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Chang R, Chang C, Cai Y, Liao R. An efficient, amine-specific iTRAQ labeling method improves the peptide and protein identification rates. J Proteomics 2024; 305:105244. [PMID: 38942233 DOI: 10.1016/j.jprot.2024.105244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/21/2024] [Accepted: 06/25/2024] [Indexed: 06/30/2024]
Abstract
Isotope tags for relative and absolute quantification (iTRAQ) are among the most widely used proteomics quantification techniques. These tags can be rapidly coupled to the primary amines of proteins/peptides through chemical reactions under mild conditions, making this technique universally applicable to any kind of sample. However, iTRAQ reagents also partially react with the hydroxyl groups of serine, threonine and tyrosine residues, particularly when these residues coexist with a histidine residue in the same peptide. This overlabeling of peptides causes systematic biases and significantly compromises protein/peptide identification rates. In this study, we report a novel iTRAQ labeling method that overcomes the detrimental overlabeling while providing high amine labeling efficiency. The impacts of reaction temperature, reactant concentrations, reaction time, buffer compositions, and pH on iTRAQ labeling performance were investigated in-depth. In a comparison experiment between our method and the standard labeling method provided by the iTRAQ manufacturer, our method reduced the number of overlabeled peptides by 55-fold while achieving comparable amine labeling efficiency. This improvement allowed our method to eliminates the systematic bias against histidyl- and hydroxyl-containing peptides, and more importantly, enabled the identification of 23.9% more peptides and 9.8% more proteins. SIGNIFICANCE: In addition to amines, the hydroxyl groups in serine, threonine, and tyrosine residues can also partially labeled by iTRAQ reagents, which leads to systematic biases and significantly compromises the analytical sensitivity. To address this issue, we developed a novel iTRAQ labeling method that overcomes the detrimental overlabeling while providing high labeling efficiency of amines. When benchmarking our method against the standard method provided by the reagent manufacturer, our method achieved comparable labeling efficiency but reduced the overlabeled species by 55-fold. This significant improvement eliminated the systematic biases, and more importantly, enabled the identification of 23.9% more peptides and 9.8% more proteins, demonstrating its superior performance and potential to enhance proteome quantification using iTRAQ labeling.
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Affiliation(s)
- Ruomeng Chang
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
| | - Chenchen Chang
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
| | - Yan Cai
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
| | - Rijing Liao
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China.
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2
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Plouviez M, Dubreucq E. Key Proteomics Tools for Fundamental and Applied Microalgal Research. Proteomes 2024; 12:13. [PMID: 38651372 PMCID: PMC11036299 DOI: 10.3390/proteomes12020013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 03/28/2024] [Accepted: 04/02/2024] [Indexed: 04/25/2024] Open
Abstract
Microscopic, photosynthetic prokaryotes and eukaryotes, collectively referred to as microalgae, are widely studied to improve our understanding of key metabolic pathways (e.g., photosynthesis) and for the development of biotechnological applications. Omics technologies, which are now common tools in biological research, have been shown to be critical in microalgal research. In the past decade, significant technological advancements have allowed omics technologies to become more affordable and efficient, with huge datasets being generated. In particular, where studies focused on a single or few proteins decades ago, it is now possible to study the whole proteome of a microalgae. The development of mass spectrometry-based methods has provided this leap forward with the high-throughput identification and quantification of proteins. This review specifically provides an overview of the use of proteomics in fundamental (e.g., photosynthesis) and applied (e.g., lipid production for biofuel) microalgal research, and presents future research directions in this field.
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Affiliation(s)
- Maxence Plouviez
- School of Agriculture and Environment, Massey University, Palmerston North 4410, New Zealand
- The Cawthron Institute, Nelson 7010, New Zealand
| | - Eric Dubreucq
- Agropolymer Engineering and Emerging Technologies, L’Institut Agro Montpellier, 34060 Montpellier, France;
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3
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Bohn T, Balbuena E, Ulus H, Iddir M, Wang G, Crook N, Eroglu A. Carotenoids in Health as Studied by Omics-Related Endpoints. Adv Nutr 2023; 14:1538-1578. [PMID: 37678712 PMCID: PMC10721521 DOI: 10.1016/j.advnut.2023.09.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/25/2023] [Accepted: 09/01/2023] [Indexed: 09/09/2023] Open
Abstract
Carotenoids have been associated with risk reduction for several chronic diseases, including the association of their dietary intake/circulating levels with reduced incidence of obesity, type 2 diabetes, certain types of cancer, and even lower total mortality. In addition to some carotenoids constituting vitamin A precursors, they are implicated in potential antioxidant effects and pathways related to inflammation and oxidative stress, including transcription factors such as nuclear factor κB and nuclear factor erythroid 2-related factor 2. Carotenoids and metabolites may also interact with nuclear receptors, mainly retinoic acid receptor/retinoid X receptor and peroxisome proliferator-activated receptors, which play a role in the immune system and cellular differentiation. Therefore, a large number of downstream targets are likely influenced by carotenoids, including but not limited to genes and proteins implicated in oxidative stress and inflammation, antioxidation, and cellular differentiation processes. Furthermore, recent studies also propose an association between carotenoid intake and gut microbiota. While all these endpoints could be individually assessed, a more complete/integrative way to determine a multitude of health-related aspects of carotenoids includes (multi)omics-related techniques, especially transcriptomics, proteomics, lipidomics, and metabolomics, as well as metagenomics, measured in a variety of biospecimens including plasma, urine, stool, white blood cells, or other tissue cellular extracts. In this review, we highlight the use of omics technologies to assess health-related effects of carotenoids in mammalian organisms and models.
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Affiliation(s)
- Torsten Bohn
- Nutrition and Health Research Group, Department of Precision Health, Luxembourg Institute of Health, Strassen, Luxembourg.
| | - Emilio Balbuena
- Department of Molecular and Structural Biochemistry, College of Agriculture and Life Sciences, North Carolina State University, Raleigh, NC, United States; Plants for Human Health Institute, North Carolina Research Campus, North Carolina State University, Kannapolis, NC, United States
| | - Hande Ulus
- Plants for Human Health Institute, North Carolina Research Campus, North Carolina State University, Kannapolis, NC, United States
| | - Mohammed Iddir
- Nutrition and Health Research Group, Department of Precision Health, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Genan Wang
- Department of Chemical and Biomolecular Engineering, College of Engineering, North Carolina State University, Raleigh, NC, United States
| | - Nathan Crook
- Department of Chemical and Biomolecular Engineering, College of Engineering, North Carolina State University, Raleigh, NC, United States
| | - Abdulkerim Eroglu
- Department of Molecular and Structural Biochemistry, College of Agriculture and Life Sciences, North Carolina State University, Raleigh, NC, United States; Plants for Human Health Institute, North Carolina Research Campus, North Carolina State University, Kannapolis, NC, United States.
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4
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Olanrewaju GO, Kruse CPS, Wyatt SE. Functional Meta-Analysis of the Proteomic Responses of Arabidopsis Seedlings to the Spaceflight Environment Reveals Multi-Dimensional Sources of Variability across Spaceflight Experiments. Int J Mol Sci 2023; 24:14425. [PMID: 37833871 PMCID: PMC10573023 DOI: 10.3390/ijms241914425] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/14/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
The human quest for sustainable habitation of extraterrestrial environments necessitates a robust understanding of life's adaptability to the unique conditions of spaceflight. This study provides a comprehensive proteomic dissection of the Arabidopsis plant's responses to the spaceflight environment through a meta-analysis of proteomics data from four separate spaceflight experiments conducted on the International Space Station (ISS) in different hardware configurations. Raw proteomics LC/MS spectra were analyzed for differential expression in MaxQuant and Perseus software. The analysis of dissimilarities among the datasets reveals the multidimensional nature of plant proteomic responses to spaceflight, impacted by variables such as spaceflight hardware, seedling age, lighting conditions, and proteomic quantification techniques. By contrasting datasets that varied in light exposure, we elucidated proteins involved in photomorphogenesis and skotomorphogenesis in plant spaceflight responses. Additionally, with data from an onboard 1 g control experiment, we isolated proteins that specifically respond to the microgravity environment and those that respond to other spaceflight conditions. This study identified proteins and associated metabolic pathways that are consistently impacted across the datasets. Notably, these shared proteins were associated with critical metabolic functions, including carbon metabolism, glycolysis, gluconeogenesis, and amino acid biosynthesis, underscoring their potential significance in Arabidopsis' spaceflight adaptation mechanisms and informing strategies for successful space farming.
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Affiliation(s)
- Gbolaga O. Olanrewaju
- Molecular and Cellular Biology Program, Ohio University, Athens, OH 45701, USA;
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA
| | - Colin P. S. Kruse
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM 87545, USA;
| | - Sarah E. Wyatt
- Molecular and Cellular Biology Program, Ohio University, Athens, OH 45701, USA;
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA
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5
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Zhao X, Xie E. Reclaimed water influences bacterioplankton and bacteriobenthos communities differently in river networks. WATER RESEARCH 2023; 243:120389. [PMID: 37494747 DOI: 10.1016/j.watres.2023.120389] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/19/2023] [Indexed: 07/28/2023]
Abstract
Reclaimed water reuse is a promising strategy for addressing water scarcity; however, its potential ecological impact remains largely unknown. In particular, the differential effects of reclaimed water on microbial communities in various habitats remain poorly understood. Here, we aimed to elucidate the distinct effects of reclaimed water on bacterioplankton and bacteriobenthos communities in reclaimed water-receiving river networks from multiple perspectives, including community structure, co-occurrence patterns, assembly mechanisms, and nitrogen cycle function. Significant differences in microbial composition were observed between the plankton and benthic habitats, and the average numbers of amplicon sequence variants (ASVs) that originated from the wastewater treatment plants (WWTP) sites were 310.0 and 613.3, respectively, indicating a stronger association between WWTP and benthic habitats. Random forest and network co-occurrence analyses identified the genus Clostridium_sensu_stricto as a biomarker and key module hub. The assembly of bacteriobenthos communities was driven primarily by deterministic processes (58.74% for River-S and 58.94% for WWTP-S), whereas for bacterioplankton communities, this proportion was reduced to 18.02% (River-W) and 19.09% (WWTP-W). The qPCR revealed a large difference in abundance between the N cycling related genes of bacteriobenthos (average 2.47 × 106 copies/ng) and bacterioplankton (average 3.11 × 103 copies/ng) communities, and different interaction patterns with functional genes. Variance partitioning analysis (VPA) indicated that nitrogen was the most important pollutant, affecting the structure and ecological functions of microbial communities. Moreover, pathway analysis suggested that the reuse of reclaimed water may have enhanced the N-cycling functions of microbial communities and the emission of nitrous oxide.
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Affiliation(s)
- Xiaohui Zhao
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing 100038, PR China; Department of Water Ecology and Environment, China Institute of Water Resources and Hydropower Research, Beijing 100038, PR China
| | - En Xie
- College of Water Resources and Civil Engineering, China Agricultural University, 17 Qinghua Donglu, Beijing 100083, PR China; Engineering Research Center of Agricultural Water-Saving and Water Resources, Ministry of Education, China Agricultural University, Beijing 100083, PR China.
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6
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Yan M, Zheng H, Yan R, Lang L, Wang Q, Xiao B, Zhang D, Lin H, Jia Y, Pan S, Chen Q. Vinculin Identified as a Potential Biomarker in Hand-Arm Vibration Syndrome Based on iTRAQ and LC-MS/MS-Based Proteomic Analysis. J Proteome Res 2023; 22:2714-2726. [PMID: 37437295 PMCID: PMC10408646 DOI: 10.1021/acs.jproteome.3c00277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Indexed: 07/14/2023]
Abstract
Local vibration can induce vascular injuries, one example is the hand-arm vibration syndrome (HAVS) caused by hand-transmitted vibration (HTV). Little is known about the molecular mechanism of HAVS-induced vascular injuries. Herein, the iTRAQ (isobaric tags for relative and absolute quantitation) followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomics approach was applied to conduct the quantitative proteomic analysis of plasma from specimens with HTV exposure or HAVS diagnosis. Overall, 726 proteins were identified in iTRAQ. 37 proteins upregulated and 43 downregulated in HAVS. Moreover, 37 upregulated and 40 downregulated when comparing severe HAVS and mild HAVS. Among them, Vinculin (VCL) was found to be downregulated in the whole process of HAVS. The concentration of vinculin was further verified by ELISA, and the results suggested that the proteomics data was reliable. Bioinformative analyses were used, and those proteins mainly engaged in specific biological processes like binding, focal adhesion, and integrins. The potential of vinculin application in HAVS diagnosis was validated by the receiver operating characteristic curve.
