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Habib MAH, Ismail MN. Hevea brasiliensis latex proteomics: a review of analytical methods and the way forward. JOURNAL OF PLANT RESEARCH 2021; 134:43-53. [PMID: 33108557 DOI: 10.1007/s10265-020-01231-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 10/13/2020] [Indexed: 06/11/2023]
Abstract
Natural rubber or latex from the Hevea brasiliensis is an important commodity in various economic sectors in today's modern society. Proteins have been detected in latex since the early twentieth century, and they are known to regulate various biological pathways within the H. brasiliensis trees such as the natural rubber biosynthesis, defence against pathogens, wound healing, and stress tolerance. However, the exact mechanisms of the pathways are still not clear. Proteomic analyses on latex have found various proteins and revealed how they fit into the mechanisms of the biological pathways. In the past three decades, there has been rapid latex protein identification due to the improvement of latex protein extraction methods, as well as the emergence of two-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS). In this manuscript, we reviewed the methods of latex protein extraction that keeps on improving over the past three decades as well as the results of numerous latex protein identification and quantitation.
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Affiliation(s)
- Mohd Afiq Hazlami Habib
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia (USM), 11800, Pulau Pinang, Malaysia
| | - Mohd Nazri Ismail
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia (USM), 11800, Pulau Pinang, Malaysia.
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia (USM), 11800, Pulau Pinang, Malaysia.
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Wang D, Peng C, Zheng X, Chang L, Xu B, Tong Z. Secretome Analysis of the Banana Fusarium Wilt Fungi Foc R1 and Foc TR4 Reveals a New Effector OASTL Required for Full Pathogenicity of Foc TR4 in Banana. Biomolecules 2020; 10:biom10101430. [PMID: 33050283 PMCID: PMC7601907 DOI: 10.3390/biom10101430] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/25/2020] [Accepted: 10/07/2020] [Indexed: 12/16/2022] Open
Abstract
Banana Fusarium wilt (BFW), which is one of the most important banana diseases worldwide, is mainly caused by Fusarium oxysporum f. sp. cubense tropic race 4 (Foc TR4). In this study, we conducted secretome analysis of Foc R1 and Foc TR4 and discovered a total of 120 and 109 secretory proteins (SPs) from Foc R1 cultured alone or with banana roots, respectively, and 129 and 105 SPs respectively from Foc TR4 cultured under the same conditions. Foc R1 and Foc TR4 shared numerous SPs associated with hydrolase activity, oxidoreductase activity, and transferase activity. Furthermore, in culture with banana roots, Foc R1 and Foc TR4 secreted many novel SPs, of which approximately 90% (Foc R1; 57/66; Foc TR4; 50/55) were unconventional SPs without signal peptides. Comparative analysis of SPs in Foc R1 and Foc TR4 revealed that Foc TR4 not only generated more specific SPs but also had a higher proportion of SPs involved in various metabolic pathways, such as phenylalanine metabolism and cysteine and methionine metabolism. The cysteine biosynthesis enzyme O-acetylhomoserine (thiol)-lyase (OASTL) was the most abundant root inducible Foc TR4-specific SP. In addition, knockout of the OASTL gene did not affect growth of Foc TR4; but resulted in the loss of pathogenicity in banana 'Brazil'. We speculated that OASTL functions in banana by interfering with the biosynthesis of cysteine, which is the precursor of an enormous number of sulfur-containing defense compounds. Overall, our studies provide a basic understanding of the SPs in Foc R1 and Foc TR4; including a novel effector in Foc TR4.
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Affiliation(s)
- Dan Wang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (D.W.); (C.P.); (X.Z.); (L.C.)
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Cunzhi Peng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (D.W.); (C.P.); (X.Z.); (L.C.)
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Xingmei Zheng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (D.W.); (C.P.); (X.Z.); (L.C.)
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Lili Chang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (D.W.); (C.P.); (X.Z.); (L.C.)
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Bingqiang Xu
- Haikou Experimental Station (Institute of Tropical Fruit Tree Research) Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Key Laboratory of Banana Genetics and Improvement, Haikou 571101, China
- Correspondence: (B.X.); (Z.T.)
| | - Zheng Tong
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (D.W.); (C.P.); (X.Z.); (L.C.)
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Correspondence: (B.X.); (Z.T.)
