1
|
Boschetti E, Righetti PG. Low-Abundance Protein Enrichment for Medical Applications: The Involvement of Combinatorial Peptide Library Technique. Int J Mol Sci 2023; 24:10329. [PMID: 37373476 DOI: 10.3390/ijms241210329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/09/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
The discovery of low- and very low-abundance proteins in medical applications is considered a key success factor in various important domains. To reach this category of proteins, it is essential to adopt procedures consisting of the selective enrichment of species that are present at extremely low concentrations. In the past few years pathways towards this objective have been proposed. In this review, a general landscape of the enrichment technology situation is made first with the presentation and the use of combinatorial peptide libraries. Then, a description of this peculiar technology for the identification of early-stage biomarkers for well-known pathologies with concrete examples is given. In another field of medical applications, the determination of host cell protein traces potentially present in recombinant therapeutic proteins, such as antibodies, is discussed along with their potentially deleterious effects on the health of patients on the one hand, and on the stability of these biodrugs on the other hand. Various additional applications of medical interest are disclosed for biological fluids investigations where the target proteins are present at very low concentrations (e.g., protein allergens).
Collapse
|
2
|
Woo J, Clair GC, Williams SM, Feng S, Tsai CF, Moore RJ, Chrisler WB, Smith RD, Kelly RT, Paša-Tolić L, Ansong C, Zhu Y. Three-dimensional feature matching improves coverage for single-cell proteomics based on ion mobility filtering. Cell Syst 2022; 13:426-434.e4. [PMID: 35298923 PMCID: PMC9119937 DOI: 10.1016/j.cels.2022.02.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/04/2021] [Accepted: 02/17/2022] [Indexed: 12/13/2022]
Abstract
Single-cell proteomics (scProteomics) promises to advance our understanding of cell functions within complex biological systems. However, a major challenge of current methods is their inability to identify and provide accurate quantitative information for low-abundance proteins. Herein, we describe an ion-mobility-enhanced mass spectrometry acquisition and peptide identification method, transferring identification based on FAIMS filtering (TIFF), to improve the sensitivity and accuracy of label-free scProteomics. TIFF extends the ion accumulation times for peptide ions by filtering out singly charged ions. The peptide identities are assigned by a three-dimensional MS1 feature matching approach (retention time, accurate mass, and FAIMS compensation voltage). The TIFF method enabled unbiased proteome analysis to a depth of >1,700 proteins in single HeLa cells, with >1,100 proteins consistently identified. As a demonstration, we applied the TIFF method to obtain temporal proteome profiles of >150 single murine macrophage cells during lipopolysaccharide stimulation and identified time-dependent proteome changes. A record of this paper's transparent peer review process is included in the supplemental information.
Collapse
Affiliation(s)
- Jongmin Woo
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Geremy C Clair
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Sarah M Williams
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Song Feng
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - William B Chrisler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Ryan T Kelly
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA; Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Charles Ansong
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
| |
Collapse
|
3
|
Shi J, Xiao J, Li J, Wang X, Her L, Sorensen MJ, Zhu HJ. FRACPRED-2D-PRM: A Fraction Prediction Algorithm-Assisted 2D Liquid Chromatography-Based Parallel Reaction Monitoring-Mass Spectrometry Approach for Measuring Low-Abundance Proteins in Human Plasma. Proteomics 2020; 20:e2000175. [PMID: 33085175 DOI: 10.1002/pmic.202000175] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/09/2020] [Indexed: 11/09/2022]
Abstract
Multidimensional fractionation-based enrichment methods improve the sensitivity of proteomic analysis for low-abundance proteins. However, a major limitation of conventional multidimensional proteomics is the extensive labor and instrument time required for analyzing many fractions obtained from the first dimension separation. Here, a fraction prediction algorithm-assisted 2D LC-based parallel reaction monitoring-mass spectrometry (FRACPRED-2D-PRM) approach for measuring low-abundance proteins in human plasma is presented. Plasma digests are separated by the first dimension high-pH RP-LC with data-dependent acquisition (DDA). The FRACPRED algorithm is then usedto predict the retention times of undetectable target peptides according to those of other abundant plasma peptides during the first dimension separation. Fractions predicted to contain target peptides are analyzed by the second dimension low-pH nano RP-LC PRM. The accuracy and robustness of fraction prediction with the FRACPRED algorithm are demonstrated by measuring two low-abundance proteins, aldolase B and carboxylesterase 1, in human plasma. The FRACPRED-2D-PRM proteomics approach demonstrates markedly improved efficiency and sensitivity over conventional 2D-LC proteomics assays. It is expected that this approach will be widely used in the study of low-abundance proteins in plasma and other complex biological samples.