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Affiliation(s)
- Maosheng Yan
- Guangdong
Province Hospital for Occupational Disease Prevention and Treatment, Guangdong Provincial Key Laboratory of Occupational
Disease Prevention and Treatment, Guangzhou, Guangdong 510230, China
- Department
of Public Health, Guangzhou Medical University, Guangzhou, Guangdong 510000, China
| | - Hanjun Zheng
- Guangdong
Province Hospital for Occupational Disease Prevention and Treatment, Guangdong Provincial Key Laboratory of Occupational
Disease Prevention and Treatment, Guangzhou, Guangdong 510230, China
- Department
of Public Health, Guangzhou Medical University, Guangzhou, Guangdong 510000, China
| | - Rong Yan
- The
Centers for Disease Control and Prevention of Haizhu District, Guangzhou, Guangdong 510230, China
| | - Li Lang
- Guangdong
Province Hospital for Occupational Disease Prevention and Treatment, Guangdong Provincial Key Laboratory of Occupational
Disease Prevention and Treatment, Guangzhou, Guangdong 510230, China
| | - Qia Wang
- Guangdong
Province Hospital for Occupational Disease Prevention and Treatment, Guangdong Provincial Key Laboratory of Occupational
Disease Prevention and Treatment, Guangzhou, Guangdong 510230, China
| | - Bin Xiao
- Guangdong
Province Hospital for Occupational Disease Prevention and Treatment, Guangdong Provincial Key Laboratory of Occupational
Disease Prevention and Treatment, Guangzhou, Guangdong 510230, China
| | - Danying Zhang
- Guangdong
Province Hospital for Occupational Disease Prevention and Treatment, Guangdong Provincial Key Laboratory of Occupational
Disease Prevention and Treatment, Guangzhou, Guangdong 510230, China
| | - Hansheng Lin
- Guangdong
Province Hospital for Occupational Disease Prevention and Treatment, Guangdong Provincial Key Laboratory of Occupational
Disease Prevention and Treatment, Guangzhou, Guangdong 510230, China
| | - Yanxia Jia
- Department
of Public Health, Shanxi Medical University, Tai Yuan, Shanxi 030000, China
| | - Siyu Pan
- Guangdong
Province Hospital for Occupational Disease Prevention and Treatment, Guangdong Provincial Key Laboratory of Occupational
Disease Prevention and Treatment, Guangzhou, Guangdong 510230, China
- Department
of Public Health, Guangdong Pharmaceutical
University, Guangzhou, Guangdong 510230, China
| | - Qingsong Chen
- Department
of Public Health, Guangdong Pharmaceutical
University, Guangzhou, Guangdong 510230, China
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7
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Révész Á, Hevér H, Steckel A, Schlosser G, Szabó D, Vékey K, Drahos L. Collision energies: Optimization strategies for bottom-up proteomics. MASS SPECTROMETRY REVIEWS 2023; 42:1261-1299. [PMID: 34859467 DOI: 10.1002/mas.21763] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 11/17/2021] [Accepted: 11/17/2021] [Indexed: 06/07/2023]
Abstract
Mass-spectrometry coupled to liquid chromatography is an indispensable tool in the field of proteomics. In the last decades, more and more complex and diverse biochemical and biomedical questions have arisen. Problems to be solved involve protein identification, quantitative analysis, screening of low abundance modifications, handling matrix effect, and concentrations differing by orders of magnitude. This led the development of more tailored protocols and problem centered proteomics workflows, including advanced choice of experimental parameters. In the most widespread bottom-up approach, the choice of collision energy in tandem mass spectrometric experiments has outstanding role. This review presents the collision energy optimization strategies in the field of proteomics which can help fully exploit the potential of MS based proteomics techniques. A systematic collection of use case studies is then presented to serve as a starting point for related further scientific work. Finally, this article discusses the issue of comparing results from different studies or obtained on different instruments, and it gives some hints on methodology transfer between laboratories based on measurement of reference species.
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Affiliation(s)
- Ágnes Révész
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Helga Hevér
- Chemical Works of Gedeon Richter Plc, Budapest, Hungary
| | - Arnold Steckel
- Department of Analytical Chemistry, MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Institute of Chemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Gitta Schlosser
- Department of Analytical Chemistry, MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Institute of Chemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Dániel Szabó
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Károly Vékey
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - László Drahos
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
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8
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Guo Y, Chowdhury T, Seshadri M, Cupp-Sutton KA, Wang Q, Yu D, Wu S. Optimization of Higher-Energy Collisional Dissociation Fragmentation Energy for Intact Protein-Level Tandem Mass Tag Labeling. J Proteome Res 2023; 22:1406-1418. [PMID: 36603205 PMCID: PMC10164041 DOI: 10.1021/acs.jproteome.2c00549] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Isobaric chemical tag labeling (e.g., TMT) is a commonly used approach in quantitative proteomics, and quantification is enabled through detection of low-mass reporter ions generated after MS2 fragmentation. Recently, we have introduced and optimized an intact protein-level TMT labeling platform that demonstrated >90% labeling efficiency in complex samples with top-down proteomics. Higher-energy collisional dissociation (HCD) is commonly utilized for isobaric tag-labeled peptide fragmentation because it produces accurate reporter ion intensities and avoids loss of low mass ions. HCD energies have been optimized for isobaric tag labeled-peptides but have not been systematically evaluated for isobaric tag-labeled intact proteins. In this study, we report a systematic evaluation of normalized HCD fragmentation energies (NCEs) on TMT-labeled HeLa cell lysate using top-down proteomics. Our results suggested that reporter ions often result in higher ion intensities at higher NCEs. Optimal fragmentation of intact proteins for identification, however, required relatively lower NCE. We further demonstrated that a stepped NCE scheme with energies from 30% to 50% resulted in optimal quantification and identification of TMT-labeled HeLa proteins. These parameters resulted in an average reporter ion intensity of ∼4E4 and average proteoform spectrum matches (PrSMs) of >1000 per RPLC-MS/MS run with a 1% false discovery rate (FDR) cutoff.
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Affiliation(s)
- Yanting Guo
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Trishika Chowdhury
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Meena Seshadri
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Kellye A Cupp-Sutton
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Qingyu Wang
- School of Meteorology, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Dahang Yu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Si Wu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
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9
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Liu P, Ye DM, Chen M, Zhang J, Huang XH, Shen LL, Xia KK, Xu XJ, Xu YC, Guo YL, Wang YC, Huang F. Scaling-up and proteomic analysis reveals photosynthetic and metabolic insights toward prolonged H 2 photoproduction in Chlamydomonas hpm91 mutant lacking proton gradient regulation 5 (PGR5). PHOTOSYNTHESIS RESEARCH 2022; 154:397-411. [PMID: 35974136 PMCID: PMC9722884 DOI: 10.1007/s11120-022-00945-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
Clean and sustainable H2 production is crucial to a carbon-neutral world. H2 generation by Chlamydomonas reinhardtii is an attractive approach for solar-H2 from H2O. However, it is currently not large-scalable because of lacking desirable strains with both optimal H2 productivity and sufficient knowledge of underlying molecular mechanism. We hereby carried out extensive and in-depth investigations of H2 photoproduction of hpm91 mutant lacking PGR5 (Proton Gradient Regulation 5) toward its up-scaling and fundamental mechanism issues. We show that hpm91 is at least 100-fold scalable (up to 10 L) with continuous H2 collection of 7287 ml H2/10L-HPBR in averagely 26 days under sulfur deprivation. Also, we show that hpm91 is robust and active during sustained H2 photoproduction, most likely due to decreased intracellular ROS relative to wild type. Moreover, we obtained quantitative proteomic profiles of wild type and hpm91 at four representing time points of H2 evolution, leading to 2229 and 1350 differentially expressed proteins, respectively. Compared to wild type, major proteome alterations of hpm91 include not only core subunits of photosystems and those related to anti-oxidative responses but also essential proteins in photosynthetic antenna, C/N metabolic balance, and sulfur assimilation toward both cysteine biosynthesis and sulfation of metabolites during sulfur-deprived H2 production. These results reveal not only new insights of cellular and molecular basis of enhanced H2 production in hpm91 but also provide additional candidate gene targets and modules for further genetic modifications and/or in artificial photosynthesis mimics toward basic and applied research aiming at advancing solar-H2 technology.
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Affiliation(s)
- Peng Liu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - De-Min Ye
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mei Chen
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jin Zhang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xia-He Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Li-Li Shen
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ke-Ke Xia
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Xiao-Jing Xu
- BGI-Shenzhen, Shenzhen, 518083, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yong-Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ya-Long Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Ying-Chun Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Fang Huang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
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10
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Immunoreactivity Profiling of Anti-Chinese Hamster Ovarian Host Cell Protein Antibodies by Isobaric Labeled Affinity Purification-Mass Spectrometry Reveals Low-Recovery Proteins. J Chromatogr A 2022; 1685:463645. [DOI: 10.1016/j.chroma.2022.463645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 11/13/2022]
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11
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Li H, Wan B, Jiang D, Ji P, Zhao M, Li X, Li R, Qiao S. Proteomic Investigation Reveals Eukaryotic Translation Initiation Factor 5A Involvement in Porcine Reproductive and Respiratory Syndrome Virus Infection in vitro. Front Vet Sci 2022; 9:861137. [PMID: 35498732 PMCID: PMC9043857 DOI: 10.3389/fvets.2022.861137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/18/2022] [Indexed: 12/05/2022] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV), one of the most serious animal pathogens in the world, has caused enormous global swine industry losses. An in-depth investigation of the PRRSV-host interaction would be beneficial for preventing and controlling PRRSV infections and transmission. In this study, we performed label-free quantitative proteomic assays to investigate proteome dynamics of porcine alveolar macrophages (PAMs) during infection with highly pathogenic PRRSV (HP-PRRSV) strain HN07-1. Analysis of the results led to identification of 269 significantly differentially expressed host cellular proteins, of which levels of proteins belonging to the eukaryotic translation initiation factor (eIF) family were found to be decreased in abundance in HP-PRRSV-infected PAMs. Furthermore, knockdown of eIF5A expression was demonstrated to markedly suppress HP-PRRSV propagation, as reflected by reduced progeny virus titers in vitro. These results highlight the importance of eIF5A in PRRSV infection, while also demonstrating that PAMs down-regulate eIF5A expression as a host cell antiviral strategy. Results of the current study deepen our understanding of PRRSV pathogenesis and provide novel insights to guide development of effective strategies to combat the virus.
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Affiliation(s)
- Huawei Li
- Henan Key Laboratory of Innovation and Utilization of Unconventional Feed Resources, Henan University of Animal Husbandry and Economy, Zhengzhou, China
| | - Bo Wan
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Dawei Jiang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Pengchao Ji
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Mengmeng Zhao
- School of Life Science and Engineering, Foshan University, Foshan, China
| | - Xinfeng Li
- Henan Key Laboratory of Innovation and Utilization of Unconventional Feed Resources, Henan University of Animal Husbandry and Economy, Zhengzhou, China
| | - Rui Li
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China
- *Correspondence: Rui Li
| | - Songlin Qiao
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China
- Songlin Qiao
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12
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Cruz Villarreal J, Kruithoff R, Egatz-Gomez A, Coleman PD, Ros R, Sandrin TR, Ros A. MIMAS: microfluidic platform in tandem with MALDI mass spectrometry for protein quantification from small cell ensembles. Anal Bioanal Chem 2022; 414:3945-3958. [PMID: 35385983 PMCID: PMC9188328 DOI: 10.1007/s00216-022-04038-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 11/26/2022]
Abstract
Understanding cell-to-cell variation at the molecular level provides relevant information about biological phenomena and is critical for clinical and biological research. Proteins carry important information not available from single-cell genomics and transcriptomics studies; however, due to the minute amount of proteins in single cells and the complexity of the proteome, quantitative protein analysis at the single-cell level remains challenging. Here, we report an integrated microfluidic platform in tandem with matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) for the detection and quantification of targeted proteins from small cell ensembles (> 10 cells). All necessary steps for the assay are integrated on-chip including cell lysis, protein immunocapture, tryptic digestion, and co-crystallization with the matrix solution for MALDI-MS analysis. We demonstrate that our approach is suitable for protein quantification by assessing the apoptotic protein Bcl-2 released from MCF-7 breast cancer cells, ranging from 26 to 223 cells lysed on-chip (8.75 nL wells). A limit of detection (LOD) of 11.22 nM was determined, equivalent to 5.91 × 107 protein molecules per well. Additionally, the microfluidic platform design was further improved, establishing the successful quantification of Bcl-2 protein from MCF-7 cell ensembles ranging from 8 to 19 cells in 4 nL wells. The LOD in the smaller well designs for Bcl-2 resulted in 14.85 nM, equivalent to 3.57 × 107 protein molecules per well. This work shows the capability of our approach to quantitatively assess proteins from cell lysate on the MIMAS platform for the first time. These results demonstrate our approach constitutes a promising tool for quantitative targeted protein analysis from small cell ensembles down to single cells, with the capability for multiplexing through parallelization and automation.
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Affiliation(s)
- Jorvani Cruz Villarreal
- School of Molecular Sciences, Arizona State University, Temple, AZ, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Rory Kruithoff
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ, USA
| | - Ana Egatz-Gomez
- School of Molecular Sciences, Arizona State University, Temple, AZ, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Paul D Coleman
- School of Life Sciences, Arizona State University, Temple, AZ, USA
- ASU-Banner Neurodegenerative Research Center, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Robert Ros
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ, USA
- Center for Single Molecule Biophysics, The Biodesign Institute, Arizona State University, Temple, AZ, USA
| | - Todd R Sandrin
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, AZ, USA
- Julie Ann Wrigley Global Futures Laboratory, Arizona State University, Tempe, AZ, USA
| | - Alexandra Ros
- School of Molecular Sciences, Arizona State University, Temple, AZ, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, USA.