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Ippoushi K, Tanaka Y, Wakagi M, Hashimoto N. Evaluation of protein extraction methods for β-conglycinin quantification in soybeans and soybean products. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2020.109871] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Identification and Characterization of Glycoproteins and Their Responsive Patterns upon Ethylene Stimulation in the Rubber Latex. Int J Mol Sci 2020; 21:ijms21155282. [PMID: 32722428 PMCID: PMC7432319 DOI: 10.3390/ijms21155282] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 07/19/2020] [Accepted: 07/23/2020] [Indexed: 12/15/2022] Open
Abstract
Natural rubber is an important industrial material, which is obtained from the only commercially cultivated rubber tree, Hevea brasiliensis. In rubber latex production, ethylene has been extensively used as a stimulant. Recent research showed that post-translational modifications (PTMs) of latex proteins, such as phosphorylation, glycosylation and ubiquitination, are crucial in natural rubber biosynthesis. In this study, comparative proteomics was performed to identify the glycosylated proteins in rubber latex treated with ethylene for different days. Combined with Pro-Q Glycoprotein gel staining and mass spectrometry techniques, we provided the first visual profiling of glycoproteomics of rubber latex and finally identified 144 glycosylated protein species, including 65 differentially accumulated proteins (DAPs) after treating with ethylene for three and/or five days. Gene Ontology (GO) functional annotation showed that these ethylene-responsive glycoproteins are mainly involved in cell parts, membrane components and metabolism. Pathway analysis demonstrated that these glycosylated rubber latex proteins are mainly involved in carbohydrate metabolism, energy metabolism, degradation function and cellular processes in rubber latex metabolism. Protein-protein interaction analysis revealed that these DAPs are mainly centered on acetyl-CoA acetyltransferase and hydroxymethylglutaryl-CoA synthase (HMGS) in the mevalonate pathway for natural rubber biosynthesis. In our glycoproteomics, three protein isoforms of HMGS2 were identified from rubber latex, and only one HMGS2 isoform was sharply increased in rubber latex by ethylene treatment for five days. Furthermore, the HbHMGS2 gene was over-expressed in a model rubber-producing grass Taraxacum Kok-saghyz and rubber content in the roots of transgenic rubber grass was significantly increased over that in the wild type plant, indicating HMGS2 is the key component for natural rubber production.
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Xie Q, Ding G, Zhu L, Yu L, Yuan B, Gao X, Wang D, Sun Y, Liu Y, Li H, Wang X. Proteomic Landscape of the Mature Roots in a Rubber-Producing Grass Taraxacum Kok-saghyz. Int J Mol Sci 2019; 20:ijms20102596. [PMID: 31137823 PMCID: PMC6566844 DOI: 10.3390/ijms20102596] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 05/23/2019] [Accepted: 05/24/2019] [Indexed: 12/25/2022] Open
Abstract
The rubber grass Taraxacum kok-saghyz (TKS) contains large amounts of natural rubber (cis-1,4-polyisoprene) in its enlarged roots and it is an alternative crop source of natural rubber. Natural rubber biosynthesis (NRB) and storage in the mature roots of TKS is a cascade process involving many genes, proteins and their cofactors. The TKS genome has just been annotated and many NRB-related genes have been determined. However, there is limited knowledge about the protein regulation mechanism for NRB in TKS roots. We identified 371 protein species from the mature roots of TKS by combining two-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS). Meanwhile, a large-scale shotgun analysis of proteins in TKS roots at the enlargement stage was performed, and 3545 individual proteins were determined. Subsequently, all identified proteins from 2-DE gel and shotgun MS in TKS roots were subject to gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses and most proteins were involved in carbon metabolic process with catalytic activity in membrane-bounded organelles, followed by proteins with binding ability, transportation and phenylpropanoid biosynthesis activities. Fifty-eight NRB-related proteins, including eight small rubber particle protein (SRPP) and two rubber elongation factor(REF) members, were identified from the TKS roots, and these proteins were involved in both mevalonate acid (MVA) and methylerythritol phosphate (MEP) pathways. To our best knowledge, it is the first high-resolution draft proteome map of the mature TKS roots. Our proteomics of TKS roots revealed both MVA and MEP pathways are important for NRB, and SRPP might be more important than REF for NRB in TKS roots. These findings would not only deepen our understanding of the TKS root proteome, but also provide new evidence on the roles of these NRB-related proteins in the mature TKS roots.
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Affiliation(s)
- Quanliang Xie
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, College of Life Sciences, Shihezi University, Shihezi 832003, China.
- Key Laboratory for Ecology of Tropical Islands, Ministry of Education, College of Life Sciences, Hainan Normal University, Haikou 571158, