadv.abl8716] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 03/16/2022] [Indexed: 06/04/2023]
Abstract
Several subunits in the matrix domain of mitochondrial complex I (CI) have been posited to be redox sensors for CI, but how elevated levels of reactive oxygen species (ROS) impinge on CI assembly is unknown. We report that genetic disruption of the mitochondrial NADPH-generating enzyme, isocitrate dehydrogenase 2 (IDH2), in Drosophila flight muscles results in elevated ROS levels and impairment of assembly of the oxidative phosphorylation system (OXPHOS). Mechanistically, this begins with an inhibition of biosynthesis of the matrix domain of CI and progresses to involve multiple OXPHOS complexes. Despite activation of multiple compensatory mechanisms, including enhanced coenzyme Q biosynthesis and the mitochondrial unfolded protein response, ferroptotic cell death ensues. Disruption of enzymes that eliminate hydrogen peroxide, but not those that eliminate the superoxide radical, recapitulates the phenotype, thereby implicating hydrogen peroxide as the signaling molecule involved. Thus, IDH2 modulates the assembly of the matrix domain of CI and ultimately that of the entire OXPHOS.
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Affiliation(s)
- Anjaneyulu Murari
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Naga S. V. Goparaju
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Shauna-Kay Rhooms
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Kaniz F. B. Hossain
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Felix G. Liang
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Wilf Family Cardiovascular Research Institute, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Christian J. Garcia
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Cindy Osei
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Tong Liu
- Center for Advanced Proteomics Research, Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers University—New Jersey Medical School, Newark, NJ 07103, USA
| | - Hong Li
- Center for Advanced Proteomics Research, Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers University—New Jersey Medical School, Newark, NJ 07103, USA
| | - Richard N. Kitsis
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Wilf Family Cardiovascular Research Institute, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Rajesh Patel
- Department of Pathology and Laboratory Medicine, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | - Edward Owusu-Ansah
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA
- The Robert N. Butler Columbia Aging Center, Columbia University Irving Medical Center, New York, NY 10032, USA
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Wang Q, Zhuang J, Ni S, Luo H, Zheng K, Li X, Lan C, Zhao D, Bai Y, Jia B, Hu Z. Overexpressing CrePAPS Polyadenylate Activity Enhances Protein Translation and Accumulation in Chlamydomonas reinhardtii. Mar Drugs 2022; 20:276. [PMID: 35621927 PMCID: PMC9147819 DOI: 10.3390/md20050276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/15/2022] [Accepted: 04/15/2022] [Indexed: 02/01/2023] Open
Abstract
The alga Chlamydomonas reinhardtii is a potential platform for recombinant protein expression in the future due to various advantages. Dozens of C. reinhardtii strains producing genetically engineered recombinant therapeutic protein have been reported. However, owing to extremely low protein expression efficiency, none have been applied for industrial purposes. Improving protein expression efficiency at the molecular level is, therefore, a priority. The 3'-end poly(A) tail of mRNAs is strongly correlated with mRNA transcription and protein translation efficiency. In this study, we identified a canonical C. reinhardtii poly(A) polymerase (CrePAPS), verified its polyadenylate activity, generated a series of overexpressing transformants, and performed proteomic analysis. Proteomic results demonstrated that overexpressing CrePAPS promoted ribosomal assembly and enhanced protein accumulation. The accelerated translation was further verified by increased crude and dissolved protein content detected by Kjeldahl and bicinchoninic acid (BCA) assay approaches. The findings provide a novel direction in which to exploit photosynthetic green algae as a recombinant protein expression platform.
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Affiliation(s)
- Quan Wang
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (Q.W.); (J.Z.); (S.N.); (H.L.); (K.Z.); (X.L.); (C.L.); (D.Z.); (Y.B.)
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Jieyi Zhuang
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (Q.W.); (J.Z.); (S.N.); (H.L.); (K.Z.); (X.L.); (C.L.); (D.Z.); (Y.B.)
| | - Shuai Ni
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (Q.W.); (J.Z.); (S.N.); (H.L.); (K.Z.); (X.L.); (C.L.); (D.Z.); (Y.B.)
| | - Haolin Luo
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (Q.W.); (J.Z.); (S.N.); (H.L.); (K.Z.); (X.L.); (C.L.); (D.Z.); (Y.B.)
| | - Kaijie Zheng
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (Q.W.); (J.Z.); (S.N.); (H.L.); (K.Z.); (X.L.); (C.L.); (D.Z.); (Y.B.)
| | - Xinyi Li
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (Q.W.); (J.Z.); (S.N.); (H.L.); (K.Z.); (X.L.); (C.L.); (D.Z.); (Y.B.)
| | - Chengxiang Lan
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (Q.W.); (J.Z.); (S.N.); (H.L.); (K.Z.); (X.L.); (C.L.); (D.Z.); (Y.B.)
| | - Di Zhao
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (Q.W.); (J.Z.); (S.N.); (H.L.); (K.Z.); (X.L.); (C.L.); (D.Z.); (Y.B.)
| | - Yongsheng Bai
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (Q.W.); (J.Z.); (S.N.); (H.L.); (K.Z.); (X.L.); (C.L.); (D.Z.); (Y.B.)
| | - Bin Jia
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (Q.W.); (J.Z.); (S.N.); (H.L.); (K.Z.); (X.L.); (C.L.); (D.Z.); (Y.B.)
- Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen 518055, China
| | - Zhangli Hu
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (Q.W.); (J.Z.); (S.N.); (H.L.); (K.Z.); (X.L.); (C.L.); (D.Z.); (Y.B.)
- Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen 518055, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
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Mizero B, Villacrés C, Spicer V, Viner R, Saba J, Patel B, Snovida S, Jensen P, Huhmer A, Krokhin OV. Retention Time Prediction for TMT-Labeled Peptides in Proteomic LC-MS Experiments. J Proteome Res 2022; 21:1218-1228. [PMID: 35363494 DOI: 10.1021/acs.jproteome.1c00833] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present the first detailed study of chromatographic behavior of peptides labeled with tandem mass tags (TMT and TMTpro) in 2D LC for proteomic applications. Carefully designed experimental procedures have permitted generating data sets of over 100,000 nonlabeled and TMT-labeled peptide pairs for the low pH RP in the second separation dimension and data sets of over 10,000 peptide pairs for high-pH RP, HILIC (amide and silica), and SCX separations in the first separation dimension. The average increase in peptide RPLC (0.1% formic acid) retention upon TMT labeling was found to be 3.3% acetonitrile (linear water/acetonitrile gradients), spanning a range of -4 to 10.3%. In addition to the bulk peptide properties such as length, hydrophobicity, and the number of labeled residues, we found several sequence-dependent features mostly associated with differences in N-terminal chemistry. The behavior of TMTpro-labeled peptides was found to be very similar except for a slightly higher hydrophobicity: an average retention shift of 3.7% acetonitrile. The respective versions of the sequence-specific retention calculator (SSRCalc) model have been developed to accommodate both TMT chemistries, showing identical prediction accuracy (R2 ∼ 0.98) for labeled and nonlabeled peptides. Higher retention for TMT-labeled peptides was observed for high-pH RP and HILIC separations, while SCX selectivity remained virtually unchanged.
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Affiliation(s)
- Benilde Mizero
- Department of Chemistry, University of Manitoba, Winnipeg R3T 2N2, Canada
| | - Carina Villacrés
- Manitoba Centre for Proteomics and Systems Biology, Winnipeg R3E 3P4, Canada
| | - Victor Spicer
- Manitoba Centre for Proteomics and Systems Biology, Winnipeg R3E 3P4, Canada
| | - Rosa Viner
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Julian Saba
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | | | - Sergei Snovida
- Thermo Fisher Scientific, Rockford, Illinois 61101, United States
| | - Penny Jensen
- Thermo Fisher Scientific, Rockford, Illinois 61101, United States
| | - Andreas Huhmer
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Oleg V Krokhin
- Department of Chemistry, University of Manitoba, Winnipeg R3T 2N2, Canada.,Manitoba Centre for Proteomics and Systems Biology, Winnipeg R3E 3P4, Canada.,Department of Internal Medicine, University of Manitoba, Winnipeg R3E 3P4, Canada
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CPEB1 directs muscle stem cell activation by reprogramming the translational landscape. Nat Commun 2022; 13:947. [PMID: 35177647 PMCID: PMC8854658 DOI: 10.1038/s41467-022-28612-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/14/2022] [Indexed: 11/08/2022] Open
Abstract
Skeletal muscle stem cells, also called Satellite Cells (SCs), are actively maintained in quiescence but can activate quickly upon extrinsic stimuli. However, the mechanisms of how quiescent SCs (QSCs) activate swiftly remain elusive. Here, using a whole mouse perfusion fixation approach to obtain bona fide QSCs, we identify massive proteomic changes during the quiescence-to-activation transition in pathways such as chromatin maintenance, metabolism, transcription, and translation. Discordant correlation of transcriptomic and proteomic changes reveals potential translational regulation upon SC activation. Importantly, we show Cytoplasmic Polyadenylation Element Binding protein 1 (CPEB1), post-transcriptionally affects protein translation during SC activation by binding to the 3' UTRs of different transcripts. We demonstrate phosphorylation-dependent CPEB1 promoted Myod1 protein synthesis by binding to the cytoplasmic polyadenylation elements (CPEs) within its 3' UTRs to regulate SC activation and muscle regeneration. Our study characterizes CPEB1 as a key regulator to reprogram the translational landscape directing SC activation and subsequent proliferation.
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66
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Leetanasaksakul K, Roytrakul S, Phaonakrop N, Kittisenachai S, Thaisakun S, Srithuanok N, Sriroth K, Soulard L. Discovery of potential protein biomarkers associated with sugarcane white leaf disease susceptibility using a comparative proteomic approach. PeerJ 2022; 10:e12740. [PMID: 35036104 PMCID: PMC8742537 DOI: 10.7717/peerj.12740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 12/13/2021] [Indexed: 01/07/2023] Open
Abstract
Sugarcane white leaf disease (SCWLD) is caused by phytoplasma, a serious sugarcane phytoplasma pathogen, which causes significant decreases in crop yield and sugar quality. The identification of proteins involved in the defense mechanism against SCWLD phytoplasma may help towards the development of varieties resistant to SCWLD. We investigated the proteomes of four sugarcane varieties with different levels of susceptibility to SCWLD phytoplasma infection, namely K88-92 and K95-84 (high), KK3 (moderate), and UT1 (low) by quantitative label-free nano-liquid chromatography-tandem mass spectrometry (nano LC-MS/MS). A total of 248 proteins were identified and compared among the four sugarcane varieties. Two potential candidate protein biomarkers for reduced susceptibility to SCWLD phytoplasma were identified as proteins detected only in UT1. The functions of these proteins are associated with protein folding, metal ion binding, and oxidoreductase. The candidate biomarkers could be useful for further study of the sugarcane defense mechanism against SCWLD phytoplasma, and in molecular and conventional breeding strategies for variety improvement.