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13
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Qian C, Huang M, Du Y, Song J, Mu H, Wei Y, Zhang S, Yin Z, Yuan C, Liu B, Liu B. Chemotaxis and Shorter O-Antigen Chain Length Contribute to the Strong Desiccation Tolerance of a Food-Isolated Cronobacter sakazakii Strain. Front Microbiol 2022; 12:779538. [PMID: 35058898 PMCID: PMC8764414 DOI: 10.3389/fmicb.2021.779538] [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: 09/19/2021] [Accepted: 11/18/2021] [Indexed: 12/02/2022] Open
Abstract
Cronobacter sakazakii is an opportunistic pathogen causing a lethality rate as high as 80% in infants. Desiccation tolerance ensures its survival in powdered infant formula (PIF) and contributes to the increased exposure to neonates, resulting in neonatal meningitis, septicemia, and necrotizing enterocolitis. This study showed that a food-isolated C. sakazakii G4023 strain exhibited a stronger desiccation tolerance than C. sakazakii ATCC 29544 strain. Considering the proven pathogenicity of G4023, it could be a big threat to infants. Transcriptome and proteome were performed to provide new insights into the desiccation adaptation mechanisms of G4023. Integrated analyses of these omics suggested that 331 genes were found regulated at both transcriptional and protein levels (≥2.0- and ≥1.5-fold, respectively). Deletion of chemotaxis system encoded genes cheA and cheW resulted in decreased tolerance in both short- and long-term desiccation. Reduced O-antigen chain length contributed to the biofilm formation and desiccation tolerance in the short term rather than the long term. In addition, biosynthesis of flagella, arginine and its transport system, and Fe/S cluster were also observed regulated in desiccated G4023. A better understanding of desiccation adaptation mechanisms of G4023 could in turn guide the operations during production and preservation of PIF or other food to reduce survival odds of G4023 and lower its exposure to get to infants.
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Affiliation(s)
- Chengqian Qian
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Min Huang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Yuhui Du
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, Beijing, China
| | - Jingjie Song
- Shenzhen Institute of Respiratory Diseases, The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
| | - Huiqian Mu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Yi Wei
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Si Zhang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Zhiqiu Yin
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Tai'an, China
| | - Chao Yuan
- Department of Sanitary Toxicology and Chemistry, School of Public Health, Tianjin Medical University, Tianjin, China
| | - Bin Liu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Bin Liu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China.,The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, China.,Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, China
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14
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Proteomic analysis of extracellular vesicles enriched serum associated with future ischemic stroke. Sci Rep 2021; 11:24024. [PMID: 34912031 PMCID: PMC8674262 DOI: 10.1038/s41598-021-03497-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 12/06/2021] [Indexed: 11/15/2022] Open
Abstract
Identifying new biomarkers beyond the established risk factors that make it possible to predict and prevent ischemic stroke has great significance. Extracellular vesicles are powerful cell‒cell messengers, containing disease-specific biomolecules, which makes them powerful diagnostic candidates. Therefore, this study aimed to identify proteins derived from extracellular vesicles enriched serum related to future ischemic stroke events, using a proteomic method. Of Japanese subjects who voluntarily participated in health checkups at our institute a number of times, 10 subjects (6 males and 4 females, age: 64.2 ± 3.9 years) who developed symptomatic ischemic stroke (7.3 ± 4.4 years’ follow-up) and 10 age‒sex matched controls without brain lesions (6.7 ± 2.8 years’ follow-up) were investigated. Extracellular vesicles enriched fractions were derived from serum collected at the baseline visit. Differentially expressed proteins were evaluated using isobaric tagging for relative and absolute protein quantification (iTRAQ)-based proteomic analysis. Of the 29 proteins identified, alpha-2-macroglobulin, complement C1q subcomponent subunit B, complement C1r subcomponent, and histidine-rich glycoprotein were significantly upregulated (2.21-, 2.15-, 2.24-, and 2.16-fold, respectively) in subjects with future ischemic stroke, as compared with controls. Our study supports the concept of serum-derived extracellular vesicles enriched fractions as biomarkers for new-onset stroke. These proteins may be useful for prediction or for targeted therapy.
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Wojtkiewicz M, Berg Luecke L, Castro C, Burkovetskaya M, Mesidor R, Gundry RL. Bottom-up proteomic analysis of human adult cardiac tissue and isolated cardiomyocytes. J Mol Cell Cardiol 2021; 162:20-31. [PMID: 34437879 PMCID: PMC9620472 DOI: 10.1016/j.yjmcc.2021.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 07/07/2021] [Accepted: 08/04/2021] [Indexed: 12/30/2022]
Abstract
The heart is composed of multiple cell types, each with a specific function. Cell-type-specific approaches are necessary for defining the intricate molecular mechanisms underlying cardiac development, homeostasis, and pathology. While single-cell RNA-seq studies are beginning to define the chamber-specific cellular composition of the heart, our views of the proteome are more limited because most proteomics studies have utilized homogenized human cardiac tissue. To promote future cell-type specific analyses of the human heart, we describe the first method for cardiomyocyte isolation from cryopreserved human cardiac tissue followed by flow cytometry for purity assessment. We also describe a facile method for preparing isolated cardiomyocytes and whole cardiac tissue homogenate for bottom-up proteomic analyses. Prior experience in dissociating cardiac tissue or proteomics is not required to execute these methods. We compare different sample preparation workflows and analysis methods to demonstrate how these can impact the depth of proteome coverage achieved. We expect this how-to guide will serve as a starting point for investigators interested in general and cell-type-specific views of the cardiac proteome.
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Affiliation(s)
- Melinda Wojtkiewicz
- CardiOmics Program, Center for Heart and Vascular Research, Division of Cardiovascular Medicine, Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Linda Berg Luecke
- CardiOmics Program, Center for Heart and Vascular Research, Division of Cardiovascular Medicine, Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE 68198, USA; Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Chase Castro
- CardiOmics Program, Center for Heart and Vascular Research, Division of Cardiovascular Medicine, Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Maria Burkovetskaya
- CardiOmics Program, Center for Heart and Vascular Research, Division of Cardiovascular Medicine, Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Roneldine Mesidor
- CardiOmics Program, Center for Heart and Vascular Research, Division of Cardiovascular Medicine, Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Rebekah L Gundry
- CardiOmics Program, Center for Heart and Vascular Research, Division of Cardiovascular Medicine, Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE 68198, USA.
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16
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Sadecki PW, Balboa SJ, Lopez LR, Kedziora KM, Arthur JC, Hicks LM. Evolution of Polymyxin Resistance Regulates Colibactin Production in Escherichia coli. ACS Chem Biol 2021; 16:1243-1254. [PMID: 34232632 PMCID: PMC8601121 DOI: 10.1021/acschembio.1c00322] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The complex reservoir of metabolite-producing bacteria in the gastrointestinal tract contributes tremendously to human health and disease. Bacterial composition, and by extension gut metabolomic composition, is undoubtably influenced by the use of modern antibiotics. Herein, we demonstrate that polymyxin B, a last resort antibiotic, influences the production of the genotoxic metabolite colibactin from adherent-invasive Escherichia coli (AIEC) NC101. Colibactin can promote colorectal cancer through DNA double stranded breaks and interstrand cross-links. While the structure and biosynthesis of colibactin have been elucidated, chemical-induced regulation of its biosynthetic gene cluster and subsequent production of the genotoxin by E. coli are largely unexplored. Using a multiomic approach, we identified that polymyxin B stress enhances the abundance of colibactin biosynthesis proteins (Clb's) in multiple pks+ E. coli strains, including pro-carcinogenic AIEC, NC101; the probiotic strain, Nissle 1917; and the antibiotic testing strain, ATCC 25922. Expression analysis via qPCR revealed that increased transcription of clb genes likely contributes to elevated Clb protein levels in NC101. Enhanced production of Clb's by NC101 under polymyxin stress matched an increased production of the colibactin prodrug motif, a proxy for the mature genotoxic metabolite. Furthermore, E. coli with a heightened tolerance for polymyxin induced greater mammalian DNA damage, assessed by quantification of γH2AX staining in cultured intestinal epithelial cells. This study establishes a key link between the polymyxin B stress response and colibactin production in pks+ E. coli. Ultimately, our findings will inform future studies investigating colibactin regulation and the ability of seemingly innocuous commensal microbes to induce host disease.
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Affiliation(s)
- Patric W. Sadecki
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Samantha J. Balboa
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Lacey R. Lopez
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Katarzyna M. Kedziora
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Bioinformatics and Analytics Research Collaborative (BARC), University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Janelle C. Arthur
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Leslie M. Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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17
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Liao DJ, Cheng XP, Li N, Liang KL, Fan H, Zhang SY, Hu XQ, Fan P, Wu YS. A Comparative Study on the Incidence, Aggravation, and Remission of Lupus Nephritis Based on iTRAQ Technology. Comb Chem High Throughput Screen 2021; 23:649-657. [PMID: 32297573 DOI: 10.2174/1386207323666200416151836] [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: 06/14/2019] [Revised: 02/24/2020] [Accepted: 03/20/2020] [Indexed: 11/22/2022]
Abstract
AIM AND OBJECTIVE Lupus nephritis (LN) is one of the major complications of systemic lupus erythematosus (SLE). The specific mechanisms of pathogenesis, aggravation, and remission processes in LN have not been clarified but is of great need in the clinic. Using isobaric tags for relative and absolute quantitation (iTRAQ) technology to screen the functional proteins of LN in mice. Especially under intervention factors of lipopolysaccharide (LPS) and dexamethasone. METHODS Mrl-lps mice were intervened with LPS, dexamethasone, and normal saline (NS) using intraperitoneal injection, and c57 mice intervened with NS as control. The anti-ANA antibody enzyme-linked immunosorbent assay (ELISA) was used to verify disease severity. Kidney tissue is collected and processed for iTRAQ to screen out functional proteins closely related to the onset and development of LN. Western blot method and rt-PCR (real-time Polymerase Chain Reaction) were used for verification. RESULTS We identified 136 proteins that marked quantitative information. Among them, Hp, Igkv8-27, Itgb2, Got2, and Pcx proteins showed significant abnormal manifestations. CONCLUSION Using iTRAQ methods, the functional proteins Hp, Igkv8-27, Itgb2, Got2, and Pcx were screened out for a close relationship with the pathogenesis and development of LN, which is worth further study.
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Affiliation(s)
- Dong-Jiang Liao
- Dermatology Department of the First Affiliated Hospital of Guangzhou Medical University, Guangdong Province, China
| | - Xi-Ping Cheng
- The First Affiliated Hospital of Guangzhou Medical University, Guangdong Province, China
| | - Nan Li
- The First Affiliated Hospital of Guangzhou Medical University, Guangdong Province, China
| | - Kang-Li Liang
- The First Affiliated Hospital of Guangzhou Medical University, Guangdong Province, China
| | - Hui Fan
- The First Affiliated Hospital of Guangzhou Medical University, Guangdong Province, China
| | - Sui-Ying Zhang
- The First Affiliated Hospital of Guangzhou Medical University, Guangdong Province, China
| | - Xiao-Qian Hu
- The First Affiliated Hospital of Guangzhou Medical University, Guangdong Province, China
| | - Ping Fan
- The First Affiliated Hospital of Guangzhou Medical University, Guangdong Province, China
| | - Yuan-Sheng Wu
- Guangdong Hospital of Traditional Chinese Medicine, Guangzhou, Guangdong Province, China
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18
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Yang M, Villarreal JC, Ariyasinghe N, Kruithoff R, Ros R, Ros A. Quantitative Approach for Protein Analysis in Small Cell Ensembles by an Integrated Microfluidic Chip with MALDI Mass Spectrometry. Anal Chem 2021; 93:6053-6061. [PMID: 33819014 PMCID: PMC8128341 DOI: 10.1021/acs.analchem.0c04112] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Increasing evidence has demonstrated that cells are individually heterogeneous. Advancing the technologies for single-cell analysis will improve our ability to characterize cells, study cell biology, design and screen drugs, and aid cancer diagnosis and treatment. Most current single-cell protein analysis approaches are based on fluorescent antibody-binding technology. However, this technology is limited by high background and cross-talk of multiple tags introduced by fluorescent labels. Stable isotope labels used in mass cytometry can overcome the spectral overlap of fluorophores. Nevertheless, the specificity of each antibody and heavy-metal-tagged antibody combination must be carefully validated to ensure detection of the intended target. Thus, novel single-cell protein analysis methods without using labels are urgently needed. Moreover, the labeling approach targets already known motifs, hampering the discovery of new biomarkers relevant to single-cell population variation. Here, we report a combined microfluidic and matrix-assisted laser desorption and ionization (MALDI) mass spectrometric approach for the analysis of protein biomarkers suitable for small cell ensembles. All necessary steps for cell analysis including cell lysis, protein capture, and digestion as well as MALDI matrix deposition are integrated on a microfluidic chip prior to the downstream MALDI-time-of-flight (TOF) detection. For proof of principle, this combined method is used to assess the amount of Bcl-2, an apoptosis regulator, in metastatic breast cancer cells (MCF-7) by using an isotope-labeled peptide as an internal standard. The proposed approach will eventually provide a new means for proteome studies in small cell ensembles with the potential for single-cell analysis and improve our ability in disease diagnosis, drug discovery, and personalized therapy.