Collapse
Affiliation(s)
- Jian Shi
- Department of Clinical Pharmacy, University of Michigan, Ann Arbor, MI, 48109-1065, USA
| | - Jingcheng Xiao
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, 48109-1065, USA
| | - Jiapeng Li
- Department of Clinical Pharmacy, University of Michigan, Ann Arbor, MI, 48109-1065, USA
| | - Xinwen Wang
- Department of Clinical Pharmacy, University of Michigan, Ann Arbor, MI, 48109-1065, USA
| | - Lucy Her
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, 48109-1065, USA
| | - Matthew J Sorensen
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109-1065, USA
| | - Hao-Jie Zhu
- Department of Clinical Pharmacy, University of Michigan, Ann Arbor, MI, 48109-1065, USA
| |
Collapse
|
4
|
Min CW, Park J, Bae JW, Agrawal GK, Rakwal R, Kim Y, Yang P, Kim ST, Gupta R. In-Depth Investigation of Low-Abundance Proteins in Matured and Filling Stages Seeds of Glycine max Employing a Combination of Protamine Sulfate Precipitation and TMT-Based Quantitative Proteomic Analysis. Cells 2020; 9:E1517. [PMID: 32580392 PMCID: PMC7349688 DOI: 10.3390/cells9061517] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 02/06/2023] Open
Abstract
Despite the significant technical advancements in mass spectrometry-based proteomics and bioinformatics resources, dynamic resolution of soybean seed proteome is still limited because of the high abundance of seed storage proteins (SSPs). These SSPs occupy a large proportion of the total seed protein and hinder the identification of low-abundance proteins. Here, we report a TMT-based quantitative proteome analysis of matured and filling stages seeds of high-protein (Saedanbaek) and low-protein (Daewon) soybean cultivars by application of a two-way pre-fractionation both at the levels of proteins (by PS) and peptides (by basic pH reverse phase chromatography). Interestingly, this approach led to the identification of more than 5900 proteins which is the highest number of proteins reported to date from soybean seeds. Comparative protein profiles of Saedanbaek and Daewon led to the identification of 2200 and 924 differential proteins in mature and filling stages seeds, respectively. Functional annotation of the differential proteins revealed enrichment of proteins related to major metabolism including amino acid, major carbohydrate, and lipid metabolism. In parallel, analysis of free amino acids and fatty acids in the filling stages showed higher contents of all the amino acids in the Saedanbaek while the fatty acids contents were found to be higher in the Daewon. Taken together, these results provide new insights into proteome changes during filling stages in soybean seeds. Moreover, results reported here also provide a framework for systemic and large-scale dissection of seed proteome for the seeds rich in SSPs by two-way pre-fractionation combined with TMT-based quantitative proteome analysis.
Collapse
Affiliation(s)
- Cheol Woo Min
- Department of Plant Bioscience, Pusan National University, Miryang 50463, Korea;
| | - Joonho Park
- Interdisciplinary Program in Bioengineering, College of Engineering, Seoul National University, Seoul 03080, Korea; (J.P.); (Y.K.)
| | - Jin Woo Bae
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea;
| | - Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO 13265, Kathmandu 44600, Nepal; (G.K.A.); (R.R.)
- GRADE (Global Research Arch for Developing Education) Academy Private Limited, Adarsh Nagar-13, Birgunj 44300, Nepal
| | - Randeep Rakwal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO 13265, Kathmandu 44600, Nepal; (G.K.A.); (R.R.)
- GRADE (Global Research Arch for Developing Education) Academy Private Limited, Adarsh Nagar-13, Birgunj 44300, Nepal
- Faculty of Health and Sport Sciences, University of Tsukuba, 1-1-1Tennodai, Tsukuba 3058574, Japan
| | - Youngsoo Kim
- Interdisciplinary Program in Bioengineering, College of Engineering, Seoul National University, Seoul 03080, Korea; (J.P.); (Y.K.)
| | - Pingfang Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China;
| | - Sun Tae Kim
- Department of Plant Bioscience, Pusan National University, Miryang 50463, Korea;
| | - Ravi Gupta
- Department of Plant Bioscience, Pusan National University, Miryang 50463, Korea;
- Department of Botany, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India
| |
Collapse
|
5
|
Min CW, Gupta R, Agrawal GK, Rakwal R, Kim ST. Concepts and strategies of soybean seed proteomics using the shotgun proteomics approach. Expert Rev Proteomics 2019; 16:795-804. [PMID: 31398080 DOI: 10.1080/14789450.2019.1654860] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 08/08/2019] [Indexed: 12/30/2022]
Abstract
Introduction: The last decade has yielded significant developments in the field of proteomics, especially in mass spectrometry (MS) and data analysis tools. In particular, a shift from gel-based to MS-based proteomics has been observed, thereby providing a platform with which to construct proteome atlases for all life forms. Nevertheless, the analysis of plant proteomes, especially those of samples that contain high-abundance proteins (HAPs), such as soybean seeds, remains challenging. Areas covered: Here, we review recent progress in soybean seed proteomics and highlight advances in HAPs depletion methods and peptide pre-fractionation, identification, and quantification methods. We also suggest a pipeline for future proteomic analysis, in order to increase the dynamic coverage of the soybean seed proteome. Expert opinion: Because HAPs limit the dynamic resolution of the soybean seed proteome, the depletion of HAPs is a prerequisite of high-throughput proteome analysis, and owing to the use of two-dimensional gel electrophoresis-based proteomic approaches, few soybean seed proteins have been identified or characterized. Recent advances in proteomic technologies, which have significantly increased the proteome coverage of other plants, could be used to overcome the current complexity and limitation of soybean seed proteomics.
Collapse
Affiliation(s)
- Cheol Woo Min
- Department of Plant Bioscience, Life and industry Convergence Research Institute, Pusan National University , Miryang , Korea
| | - Ravi Gupta
- Department of Plant Bioscience, Life and industry Convergence Research Institute, Pusan National University , Miryang , Korea
| | - Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO 13265 , Kathmandu , Nepal
- GRADE (Global Research Arch for Developing Education) Academy Private Limited , Birgunj , Nepal
| | - Randeep Rakwal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO 13265 , Kathmandu , Nepal
- GRADE (Global Research Arch for Developing Education) Academy Private Limited , Birgunj , Nepal
- Faculty of Health and Sport Sciences, University of Tsukuba , Tsukuba , Ibaraki , Japan
| | - Sun Tae Kim
- Department of Plant Bioscience, Life and industry Convergence Research Institute, Pusan National University , Miryang , Korea
| |
Collapse
|
6
|
Zhang C, Shi Z, Han Y, Ren Y, Hao P. Multiparameter Optimization of Two Common Proteomics Quantification Methods for Quantifying Low-Abundance Proteins. J Proteome Res 2018; 18:461-468. [PMID: 30394099 DOI: 10.1021/acs.jproteome.8b00769] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Quantitative proteomics has been extensively applied in the screening of differentially regulated proteins in various research areas for decades, but its sensitivity and accuracy have been a bottleneck for many applications. Every step in the proteomics workflow can potentially affect the quantification of low-abundance proteins, but a systematic evaluation of their effects has not been done yet. In this work, to improve the sensitivity and accuracy of label-free quantification and tandem mass tags (TMT) labeling in quantifying low-abundance proteins, multiparameter optimization was carried out using a complex 2-proteome artificial sample mixture for a series of steps from sample preparation to data analysis, including the desalting of peptides, peptide injection amount for LC-MS/MS, MS1 resolution, the length of LC-MS/MS gradient, AGC targets, ion accumulation time, MS2 resolution, precursor coisolation threshold, data analysis software, statistical calculation methods, and protein fold changes, and the best settings for each parameter were defined. The suitable cutoffs for detecting low-abundance proteins with at least 1.5-fold and 2-fold changes were identified for label-free and TMT methods, respectively. The use of optimized parameters will significantly improve the overall performance of quantitative proteomics in quantifying low-abundance proteins and thus promote its application in other research areas.