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Affiliation(s)
- Kantinan Leetanasaksakul
- Functional Proteomics Technology, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Nueng, Khlong Luang, Pathum Thani, Thailand
| | - Sittiruk Roytrakul
- Functional Proteomics Technology, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Nueng, Khlong Luang, Pathum Thani, Thailand
| | - Narumon Phaonakrop
- Functional Proteomics Technology, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Nueng, Khlong Luang, Pathum Thani, Thailand
| | - Suthathip Kittisenachai
- Functional Proteomics Technology, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Nueng, Khlong Luang, Pathum Thani, Thailand
| | - Siriwan Thaisakun
- Functional Proteomics Technology, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Nueng, Khlong Luang, Pathum Thani, Thailand
| | - Nitiya Srithuanok
- Mitr Phol Innovation and Research Center, Khoksa-at, Phu Khiao, Chaiyaphum, Thailand
| | - Klanarong Sriroth
- Mitr Phol Innovation and Research Center, Khoksa-at, Phu Khiao, Chaiyaphum, Thailand
| | - Laurent Soulard
- Mitr Phol Innovation and Research Center, Khoksa-at, Phu Khiao, Chaiyaphum, Thailand
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67
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Zhan X, Lu M, Yang L, Yang J, Zhan X, Zheng S, Guo Y, Li B, Wen S, Li J, Li N. Ubiquitination-mediated molecular pathway alterations in human lung squamous cell carcinomas identified by quantitative ubiquitinomics. Front Endocrinol (Lausanne) 2022; 13:970843. [PMID: 36187110 PMCID: PMC9520991 DOI: 10.3389/fendo.2022.970843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/25/2022] [Indexed: 11/13/2022] Open
Abstract
Abnormal ubiquitination is extensively associated with cancers. To investigate human lung cancer ubiquitination and its potential functions, quantitative ubiquitinomics was carried out between human lung squamous cell carcinoma (LSCC) and control tissues, which characterized a total of 627 ubiquitin-modified proteins (UPs) and 1209 ubiquitinated lysine sites. Those UPs were mainly involved in cell adhesion, signal transduction, and regulations of ribosome complex and proteasome complex. Thirty three UPs whose genes were also found in TCGA database were significantly related to overall survival of LSCC. Six significant networks and 234 hub molecules were obtained from the protein-protein interaction (PPI) analysis of those 627 UPs. KEGG pathway analysis of those UPs revealed 47 statistically significant pathways, and most of which were tumor-associated pathways such as mTOR, HIF-1, PI3K-Akt, and Ras signaling pathways, and intracellular protein turnover-related pathways such as ribosome complex, ubiquitin-mediated proteolysis, ER protein processing, and proteasome complex pathways. Further, the relationship analysis of ubiquitination and differentially expressed proteins shows that ubiquitination regulates two aspects of protein turnover - synthesis and degradation. This study provided the first profile of UPs and molecular networks in LSCC tissue, which is the important resource to insight into new mechanisms, and to identify new biomarkers and therapeutic targets/drugs to treat LSCC.
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Affiliation(s)
- Xianquan Zhan
- Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
- *Correspondence: Xianquan Zhan,
| | - Miaolong Lu
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, China
| | - Lamei Yang
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
| | - Jingru Yang
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
| | - Xiaohan Zhan
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, China
| | - Shu Zheng
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
| | - Yuna Guo
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
| | - Biao Li
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, China
| | - Siqi Wen
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, China
| | - Jiajia Li
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, China
| | - Na Li
- Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
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Kongpracha P, Wiriyasermkul P, Isozumi N, Moriyama S, Kanai Y, Nagamori S. Simple but efficacious enrichment of integral membrane proteins and their interactions for in-depth membrane proteomics. Mol Cell Proteomics 2022; 21:100206. [PMID: 35085786 PMCID: PMC9062332 DOI: 10.1016/j.mcpro.2022.100206] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 12/13/2021] [Accepted: 01/20/2022] [Indexed: 12/19/2022] Open
Abstract
Membrane proteins play essential roles in various cellular processes, such as nutrient transport, bioenergetic processes, cell adhesion, and signal transduction. Proteomics is one of the key approaches to exploring membrane proteins comprehensively. Bottom–up proteomics using LC–MS/MS has been widely used in membrane proteomics. However, the low abundance and hydrophobic features of membrane proteins, especially integral membrane proteins, make it difficult to handle the proteins and are the bottleneck for identification by LC–MS/MS. Herein, to improve the identification and quantification of membrane proteins, we have stepwisely evaluated methods of membrane enrichment for the sample preparation. The enrichment methods of membranes consisted of precipitation by ultracentrifugation and treatment by urea or alkaline solutions. The best enrichment method in the study, washing with urea after isolation of the membranes, resulted in the identification of almost twice as many membrane proteins compared with samples without the enrichment. Notably, the method significantly enhances the identified numbers of multispanning transmembrane proteins, such as solute carrier transporters, ABC transporters, and G-protein–coupled receptors, by almost sixfold. Using this method, we revealed the profiles of amino acid transport systems with the validation by functional assays and found more protein–protein interactions, including membrane protein complexes and clusters. Our protocol uses standard procedures in biochemistry, but the method was efficient for the in-depth analysis of membrane proteome in a wide range of samples. Fractionation of membranes improves the identification of membrane proteins. Membranes washed with urea or alkaline increase identified transmembrane proteins. Urea wash increases the detection of multispanning transmembrane proteins. Proteomics of urea-washed membranes keeps more protein–protein interactions.
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Affiliation(s)
- Pornparn Kongpracha
- Department of Laboratory Medicine, The Jikei University School of Medicine, Tokyo, Japan; Department of Collaborative Research for Biomolecular Dynamics, Nara Medical University, Nara, Japan
| | - Pattama Wiriyasermkul
- Department of Laboratory Medicine, The Jikei University School of Medicine, Tokyo, Japan; Department of Collaborative Research for Biomolecular Dynamics, Nara Medical University, Nara, Japan
| | - Noriyoshi Isozumi
- Department of Bio-system Pharmacology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Satomi Moriyama
- Department of Collaborative Research for Biomolecular Dynamics, Nara Medical University, Nara, Japan
| | - Yoshikatsu Kanai
- Department of Bio-system Pharmacology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Shushi Nagamori
- Department of Laboratory Medicine, The Jikei University School of Medicine, Tokyo, Japan; Department of Collaborative Research for Biomolecular Dynamics, Nara Medical University, Nara, Japan.
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69
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Biochemical Mapping of Pyrodinium bahamense Unveils Molecular Underpinnings behind Organismal Processes. Int J Mol Sci 2021; 22:ijms222413332. [PMID: 34948131 PMCID: PMC8706660 DOI: 10.3390/ijms222413332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 11/17/2022] Open
Abstract
Proteins, lipids, and carbohydrates from the harmful algal bloom (HAB)-causing organism Pyrodinium bahamense were characterized to obtain insights into the biochemical processes in this environmentally relevant dinoflagellate. Shotgun proteomics using label-free quantitation followed by proteome mapping using the P. bahamense transcriptome and translated protein databases of Marinovum algicola, Alexandrium sp., Cylindrospermopsis raciborskii, and Symbiodinium kawagutii for annotation enabled the characterization of the proteins in P. bahamense. The highest number of annotated hits were obtained from M. algicola and highlighted the contribution of microorganisms associated with P. bahamense. Proteins involved in dimethylsulfoniopropionate (DMSP) degradation such as propionyl CoA synthethase and acryloyl-CoA reductase were identified, suggesting the DMSP cleavage pathway as the preferred route in this dinoflagellate. Most of the annotated proteins were involved in amino acid biosynthesis and carbohydrate degradation and metabolism, indicating the active roles of these molecules in the vegetative stage of P. bahamense. This characterization provides baseline information on the cellular machinery and the molecular basis of the ecophysiology of P. bahamense.
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Haytural H, Benfeitas R, Schedin-Weiss S, Bereczki E, Rezeli M, Unwin RD, Wang X, Dammer EB, Johnson ECB, Seyfried NT, Winblad B, Tijms BM, Visser PJ, Frykman S, Tjernberg LO. Insights into the changes in the proteome of Alzheimer disease elucidated by a meta-analysis. Sci Data 2021; 8:312. [PMID: 34862388 PMCID: PMC8642431 DOI: 10.1038/s41597-021-01090-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 10/21/2021] [Indexed: 11/10/2022] Open
Abstract
Mass spectrometry (MS)-based proteomics is a powerful tool to explore pathogenic changes of a disease in an unbiased manner and has been used extensively in Alzheimer disease (AD) research. Here, by performing a meta-analysis of high-quality proteomic studies, we address which pathological changes are observed consistently and therefore most likely are of great importance for AD pathogenesis. We retrieved datasets, comprising a total of 21,588 distinct proteins identified across 857 postmortem human samples, from ten studies using labeled or label-free MS approaches. Our meta-analysis findings showed significant alterations of 757 and 1,195 proteins in AD in the labeled and label-free datasets, respectively. Only 33 proteins, some of which were associated with synaptic signaling, had the same directional change across the individual studies. However, despite alterations in individual proteins being different between the labeled and the label-free datasets, several pathways related to synaptic signaling, oxidative phosphorylation, immune response and extracellular matrix were commonly dysregulated in AD. These pathways represent robust changes in the human AD brain and warrant further investigation.
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Affiliation(s)
- Hazal Haytural
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Solna, Sweden.
| | - Rui Benfeitas
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, S-10691, Stockholm, Sweden
| | - Sophia Schedin-Weiss
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Solna, Sweden
| | - Erika Bereczki
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Solna, Sweden
| | - Melinda Rezeli
- Division of Clinical Protein Science & Imaging, Department of Clinical Sciences (Lund) and Department of Biomedical Engineering, Lund University, Lund, Sweden
| | - Richard D Unwin
- Stoller Biomarker Discovery Centre, and Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Sciences Centre, CityLabs 1.0, Nelson Street, Manchester, M13 9NQ, UK
| | - Xusheng Wang
- Department of Biology, University of North Dakota, Grand Forks, ND, USA
| | - Eric B Dammer
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Erik C B Johnson
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Nicholas T Seyfried
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Bengt Winblad
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Solna, Sweden
- Karolinska University Hospital, Theme of Inflammation and Aging, Huddinge, Sweden
| | - Betty M Tijms
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Pieter Jelle Visser
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Solna, Sweden
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
- Alzheimer Center Limburg, School for Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Susanne Frykman
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Solna, Sweden
| | - Lars O Tjernberg
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Solna, Sweden.