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Affiliation(s)
- Mian Yang
- Department of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan City, Hubei Province, 430081, P.R.China
| | - Jorvani Cruz Villarreal
- School of Molecular Sciences, Arizona State University, Tempe AZ, 85287-1604, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe AZ, 85287-7401, USA
| | - Nethmi Ariyasinghe
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe AZ, 85287-1504, USA
- Center for Single Molecule Biophysics, The Biodesign Institute, Arizona State University, Tempe AZ, 85287, USA
| | - Rory Kruithoff
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe AZ, 85287-1504, USA
| | - Robert Ros
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe AZ, 85287-1504, USA
- Center for Single Molecule Biophysics, The Biodesign Institute, Arizona State University, Tempe AZ, 85287, USA
| | - Alexandra Ros
- School of Molecular Sciences, Arizona State University, Tempe AZ, 85287-1604, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe AZ, 85287-7401, USA
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19
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Zha W, You A. Comparative iTRAQ proteomic profiling of proteins associated with the adaptation of brown planthopper to moderately resistant vs. susceptible rice varieties. PLoS One 2020; 15:e0238549. [PMID: 32903256 PMCID: PMC7480849 DOI: 10.1371/journal.pone.0238549] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/18/2020] [Indexed: 02/06/2023] Open
Abstract
The brown planthopper (BPH), Nilaparvata lugens (Stål), is a destructive pest that poses a significant threat to rice plants worldwide. To explore how BPHs adapt to the resistant rice variety, we analyzed proteomics profiles of two virulent N. lugens populations. We focused on Biotype Y, which can survive on the moderately resistant rice variety YHY15, and Biotype I, which can survive on the susceptible rice variety TN1. We performed protein quantitation using the isobaric tag for relative and absolute quantification (iTRAQ) and then compared the expression patterns between two virulent N. lugens populations and found 258 differentially expressed proteins (DEPs). We found that 151 of the DEPs were up-regulated, while 107 were down-regulated. We evaluated transcript levels of 8 expressed genes from the iTRAQ results by qRT-PCR, which revealed transcriptional changes that were consistent with the changes at the protein level. The determination of the protein changes in two virulent N. lugens populations would help to better understanding BPH adaptation to resistant rice varieties and facilitate the better design of new control strategies for host defense against BPH.
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Affiliation(s)
- Wenjun Zha
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Aiqing You
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
- * E-mail:
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20
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Petrova EV, Kukarskikh GP, Krendeleva TE, Antal TK. The Mechanisms and Role of Photosynthetic Hydrogen Production by Green Microalgae. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720030169] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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21
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iTRAQ-based proteomic analysis after mesenchymal stem cell line transplantation for ischemic stroke. Brain Res 2020; 1742:146900. [PMID: 32445714 DOI: 10.1016/j.brainres.2020.146900] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 05/01/2020] [Accepted: 05/18/2020] [Indexed: 02/01/2023]
Abstract
Transplantation with mesenchymal stem cells (MSCs) has been reported to promote functional recovery in animal models of ischemic stroke. However, the molecular mechanisms underlying the therapeutic effects of MSC transplantation have been only partially elucidated. The purpose of this study was to comprehensively identify changes in brain proteins in rats treated with MSCs for ischemic stroke, and to explore the multi-target mechanisms of MSCs using a proteomics-based strategy. Twenty-eight proteins were found to be differentially expressed following B10 MSC transplantation in adult male Wistar rats, as assessed using isobaric tagging for relative and absolute protein quantification (iTRAQ). Subsequent bioinformatic analysis revealed that these proteins were mainly associated with energy metabolism, glutamate excitotoxicity, oxidative stress, and brain structural and functional plasticity. Immunohistochemical staining revealed decreased expression of EAAT1 in the phosphate-buffered saline group as opposed to normal levels in the B10 transplantation group. Furthermore, ATP levels were also significantly higher in the B10 transplantation group, thus supporting the iTRAQ results. Our results suggest that the therapeutic effects of B10 transplantation might arise from the modulation of the acute ischemic cascade via multiple molecular pathways. Thus, our findings provide valuable clues to elucidate the mechanisms underlying the therapeutic effects of MSC transplantation in ischemic stroke.
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22
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Piragasam RS, Hussain SF, Chaulk SG, Siddiqi ZA, Fahlman RP. Label-free proteomic analysis reveals large dynamic changes to the cellular proteome upon expression of the miRNA-23a-27a-24-2 microRNA cluster. Biochem Cell Biol 2020; 98:61-69. [DOI: 10.1139/bcb-2019-0014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
In deciphering the regulatory networks of gene expression controlled by the small non-coding RNAs known as microRNAs (miRNAs), a major challenge has been with the identification of the true mRNA targets by these RNAs within the context of the enormous numbers of predicted targets for each of these small RNAs. To facilitate the system-wide identification of miRNA targets, a variety of system wide methods, such as proteomics, have been implemented. Here we describe the utilization of quantitative label-free proteomics and bioinformatics to identify the most significant changes to the proteome upon expression of the miR-23a-27a-24-2 miRNA cluster. In light of recent work leading to the hypothesis that only the most pronounced regulatory events by miRNAs may be physiologically relevant, our data reveal that label-free analysis circumvents the limitations of proteomic labeling techniques that limit the maximum differences that can be quantified. The result of our analysis identifies a series of novel candidate targets that are reduced in abundance by more than an order of magnitude upon the expression of the miR-23a-27a-24-2 cluster.
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Affiliation(s)
- Ramanaguru S. Piragasam
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - S. Faraz Hussain
- Department of Medicine, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Steven G. Chaulk
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Zaeem A. Siddiqi
- Department of Medicine, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Richard P. Fahlman
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
- Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
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23
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Ford MM, Lawrence SR, Werth EG, McConnell EW, Hicks LM. Label-Free Quantitative Phosphoproteomics for Algae. Methods Mol Biol 2020; 2139:197-211. [PMID: 32462588 DOI: 10.1007/978-1-0716-0528-8_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The unicellular alga Chlamydomonas reinhardtii is a model photosynthetic organism for the study of microalgal processes. Along with genomic and transcriptomic studies, proteomic analysis of Chlamydomonas has led to an increased understanding of its metabolic signaling as well as a growing interest in the elucidation of its phosphorylation networks. To this end, mass spectrometry-based proteomics has made great strides in large-scale protein quantitation as well as analysis of posttranslational modifications (PTMs) in a high-throughput manner. An accurate quantification of dynamic PTMs, such as phosphorylation, requires high reproducibility and sensitivity due to the substoichiometric levels of modified peptides, which can make depth of coverage challenging. Here we present a method using TiO2-based phosphopeptide enrichment paired with label-free LC-MS/MS for phosphoproteome quantification. Three technical replicate samples in Chlamydomonas were processed and analyzed using this approach, quantifying a total of 1775 phosphoproteins with a total of 3595 phosphosites. With a median CV of 21% across quantified phosphopeptides, implementation of this method for differential studies provides highly reproducible analysis of phosphorylation events. While the culturing and extraction methods used are specific to facilitate coverage in algal species, this approach is widely applicable and can easily extend beyond algae to other photosynthetic organisms with minor modifications.
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Affiliation(s)
- Megan M Ford
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sheldon R Lawrence
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Emily G Werth
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Evan W McConnell
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Leslie M Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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24
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Wu JS, Liu Q, Fang SH, Liu X, Zheng M, Wang TM, Zhang H, Liu P, Zhou H, Ma YM. Quantitative Proteomics Reveals the Protective Effects of Huangqi Decoction Against Acute Cholestatic Liver Injury by Inhibiting the NF-κB/IL-6/STAT3 Signaling Pathway. J Proteome Res 2019; 19:677-687. [DOI: 10.1021/acs.jproteome.9b00563] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
| | - Qian Liu
- Department of Analytical Chemistry and CAS Key Laboratory for Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, Number 19A Yuquan Road, Beijing 100049, China
| | - Shan-Hua Fang
- Department of Analytical Chemistry and CAS Key Laboratory for Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Xing Liu
- Department of Analytical Chemistry and CAS Key Laboratory for Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | | | | | - Hua Zhang
- Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Institute of Liver Diseases, Shuguang Hospital, Shanghai 201203, China
| | - Ping Liu
- Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Institute of Liver Diseases, Shuguang Hospital, Shanghai 201203, China
| | - Hu Zhou
- Department of Analytical Chemistry and CAS Key Laboratory for Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, Number 19A Yuquan Road, Beijing 100049, China
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25
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Ran W, Wang H, Liu Y, Qi M, Xiang Q, Yao C, Zhang Y, Lan X. Storage of starch and lipids in microalgae: Biosynthesis and manipulation by nutrients. BIORESOURCE TECHNOLOGY 2019; 291:121894. [PMID: 31387839 DOI: 10.1016/j.biortech.2019.121894] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 07/22/2019] [Accepted: 07/23/2019] [Indexed: 05/28/2023]
Abstract
Microalgae accumulate starch and lipid as storage metabolites under nutrient depletion, which can be used as sustainable feedstock for biorefinery. Omics analysis coupled with enzymatic and genetic verifications uncovered a partial picture of pathways and important enzymes or regulators related to starch and lipid biosynthesis as well as the carbon partitioning between them under nutrient depletion conditions. Depletion of macronutrients (N, P, and S) resulted in considerable enhancement of starch and/or lipid content in microalgae, but the accompanying declined photosynthesis hampered the achievements of high concentrations. This review summarized the current knowledge on the pathways and the committed steps as well as their carbon allocation involved in starch and lipid biosynthesis, and focused on the manipulation of different nutrients and the alleviation of oxidative stress for enhanced storage metabolites production. The biological and engineering approaches to cope with the conflict between biomass production and storage metabolites accumulation are proposed.
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Affiliation(s)
- Wenyi Ran
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, China
| | - Haitao Wang
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, Liaoning 116034, China
| | - Yinghui Liu
- Information Management Center of Sichuan University, Chengdu, Sichuan 610065, China
| | - Man Qi
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, China
| | - Qi Xiang
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, China
| | - Changhong Yao
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, China.
| | - Yongkui Zhang
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, China
| | - Xianqiu Lan
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, China
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Deng Y, Ruan Y, Ma B, Timmons MB, Lu H, Xu X, Zhao H, Yin X. Multi-omics analysis reveals niche and fitness differences in typical denitrification microbial aggregations. ENVIRONMENT INTERNATIONAL 2019; 132:105085. [PMID: 31415965 DOI: 10.1016/j.envint.2019.105085] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/03/2019] [Accepted: 08/04/2019] [Indexed: 06/10/2023]
Abstract
Suspended floc and fixed biofilm are two commonly applied strategies for heterotrophic denitrification in wastewater treatment. These two strategies use different carbon sources and reside within different ecological niches for microbial aggregation, which were hypothesized to show distinct microbial structures and metabolic fitness. We surveyed three floc reactors and three biofilm reactors for denitrification and determined if there were distinct microbial aggregations. Multiple molecular omics approaches were used to determine the microbial community composition, co-occurrence network and metabolic pathways. Proteobacteria was the dominating and most active phylum among all samples. Carbon source played an important role in shaping the microbial community composition while the distribution of functional protein was largely influenced by salinity. We found that the topological network features had different ecological patterns and that the microorganisms in the biofilm reactors had more nodes but less interactions than those in floc reactors. The large niche differences in the biofilm reactors explained the observed high microbial diversity, functional redundancy and resulting high system stability. We also observed a lower proportion of denitrifiers and higher resistance to oxygen and salinity perturbation in the biofilm reactors than the floc reactors. Our findings support our hypothesis that niche differences caused a distinct microbial structure and increased microbial ecology distribution, which has the potential to improve system efficiency and stability.