Collapse
Affiliation(s)
- Chengqian Zhang
- School of Life Science and Technology , ShanghaiTech University , 393 Middle Huaxia Road , Shanghai 201210 , China
| | - Zhaomei Shi
- School of Life Science and Technology , ShanghaiTech University , 393 Middle Huaxia Road , Shanghai 201210 , China
| | - Ying Han
- School of Life Science and Technology , ShanghaiTech University , 393 Middle Huaxia Road , Shanghai 201210 , China
| | - Yan Ren
- BGI-Shenzhen , Beishan Industrial Zone 11th building , Yantian District, Shenzhen , Guangdong 518083 , China.,China National GeneBank , BGI-Shenzhen , Jinsha Road , Shenzhen 518120 , China
| | - Piliang Hao
- School of Life Science and Technology , ShanghaiTech University , 393 Middle Huaxia Road , Shanghai 201210 , China
| |
Collapse
|
7
|
Gupta R, Min CW, Wang Y, Kim YC, Agrawal GK, Rakwal R, Kim ST. Expect the Unexpected Enrichment of "Hidden Proteome" of Seeds and Tubers by Depletion of Storage Proteins. Front Plant Sci 2016; 7:761. [PMID: 27313590 PMCID: PMC4887479 DOI: 10.3389/fpls.2016.00761] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 05/17/2016] [Indexed: 05/03/2023]
Abstract
Dynamic resolution of seed and tuber protein samples is highly limited due to the presence of high-abundance storage proteins (SPs). These proteins inevitably obscure the low-abundance proteins (LAPs) impeding their identification and characterization. To facilitate the detection of LAPs, several methods have been developed during the past decade, enriching the proteome with extreme proteins. Most of these methods, if not all, are based on the specific removal of SPs which ultimately magnify the proteome coverage. In this mini-review, we summarize the available methods that have been developed over the years for the enrichment of LAPs either from seeds or tubers. Incorporation of these methods during the protein extraction step will be helpful in understanding the seed/tuber biology in greater detail.
Collapse
Affiliation(s)
- Ravi Gupta
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National UniversityMiryang, South Korea
| | - Cheol W. Min
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National UniversityMiryang, South Korea
| | - Yiming Wang
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Yong C. Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National UniversityMiryang, South Korea
| | - Ganesh K. Agrawal
- Research Laboratory for Biotechnology and BiochemistryKathmandu, Nepal
- Global Research Arch for Developing Education, Academy Pvt. Ltd.Birgunj, Nepal
| | - Randeep Rakwal
- Global Research Arch for Developing Education, Academy Pvt. Ltd.Birgunj, Nepal
- Faculty of Health and Sport Sciences and Tsukuba International Academy for Sport Studies, University of TsukubaIbaraki, Japan
| | - Sun T. Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National UniversityMiryang, South Korea
- *Correspondence: Sun T. Kim,
| |
Collapse
|
8
|
Lancrajan I, Schneider-Stock R, Naschberger E, Schellerer VS, Stürzl M, Enz R. Absolute quantification of DcR3 and GDF15 from human serum by LC-ESI MS. J Cell Mol Med 2015; 19:1656-71. [PMID: 25823874 PMCID: PMC4511363 DOI: 10.1111/jcmm.12540] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 12/16/2014] [Indexed: 12/22/2022] Open
Abstract
Biomarkers are widely used in clinical diagnosis, prognosis and therapy monitoring. Here, we developed a protocol for the efficient and selective enrichment of small and low concentrated biomarkers from human serum, involving a 95% effective depletion of high-abundant serum proteins by partial denaturation and enrichment of low-abundant biomarkers by size exclusion chromatography. The recovery of low-abundance biomarkers was above 97%. Using this protocol, we quantified the tumour markers DcR3 and growth/differentiation factor (GDF)15 from 100 μl human serum by isotope dilution mass spectrometry, using 15N metabolically labelled and concatamerized fingerprint peptides for the both proteins. Analysis of three different fingerprint peptides for each protein by liquid chromatography electrospray ionization mass spectrometry resulted in comparable concentrations in three healthy human serum samples (DcR3: 27.23 ± 2.49 fmol/ml; GDF15: 98.11 ± 0.49 fmol/ml). In contrast, serum levels were significantly elevated in tumour patients for DcR3 (116.94 ± 57.37 fmol/ml) and GDF15 (164.44 ± 79.31 fmol/ml). Obtained data were in good agreement with ELISA and qPCR measurements, as well as with literature data. In summary, our protocol allows the reliable quantification of biomarkers, shows a higher resolution at low biomarker concentrations than antibody-based strategies, and offers the possibility of multiplexing. Our proof-of-principle studies in patient sera encourage the future analysis of the prognostic value of DcR3 and GDF15 for colon cancer patients in larger patient cohorts.