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Wei FR, Gao CH, Wang JY, Yang YT, Shi F, Zheng B. Label-Free Quantitative Proteomic Analysis of Three Strains of Viscerotropic Leishmania Isolated from Patients with Different Epidemiological Types of Visceral Leishmaniasis in China. Acta Parasitol 2021; 66:1366-1386. [PMID: 34019278 DOI: 10.1007/s11686-021-00387-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/29/2021] [Indexed: 11/27/2022]
Abstract
BACKGROUND There are three epidemiological types of visceral leishmaniasis in China, which are caused by Leishmania strains belonging to the L. donovani complex. The mechanisms underlying their differences in the population affected, disease latency, and animal host, etc., remain unclear. We investigated the protein abundance differences among Leishmania strains isolated from three types of visceral leishmaniasis endemic areas in China. METHODS Promastigotes of the three Leishmania strains were cultured to the log phase and harvested. The protein tryptic digests were analyzed with liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS), followed by label-free quantitative analysis. The MS experiment was performed on a Q Exactive mass spectrometer. Raw spectra were quantitatively analyzed with the MaxQuant software (ver 1.3.0.5) and matched with the reference database. Differentially expressed proteins were analyzed using the bioinformatics method. The MS analysis was repeated three times for each sample. RESULTS A total of 5012 proteins were identified across the KS-2, JIASHI-5 and SC6 strains in at least 2 of the three samples replicate. Of them, 1758 were identified to be differentially expressed at least between 2 strains, including 349 with known names. These differentially expressed proteins with known names are involved in biological functions such as energy and lipid metabolic process, nucleotide acid metabolic process, amino acid metabolic process, response to stress, cell membrane/cytoskeleton, cell cycle and proliferation, biological adhesion and proteolysis, localization and transport, regulation of the biological process, and signal transduction. CONCLUSION The differentially expressed proteins and their related biological functions may shed light on the pathogenicity of Leishmania and targets for the development of vaccines and medicines.
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Affiliation(s)
- Fu-Rong Wei
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Ministry of Health, Shanghai, 200025, China
| | - Chun-Hua Gao
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Ministry of Health, Shanghai, 200025, China
| | - Jun-Yun Wang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Ministry of Health, Shanghai, 200025, China.
| | - Yue-Tao Yang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Ministry of Health, Shanghai, 200025, China
| | - Feng Shi
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Ministry of Health, Shanghai, 200025, China
| | - Bin Zheng
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Ministry of Health, Shanghai, 200025, China.
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72
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Abreha KB, Alexandersson E, Resjö S, Lankinen Å, Sueldo D, Kaschani F, Kaiser M, van der Hoorn RAL, Levander F, Andreasson E. Leaf Apoplast of Field-Grown Potato Analyzed by Quantitative Proteomics and Activity-Based Protein Profiling. Int J Mol Sci 2021; 22:12033. [PMID: 34769464 PMCID: PMC8584485 DOI: 10.3390/ijms222112033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 01/11/2023] Open
Abstract
Multiple biotic and abiotic stresses challenge plants growing in agricultural fields. Most molecular studies have aimed to understand plant responses to challenges under controlled conditions. However, studies on field-grown plants are scarce, limiting application of the findings in agricultural conditions. In this study, we investigated the composition of apoplastic proteomes of potato cultivar Bintje grown under field conditions, i.e., two field sites in June-August across two years and fungicide treated and untreated, using quantitative proteomics, as well as its activity using activity-based protein profiling (ABPP). Samples were clustered and some proteins showed significant intensity and activity differences, based on their field site and sampling time (June-August), indicating differential regulation of certain proteins in response to environmental or developmental factors. Peroxidases, class II chitinases, pectinesterases, and osmotins were among the proteins more abundant later in the growing season (July-August) as compared to early in the season (June). We did not detect significant differences between fungicide Shirlan treated and untreated field samples in two growing seasons. Using ABPP, we showed differential activity of serine hydrolases and β-glycosidases under greenhouse and field conditions and across a growing season. Furthermore, the activity of serine hydrolases and β-glycosidases, including proteins related to biotic stress tolerance, decreased as the season progressed. The generated proteomics data would facilitate further studies aiming at understanding mechanisms of molecular plant physiology in agricultural fields and help applying effective strategies to mitigate biotic and abiotic stresses.
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Affiliation(s)
- Kibrom B. Abreha
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, SE-234 22 Lomma, Sweden; (E.A.); (S.R.); (Å.L.); (E.A.)
| | - Erik Alexandersson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, SE-234 22 Lomma, Sweden; (E.A.); (S.R.); (Å.L.); (E.A.)
| | - Svante Resjö
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, SE-234 22 Lomma, Sweden; (E.A.); (S.R.); (Å.L.); (E.A.)
| | - Åsa Lankinen
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, SE-234 22 Lomma, Sweden; (E.A.); (S.R.); (Å.L.); (E.A.)
| | - Daniela Sueldo
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK; (D.S.); (R.A.L.v.d.H.)
| | - Farnusch Kaschani
- Chemische Biologie, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany; (F.K.); (M.K.)
| | - Markus Kaiser
- Chemische Biologie, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany; (F.K.); (M.K.)
| | - Renier A. L. van der Hoorn
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK; (D.S.); (R.A.L.v.d.H.)
| | - Fredrik Levander
- Department of Immunotechnology, Lund University, SE-221 00 Lund, Sweden;
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Lund University, SE-221 00 Lund, Sweden
| | - Erik Andreasson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, SE-234 22 Lomma, Sweden; (E.A.); (S.R.); (Å.L.); (E.A.)
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73
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Gaspar VP, Ibrahim S, Zahedi RP, Borchers CH. Utility, promise, and limitations of liquid chromatography-mass spectrometry-based therapeutic drug monitoring in precision medicine. JOURNAL OF MASS SPECTROMETRY : JMS 2021; 56:e4788. [PMID: 34738286 PMCID: PMC8597589 DOI: 10.1002/jms.4788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 05/03/2023]
Abstract
Therapeutic drug monitoring (TDM) is typically referred to as the measurement of the concentration of drugs in patient blood. Although in the past, TDM was restricted to drugs with a narrow therapeutic range in order to avoid drug toxicity, TDM has recently become a major tool for precision medicine being applied to many more drugs. Through compensating for interindividual differences in a drug's pharmacokinetics, improved dosing of individual patients based on TDM ensures maximum drug effectiveness while minimizing side effects. This is especially relevant for individuals that present a particularly high intervariability in pharmacokinetics, such as newborns, or for critically/severely ill patients. In this article, we will review the applications for and limitations of TDM, discuss for which patients TDM is most beneficial and why, examine which techniques are being used for TDM, and demonstrate how mass spectrometry is increasingly becoming a reliable and convenient alternative for the TDM of different classes of drugs. We will also highlight the advances, challenges, and limitations of the existing repertoire of TDM methods and discuss future opportunities for TDM-based precision medicine.
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Affiliation(s)
- Vanessa P. Gaspar
- Segal Cancer Proteomics CentreMcGill UniversityMontrealQuebecCanada
- Gerald Bronfman Department of OncologyMcGill UniversityMontrealQuebecCanada
| | - Sahar Ibrahim
- Segal Cancer Proteomics CentreMcGill UniversityMontrealQuebecCanada
- Division of Experimental MedicineMcGill UniversityMontrealQuebecCanada
- Clinical Pathology DepartmentMenoufia UniversityShibin el KomEgypt
| | - René P. Zahedi
- Segal Cancer Proteomics CentreMcGill UniversityMontrealQuebecCanada
- Center for Computational and Data‐Intensive Science and EngineeringSkolkovo Institute of Science and TechnologyMoscowRussia
| | - Christoph H. Borchers
- Segal Cancer Proteomics CentreMcGill UniversityMontrealQuebecCanada
- Gerald Bronfman Department of OncologyMcGill UniversityMontrealQuebecCanada
- Center for Computational and Data‐Intensive Science and EngineeringSkolkovo Institute of Science and TechnologyMoscowRussia
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74
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Modahl CM, Saviola AJ, Mackessy SP. Integration of transcriptomic and proteomic approaches for snake venom profiling. Expert Rev Proteomics 2021; 18:827-834. [PMID: 34663159 DOI: 10.1080/14789450.2021.1995357] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Snake venoms contain many protein and peptide isoforms with high levels of sequence variation, even within a single species. AREAS COVERED In this review, we highlight several examples, from both published and unpublished work in our lab, demonstrating how a combined venom gland transcriptome and proteome methodology allows for comprehensive characterization of venoms, including those from understudied rear-fanged snake species, and we provide recommendations for using these approaches. EXPERT OPINION When characterizing venoms, peptide mass fingerprinting using databases built predominately from protein sequences originating from model organisms can be disadvantageous, especially when the intention is to document protein diversity. Therefore, the use of species-specific venom gland transcriptomes corrects for the absence of these unique peptide sequences in databases. The integration of transcriptomics and proteomics improves the accuracy of either approach alone for venom profiling.
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Affiliation(s)
| | - Anthony J Saviola
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, USA
| | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, Greeley, USA
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75
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Exercising D. melanogaster Modulates the Mitochondrial Proteome and Physiology. The Effect on Lifespan Depends upon Age and Sex. Int J Mol Sci 2021; 22:ijms222111606. [PMID: 34769041 PMCID: PMC8583977 DOI: 10.3390/ijms222111606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/21/2021] [Accepted: 10/25/2021] [Indexed: 11/17/2022] Open
Abstract
Ageing is a major risk factor for many of the most prevalent diseases, including neurodegenerative diseases, cancer, and heart disease. As the global population continues to age, behavioural interventions that can promote healthy ageing will improve quality of life and relieve the socioeconomic burden that comes with an aged society. Exercise is recognised as an effective intervention against many diseases of ageing, but we do not know the stage in an individual’s lifetime at which exercise is most effective at promoting healthy ageing, and whether or not it has a direct effect on lifespan. We exercised w1118 Drosophila melanogaster, investigating the effects of sex and group size at different stages of their lifetime, and recorded their lifespan. Climbing scores at 30 days were measured to record differences in fitness in response to exercise. We also assessed the mitochondrial proteome of w1118 Drosophila that had been exercised for one week, alongside mitochondrial respiration measured using high-resolution respirometry, to determine changes in mitochondrial physiology in response to exercise. We found that age-targeted exercise interventions improved the lifespan of both male and female Drosophila, and grouped males exercised in late life had improved climbing scores when compared with those exercised throughout their entire lifespan. The proteins of the electron transport chain were significantly upregulated in expression after one week of exercise, and complex-II-linked respiration was significantly increased in exercised Drosophila. Taken together, our findings provide a basis to test specific proteins, and complex II of the respiratory chain, as important effectors of exercise-induced healthy ageing.