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Affiliation(s)
- Yale Deng
- Institute of Agricultural Bio-Environmental Engineering, College of Bio-systems Engineering and Food Science, Zhejiang University, 310058 Hangzhou, China; Aquaculture and Fisheries Group, Department of Animal Sciences, Wageningen University, 6708 WD Wageningen, the Netherlands
| | - Yunjie Ruan
- Institute of Agricultural Bio-Environmental Engineering, College of Bio-systems Engineering and Food Science, Zhejiang University, 310058 Hangzhou, China; Academy of Rural Development, Zhejiang University, 310058 Hangzhou, China; Department of Biological and Environmental Engineering, Cornell University, Riley Robb Hall, Ithaca, NY 14853, USA.
| | - Bin Ma
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, 310058 Hangzhou, China
| | - Michael B Timmons
- Department of Biological and Environmental Engineering, Cornell University, Riley Robb Hall, Ithaca, NY 14853, USA
| | - Huifeng Lu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, 310058 Hangzhou, China
| | - Xiangyang Xu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, 310058 Hangzhou, China
| | - Heping Zhao
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, 310058 Hangzhou, China
| | - Xuwang Yin
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
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Zhang SZ, Wang J, Zhu LB, Toufeeq S, Xu X, You LL, Li B, Hu P, Xu JP. Quantitative label-free proteomic analysis reveals differentially expressed proteins in the digestive juice of resistant versus susceptible silkworm strains and their predicted impacts on BmNPV infection. J Proteomics 2019; 210:103527. [PMID: 31610263 PMCID: PMC7102787 DOI: 10.1016/j.jprot.2019.103527] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/31/2019] [Accepted: 09/10/2019] [Indexed: 12/13/2022]
Abstract
Bombyx mori nucleopolyhedrovirus (BmNPV) is a major pathogen causing severe economic loss. Previous studies have revealed that some proteins in silkworm digestive juice show antiviral activity. In this study, antiviral activity examination of different resistant strains showed that the digestive juice of the resistant strain (A35) had higher inhibition to virus than the susceptible strain (P50). Subsequently, the label-free quantitative proteomics was used to study the midgut digestive juice response to BmNPV infection in P50 and A35 strains. A total of 98 proteins were identified, of which 80 were differentially expressed proteins (DEPs) with 54 enzymes and 26 nonenzymatic proteins by comparing the proteomes of infected and non-infected P50 and A35 silkworms. These DEPs are mainly involved in metabolism, proteolysis, neuroactive ligand receptor interaction, starch and sucrose metabolism and glutathione metabolism. After removing the genetic background and individual immune stress response proteins, 9 DEPs were identified potentially involved in resistance to BmNPV. Further studies showed that a serine protease, an alkaline phosphatase and serine protease inhibitor 2 isoform X1 were differentially expressed in A35 compared to P50 or post BmNPV infection. Taken together, these results provide insights into the potential mechanisms for silkworm digestive juice to provide resistance to BmNPV infection. Signifcance: Bombyx mori nucleopolyhedrovirus (BmNPV) is highly pathogenic, which has a great impact on the sericulture. BmNPV entered the midgut lumen and exposed to digestive juices after oral infection. Previous studies have revealed that some proteins in silkworm digestive juice show antiviral activity, however, current information on the digestive juice proteome of high resistant silkworm strain after BmNPV challenge compared to susceptible strain is incomprehensive. Here, we combined label-free quantification method, bioinformatics, RT-qPCR and western blot analysis and found that BmNPV infection causes some protein changes in the silkworm midgut digestive juice. The DEPs were identified in the digestive juices of different resistant strains following BmNPV infection, and screened out some proteins potentially related to resistance to BmNPV. Three important differentially expression proteins were validated by independent approaches. These findings uncover the potential role of silkworm digestive juice in providing resistance to BmNPV and supplemented the profile of the proteome of the digestive juices in B. mori.
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Affiliation(s)
- Shang-Zhi Zhang
- School of Life Sciences, Anhui Agricultural University, Hefei, China; Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, China
| | - Jie Wang
- School of Life Sciences, Anhui Agricultural University, Hefei, China; Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, China
| | - Lin-Bao Zhu
- School of Life Sciences, Anhui Agricultural University, Hefei, China; Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, China
| | - Shahzad Toufeeq
- School of Life Sciences, Anhui Agricultural University, Hefei, China; Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, China
| | - Xin Xu
- School of Life Sciences, Anhui Agricultural University, Hefei, China; Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, China
| | - Ling-Ling You
- School of Life Sciences, Anhui Agricultural University, Hefei, China; Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, China
| | - Bing Li
- School of Life Sciences, Anhui Agricultural University, Hefei, China; Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, China
| | - Pei Hu
- School of Life Sciences, Anhui Agricultural University, Hefei, China; Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, China
| | - Jia-Ping Xu
- School of Life Sciences, Anhui Agricultural University, Hefei, China; Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, China.
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28
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Yang W, Shi J, Zhou Y, Liu T, Li J, Hong F, Zhang K, Liu N. Co-expression Network Analysis Identified Key Proteins in Association With Hepatic Metastatic Colorectal Cancer. Proteomics Clin Appl 2019; 13:e1900017. [PMID: 31397080 DOI: 10.1002/prca.201900017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 07/16/2019] [Indexed: 12/24/2022]
Abstract
PURPOSE Intense efforts have been made in colorectal cancer (CRC) treatment in recent decades. However, the mechanism of development and metastasis of CRC has not been fully cleared. This study is designed to identify key proteins involved in stage III and hepatic metastatic CRC. EXPERIMENT DESIGN Protein expression profiles of paired tumor and benign tissue samples from stage III and hepatic metastatic CRC patients are characterized by using a label-free proteomics approach. Key proteins relevant to hepatic metastatic CRC are revealed by weighted gene correlation network analysis (WGCNA) and other bioinformatics tools. RESULTS WGCNA reveals three hub modules: CRC without specific stage (turquoise), stage III CRC (blue), and hepatic metastatic CRC (green). Nine key proteins (heat shock protein family D member 1 (HSPD1), eukaryotic translation elongation factor 1 gamma, heterogeneous nuclear ribonucleoprotein A2/B1, fibrinogen beta chain (FGB), Talin 1, adaptor related protein complex 2 subunit alpha 2, serrate RNA effector molecule homolog, apolipoprotein C3, phosphoglucomutase 5) are identified. Moreover, upregulation of HSPD1 is validated in CRC tissue by the immunohistochemistry. Upregulation of fibrinogen is validated in metastatic CRC by plasma fibrinogen assay. CONCLUSION AND CLINICAL RELEVANCE This study provides the proteomic analysis of stage III and hepatic metastatic CRC to identify key proteins of CRC. FGB plays a key role to serve as diagnostic and therapeutic biomarkers for hepatic metastatic CRC.
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Affiliation(s)
- Wang Yang
- Gastrointestinal Surgery, The Second Hospital of Jilin University, Changchun, 130041, China.,College of Clinical Medicine, Jilin University, Changchun, 130012, China
| | - Jian Shi
- Gastrointestinal Surgery, The Second Hospital of Jilin University, Changchun, 130041, China
| | - Yan Zhou
- Gastrointestinal Surgery, The Second Affiliated Hospital of Shandong University, Jinan, 250033, China
| | - Tongjun Liu
- Gastrointestinal Surgery, The Second Hospital of Jilin University, Changchun, 130041, China
| | - Jiannan Li
- Gastrointestinal Surgery, The Second Hospital of Jilin University, Changchun, 130041, China
| | - Feng Hong
- Institute of Liver Diseases, Affiliated Hospital of Jining Medical University, Jining, 272067, P. R. China
| | - Kai Zhang
- Gastrointestinal Surgery, The Second Hospital of Jilin University, Changchun, 130041, China
| | - Ning Liu
- Central Laboratory, The Second Hospital of Jilin University, Changchun, 130041, China.,Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun, 130062, China
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29
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Ma H, Li R, Di X, Jin X, Wang Y, Lai B, Shi C, Ji M, Zhu X, Wang K. ITRAQ-based proteomic analysis reveals possible target-related proteins in human adrenocortical adenomas. BMC Genomics 2019; 20:655. [PMID: 31419939 PMCID: PMC6697928 DOI: 10.1186/s12864-019-6030-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 08/12/2019] [Indexed: 01/22/2023] Open
Abstract
Background Adrenocortical adenomas (ACAs) can lead to the autonomous secretion of aldosterone responsible for primary aldosteronism (PA), which is the most common form of secondary arterial hypertension. However, the authentic fundamental mechanisms underlying ACAs remain unclear. Objective Isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomics and bioinformatics analyses from etiological studies of ACAs were performed to screen the differentially expressed proteins (DEPs) and investigate the relevant mechanisms of their occurrence and development. Results could help determine therapeutic targets of clinical significance. Methods In the present study, iTRAQ-based proteomics was applied to analyze ACA tissue samples from normal adrenal cortex tissues adjacent to the tumor. Using proteins extracted from a panel of four pairs of ACA samples, we identified some upregulated proteins and other downregulated proteins in all four pairs of ACA samples compared with adjacent normal tissue. Subsequently, we predicted protein–protein interaction networks of three DEPs to determine the authentic functional factors in ACA. Results A total of 753 DEPs were identified, including 347 upregulated and 406 downregulated proteins. The expression of three upregulated proteins (E2F3, KRT6A, and ALDH1A2) was validated by Western blot in 24 ACA samples. Our data suggested that some DEPs might be important hallmarks during the development of ACA. Conclusions This study is the first proteomic research to investigate alterations in protein levels and affected pathways in ACA using the iTRAQ technique. Thus, this study not only provides a comprehensive dataset on overall protein changes but also sheds light on its potential molecular mechanism in human ACAs. Electronic supplementary material The online version of this article (10.1186/s12864-019-6030-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- He Ma
- Department of Respiratory Medicine, the Second Hospital of Jilin University, Changchun, China.,Department of Anesthesiology, the Second Hospital of Jilin University, Changchun, China
| | - Ranwei Li
- Department of Urinary Surgery, the Second Hospital of Jilin University, Changchun, China
| | - Xin Di
- Department of Respiratory Medicine, the Second Hospital of Jilin University, Changchun, China
| | - Xin Jin
- Department of Hematology, the Second Hospital of Jilin University, Changchun, China
| | - Yan Wang
- Department of Respiratory Medicine, the Second Hospital of Jilin University, Changchun, China
| | - Bingjie Lai
- Department of Intensive Care Unit, the Second Hospital of Jilin University, Changchun, China
| | - Cailian Shi
- Department of Anesthesiology, the Second Hospital of Jilin University, Changchun, China
| | - Mingxin Ji
- Department of Anesthesiology, the Second Hospital of Jilin University, Changchun, China
| | - Xinran Zhu
- Department of Anesthesiology, the Second Hospital of Jilin University, Changchun, China
| | - Ke Wang
- Department of Respiratory Medicine, the Second Hospital of Jilin University, Changchun, China.
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30
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Sum of peak intensities outperforms peak area integration in iTRAQ protein expression measurement by LC-MS/MS using a TripleTOF 5600+ platform. Biosci Rep 2019; 39:BSR20190904. [PMID: 31110078 PMCID: PMC6554230 DOI: 10.1042/bsr20190904] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 05/08/2019] [Accepted: 05/16/2019] [Indexed: 11/17/2022] Open
Abstract
In the field of quantitative proteomics, the Isobaric Tags for Relative and Absolute Quantitation (iTRAQ) technology has demonstrated efficacy for proteome monitoring despite its lack of a consensus for data handling. In the present study, after peptide and protein identification, we compared the widespread quantitation method based on the calculation of MS/MS reporter ion peaks areas ratios (ProteinPilot) to the alternative method based on the calculation of ratios of the sum of peak intensities (jTRAQx [Quant]) and we processed output data with the in-house Customizable iTRAQ Ratios Calculator (CiR-C) algorithm. Quantitation based on peak area ratios displayed no significant linear correlation with Western blot quantitation. In contrast, quantitation based on the sum of peak intensities displayed a significant linear association with Western blot quantitation (non-zero slope; Pearson correlation coefficient test, r = 0.296, P=0.010**) with an average bias of 0.087 ± 0.500 and 95% Limits of Agreement from −0.893 to 1.068. We proposed the Mascot-jTRAQx-CiR-C strategy as a simple yet powerful data processing adjunct to the iTRAQ technology.
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31
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Pu Y, Walley JW, Shen Z, Lang MG, Briggs SP, Estelle M, Kelley DR. Quantitative Early Auxin Root Proteomics Identifies GAUT10, a Galacturonosyltransferase, as a Novel Regulator of Root Meristem Maintenance. Mol Cell Proteomics 2019; 18:1157-1170. [PMID: 30918009 PMCID: PMC6553934 DOI: 10.1074/mcp.ra119.001378] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Indexed: 11/25/2022] Open
Abstract
Auxin induces rapid gene expression changes throughout root development. How auxin-induced transcriptional responses relate to changes in protein abundance is not well characterized. This report identifies early auxin responsive proteins in roots at 30 min and 2 h after hormone treatment using a quantitative proteomics approach in which 3,514 proteins were reliably quantified. A comparison of the >100 differentially expressed proteins at each the time point showed limited overlap, suggesting a dynamic and transient response to exogenous auxin. Several proteins with established roles in auxin-mediated root development exhibited altered abundance, providing support for this approach. While novel targeted proteomics assays demonstrate that all six auxin receptors remain stable in response to hormone. Additionally, 15 of the top responsive proteins display root and/or auxin response phenotypes, demonstrating the validity of these differentially expressed proteins. Auxin signaling in roots dictates proteome reprogramming of proteins enriched for several gene ontology terms, including transcription, translation, protein localization, thigmatropism, and cell wall modification. In addition, we identified auxin-regulated proteins that had not previously been implicated in auxin response. For example, genetic studies of the auxin responsive protein galacturonosyltransferase 10 demonstrate that this enzyme plays a key role in root development. Altogether these data complement and extend our understanding of auxin response beyond that provided by transcriptome studies and can be used to uncover novel proteins that may mediate root developmental programs.