Collapse
Affiliation(s)
- Ioana Lancrajan
- Institute of Biochemistry (Emil-Fischer-Centre), Friedrich-Alexander-University of Erlangen-Nuremberg, Erlangen, Germany
| | - Regine Schneider-Stock
- Experimental Tumorpathology, Institute of Pathology, Friedrich-Alexander-University of Erlangen-Nuremberg, Erlangen, Germany
| | - Elisabeth Naschberger
- Division of Molecular and Experimental Surgery, University Medical Centre Erlangen, Erlangen, Germany
| | - Vera S Schellerer
- Department of Surgery, University Medical Centre Erlangen, 91054, Erlangen
| | - Michael Stürzl
- Division of Molecular and Experimental Surgery, University Medical Centre Erlangen, Erlangen, Germany
| | - Ralf Enz
- Institute of Biochemistry (Emil-Fischer-Centre), Friedrich-Alexander-University of Erlangen-Nuremberg, Erlangen, Germany
| |
Collapse
|
9
|
Gupta R, Wang Y, Agrawal GK, Rakwal R, Jo IH, Bang KH, Kim ST. Time to dig deep into the plant proteome: a hunt for low-abundance proteins. Front Plant Sci 2015; 6:22. [PMID: 25688253 PMCID: PMC4311630 DOI: 10.3389/fpls.2015.00022] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 01/12/2015] [Indexed: 05/04/2023]
Affiliation(s)
- Ravi Gupta
- Plant Functional Genomics Laboratory, Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National UniversityMiryang, South Korea
| | - Yiming Wang
- Plant Proteomics Group, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Ganesh K. Agrawal
- Research Laboratory for Biotechnology and BiochemistryKathmandu, Nepal
- Global Research Arch for Developing Education (GRADE) Academy Pvt. LtdBirgunj, Nepal
| | - Randeep Rakwal
- Research Laboratory for Biotechnology and BiochemistryKathmandu, Nepal
- Global Research Arch for Developing Education (GRADE) Academy Pvt. LtdBirgunj, Nepal
- Organization for Educational Initiatives, University of TsukubaTsukuba, Japan
- Department of Anatomy I, Showa University School of MedicineTokyo, Japan
| | - Ick H. Jo
- Department of Herbal Crop Research, Rural Development AdministrationEumseong, South Korea
| | - Kyong H. Bang
- Department of Herbal Crop Research, Rural Development AdministrationEumseong, South Korea
| | - Sun T. Kim
- Plant Functional Genomics Laboratory, Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National UniversityMiryang, South Korea
- *Correspondence:
| |
Collapse
|
10
|
López-Castillo LM, López-Arciniega JAI, Guerrero-Rangel A, Valdés-Rodríguez S, Brieba LG, García-Lara S, Winkler R. Identification of B6T173 (ZmPrx35) as the prevailing peroxidase in highly insect-resistant maize (Zea mays, p84C3) kernels by activity-directed purification. Front Plant Sci 2015; 6:670. [PMID: 26379694 PMCID: PMC4553411 DOI: 10.3389/fpls.2015.00670] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 08/13/2015] [Indexed: 05/03/2023]
Abstract
Plant peroxidases (PODs) are involved in diverse physiological processes, including defense against pathogens and insects. Contrary to their biological importance, only very few plant PODs have been proven on protein level, because their low abundance makes them difficult to detect in standard proteomics work-flows. A statistically significant positive correlation between POD activity and post-harvest insect resistance has been found for maize (Zea mays, p84C3) kernels. In combining activity-directed protein purification, genomic and proteomic tools we found that protein B6T173 (ZmPrx35) is responsible for the majority of the POD activity of the kernel. We successfully produced recombinant ZmPrx35 protein in Escherichia coli and demonstrate both, in vitro activity and the presence of a haem (heme) cofactor of the enzyme. Our findings support the screening for insect resistant maize variants and the construction of genetically optimized maize plants.