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76
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Abstract
Streptomyces coelicolor is a model organism for the study of Streptomyces, a genus of Gram-positive bacteria that undergoes a complex life cycle and produces a broad repertoire of bioactive metabolites and extracellular enzymes. This study investigated the production and characterization of membrane vesicles (MVs) in liquid cultures of S. coelicolor M145 from a structural and biochemical point of view; this was achieved by combining microscopic, physical and -omics analyses. Two main populations of MVs, with different size and cargo, were isolated and purified. S. coelicolor MV cargo was determined being complex and containing different kinds of proteins and metabolites. In particular, a whole of 166 proteins involved in cell metabolism/differentiation, molecular processing/transport, and stress response was identified in MVs, the latter functional class being also important for bacterial morpho-physiological differentiation. A subset of these proteins was protected from degradation following treatment of MVs with proteinase K, indicating their localization inside the vesicles. Moreover, S. coelicolor MVs contained an array of metabolites, such as antibiotics, vitamins, amino acids and components of carbon metabolism. In conclusion, this analysis provides detailed information on S. coelicolor MVs under basal conditions and corresponding content, which may be useful in a next future to elucidate vesicle biogenesis and functions. Importance Streptomycetes are widely distributed in nature, and they are characterized by a complex life cycle that involves morphological differentiation. They are very relevant in industry because they produce about a half of the antibiotics used clinically and other important pharmaceutical products having natural origin. Streptomyces coelicolor is a model organism for the study of bacterial differentiation and bioactive molecule production. S. coelicolor produces extracellular vesicles carrying many molecules such as proteins and metabolites, including antibiotics. The elucidation of S. coelicolor extracellular vesicle cargo will help to understand different aspects of streptomycete physiology, such as cell communication during differentiation and response to environmental stimuli. Moreover, the capability of carrying different kind of biomolecules opens up new biotechnological possibilities related to drug delivery. Indeed, the decoding of molecular mechanisms involved in cargo selection may lead to the customization of the content of extracellular vesicles.
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77
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Kwon YW, Jo HS, Bae S, Seo Y, Song P, Song M, Yoon JH. Application of Proteomics in Cancer: Recent Trends and Approaches for Biomarkers Discovery. Front Med (Lausanne) 2021; 8:747333. [PMID: 34631760 PMCID: PMC8492935 DOI: 10.3389/fmed.2021.747333] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 08/26/2021] [Indexed: 12/12/2022] Open
Abstract
Proteomics has become an important field in molecular sciences, as it provides valuable information on the identity, expression levels, and modification of proteins. For example, cancer proteomics unraveled key information in mechanistic studies on tumor growth and metastasis, which has contributed to the identification of clinically applicable biomarkers as well as therapeutic targets. Several cancer proteome databases have been established and are being shared worldwide. Importantly, the integration of proteomics studies with other omics is providing extensive data related to molecular mechanisms and target modulators. These data may be analyzed and processed through bioinformatic pipelines to obtain useful information. The purpose of this review is to provide an overview of cancer proteomics and recent advances in proteomic techniques. In particular, we aim to offer insights into current proteomics studies of brain cancer, in which proteomic applications are in a relatively early stage. This review covers applications of proteomics from the discovery of biomarkers to the characterization of molecular mechanisms through advances in technology. Moreover, it addresses global trends in proteomics approaches for translational research. As a core method in translational research, the continued development of this field is expected to provide valuable information at a scale beyond that previously seen.
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Affiliation(s)
- Yang Woo Kwon
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu, South Korea
| | - Han-Seul Jo
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu, South Korea
| | - Sungwon Bae
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu, South Korea
| | - Youngsuk Seo
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu, South Korea
| | - Parkyong Song
- Department of Convergence Medicine, Pusan National University School of Medicine, Yangsan, South Korea
| | - Minseok Song
- Department of Life Sciences, Yeungnam University, Gyeongsan, South Korea
| | - Jong Hyuk Yoon
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu, South Korea
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78
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Rangama S, Lidbury IDEA, Holden JM, Borsetto C, Murphy ARJ, Hawkey PM, Wellington EMH. Mechanisms Involved in the Active Secretion of CTX-M-15 β-Lactamase by Pathogenic Escherichia coli ST131. Antimicrob Agents Chemother 2021; 65:e0066321. [PMID: 34310213 PMCID: PMC8448145 DOI: 10.1128/aac.00663-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 07/19/2021] [Indexed: 11/20/2022] Open
Abstract
Infections caused by antimicrobial-resistant bacterial pathogens are fast becoming an important global health issue. Strains of Escherichia coli are common causal agents of urinary tract infection and can carry multiple resistance genes. This includes the gene blaCTX-M-15, which encodes an extended-spectrum beta-lactamase (ESBL). While studying antimicrobial resistance (AMR) in the environment, we isolated several strains of E. coli ST131 downstream of a wastewater treatment plan (WWTP) in a local river. These isolates were surviving in the river sediment, and characterization proved that a multiresistant phenotype was evident. Here, we show that E. coli strain 48 (river isolate ST131) provided a protective effect against a third-generation cephalosporin (cefotaxime) for susceptible E. coli strain 33 (river isolate ST3576) through secretion of a functional ESBL into the growth medium. Furthermore, extracellular ESBL activity was stable for at least 24 h after secretion. Proteomic and molecular genetic analyses identified CTX-M-15 as the major secreted ESBL responsible for the observed protective effect. In contrast to previous studies, outer membrane vesicles (OMVs) were not the route for CTX-M-15 secretion. Indeed, mutation of the type I secretion system led to a significant reduction in the growth of the ESBL-producing strain as well as a significantly reduced ability to confer protective effect. We speculate that CTX-M-15 secretion, mediated through active secretion using molecular machinery, provides a public goods service by facilitating the survival of otherwise susceptible bacteria in the presence of cefotaxime.
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Affiliation(s)
- Severine Rangama
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Ian D. E. A. Lidbury
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Department of Animal and Plant Science, The University of Sheffield, Sheffield, United Kingdom
| | - Jennifer M. Holden
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Micropathology Ltd., University of Warwick Science Park, Coventry, United Kingdom
| | - Chiara Borsetto
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | | | - Peter M. Hawkey
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom
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79
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Graf AC, Striesow J, Pané-Farré J, Sura T, Wurster M, Lalk M, Pieper DH, Becher D, Kahl BC, Riedel K. An Innovative Protocol for Metaproteomic Analyses of Microbial Pathogens in Cystic Fibrosis Sputum. Front Cell Infect Microbiol 2021; 11:724569. [PMID: 34513734 PMCID: PMC8432295 DOI: 10.3389/fcimb.2021.724569] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 08/11/2021] [Indexed: 12/28/2022] Open
Abstract
Hallmarks of cystic fibrosis (CF) are increased viscosity of mucus and impaired mucociliary clearance within the airways due to mutations of the cystic fibrosis conductance regulator gene. This facilitates the colonization of the lung by microbial pathogens and the concomitant establishment of chronic infections leading to tissue damage, reduced lung function, and decreased life expectancy. Although the interplay between key CF pathogens plays a major role during disease progression, the pathophysiology of the microbial community in CF lungs remains poorly understood. Particular challenges in the analysis of the microbial population present in CF sputum is (I) the inhomogeneous, viscous, and slimy consistence of CF sputum, and (II) the high number of human proteins masking comparably low abundant microbial proteins. To address these challenges, we used 21 CF sputum samples to develop a reliable, reproducible and widely applicable protocol for sputum processing, microbial enrichment, cell disruption, protein extraction and subsequent metaproteomic analyses. As a proof of concept, we selected three sputum samples for detailed metaproteome analyses and complemented and validated metaproteome data by 16S sequencing, metabolomic as well as microscopic analyses. Applying our protocol, the number of bacterial proteins/protein groups increased from 199-425 to 392-868 in enriched samples compared to nonenriched controls. These early microbial metaproteome data suggest that the arginine deiminase pathway and multiple proteases and peptidases identified from various bacterial genera could so far be underappreciated in their contribution to the CF pathophysiology. By providing a standardized and effective protocol for sputum processing and microbial enrichment, our study represents an important basis for future studies investigating the physiology of microbial pathogens in CF in vivo – an important prerequisite for the development of novel antimicrobial therapies to combat chronic recurrent airway infection in CF.
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Affiliation(s)
- Alexander C Graf
- Institute of Microbiology, Department of Microbial Physiology & Molecular Biology, University of Greifswald, Greifswald, Germany
| | - Johanna Striesow
- Research Group ZIK Plasmatis, Leibniz Institute for Plasma Science and Technology, Greifswald, Germany
| | - Jan Pané-Farré
- Center for Synthetic Microbiology, Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Thomas Sura
- Institute of Microbiology, Department of Microbial Proteomics, University of Greifswald, Greifswald, Germany
| | - Martina Wurster
- Institute of Biochemistry, Department of Cellular Biochemistry & Metabolomics, University of Greifswald, Greifswald, Germany
| | - Michael Lalk
- Institute of Biochemistry, Department of Cellular Biochemistry & Metabolomics, University of Greifswald, Greifswald, Germany
| | - Dietmar H Pieper
- Research Group Microbial Interactions and Processes, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Dörte Becher
- Institute of Microbiology, Department of Microbial Proteomics, University of Greifswald, Greifswald, Germany
| | - Barbara C Kahl
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Katharina Riedel
- Institute of Microbiology, Department of Microbial Physiology & Molecular Biology, University of Greifswald, Greifswald, Germany
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Global Proteome Profiling to Assess Changes in Protein Abundance Using Isobaric Labeling and Liquid Chromatography-Tandem Mass Spectrometry. Methods Mol Biol 2021. [PMID: 34432251 DOI: 10.1007/978-1-0716-1665-9_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Protein degradation is a critical component of all facets of cell biology, and recently methods have been developed to make use of targeted protein degradation as both an investigative tool and a potential therapeutic avenue. Mass spectrometry-based proteomic studies have allowed detailed characterization of changes in protein level and the biology underlying growth, development, and disease. Current methods and instrumentation allow identification and quantitative analysis of thousands of proteins in a single assay. The method described here involves cell lysis and digestion to peptides, labeling peptides with isobaric tagging TMT reagents, basic reversed phase fractionation, and liquid chromatography-tandem mass spectrometry analysis of the enriched peptides.