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Affiliation(s)
- Yunting Pu
- From the Departments of ‡Genetics, Development and Cell Biology
| | - Justin W Walley
- ¶Plant Pathology and Microbiology, Iowa State University, Ames, IA
| | - Zhouxin Shen
- §Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA
| | - Michelle G Lang
- From the Departments of ‡Genetics, Development and Cell Biology
| | - Steven P Briggs
- §Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA
| | - Mark Estelle
- §Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA
| | - Dior R Kelley
- From the Departments of ‡Genetics, Development and Cell Biology,
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Sun YZ, Li JF, Wei ZD, Jiang HH, Hong YX, Zheng S, Qi RQ, Gao XH. Proteomic and bioinformatic analysis of condyloma acuminata: mild hyperthermia treatment reveals compromised HPV infectivity of keratinocytes via regulation of metabolism, differentiation and anti-viral responses. Int J Hyperthermia 2019; 36:383-393. [PMID: 30909744 DOI: 10.1080/02656736.2019.1578420] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Hyperthermia has proved successful in treating cutaneous human papillomavirus infectious diseases such as plantar wart and condyloma acuminata (CA). Moreover, this treatment provides improved therapeutic efficacy in these conditions as compared with conventional therapies. OBJECTIVES To investigate the global proteome changes in CA in response to hyperthermia and achieve a better understanding of the mechanisms of hyperthermia therapy against HPV-infectious diseases. METHODS CA tissue was obtained from patients undergoing pathological examinations. Diagnosis was verified as based on results of both HE staining and HPV-DNA PCR assay. Hyperthermia was achieved with a 44 °C water bath. Differentially expressed proteins (DEPs) were identified by iTRAQ labeling, SCX chromatography and LC-MS/MS assay. Validation of proteomic results was performed using real-time qPCR and western blot, while bioinformatic analysis of DEPs was accomplished by R 3.4.1, STRING and Cytoscape softwares. RESULTS In response to hyperthermia, a total of 102 DEPs were identified with 37 being upregulated and 65 downregulated. Among these DEPs, hyperthermia induced proteins involved with anti-viral processes such as OAS1, MX1, BANF1, CANX and AP1S1, whereas it inhibited proteins that participated in cellular metabolism, such as GALT, H6PD, EXOSC4 and EXOSC6; protein translation, such as RPS4Y1; as well as keratinocyte differentiation, such as KRT5, KRT27, KRT75, KRT76 and H2AFY2. CONCLUSIONS Hyperthermia inhibited enzymes and molecules responsible for metabolism modulation and keratinocyte differentiation in CA tissue, whereas it promoted factors involved in anti-viral responses. Such effects may, in part, contribute to the efficacy of local hyperthermia therapy against HPV infection.
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Affiliation(s)
- Yu-Zhe Sun
- a Graduate School, China Medical University , Shenyang , China.,b Department of Dermatology , The First Hospital of China Medical University and Key Laboratory of Immunodermatology, Ministry of Health and Ministry of Education , Shenyang , China
| | - Jia-Feng Li
- a Graduate School, China Medical University , Shenyang , China.,c Department of Pathology , The First Hospital of China Medical University , Shenyang , China
| | - Zhen-Dong Wei
- d Department of Dermatology , the 2nd Affiliated Hospital of Dalian Medical University , Dalian , China
| | - Hang-Hang Jiang
- b Department of Dermatology , The First Hospital of China Medical University and Key Laboratory of Immunodermatology, Ministry of Health and Ministry of Education , Shenyang , China
| | - Yu-Xiao Hong
- b Department of Dermatology , The First Hospital of China Medical University and Key Laboratory of Immunodermatology, Ministry of Health and Ministry of Education , Shenyang , China
| | - Song Zheng
- b Department of Dermatology , The First Hospital of China Medical University and Key Laboratory of Immunodermatology, Ministry of Health and Ministry of Education , Shenyang , China
| | - Rui-Qun Qi
- b Department of Dermatology , The First Hospital of China Medical University and Key Laboratory of Immunodermatology, Ministry of Health and Ministry of Education , Shenyang , China
| | - Xing-Hua Gao
- a Graduate School, China Medical University , Shenyang , China.,b Department of Dermatology , The First Hospital of China Medical University and Key Laboratory of Immunodermatology, Ministry of Health and Ministry of Education , Shenyang , China
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Li Z, Kuang W, Liu Y, Peng D, Bai L. Proteomic Analysis of Horseweed (Conyza canadensis) Subjected to Caprylic Acid Stress. Proteomics 2019; 19:e1800294. [PMID: 30865362 DOI: 10.1002/pmic.201800294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 02/02/2019] [Indexed: 11/08/2022]
Abstract
Caprylic acid (CAP) is anticipated to be a potential biocontrol herbicide in the control of weeds, however the molecular mechanism of how CAP affects weeds is poorly understood. Here, the physiological and biochemical (protein-level) changes in horseweed (Conyza canadensis L.) are studied under CAP treatment, with infrared gas analyzer and label-free quantitative proteomics methods. In total, 112 differentially-accumulated proteins (DAPs) (>1.5 fold change, p < 0.05) are present between treated horseweed and control samples, with 46 up-regulated and 66 down-regulated proteins. These DAPs are involved in 28 biochemical pathways, including photosynthesis pathways. In particular, six photosynthesis proteins show significant abundance changes in the CAP-treated horseweed. The qRT-PCR results confirm three of the six genes involved in photosynthesis. Moreover, by measuring photosynthesis characteristics, CAP was shown to decrease photosynthetic rate, stomatal conductance, intercellular CO2 concentration, and the transpiration rate of horseweed. These results suggest that photosystem I is one of the main biological processes involved in the response of horseweed to CAP.
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Affiliation(s)
- Zuren Li
- Hunan Academy of Agricultural Sciences, Hunan Agricultural Biotechnology Research Institute, Changsha, 410125, China.,College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Wei Kuang
- Hunan Academy of Agricultural Sciences, Hunan Agricultural Biotechnology Research Institute, Changsha, 410125, China
| | - Yongbo Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Di Peng
- Hunan Academy of Agricultural Sciences, Hunan Agricultural Biotechnology Research Institute, Changsha, 410125, China
| | - Lianyang Bai
- Hunan Academy of Agricultural Sciences, Hunan Agricultural Biotechnology Research Institute, Changsha, 410125, China.,College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, 410128, China
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34
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Label-free quantification of protein expression in the rainbow trout (Oncorhynchus mykiss) in response to short-term exposure to heat stress. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 30:158-168. [PMID: 30851505 DOI: 10.1016/j.cbd.2019.02.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 01/21/2019] [Accepted: 02/26/2019] [Indexed: 12/25/2022]
Abstract
Rainbow trout (Oncorhynchus mykiss) are a cold-water salmonid species that is highly susceptible to heat stress. Summer temperature stress is a common issue in trout aquaculture. To better understand the molecular mechanisms of the heat-stress response in the trout, we used label-free quantitative proteome techniques to identify differentially expressed proteins in the livers of rainbow trout exposed to heat stress. We identified 3362 proteins and 152 differentially expressed proteins (p < 0.05; fold-change >2). Of these, 37 were uniquely expressed in the heat-stress group and 35 were uniquely expressed in the control group. In addition, 42 proteins were significantly upregulated (fold-change >2) and 38 proteins were significantly downregulated (fold-change >2). GO (Gene Ontology) analysis indicated that these differentially expressed proteins were primarily expressed in the nucleus, extracellular matrix, and cytoplasm, and were associated with a variety of functions, including protein binding/bridging and enzyme facilitation. KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis of the differentially expressed proteins showed that, during high temperature stress, many biological processes were extensively altered, particularly the estrogen signaling pathway, the complement and coagulation cascades, and the platelet activation pathway. Our study focused on the identification of a systematic approach for the characterization of regulatory networks. Our results provide a framework for further studies of the heat-stress response in fish.
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Smith BJ, Martins-de-Souza D, Fioramonte M. A Guide to Mass Spectrometry-Based Quantitative Proteomics. Methods Mol Biol 2019; 1916:3-39. [PMID: 30535679 DOI: 10.1007/978-1-4939-8994-2_1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Proteomics has become an attractive science in the postgenomic era, given its capacity to identify up to thousands of molecules in a single, complex sample and quantify them in an absolute and/or relative manner. The use of these techniques enables understanding of cellular and molecular mechanisms of diseases and other biological conditions, as well as identification and screening of protein biomarkers. Here we provide a straightforward, up-to-date compilation and comparison of the main quantitation techniques used in comparative proteomics such as in vitro and in vivo stable isotope labeling and label-free techniques. Additionally, this chapter includes common methods for data acquisition in proteomics and some appropriate methods for data processing. This compilation can serve as a reference for scientists who are new to, or already familiar with, quantitative proteomics.
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Affiliation(s)
- Bradley J Smith
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- Center for Neurobiology, University of Campinas (UNICAMP), Campinas, Brazil
- Instituto Nacional de Biomarcadores em Neuropsiquiatria (INBION), Conselho Nacional de Desenvolvimento Cientifico e Tecnologico, Sao Paulo, Brazil
| | - Mariana Fioramonte
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil.
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Carlyle BC, Trombetta BA, Arnold SE. Proteomic Approaches for the Discovery of Biofluid Biomarkers of Neurodegenerative Dementias. Proteomes 2018; 6:32. [PMID: 30200280 PMCID: PMC6161166 DOI: 10.3390/proteomes6030032] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 08/22/2018] [Accepted: 08/29/2018] [Indexed: 12/11/2022] Open
Abstract
Neurodegenerative dementias are highly complex disorders driven by vicious cycles of intersecting pathophysiologies. While most can be definitively diagnosed by the presence of disease-specific pathology in the brain at postmortem examination, clinical disease presentations often involve substantially overlapping cognitive, behavioral, and functional impairment profiles that hamper accurate diagnosis of the specific disease. As global demographics shift towards an aging population in developed countries, clinicians need more sensitive and specific diagnostic tools to appropriately diagnose, monitor, and treat neurodegenerative conditions. This review is intended as an overview of how modern proteomic techniques (liquid chromatography mass spectrometry (LC-MS/MS) and advanced capture-based technologies) may contribute to the discovery and establishment of better biofluid biomarkers for neurodegenerative disease, and the limitations of these techniques. The review highlights some of the more interesting technical innovations and common themes in the field but is not intended to be an exhaustive systematic review of studies to date. Finally, we discuss clear reporting principles that should be integrated into all studies going forward to ensure data is presented in sufficient detail to allow meaningful comparisons across studies.
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Affiliation(s)
- Becky C Carlyle
- Massachusetts General Hospital Department of Neurology, Charlestown, MA 02129, USA.
| | - Bianca A Trombetta
- Massachusetts General Hospital Department of Neurology, Charlestown, MA 02129, USA.
| | - Steven E Arnold
- Massachusetts General Hospital Department of Neurology, Charlestown, MA 02129, USA.
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Arora N, Pienkos PT, Pruthi V, Poluri KM, Guarnieri MT. Leveraging algal omics to reveal potential targets for augmenting TAG accumulation. Biotechnol Adv 2018; 36:1274-1292. [PMID: 29678388 DOI: 10.1016/j.biotechadv.2018.04.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 04/11/2018] [Accepted: 04/15/2018] [Indexed: 02/08/2023]
Abstract
Ongoing global efforts to commercialize microalgal biofuels have expedited the use of multi-omics techniques to gain insights into lipid biosynthetic pathways. Functional genomics analyses have recently been employed to complement existing sequence-level omics studies, shedding light on the dynamics of lipid synthesis and its interplay with other cellular metabolic pathways, thus revealing possible targets for metabolic engineering. Here, we review the current status of algal omics studies to reveal potential targets to augment TAG accumulation in various microalgae. This review specifically aims to examine and catalog systems level data related to stress-induced TAG accumulation in oleaginous microalgae and inform future metabolic engineering strategies to develop strains with enhanced bioproductivity, which could pave a path for sustainable green energy.
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Affiliation(s)
- Neha Arora
- Department of Biotechnology, Indian Institute of Technology Roorkee, Uttarakhand 247667, India
| | - Philip T Pienkos
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Vikas Pruthi
- Department of Biotechnology, Indian Institute of Technology Roorkee, Uttarakhand 247667, India
| | - Krishna Mohan Poluri
- Department of Biotechnology, Indian Institute of Technology Roorkee, Uttarakhand 247667, India
| | - Michael T Guarnieri
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, USA.