Collapse
Affiliation(s)
- Laura M. López-Castillo
- Laboratory of Biochemical and Instrumental Analysis, Department of Biotechnology and Biochemistry, Cinvestav Unidad IrapuatoIrapuato, Mexico
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada del Centro de Investigación y de Estudios Avanzados – Instituto Politécnico NacionalIrapuato, Mexico
| | - Janet A. I. López-Arciniega
- Laboratory of Biochemical and Instrumental Analysis, Department of Biotechnology and Biochemistry, Cinvestav Unidad IrapuatoIrapuato, Mexico
| | | | | | - Luis G. Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada del Centro de Investigación y de Estudios Avanzados – Instituto Politécnico NacionalIrapuato, Mexico
| | | | - Robert Winkler
- Laboratory of Biochemical and Instrumental Analysis, Department of Biotechnology and Biochemistry, Cinvestav Unidad IrapuatoIrapuato, Mexico
- *Correspondence: Robert Winkler, Laboratory of Biochemical and Instrumental Analysis, Department of Biotechnology and Biochemistry, Cinvestav Unidad Irapuato, Km. 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Guanajuato, Mexico,
| |
Collapse
|
11
|
Baracat-Pereira MC, de Oliveira Barbosa M, Magalhães MJ, Carrijo LC, Games PD, Almeida HO, Sena Netto JF, Pereira MR, de Barros EG. Separomics applied to the proteomics and peptidomics of low-abundance proteins: Choice of methods and challenges - A review. Genet Mol Biol 2012; 35:283-91. [PMID: 22802713 PMCID: PMC3392880 DOI: 10.1590/s1415-47572012000200009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The enrichment and isolation of proteins are considered limiting steps in proteomic studies. Identification of proteins whose expression is transient, those that are of low-abundance, and of natural peptides not described in databases, is still a great challenge. Plant extracts are in general complex, and contaminants interfere with the identification of proteins involved in important physiological processes, such as plant defense against pathogens. This review discusses the challenges and strategies of separomics applied to the identification of low-abundance proteins and peptides in plants, especially in plants challenged by pathogens. Separomics is described as a group of methodological strategies for the separation of protein molecules for proteomics. Several tools have been used to remove highly abundant proteins from samples and also non-protein contaminants. The use of chromatographic techniques, the partition of the proteome into subproteomes, and an effort to isolate proteins in their native form have allowed the isolation and identification of rare proteins involved in different processes.
Collapse
Affiliation(s)
- Maria Cristina Baracat-Pereira
- Departamento de Bioquímica e Biologia Molecular, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Meire de Oliveira Barbosa
- Departamento de Bioquímica e Biologia Molecular, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Marcos Jorge Magalhães
- Departamento de Bioquímica e Biologia Molecular, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Lanna Clicia Carrijo
- Departamento de Bioquímica e Biologia Molecular, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Patrícia Dias Games
- Departamento de Bioquímica e Biologia Molecular, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Hebréia Oliveira Almeida
- Departamento de Bioquímica e Biologia Molecular, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - José Fabiano Sena Netto
- Departamento de Bioquímica e Biologia Molecular, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | | | | |
Collapse
|