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81
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Proteomic Analysis Reveals Key Proteins in Extracellular Vesicles Cargo Associated with Idiopathic Pulmonary Fibrosis In Vitro. Biomedicines 2021; 9:biomedicines9081058. [PMID: 34440261 PMCID: PMC8394197 DOI: 10.3390/biomedicines9081058] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/13/2021] [Accepted: 08/17/2021] [Indexed: 12/29/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, irreversible, and highly fatal disease. It is characterized by the increased activation of both fibroblast and myofibroblast that results in excessive extracellular matrix (ECM) deposition. Extracellular vesicles (EVs) have been described as key mediators of intercellular communication in various pathologies. However, the role of EVs in the development of IPF remains poorly understood. This study aimed to characterize the differentially expressed proteins contained within EVs cargo derived from the fibroblast cell lines LL97A (IPF-1) and LL29 (IPF-2) isolated from lungs bearing IPF as compared to those derived from the fibroblast cell lines CCD8Lu (NL-1) and CCD19Lu (NL-2) isolated from healthy donors. Isolated EVs were subjected to label-free quantitative proteomic analysis by LC-MS/MS, and as a result, 331 proteins were identified. Differentially expressed proteins were obtained after the pairwise comparison, including all experimental groups. A total of 86 differentially expressed proteins were identified in either one or more comparison groups. Of note, proteins involved in fibrogenic processes, such as tenascin-c (TNC), insulin-like-growth-factor-binding protein 7 (IGFBP7), fibrillin-1 (FBN1), alpha-2 collagen chain (I) (COL1A2), alpha-1 collagen chain (I) (COL1A1), and lysyl oxidase homolog 1 (LOXL1), were identified in EVs cargo isolated from IPF cell lines. Additionally, KEGG pathway enrichment analysis revealed that differentially expressed proteins participate in focal adhesion, PI3K-Akt, and ECM–receptor interaction signaling pathways. In conclusion, our findings reveal that proteins contained within EVs cargo might play key roles during IPF pathogenesis.
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82
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Murari A, Rhooms SK, Garcia C, Liu T, Li H, Mishra B, Deshong C, Owusu-Ansah E. Dissecting the concordant and disparate roles of NDUFAF3 and NDUFAF4 in mitochondrial complex I biogenesis. iScience 2021; 24:102869. [PMID: 34386730 PMCID: PMC8346666 DOI: 10.1016/j.isci.2021.102869] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/12/2021] [Accepted: 07/14/2021] [Indexed: 11/19/2022] Open
Abstract
Distinct sub-assemblies (modules) of mitochondrial complex I (CI) are assembled with the assistance of CI Assembly Factors (CIAFs) through mechanisms that are incompletely defined. Here, using genetic analyses in Drosophila, we report that when either of the CIAFs – NDUFAF3 or NDUFAF4 – is disrupted, biogenesis of the Q-, N-, and PP-b-modules of CI is impaired. This is due, at least in part, to the compromised integration of NDUFS3 and NDUFS5 into the Q-, and PP-b-modules, respectively, coupled with a destabilization of another CIAF, TIMMDC1, in assembly intermediates. Notably, forced expression of NDUFAF4 rescues the biogenesis defects in the Q-module and some aspects of the defects in the PP-b-module of CI when NDUFAF3 is disrupted. Altogether, our studies furnish new fundamental insights into the mechanism by which NDUFAF3 and NDUFAF4 regulate CI assembly and raises the possibility that certain point mutations in NDUFAF3 may be rescued by overexpression of NDUFAF4. Disruption of NDUFAF3 and NDUFAF4 in Drosophila muscles destabilizes TIMMDC1 NDUFAF3 and NDUFAF4 regulate biogenesis of the N, Q, and Pp modules NDUFAF4 ameliorates some of the CI biogenesis defects in NDUFAF3 mutants
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Affiliation(s)
- Anjaneyulu Murari
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Shauna-Kay Rhooms
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Christian Garcia
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Tong Liu
- Center for Advanced Proteomics Research, Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers University - New Jersey Medical School, Newark, NJ 07103, USA
| | - Hong Li
- Center for Advanced Proteomics Research, Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers University - New Jersey Medical School, Newark, NJ 07103, USA
| | - Bibhuti Mishra
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Cassie Deshong
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Edward Owusu-Ansah
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA
- The Robert N. Butler Columbia Aging Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Corresponding author
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83
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Calvete JJ, Lomonte B, Saviola AJ, Bonilla F, Sasa M, Williams DJ, Undheim EA, Sunagar K, Jackson TN. Mutual enlightenment: A toolbox of concepts and methods for integrating evolutionary and clinical toxinology via snake venomics and the contextual stance. Toxicon X 2021; 9-10:100070. [PMID: 34195606 PMCID: PMC8234350 DOI: 10.1016/j.toxcx.2021.100070] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/01/2021] [Accepted: 06/07/2021] [Indexed: 12/21/2022] Open
Abstract
Snakebite envenoming is a neglected tropical disease that may claim over 100,000 human lives annually worldwide. Snakebite occurs as the result of an interaction between a human and a snake that elicits either a defensive response from the snake or, more rarely, a feeding response as the result of mistaken identity. Snakebite envenoming is therefore a biological and, more specifically, an ecological problem. Snake venom itself is often described as a "cocktail", as it is a heterogenous mixture of molecules including the toxins (which are typically proteinaceous) responsible for the pathophysiological consequences of envenoming. The primary function of venom in snake ecology is pre-subjugation, with defensive deployment of the secretion typically considered a secondary function. The particular composition of any given venom cocktail is shaped by evolutionary forces that include phylogenetic constraints associated with the snake's lineage and adaptive responses to the snake's ecological context, including the taxa it preys upon and by which it is predated upon. In the present article, we describe how conceptual frameworks from ecology and evolutionary biology can enter into a mutually enlightening relationship with clinical toxinology by enabling the consideration of snakebite envenoming from an "ecological stance". We detail the insights that may emerge from such a perspective and highlight the ways in which the high-fidelity descriptive knowledge emerging from applications of -omics era technologies - "venomics" and "antivenomics" - can combine with evolutionary explanations to deliver a detailed understanding of this multifactorial health crisis.
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Affiliation(s)
- Juan J. Calvete
- Evolutionary and Translational Venomics Laboratory, Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain
| | - Bruno Lomonte
- Unidad de Proteómica, Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Anthony J. Saviola
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Fabián Bonilla
- Laboratorio de Investigación en Animales Peligrosos (LIAP), Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Mahmood Sasa
- Laboratorio de Investigación en Animales Peligrosos (LIAP), Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
- Museo de Zoología, Centro de Investigaciones en Biodiversidad y Ecología Tropical, Universidad de Costa Rica, Costa Rica
| | | | - Eivind A.B. Undheim
- Centre for Biodiversity Dynamics, Department of Biology, NTNU, Trondheim, Norway
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Kartik Sunagar
- Evolutionary Venomics Lab, Centre for Ecological Sciences, Indian Institute of Science, Bangalore, Karnataka, India
| | - Timothy N.W. Jackson
- Australian Venom Research Unit, Department of Pharmacology and Therapeutics, University of Melbourne, Melbourne, Australia
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84
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Ishikawa S, Ishizawa K, Tanaka A, Kimura H, Kitabatake K, Sugano A, Edamatsu K, Ueda S, Iino M. Identification of Salivary Proteomic Biomarkers for Oral Cancer Screening. In Vivo 2021; 35:541-547. [PMID: 33402507 DOI: 10.21873/invivo.12289] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND/AIM The current study aimed to identify biomarkers for differentiating between patients with oral cancer (OC) and healthy controls (HCs) on the basis of the comprehensive proteomic analyses of saliva samples by using liquid chromatography-mass spectrometry (LC-MS/MS). PATIENTS AND METHODS Unstimulated saliva samples were collected from 39 patients with OC and from 31 HCs. Proteins in the saliva were comprehensively analyzed using LC-MS/MS. To differentiate between patients with OC and HCs, a multiple logistic regression model was developed for evaluating the discriminatory ability of a combination of multiple markers. RESULTS A total of 23 proteins were significantly differentially expressed between the patients with OC and the HCs. Six out of the 23 proteins, namely α-2-macroglobulin-like protein 1, cornulin, hemoglobin subunit β, Ig k chain V-II region Vk167, kininogen-1 and transmembrane protease serine 11D, were selected using the forward-selection method and applied to the multiple logistic regression model. The area under the curve for discriminating between patients with OC and HCs was 0.957 when the combination of the six metabolites was used (95% confidence interval=0.915-0.998; p<0.001). Furthermore, these candidate proteins did not show a stage-specific difference. CONCLUSION The results of the current study showed that six salivary proteins are potential non-invasive biomarkers for OC screening.