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McConnell EW, Werth EG, Hicks LM. The phosphorylated redox proteome of Chlamydomonas reinhardtii: Revealing novel means for regulation of protein structure and function. Redox Biol 2018; 17:35-46. [PMID: 29673699 PMCID: PMC6006682 DOI: 10.1016/j.redox.2018.04.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/02/2018] [Accepted: 04/03/2018] [Indexed: 01/16/2023] Open
Abstract
Post-translational modifications (PTMs) are covalent modifications to protein residues which may alter both conformation and activity, thereby modulating signaling and metabolic processes. While PTMs have been largely investigated independently, examination into how different modification interact, or crosstalk, will reveal a more complete understanding of the reciprocity of signaling cascades across numerous pathways. Combinatorial reversible thiol oxidation and phosphorylation in eukaryotes is largely recognized, but rigorous approaches for experimental discovery are underdeveloped. To begin meaningful interrogation of PTM crosstalk in systems biology research, knowledge of targeted proteins must be advanced. Herein, we demonstrate protein-level enrichment of reversibly oxidized proteoforms in Chlamydomonas reinhardtii with subsequent phosphopeptide analysis to determine the extent of phosphorylation in the redox thiol proteome. Label-free quantification was used to quantify 3353 oxidized Cys-sites on 1457 enriched proteins, where sequential phosphopeptide enrichment measured 1094 sites of phosphorylation on 720 proteins with 23% (172 proteins) also identified as reversibly oxidized. Proteins identified with both reversible oxidation and phosphorylation were involved in signaling transduction, ribosome and translation-related machinery, and metabolic pathways. Several redox-modified Calvin-Benson cycle proteins were found phosphorylated and many kinases/phosphatases involved in phosphorylation-dependent photosynthetic state transition and stress-response pathways had sites of reversible oxidation. Identification of redox proteins serves as a crucial element in understanding stress response in photosynthetic organisms and beyond, whereby knowing the ensemble of modifications co-occurring with oxidation highlights novel mechanisms for cellular control. Quantified reversible oxidation on protein cysteine residues. Sequential phosphopeptide enrichment to define the phosphorylated redox proteome. Found >3000 oxidized cysteines and >1000 phosphosites in Chlamydomonas reinhardtii. Co-modified proteins discovered across diverse metabolic and signaling pathways.
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Affiliation(s)
- Evan W McConnell
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Emily G Werth
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Leslie M Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.
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Song H, Fang S, Gao J, Wang J, Cao Z, Guo Z, Huang Q, Qu Y, Zhou H, Yu J. Quantitative Proteomic Study Reveals Up-Regulation of cAMP Signaling Pathway-Related Proteins in Mild Traumatic Brain Injury. J Proteome Res 2017; 17:858-869. [PMID: 29215295 DOI: 10.1021/acs.jproteome.7b00618] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Traumatic brain injury (TBI), as a neurological injury, becomes a leading cause of disability and mortality due to lacking effective therapy. About 75% of TBI is mild traumatic brain injury (mTBI). However, the complex molecular mechanisms underlying mTBI pathophysiology remains to be elucidated. In this study, iTRAQ-based quantitative proteomic approach was employed to measure temporal-global proteome changes of rat brain tissues from different time points (1 day, 7 day and 6 months) post single mTBI (smTBI) and repetitive mTBI (rmTBI). A total of 5169 proteins were identified, of which, 237 proteins were significantly changed between control rats and mTBI model rats. Fuzzy c-means (FCM) clustering analysis classified these 237 proteins into six clusters according to their temporal pattern of protein abundance. Functional bioinformatics analysis and protein-protein interaction (PPI) network mapping of these FCM clusters showed that phosphodiesterase 10A (Pde10a) and guanine nucleotide-binding protein G (olf) subunit alpha (Gnal) were the node proteins in the cAMP signaling pathway. Other biological processes, such as cell adhesion, autophagy, myelination, microtubule depolymerization and brain development, were also over-represented in FCM clusters. Further Western Blot experiments confirmed that Pde10a and Gnal were acutely up-regulated in severity-dependent manner by mTBI, but these two proteins could not be down-regulated to basal level at the time point of 6 months post repetitive mTBI. Our study demonstrated that different severity of mTBI cause significant temporal profiling change at the proteomic level and pointed out the cAMP signaling pathway-related proteins, Pde10a and Gnal, may play important roles in the pathogenesis and recovery of mTBI.
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Affiliation(s)
- Hai Song
- Department of Forensic Medicine, Kunming Medical University , Kunming, Yunnan 650032, China.,Department of Neurosurgery, The First Affiliated Hospital of Kunming Medical University , Kunming, Yunnan 650032, China
| | - Shanhua Fang
- E-Institute of Shanghai Municipal Education Committee, Shanghai University of Traditional Chinese Medicine , 1200 Cai Lun Road, Shanghai 201203, China
| | - Jing Gao
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203, China
| | - Jiaxong Wang
- Department of Forensic Medicine, Kunming Medical University , Kunming, Yunnan 650032, China.,Department of Neurosurgery, The First Affiliated Hospital of Kunming Medical University , Kunming, Yunnan 650032, China
| | - Zhenzhen Cao
- Department of Anatomy and Histology, Kunming Medical University , Kunming, Yunnan 650032, China
| | - Zeyun Guo
- Department of Anatomy and Histology, Kunming Medical University , Kunming, Yunnan 650032, China
| | - Qiongping Huang
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203, China
| | - Yongqang Qu
- Department of Forensic Medicine, Kunming Medical University , Kunming, Yunnan 650032, China
| | - Hu Zhou
- E-Institute of Shanghai Municipal Education Committee, Shanghai University of Traditional Chinese Medicine , 1200 Cai Lun Road, Shanghai 201203, China.,Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203, China
| | - Jianyun Yu
- Department of Forensic Medicine, Kunming Medical University , Kunming, Yunnan 650032, China
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Carlyle BC, Kitchen RR, Kanyo JE, Voss EZ, Pletikos M, Sousa AMM, Lam TT, Gerstein MB, Sestan N, Nairn AC. A multiregional proteomic survey of the postnatal human brain. Nat Neurosci 2017; 20:1787-1795. [PMID: 29184206 PMCID: PMC5894337 DOI: 10.1038/s41593-017-0011-2] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 09/27/2017] [Indexed: 12/13/2022]
Abstract
Detailed observations of transcriptional, translational and post-translational events in the human brain are essential to improving our understanding of its development, function and vulnerability to disease. Here, we exploited label-free quantitative tandem mass-spectrometry to create an in-depth proteomic survey of regions of the postnatal human brain, ranging in age from early infancy to adulthood. Integration of protein data with existing matched whole-transcriptome sequencing (RNA-seq) from the BrainSpan project revealed varied patterns of protein-RNA relationships, with generally increased magnitudes of protein abundance differences between brain regions compared to RNA. Many of the differences amplified in protein data were reflective of cytoarchitectural and functional variation between brain regions. Comparing structurally similar cortical regions revealed significant differences in the abundances of receptor-associated and resident plasma membrane proteins that were not readily observed in the RNA expression data.
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Affiliation(s)
- Becky C Carlyle
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
| | - Robert R Kitchen
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- Department of Molecular Biophysics & Biochemistry, Yale School of Medicine, New Haven, CT, USA
| | - Jean E Kanyo
- W.M. Keck Biotechnology Resource Laboratory, Yale School of Medicine, New Haven, CT, USA
| | - Edward Z Voss
- W.M. Keck Biotechnology Resource Laboratory, Yale School of Medicine, New Haven, CT, USA
| | - Mihovil Pletikos
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - André M M Sousa
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - TuKiet T Lam
- Department of Molecular Biophysics & Biochemistry, Yale School of Medicine, New Haven, CT, USA
- W.M. Keck Biotechnology Resource Laboratory, Yale School of Medicine, New Haven, CT, USA
| | - Mark B Gerstein
- Department of Molecular Biophysics & Biochemistry, Yale School of Medicine, New Haven, CT, USA
| | - Nenad Sestan
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA.
- Departments of Genetics and Psychiatry, Section of Comparative Medicine, and Yale Child Study Center, Yale School of Medicine, New Haven, CT, USA.
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale School of Medicine, New Haven, CT, USA.
| | - Angus C Nairn
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA.
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale School of Medicine, New Haven, CT, USA.
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41
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Yang W, Gao Y, Qian Y, Li J, Hu Q. iTRAQ-based quantitative analysis of alveolar bone resorption in rats with experimental periodontitis. Arch Oral Biol 2017. [DOI: 10.1016/j.archoralbio.2017.05.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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42
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Zhou X, Xing X, Hou J, Liu J. Quantitative proteomics analysis of proteins involved in alkane uptake comparing the profiling of Pseudomonas aeruginosa SJTD-1 in response to n-octadecane and n-hexadecane. PLoS One 2017; 12:e0179842. [PMID: 28662172 PMCID: PMC5491041 DOI: 10.1371/journal.pone.0179842] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 06/05/2017] [Indexed: 12/22/2022] Open
Abstract
While many data are available on genes encoding proteins for degradation of hydrocarbons in bacteria, the impact of alkane on transporter protein expression is unclear. Pseudomonas aeruginosa SJTD-1 is a strain that can consume medium- and long-chain n-alkanes. In order to study the proteins involved in n-octadecane uptake, we use iTRAQ and label free comparative proteomics analysis to identify the proteins of alkane uptake in response to n-octadecane (C18) comparing with n-hexadecane (C16) in P. aeruginosa SJTD-1. A total of 1102 and 1249 proteins were identified by iTRAQ-based and label free quantitative methodologies, respectively. By application of 1.5 (iTRAQ) or 2-fold (label free) for upregulated and 0.65 (iTRAQ) or 0.5-fold (label free) for downregulated cutoff values, 91 and 99 proteins were found to be differentially expressed comparing SJTD-1 cultivated on C18 with C16 respectively. There are six proteins with the common differential expression by iTRAQ and label free-based methods. Results of bioinformational analysis suggested the involvement of bacterial chemotaxis in responds to C18. Additionally, quantitative reverse transcriptase PCR (qRT-PCR) results confirmed C18-induced change in levels of FleQ, FliC, NirS, FadL and FadD proteins and the role of the proteins in n-octadecane uptake was further discussed in P. aeruginosa. In conclusion, results of the present study provided information about possible target-related proteins of bacterial chemotaxis, swimming performance, alkane transport to stimulus of n-ctadecane rather than n-hexadecane in P. aeruginosa SJTD-1.
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Affiliation(s)
- Xuefeng Zhou
- School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xuejiao Xing
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Jingli Hou
- Instrumental Analysis Center of Shanghai Jiao Tong University, Shanghai, China
- * E-mail:
| | - Jianhua Liu
- School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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43
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Zhang B, Chamba Y, Shang P, Wang Z, Ma J, Wang L, Zhang H. Comparative transcriptomic and proteomic analyses provide insights into the key genes involved in high-altitude adaptation in the Tibetan pig. Sci Rep 2017. [PMID: 28623314 PMCID: PMC5473931 DOI: 10.1038/s41598-017-03976-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Tibetan pigs that inhabit the Tibetan Plateau exhibit striking phenotypic and physiological differences from lowland pigs, and have adapted well to extreme conditions. However, the mechanisms involved in regulating gene expression at high altitude in these animals are not fully understood. In this study, we obtained transcriptomic and proteomic data from the heart tissues of Tibetan and Yorkshire pigs raised in the highlands (TH and YH) and lowlands (TL and YL) via RNA-seq and iTRAQ (isobaric tags for relative and absolute quantitation) analyses, respectively. Comparative analyses of TH vs. YH, TH vs.TL, TL vs. YL, and YH vs. YL yielded 299, 169, 242, and 368 differentially expressed genes (DEGs), and 473, 297, 394, and 297 differentially expressed proteins (DEPs), respectively. By functional annotation of these DEGs and DEPs, genes that were enriched in the HIF-1 signaling pathway (NPPA, ERK2, ENO3, and EGLN3), VEGF signaling pathway (ERK2, A2M, FGF1, CTGF, and DPP4), and hypoxia-related processes (CRYAB, EGLN3, TGFB2, DPP4, and ACE) were identified as important candidate genes for high-altitude adaptation in the Tibetan pig. This study enhances our understanding of the molecular mechanisms involved in hypoxic adaptation in pigs, and furthers our understanding of human hypoxic diseases.
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Affiliation(s)
- Bo Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd., Beijing, 100193, China
| | - Yangzom Chamba
- Tibet Agriculture and Animal Husbandry College, Linzhi, Tibet, 860000, China
| | - Peng Shang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd., Beijing, 100193, China.,Tibet Agriculture and Animal Husbandry College, Linzhi, Tibet, 860000, China
| | - Zhixiu Wang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd., Beijing, 100193, China
| | - Jun Ma
- National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd., Beijing, 100193, China
| | - Liyuang Wang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd., Beijing, 100193, China
| | - Hao Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd., Beijing, 100193, China.