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Affiliation(s)
- Shigeo Ishikawa
- Department of Dentistry, Oral and Maxillofacial Plastic and Reconstructive Surgery, Faculty of Medicine, Yamagata University, Yamagata, Japan;
| | - Kenichi Ishizawa
- Department of Neurology, Hematology, Metabolism, Endocrinology and Diabetology, Faculty of Medicine, Yamagata University, Yamagata, Japan
| | - Atsushi Tanaka
- Pharmaceutical Sciences, Graduate School of Medical Science, Yamagata University, Yamagata, Japan.,Institute for Promotion of Medical Science Research, Faculty of Medicine, Yamagata University, Yamagata, Japan
| | - Hirohito Kimura
- Institute for Promotion of Medical Science Research, Faculty of Medicine, Yamagata University, Yamagata, Japan
| | | | - Ayako Sugano
- Department of Dentistry, Oral and Maxillofacial Plastic and Reconstructive Surgery, Faculty of Medicine, Yamagata University, Yamagata, Japan
| | - Kaoru Edamatsu
- Department of Dentistry, Oral and Maxillofacial Plastic and Reconstructive Surgery, Faculty of Medicine, Yamagata University, Yamagata, Japan
| | - Shohei Ueda
- Department of Dentistry, Oral and Maxillofacial Plastic and Reconstructive Surgery, Faculty of Medicine, Yamagata University, Yamagata, Japan
| | - Mitsuyoshi Iino
- Department of Dentistry, Oral and Maxillofacial Plastic and Reconstructive Surgery, Faculty of Medicine, Yamagata University, Yamagata, Japan
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85
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Song J, Liu C, Wang X, Xu B, Liu X, Li Y, Xia J, Li Y, Zhang C, Li D, Sun H. O-GlcNAcylation Quantification of Certain Protein by the Proximity Ligation Assay and Clostridium perfringen OGA D298N(CpOGA D298N). ACS Chem Biol 2021; 16:1040-1049. [PMID: 34105348 DOI: 10.1021/acschembio.1c00185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
O-GlcNAcylation is an O-linked β-N-acetyl-glucosamine (O-GlcNAc)-monosaccharide modification of serine or threonine in proteins that plays a vital role in many critical cellular processes. Owing to its low molecular weight, uncharged property, and difficulty in distinguishing from β-N-acetyl-galactosamine (GalNAc), the lack of high specificity and avidity tools and sophisticated quantification methods have always been the bottleneck in analyzing O-GlcNAc functions. Here, we compared glycan array data of the mutant of Clostridium perfringen OGA (CpOGAD298N), O-GlcNAc antibody CTD110.6, and several lectins. We found that CpOGAD298N can effectively distinguish GlcNAc from GalNAc. Glycan array analysis and isothermal titration calorimetry (ITC) show that CpOGAD298N has a GlcNAc specific binding characteristic. CpOGAD298N could be used in far-western, flow cytometry analysis, and confocal imaging to demonstrate the existence of O-GlcNAc proteins. Using the CpOGAD298N affinity column, we identified 84 highly confident O-GlcNAc modified peptides from 82 proteins in the MCF-7 cell line and 33 highly confident peptides in 33 proteins from mouse liver tissue; most of them are novel O-GlcNAc proteins and could not bind with wheat germ agglutinin (WGA). Besides being used as a facile enrichment tool, a combination of CpOGAD298N with the proximity ligation assay (PLA) is successfully used to quantify O-GlcNAc modified histone H2B, which is as low as femtomoles in MCF-7 cell lysate. These results suggest that CpOGAD298N is a specific tool for detection (far-western, flow cytometry analysis, and confocal imaging) and enrichment of O-GlcNAcylated proteins and peptides, and the CpOGAD298N-PLA method is useful for quantifying certain O-GlcNAc protein.
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Affiliation(s)
- Jiaqi Song
- College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei Province, People’s Republic of China
| | - Chenglong Liu
- College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei Province, People’s Republic of China
| | - Xueqing Wang
- College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei Province, People’s Republic of China
| | - Bo Xu
- College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei Province, People’s Republic of China
| | - Xiaomei Liu
- College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei Province, People’s Republic of China
| | - Yang Li
- College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei Province, People’s Republic of China
| | - Jing Xia
- College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei Province, People’s Republic of China
| | - Yan Li
- College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei Province, People’s Republic of China
| | - Can Zhang
- College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei Province, People’s Republic of China
| | - Danni Li
- College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei Province, People’s Republic of China
| | - Hui Sun
- College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei Province, People’s Republic of China
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86
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Damm M, Hempel BF, Süssmuth RD. Old World Vipers-A Review about Snake Venom Proteomics of Viperinae and Their Variations. Toxins (Basel) 2021; 13:toxins13060427. [PMID: 34204565 PMCID: PMC8235416 DOI: 10.3390/toxins13060427] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/11/2021] [Accepted: 06/16/2021] [Indexed: 12/12/2022] Open
Abstract
Fine-tuned by millions of years of evolution, snake venoms have frightened but also fascinated humanity and nowadays they constitute potential resources for drug development, therapeutics and antivenoms. The continuous progress of mass spectrometry techniques and latest advances in proteomics workflows enabled toxinologists to decipher venoms by modern omics technologies, so-called ‘venomics’. A tremendous upsurge reporting on snake venom proteomes could be observed. Within this review we focus on the highly venomous and widely distributed subfamily of Viperinae (Serpentes: Viperidae). A detailed public literature database search was performed (2003–2020) and we extensively reviewed all compositional venom studies of the so-called Old-World Vipers. In total, 54 studies resulted in 89 venom proteomes. The Viperinae venoms are dominated by four major, four secondary, six minor and several rare toxin families and peptides, respectively. The multitude of different venomics approaches complicates the comparison of venom composition datasets and therefore we differentiated between non-quantitative and three groups of quantitative workflows. The resulting direct comparisons within these groups show remarkable differences on the intra- and interspecies level across genera with a focus on regional differences. In summary, the present compilation is the first comprehensive up-to-date database on Viperinae venom proteomes and differentiating between analytical methods and workflows.
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Affiliation(s)
- Maik Damm
- Department of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany;
| | - Benjamin-Florian Hempel
- BIH Center for Regenerative Therapies, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, (BCRT), 10117 Berlin, Germany;
| | - Roderich D. Süssmuth
- Department of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany;
- Correspondence: ; Tel.: +49-(0)30-314-24205
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87
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Abstract
The abundance, localization, modifications, and protein-protein interactions of many host cell and virus proteins can change dynamically throughout the course of any viral infection. Studying these changes is critical for a comprehensive understanding of how viruses replicate and cause disease, as well as for the development of antiviral therapeutics and vaccines. Previously, we developed a mass spectrometry-based technique called quantitative temporal viromics (QTV), which employs isobaric tandem mass tags (TMTs) to allow precise comparative quantification of host and virus proteomes through a whole time course of infection. In this review, we discuss the utility and applications of QTV, exemplified by numerous studies that have since used proteomics with a variety of quantitative techniques to study virus infection through time. Expected final online publication date for the Annual Review of Virology, Volume 8 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
| | - Michael P Weekes
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom;
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88
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Zhang Y, Cheng P, Wang J, Abdalmegeed D, Li Y, Wu M, Dai C, Wan S, Guan R, Pu H, Shen W. Nitric Oxide Is Associated With Heterosis of Salinity Tolerance in Brassica napus L. FRONTIERS IN PLANT SCIENCE 2021; 12:649888. [PMID: 34122475 PMCID: PMC8194068 DOI: 10.3389/fpls.2021.649888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/13/2021] [Indexed: 06/01/2023]
Abstract
Heterosis is most frequently manifested as the superior performance of a hybrid than either of the parents, especially under stress conditions. Nitric oxide (NO) is a well-known gaseous signaling molecule that acts as a functional component during plant growth, development, and defense responses. In this study, the Brassica napus L. hybrid (F1, NJ4375 × MB1942) showed significant heterosis under salt stress, during both germination and post-germination periods. These phenotypes in the hybrid were in parallel with the better performance in redox homeostasis, including alleviation of reactive oxygen species accumulation and lipid peroxidation, and ion homeostasis, evaluated as a lower Na/K ratio in the leaves than parental lines. Meanwhile, stimulation of endogenous NO was more pronounced in hybrid plants, compared with parental lines, which might be mediated by nitrate reductase. Proteomic and biochemical analyses further revealed that protein abundance related to several metabolic processes, including chlorophyll biosynthesis, proline metabolism, and tricarboxylic acid cycle metabolism pathway, was greatly suppressed by salt stress in the two parental lines than in the hybrid. The above responses in hybrid plants were intensified by a NO-releasing compound, but abolished by a NO scavenger, both of which were matched with the changes in chlorophyll and proline contents. It was deduced that the above metabolic processes might play important roles in heterosis upon salt stress. Taken together, we proposed that heterosis derived from F1 hybridization in salt stress tolerance might be mediated by NO-dependent activation of defense responses and metabolic processes.
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Affiliation(s)
- Yihua Zhang
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, China
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
- Ministry of Agriculture’s Key Laboratory of Cotton and Rapeseed, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- College of Life Sciences, Shanxi Agricultural University, Taigu, China
| | - Pengfei Cheng
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jun Wang
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Dyaaaldin Abdalmegeed
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Ying Li
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Mangteng Wu
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Chen Dai
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Shubei Wan
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Rongzhan Guan
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Huiming Pu
- Ministry of Agriculture’s Key Laboratory of Cotton and Rapeseed, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Wenbiao Shen
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, China
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89
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Abstract
Biomarkers factor into the diagnosis and treatment of almost every patient with cancer. The innovation in proteomics follows improvement of mass spectrometry techniques and data processing strategy. Recently, proteomics and typical biological studies have been the answer for clinical applications. The clinical proteomics techniques are now actively adapted to protein identification in large patient cohort, biomarker development for more sensitive and specific screening based on quantitative data. And, it is important for clinical, translational researchers to be acutely aware of the issues surrounding appropriate biomarker development, in order to facilitate entry of clinically useful biomarkers into the clinic. Here, we discuss in detail include the case research for clinical proteomics. Furthermore, we give an overview on the current developments and novel findings in proteomics-based cancer biomarker research.
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90
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Walsh BJC, Giedroc DP. Proteomics Profiling of S-sulfurated Proteins in Acinetobacter baumannii. Bio Protoc 2021; 11:e4000. [PMID: 34124301 DOI: 10.21769/bioprotoc.4000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 02/10/2021] [Accepted: 02/18/2021] [Indexed: 11/02/2022] Open
Abstract
Hydrogen sulfide (H2S) is emerging as an important modulator in bacterial cytoprotection against the host immune response in infected animals, which may well be attributed to downstream highly oxidized sulfur species, termed reactive sulfur species (RSS), derived from H2S. One mechanism by which H2S/RSS may signal in the cell is through proteome S-sulfuration (persulfidation), which is the conversion of protein thiols (-SH) to protein persulfides (-SSH). While several analytical methods have been developed to profile sites of protein persulfidation, few have been applied to bacterial cells. The analytical workflow presented here was recently utilized to profile proteome persulfidation in the major human pathogen Acinetobacter baumannii treated with an exogenous sulfide source, Na2S. The data obtained using this protocol allow quantitation of the change in persulfidation status of each cysteine in the proteome normalized to the change in protein abundance, thus identifying sites of persulfidation that may constitute regulatory modifications. These can be validated using follow-up biochemical studies.
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Affiliation(s)
- Brenna J C Walsh
- Department of Chemistry, Indiana University, Bloomington, IN 47405 7102, USA
| | - David P Giedroc
- Department of Chemistry, Indiana University, Bloomington, IN 47405 7102, USA.,Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
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91
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Peikert K, Federti E, Matte A, Constantin G, Pietronigro EC, Fabene PF, Defilippi P, Turco E, Del Gallo F, Pucci P, Amoresano A, Illiano A, Cozzolino F, Monti M, Garello F, Terreno E, Alper SL, Glaß H, Pelzl L, Akgün K, Ziemssen T, Ordemann R, Lang F, Brunati AM, Tibaldi E, Andolfo I, Iolascon A, Bertini G, Buffelli M, Zancanaro C, Lorenzetto E, Siciliano A, Bonifacio M, Danek A, Walker RH, Hermann A, De Franceschi L. Therapeutic targeting of Lyn kinase to treat chorea-acanthocytosis. Acta Neuropathol Commun 2021; 9:81. [PMID: 33941276 PMCID: PMC8091687 DOI: 10.1186/s40478-021-01181-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 04/14/2021] [Indexed: 11/18/2022] Open
Abstract
Chorea-Acanthocytosis (ChAc) is a devastating, little understood, and currently untreatable neurodegenerative disease caused by VPS13A mutations. Based on our recent demonstration that accumulation of activated Lyn tyrosine kinase is a key pathophysiological event in human ChAc cells, we took advantage of Vps13a−/− mice, which phenocopied human ChAc. Using proteomic approach, we found accumulation of active Lyn, γ-synuclein and phospho-tau proteins in Vps13a−/− basal ganglia secondary to impaired autophagy leading to neuroinflammation. Mice double knockout Vps13a−/− Lyn−/− showed normalization of red cell morphology and improvement of autophagy in basal ganglia. We then in vivo tested pharmacologic inhibitors of Lyn: dasatinib and nilotinib. Dasatinib failed to cross the mouse brain blood barrier (BBB), but the more specific Lyn kinase inhibitor nilotinib, crosses the BBB. Nilotinib ameliorates both Vps13a−/− hematological and neurological phenotypes, improving autophagy and preventing neuroinflammation. Our data support the proposal to repurpose nilotinib as new therapeutic option for ChAc patients.
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92
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Nalbantoglu S, Karadag A. Metabolomics bridging proteomics along metabolites/oncometabolites and protein modifications: Paving the way toward integrative multiomics. J Pharm Biomed Anal 2021; 199:114031. [PMID: 33857836 DOI: 10.1016/j.jpba.2021.114031] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 03/02/2021] [Accepted: 03/16/2021] [Indexed: 02/08/2023]
Abstract
Systems biology adopted functional and integrative multiomics approaches enable to discover the whole set of interacting regulatory components such as genes, transcripts, proteins, metabolites, and metabolite dependent protein modifications. This interactome build up the midpoint of protein-protein/PTM, protein-DNA/RNA, and protein-metabolite network in a cell. As the key drivers in cellular metabolism, metabolites are precursors and regulators of protein post-translational modifications [PTMs] that affect protein diversity and functionality. The precisely orchestrated core pattern of metabolic networks refer to paradigm 'metabolites regulate PTMs, PTMs regulate enzymes, and enzymes modulate metabolites' through a multitude of feedback and feed-forward pathway loops. The concept represents a flawless PTM-metabolite-enzyme(protein) regulomics underlined in reprogramming cancer metabolism. Immense interconnectivity of those biomolecules in their spectacular network of intertwined metabolic pathways makes integrated proteomics and metabolomics an excellent opportunity, and the central component of integrative multiomics framework. It will therefore be of significant interest to integrate global proteome and PTM-based proteomics with metabolomics to achieve disease related altered levels of those molecules. Thereby, present update aims to highlight role and analysis of interacting metabolites/oncometabolites, and metabolite-regulated PTMs loop which may function as translational monitoring biomarkers along the reprogramming continuum of oncometabolism.
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Affiliation(s)
- Sinem Nalbantoglu
- TUBITAK Marmara Research Center, Gene Engineering and Biotechnology Institute, Molecular, Oncology Laboratory, Gebze, Kocaeli, Turkey.
| | - Abdullah Karadag
- TUBITAK Marmara Research Center, Gene Engineering and Biotechnology Institute, Molecular, Oncology Laboratory, Gebze, Kocaeli, Turkey
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93
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Xiang Y, Sang Z, Bitton L, Xu J, Liu Y, Schneidman-Duhovny D, Shi Y. Integrative proteomics identifies thousands of distinct, multi-epitope, and high-affinity nanobodies. Cell Syst 2021; 12:220-234.e9. [PMID: 33592195 PMCID: PMC7979497 DOI: 10.1016/j.cels.2021.01.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 10/13/2020] [Accepted: 01/20/2021] [Indexed: 12/15/2022]
Abstract
The antibody immune response is essential for the survival of mammals. However, we still lack a systematic understanding of the antibody repertoire. Here, we developed a proteomic strategy to survey, at an unprecedented scale, the landscape of antigen-engaged, circulating camelid heavy-chain antibodies, whose minimal binding fragments are called VHH antibodies or nanobodies. The sensitivity and robustness of this approach were validated with three antigens spanning orders of magnitude in immune responses; thousands of distinct, high-affinity nanobody families were reliably identified and quantified. Using high-throughput structural modeling, cross-linking mass spectrometry, mutagenesis, and deep learning, we mapped and analyzed the epitopes of >100,000 antigen-nanobody complexes. Our results revealed a surprising diversity of ultrahigh-affinity camelid nanobodies for specific antigen binding on various dominant epitope clusters. Nanobodies utilize both shape and charge complementarity to enable highly selective antigen binding. Interestingly, we found that nanobody-antigen binding can mimic conserved intracellular protein-protein interactions. A record of this paper's Transparent Peer Review process is included in the Supplemental information.
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Affiliation(s)
- Yufei Xiang
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zhe Sang
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA; University of Pittsburgh, Carnegie Mellon University Program for Computational Biology, Pittsburgh, PA, USA
| | - Lirane Bitton
- School of Computer Science and Engineering, Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| | - Jianquan Xu
- Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yang Liu
- Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dina Schneidman-Duhovny
- School of Computer Science and Engineering, Institute of Life Sciences, The Hebrew University of Jerusalem, Israel.
| | - Yi Shi
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA; University of Pittsburgh, Carnegie Mellon University Program for Computational Biology, Pittsburgh, PA, USA.
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94
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Kim TK, Tirloni L, Bencosme-Cuevas E, Kim TH, Diedrich JK, Yates JR, Mulenga A. Borrelia burgdorferi infection modifies protein content in saliva of Ixodes scapularis nymphs. BMC Genomics 2021; 22:152. [PMID: 33663385 PMCID: PMC7930271 DOI: 10.1186/s12864-021-07429-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 02/08/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Lyme disease (LD) caused by Borrelia burgdorferi is the most prevalent tick-borne disease. There is evidence that vaccines based on tick proteins that promote tick transmission of B. burgdorferi could prevent LD. As Ixodes scapularis nymph tick bites are responsible for most LD cases, this study sought to identify nymph tick saliva proteins associated with B. burgdorferi transmission using LC-MS/MS. Tick saliva was collected using a non-invasive method of stimulating ticks (uninfected and infected: unfed, and every 12 h during feeding through 72 h, and fully-fed) to salivate into 2% pilocarpine-PBS for protein identification using LC-MS/MS. RESULTS We identified a combined 747 tick saliva proteins of uninfected and B. burgdorferi infected ticks that were classified into 25 functional categories: housekeeping-like (48%), unknown function (18%), protease inhibitors (9%), immune-related (6%), proteases (8%), extracellular matrix (7%), and small categories that account for <5% each. Notably, B. burgdorferi infected ticks secreted high number of saliva proteins (n=645) than uninfected ticks (n=376). Counter-intuitively, antimicrobial peptides, which function to block bacterial infection at tick feeding site were suppressed 23-85 folds in B. burgdorferi infected ticks. Similar to glycolysis enzymes being enhanced in mammalian cells exposed to B. burgdorferi : eight of the 10-glycolysis pathway enzymes were secreted at high abundance by B. burgdorferi infected ticks. Of significance, rabbits exposed to B. burgdorferi infected ticks acquired potent immunity that caused 40-60% mortality of B. burgdorferi infected ticks during the second infestation compared to 15-28% for the uninfected. This might be explained by ELISA data that show that high expression levels of immunogenic proteins in B. burgdorferi infected ticks. CONCLUSION Data here suggest that B. burgdorferi infection modified protein content in tick saliva to promote its survival at the tick feeding site. For instance, enzymes; copper/zinc superoxide dismutase that led to production of H2O2 that is toxic to B. burgdorferi were suppressed, while, catalase and thioredoxin that neutralize H2O2, and pyruvate kinase which yields pyruvate that protects Bb from H2O2 killing were enhanced. We conclude data here is an important resource for discovery of effective antigens for a vaccine to prevent LD.
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Affiliation(s)
- Tae Kwon Kim
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
- Department of Diagnostic Medicine and Veterinary Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, United States of America
| | - Lucas Tirloni
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Hamilton, Montana, United States of America
| | - Emily Bencosme-Cuevas
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
| | - Tae Heung Kim
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, United States of America
- Mass Spectrometry Core, Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - Albert Mulenga
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America.
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95
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Proteome-wide and matrisome-specific alterations during human pancreas development and maturation. Nat Commun 2021; 12:1020. [PMID: 33589611 PMCID: PMC7884717 DOI: 10.1038/s41467-021-21261-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 01/19/2021] [Indexed: 01/31/2023] Open
Abstract
The extracellular matrix (ECM) is unique to each tissue and capable of guiding cell differentiation, migration, morphology, and function. The ECM proteome of different developmental stages has not been systematically studied in the human pancreas. In this study, we apply mass spectrometry-based quantitative proteomics strategies using N,N-dimethyl leucine isobaric tags to delineate proteome-wide and ECM-specific alterations in four age groups: fetal (18-20 weeks gestation), juvenile (5-16 years old), young adults (21-29 years old) and older adults (50-61 years old). We identify 3,523 proteins including 185 ECM proteins and quantify 117 of them. We detect previously unknown proteome and matrisome features during pancreas development and maturation. We also visualize specific ECM proteins of interest using immunofluorescent staining and investigate changes in ECM localization within islet or acinar compartments. This comprehensive proteomics analysis contributes to an improved understanding of the critical roles that ECM plays throughout human pancreas development and maturation.