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Gargouri M, Bates PD, Park JJ, Kirchhoff H, Gang DR. Functional photosystem I maintains proper energy balance during nitrogen depletion in Chlamydomonas reinhardtii, promoting triacylglycerol accumulation. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:89. [PMID: 28413444 PMCID: PMC5390395 DOI: 10.1186/s13068-017-0774-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 04/05/2017] [Indexed: 05/11/2023]
Abstract
BACKGROUND Nutrient deprivation causes significant stress to the unicellular microalga, Chlamydomonas reinhardtii, which responds by significantly altering its metabolic program. Following N deprivation, the accumulation of starch and triacylglycerols (TAGs) is significantly altered following massive reprogramming of cellular metabolism. One protein that was found to change dramatically and early to this stress was TAB2, a photosystem I (PSI) translation initiation factor, whose transcript and protein levels increased significantly after only 30 min of N deprivation. A detailed physiological and omics-based analysis of an insertional mutant of Chlamydomonas with reduced TAB2 function was conducted to determine what role the functional PSI plays in regulating the cellular response to N deprivation. RESULTS The tab2 mutant displayed increased acetate assimilation and elevated starch levels during the first 6 h of N deprivation, followed by a shift toward altered amino acid synthesis, reduced TAG content and altered fatty acid profiles. These results suggested a central role for PSI in controlling cellular metabolism and its implication in regulation of lipid/starch partitioning. Time course analyses of the tab2 mutant versus wild type under N-deprived versus N replete conditions revealed changes in the ATP/NADPH ratio and suggested that TAG biosynthesis may be associated with maintaining the redox state of the cell during N deprivation. The loss of ability to accumulate TAG in the tab2 mutant co-occurred with an up-regulation of photo-protective mechanisms, suggesting that the synthesis of TAG in the wild type occurs not only as a temporal energy sink, but also as a protective electron sink. CONCLUSIONS By exploiting the tab2 mutation in the cells of C. reinhardtii cultured under autotrophic, mixotrophic, and heterotrophic conditions during nitrogen replete growth and for the first 8 days of nitrogen deprivation, we showed that TAG accumulation and lipid/starch partitioning are dynamically regulated by alterations in PSI function, which concomitantly alters the immediate ATP/NADPH demand. This occurs even without removal of nitrogen from the medium, but sufficient external carbon must nevertheless be available. Efforts to increase lipid accumulation in algae such as Chlamydomonas need to consider carefully how the energy balance of the cell is involved in or affected by such efforts and that numerous layers of metabolic and genetic regulatory control are likely to interfere with such efforts to control oil biosynthesis. Such knowledge will enable synthetic biology approaches to alter the response to the N depletion stress, leading to rewiring of the regulatory networks so that lipid accumulation could be turned on in the absence of N deprivation, allowing for the development of algal production strains with highly enhanced lipid accumulation profiles.
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Affiliation(s)
- Mahmoud Gargouri
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164 USA
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, P.O. Box 901, 2050 Hammam-Lif, Tunisia
| | - Philip D. Bates
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164 USA
- Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, MS 39406 USA
| | - Jeong-Jin Park
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164 USA
| | - Helmut Kirchhoff
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164 USA
| | - David R. Gang
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164 USA
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45
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Jiang L, Xie Y, Wei L, Zhou Q, Li N, Jiang X, Gao Y. iTRAQ-based quantitative proteomic analysis on differentially expressed proteins of rat mandibular condylar cartilage induced by reducing dietary loading. Front Med 2017; 11:97-109. [DOI: 10.1007/s11684-016-0496-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 09/13/2016] [Indexed: 12/24/2022]
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46
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Bringans SD, Ito J, Stoll T, Winfield K, Phillips M, Peters K, Davis WA, Davis TME, Lipscombe RJ. Comprehensive mass spectrometry based biomarker discovery and validation platform as applied to diabetic kidney disease. EUPA OPEN PROTEOMICS 2017; 14:1-10. [PMID: 29900119 PMCID: PMC5988498 DOI: 10.1016/j.euprot.2016.12.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 10/21/2016] [Accepted: 12/30/2016] [Indexed: 11/25/2022]
Abstract
A protein biomarker discovery workflow was applied to plasma samples from patients at different stages of diabetic kidney disease. The proteomics platform produced a panel of significant plasma biomarkers that were statistically scrutinised against the current gold standard tests on an analysis of 572 patients. Five proteins were significantly associated with diabetic kidney disease defined by albuminuria, renal impairment (eGFR) and chronic kidney disease staging (CKD Stage ≥1, ROC curve of 0.77). The results prove the suitability and efficacy of the process used, and introduce a biomarker panel with the potential to improve diagnosis of diabetic kidney disease.
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Affiliation(s)
- Scott D Bringans
- Proteomics International, PO Box 3008, Broadway, Nedlands, Perth, Western Australia, WA 6009, Australia
| | - Jun Ito
- Proteomics International, PO Box 3008, Broadway, Nedlands, Perth, Western Australia, WA 6009, Australia
| | - Thomas Stoll
- Proteomics International, PO Box 3008, Broadway, Nedlands, Perth, Western Australia, WA 6009, Australia
| | - Kaye Winfield
- Proteomics International, PO Box 3008, Broadway, Nedlands, Perth, Western Australia, WA 6009, Australia
| | - Michael Phillips
- Harry Perkins Institute of Medial Research, QQ Block, QEII Medical Centre 6 Verdun Street, Nedlands, Perth, Western Australia, WA 6009, Australia
| | - Kirsten Peters
- Proteomics International, PO Box 3008, Broadway, Nedlands, Perth, Western Australia, WA 6009, Australia.,University of Western Australia, 35 Stirling Highway, Crawley, Perth, Western Australia, WA 6009, Australia
| | - Wendy A Davis
- University of Western Australia, 35 Stirling Highway, Crawley, Perth, Western Australia, WA 6009, Australia
| | - Timothy M E Davis
- University of Western Australia, 35 Stirling Highway, Crawley, Perth, Western Australia, WA 6009, Australia
| | - Richard J Lipscombe
- Proteomics International, PO Box 3008, Broadway, Nedlands, Perth, Western Australia, WA 6009, Australia
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Li Y, Dong XM, Jin F, Shen Z, Chao Q, Wang BC. Histone Acetylation Modifications Affect Tissue-Dependent Expression of Poplar Homologs of C 4 Photosynthetic Enzyme Genes. FRONTIERS IN PLANT SCIENCE 2017; 8:950. [PMID: 28642769 PMCID: PMC5462996 DOI: 10.3389/fpls.2017.00950] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 05/22/2017] [Indexed: 05/18/2023]
Abstract
Histone modifications play important roles in regulating the expression of C4 photosynthetic genes. Given that all enzymes required for the C4 photosynthesis pathway are present in C3 plants, it has been hypothesized that this expression regulatory mechanism has been conserved. However, the relationship between histone modification and the expression of homologs of C4 photosynthetic enzyme genes has not been well determined in C3 plants. In the present study, we cloned nine hybrid poplar (Populus simonii × Populus nigra) homologs of maize (Zea mays) C4 photosynthetic enzyme genes, carbonic anhydrase (CA), pyruvate orthophosphate dikinase (PPDK), phosphoenolpyruvate carboxykinase (PCK), and phosphoenolpyruvate carboxylase (PEPC), and investigated the correlation between the expression levels of these genes and the levels of promoter histone acetylation modifications in four vegetative tissues. We found that poplar homologs of C4 homologous genes had tissue-dependent expression patterns that were mostly well-correlated with the level of histone acetylation modification (H3K9ac and H4K5ac) determined by chromatin immunoprecipitation assays. Treatment with the histone deacetylase inhibitor trichostatin A further confirmed the role of histone acetylation in the regulation of the nine target genes. Collectively, these results suggest that both H3K9ac and H4K5ac positively regulate the tissue-dependent expression pattern of the PsnCAs, PsnPPDKs, PsnPCKs, and PsnPEPCs genes and that this regulatory mechanism seems to be conserved among the C3 and C4 species. Our findings provide new insight that will aid efforts to modify the expression pattern of these homologs of C4 genes to engineer C4 plants from C3 plants.
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Affiliation(s)
- Yuan Li
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of SciencesBeijing, China
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry UniversityHarbin, China
| | - Xiu-Mei Dong
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Feng Jin
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Zhuo Shen
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Qing Chao
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Bai-Chen Wang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of SciencesBeijing, China
- *Correspondence: Bai-Chen Wang,
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Casey TM, Khan JM, Bringans SD, Koudelka T, Takle PS, Downs RA, Livk A, Syme RA, Tan KC, Lipscombe RJ. Analysis of Reproducibility of Proteome Coverage and Quantitation Using Isobaric Mass Tags (iTRAQ and TMT). J Proteome Res 2016; 16:384-392. [PMID: 28152591 DOI: 10.1021/acs.jproteome.5b01154] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This study aimed to compare the depth and reproducibility of total proteome and differentially expressed protein coverage in technical duplicates and triplicates using iTRAQ 4-plex, iTRAQ 8-plex, and TMT 6-plex reagents. The analysis was undertaken because comprehensive comparisons of isobaric mass tag reproducibility have not been widely reported in the literature. The highest number of proteins was identified with 4-plex, followed by 8-plex and then 6-plex reagents. Quantitative analyses revealed that more differentially expressed proteins were identified with 4-plex reagents than 8-plex reagents and 6-plex reagents. Replicate reproducibility was determined to be ≥69% for technical duplicates and ≥57% for technical triplicates. The results indicate that running an 8-plex or 6-plex experiment instead of a 4-plex experiment resulted in 26 or 39% fewer protein identifications, respectively. When 4-plex spectra were searched with three software tools-ProteinPilot, Mascot, and Proteome Discoverer-the highest number of protein identifications were obtained with Mascot. The analysis of negative controls demonstrated the importance of running experiments as replicates. Overall, this study demonstrates the advantages of using iTRAQ 4-plex reagents over iTRAQ 8-plex and TMT 6-plex reagents, provides estimates of technical duplicate and triplicate reproducibility, and emphasizes the value of running replicate samples.
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Affiliation(s)
- Tammy M Casey
- Proteomics International , Perth, Western Australia 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, The University of Western Australia , Nedlands, Western Australia 6009, Australia
| | - Javed M Khan
- Proteomics International , Perth, Western Australia 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, The University of Western Australia , Nedlands, Western Australia 6009, Australia
| | - Scott D Bringans
- Proteomics International , Perth, Western Australia 6009, Australia
| | - Tomas Koudelka
- Proteomics International , Perth, Western Australia 6009, Australia
| | - Pari S Takle
- Proteomics International , Perth, Western Australia 6009, Australia
| | - Rachael A Downs
- Proteomics International , Perth, Western Australia 6009, Australia
| | - Andreja Livk
- Proteomics International , Perth, Western Australia 6009, Australia
| | - Robert A Syme
- Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University , Bentley, Western Australia 6102, Australia
| | - Kar-Chun Tan
- Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University , Bentley, Western Australia 6102, Australia
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49
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Dowle AA, Wilson J, Thomas JR. Comparing the Diagnostic Classification Accuracy of iTRAQ, Peak-Area, Spectral-Counting, and emPAI Methods for Relative Quantification in Expression Proteomics. J Proteome Res 2016; 15:3550-3562. [PMID: 27546623 DOI: 10.1021/acs.jproteome.6b00308] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Diagnostic classification accuracy is critical in expression proteomics to ensure that as many true differences as possible are identified with acceptable false-positive rates. We present a comparison of the diagnostic accuracy of iTRAQ with three label-free methods, peak area, spectral counting, and emPAI, for relative quantification using a spiked proteome standard. We provide the first validation of emPAI for intersample relative quantification and find clear differences among the four quantification approaches that could be considered when designing an experiment. Spectral counting was observed to perform surprisingly well in all regards. Peak area performed best for smaller fold differences and was shown to be capable of discerning a 1.1-fold difference with acceptable specificity and sensitivity. The performance of iTRAQ was dramatically worse than the label-free methods with low abundance proteins. Using the iTRAQ data set for validation, we also demonstrate a novel iTRAQ analysis regime that avoids the use of ratios in significance testing and outperforms a common commercial alternative.
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Affiliation(s)
- Adam A Dowle
- Bioscience Technology Facility, Department of Biology, University of York , York YO10 5DD, United Kingdom
| | - Julie Wilson
- Departments of Mathematics and Chemistry, University of York , York YO10 5DD, United Kingdom
| | - Jerry R Thomas
- Bioscience Technology Facility, Department of Biology, University of York , York YO10 5DD, United Kingdom
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50
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Longworth J, Wu D, Huete-Ortega M, Wright PC, Vaidyanathan S. Proteome response of Phaeodactylum tricornutum, during lipid accumulation induced by nitrogen depletion. ALGAL RES 2016; 18:213-224. [PMID: 27812494 PMCID: PMC5070409 DOI: 10.1016/j.algal.2016.06.015] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 05/08/2016] [Accepted: 06/14/2016] [Indexed: 11/26/2022]
Abstract
Nitrogen stress is a common strategy employed to stimulate lipid accumulation in microalgae, a biofuel feedstock of topical interest. Although widely investigated, the underlying mechanism of this strategy is still poorly understood. We examined the proteome response of lipid accumulation in the model diatom, Phaeodactylum tricornutum (CCAP 1055/1), at an earlier stage of exposure to selective nitrogen exclusion than previously investigated, and at a time point when changes would reflect lipid accumulation more than carbohydrate accumulation. In total 1043 proteins were confidently identified (≥ 2 unique peptides) with 645 significant (p < 0.05) changes observed, in the LC-MS/MS based iTRAQ investigation. Analysis of significant changes in KEGG pathways and individual proteins showed that under nitrogen starvation P. tricornutum reorganizes its proteome in favour of nitrogen scavenging and reduced lipid degradation whilst rearranging the central energy metabolism that deprioritizes photosynthetic pathways. By doing this, this species appears to increase nitrogen availability inside the cell and limit its use to the pathways where it is needed most. Compared to previously published proteomic analysis of nitrogen starvation in Chlamydomonas reinhardtii, central energy metabolism and photosynthesis appear to be affected more in the diatom, whilst the green algae appears to invest its energy in reorganizing respiration and the cellular organization pathways.
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