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96
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Fu J, Luo Y, Mou M, Zhang H, Tang J, Wang Y, Zhu F. Advances in Current Diabetes Proteomics: From the Perspectives of Label- free Quantification and Biomarker Selection. Curr Drug Targets 2021; 21:34-54. [PMID: 31433754 DOI: 10.2174/1389450120666190821160207] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/17/2019] [Accepted: 07/24/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND Due to its prevalence and negative impacts on both the economy and society, the diabetes mellitus (DM) has emerged as a worldwide concern. In light of this, the label-free quantification (LFQ) proteomics and diabetic marker selection methods have been applied to elucidate the underlying mechanisms associated with insulin resistance, explore novel protein biomarkers, and discover innovative therapeutic protein targets. OBJECTIVE The purpose of this manuscript is to review and analyze the recent computational advances and development of label-free quantification and diabetic marker selection in diabetes proteomics. METHODS Web of Science database, PubMed database and Google Scholar were utilized for searching label-free quantification, computational advances, feature selection and diabetes proteomics. RESULTS In this study, we systematically review the computational advances of label-free quantification and diabetic marker selection methods which were applied to get the understanding of DM pathological mechanisms. Firstly, different popular quantification measurements and proteomic quantification software tools which have been applied to the diabetes studies are comprehensively discussed. Secondly, a number of popular manipulation methods including transformation, pretreatment (centering, scaling, and normalization), missing value imputation methods and a variety of popular feature selection techniques applied to diabetes proteomic data are overviewed with objective evaluation on their advantages and disadvantages. Finally, the guidelines for the efficient use of the computationbased LFQ technology and feature selection methods in diabetes proteomics are proposed. CONCLUSION In summary, this review provides guidelines for researchers who will engage in proteomics biomarker discovery and by properly applying these proteomic computational advances, more reliable therapeutic targets will be found in the field of diabetes mellitus.
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Affiliation(s)
- Jianbo Fu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yongchao Luo
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Minjie Mou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hongning Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jing Tang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,School of Pharmaceutical Sciences and Innovative Drug Research Centre, Chongqing University, Chongqing 401331, China
| | - Yunxia Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,School of Pharmaceutical Sciences and Innovative Drug Research Centre, Chongqing University, Chongqing 401331, China
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97
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A comparative study of evaluating missing value imputation methods in label-free proteomics. Sci Rep 2021; 11:1760. [PMID: 33469060 PMCID: PMC7815892 DOI: 10.1038/s41598-021-81279-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 12/31/2020] [Indexed: 12/29/2022] Open
Abstract
The presence of missing values (MVs) in label-free quantitative proteomics greatly reduces the completeness of data. Imputation has been widely utilized to handle MVs, and selection of the proper method is critical for the accuracy and reliability of imputation. Here we present a comparative study that evaluates the performance of seven popular imputation methods with a large-scale benchmark dataset and an immune cell dataset. Simulated MVs were incorporated into the complete part of each dataset with different combinations of MV rates and missing not at random (MNAR) rates. Normalized root mean square error (NRMSE) was applied to evaluate the accuracy of protein abundances and intergroup protein ratios after imputation. Detection of true positives (TPs) and false altered-protein discovery rate (FADR) between groups were also compared using the benchmark dataset. Furthermore, the accuracy of handling real MVs was assessed by comparing enriched pathways and signature genes of cell activation after imputing the immune cell dataset. We observed that the accuracy of imputation is primarily affected by the MNAR rate rather than the MV rate, and downstream analysis can be largely impacted by the selection of imputation methods. A random forest-based imputation method consistently outperformed other popular methods by achieving the lowest NRMSE, high amount of TPs with the average FADR < 5%, and the best detection of relevant pathways and signature genes, highlighting it as the most suitable method for label-free proteomics.
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98
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Huang L, Shao D, Wang Y, Cui X, Li Y, Chen Q, Cui J. Human body-fluid proteome: quantitative profiling and computational prediction. Brief Bioinform 2021; 22:315-333. [PMID: 32020158 PMCID: PMC7820883 DOI: 10.1093/bib/bbz160] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/22/2019] [Accepted: 10/18/2019] [Indexed: 12/15/2022] Open
Abstract
Empowered by the advancement of high-throughput bio technologies, recent research on body-fluid proteomes has led to the discoveries of numerous novel disease biomarkers and therapeutic drugs. In the meantime, a tremendous progress in disclosing the body-fluid proteomes was made, resulting in a collection of over 15 000 different proteins detected in major human body fluids. However, common challenges remain with current proteomics technologies about how to effectively handle the large variety of protein modifications in those fluids. To this end, computational effort utilizing statistical and machine-learning approaches has shown early successes in identifying biomarker proteins in specific human diseases. In this article, we first summarized the experimental progresses using a combination of conventional and high-throughput technologies, along with the major discoveries, and focused on current research status of 16 types of body-fluid proteins. Next, the emerging computational work on protein prediction based on support vector machine, ranking algorithm, and protein-protein interaction network were also surveyed, followed by algorithm and application discussion. At last, we discuss additional critical concerns about these topics and close the review by providing future perspectives especially toward the realization of clinical disease biomarker discovery.
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Affiliation(s)
- Lan Huang
- College of Computer Science and Technology in the Jilin University
| | - Dan Shao
- College of Computer Science and Technology in the Jilin University
- College of Computer Science and Technology in Changchun University
| | - Yan Wang
- College of Computer Science and Technology in the Jilin University
| | - Xueteng Cui
- College of Computer Science and Technology in the Changchun University
| | - Yufei Li
- College of Computer Science and Technology in the Changchun University
| | - Qian Chen
- College of Computer Science and Technology in the Jilin University
| | - Juan Cui
- Department of Computer Science and Engineering in the University of Nebraska-Lincoln
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99
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Shin S, Lee J, Kwon Y, Park KS, Jeong JH, Choi SJ, Bang SI, Chang JW, Lee C. Comparative Proteomic Analysis of the Mesenchymal Stem Cells Secretome from Adipose, Bone Marrow, Placenta and Wharton's Jelly. Int J Mol Sci 2021; 22:ijms22020845. [PMID: 33467726 PMCID: PMC7829982 DOI: 10.3390/ijms22020845] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 12/12/2022] Open
Abstract
Mesenchymal stem cells (MSCs) have the potential to be a viable therapy against various diseases due to their paracrine effects, such as secretion of immunomodulatory, trophic and protective factors. These cells are known to be distributed within various organs and tissues. Although they possess the same characteristics, MSCs from different sources are believed to have different secretion potentials and patterns, which may influence their therapeutic effects in disease environments. We characterized the protein secretome of adipose (AD), bone marrow (BM), placenta (PL), and Wharton’s jelly (WJ)-derived human MSCs by using conditioned media and analyzing the secretome by mass spectrometry and follow-up bioinformatics. Each MSC secretome profile had distinct characteristics depending on the source. However, the functional analyses of the secretome from different sources showed that they share similar characteristics, such as cell migration and negative regulation of programmed cell death, even though differences in the composition of the secretome exist. This study shows that the secretome of fetal-derived MSCs, such as PL and WJ, had a more diverse composition than that of AD and BM-derived MSCs, and it was assumed that their therapeutic potential was greater because of these properties.
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Affiliation(s)
- Sungho Shin
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Korea; (S.S.); (Y.K.)
- KHU-KIST Department of Converging Science and Technology, Kyung Hee University, Seoul 02447, Korea;
| | - Jeongmin Lee
- Stem Cell & Regenerative Medicine Institute, Samsung Medical Center, Seoul 06351, Korea;
- R&D Center, ENCell Co., Ltd., Seoul 06351, Korea
| | - Yumi Kwon
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Korea; (S.S.); (Y.K.)
| | - Kang-Sik Park
- KHU-KIST Department of Converging Science and Technology, Kyung Hee University, Seoul 02447, Korea;
- Department of Physiology, School of Medicine, Kyung Hee University, Seoul 02447, Korea
| | - Jae-Hoon Jeong
- Division of Radiation Cancer Research, Korea Institute of Radiological and Medical Sciences, Seoul 01812, Korea;
| | - Suk-Joo Choi
- Department of Obstetrics and Gynecology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea;
| | - Sa Ik Bang
- Department of Plastic Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea;
| | - Jong Wook Chang
- Stem Cell & Regenerative Medicine Institute, Samsung Medical Center, Seoul 06351, Korea;
- R&D Center, ENCell Co., Ltd., Seoul 06351, Korea
- Correspondence: (J.W.C.); (C.L.)
| | - Cheolju Lee
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Korea; (S.S.); (Y.K.)
- KHU-KIST Department of Converging Science and Technology, Kyung Hee University, Seoul 02447, Korea;
- Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Korea
- Correspondence: (J.W.C.); (C.L.)
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100
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Duan S, Li H, Zhang Y, Yang S, Chen Y, Qiu B, Huang C, Wang J, Li J, Zhu X, Yan X. Rabl2 GTP hydrolysis licenses BBSome-mediated export to fine-tune ciliary signaling. EMBO J 2021; 40:e105499. [PMID: 33241915 PMCID: PMC7809784 DOI: 10.15252/embj.2020105499] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 10/19/2020] [Accepted: 10/23/2020] [Indexed: 01/04/2023] Open
Abstract
Cilia of higher animals sense various environmental stimuli. Proper ciliary signaling requires appropriate extent of BBSome-mediated export of membrane receptors across ciliary barrier transition zone (TZ) through retrograde intraflagellar transport (IFT) machinery. How the barrier passage is controlled, however, remains unknown. Here, we show that small GTPase Rabl2 functions as a molecular switch for the outward TZ passage. Rabl2-GTP enters cilia by binding to IFT-B complex. Its GTP hydrolysis enables the outward TZ passage of the BBSome and its cargos with retrograde IFT machinery, whereas its persistent association leads to their shedding from IFT-B during the passing process and consequently ciliary retention. Rabl2 deficiency or expression of a GTP-locked mutant impairs the ciliary hedgehog signaling without interfering with ciliation and respectively results in different spectrums of mouse developmental disorders. We propose that the switch role of Rabl2 ensures proper turnover of the BBSome and ciliary membrane receptors to fine-tune cilia-dependent signaling for normal embryonic development and organismic homeostasis.
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Affiliation(s)
- Shichao Duan
- State Key Laboratory of Cell BiologyShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- Department of PathologyFirst Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Hao Li
- State Key Laboratory of Cell BiologyShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yirong Zhang
- State Key Laboratory of Cell BiologyShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Suming Yang
- State Key Laboratory of Cell BiologyShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yawen Chen
- State Key Laboratory of Cell BiologyShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Benhua Qiu
- State Key Laboratory of Cell BiologyShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Cheng Huang
- State Key Laboratory of Cell BiologyShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Juan Wang
- State Key Laboratory of Cell BiologyShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jinsong Li
- State Key Laboratory of Cell BiologyShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xueliang Zhu
- State Key Laboratory of Cell BiologyShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- School of Life ScienceHangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhouChina
| | - Xiumin Yan
- State Key Laboratory of Cell BiologyShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghaiChina
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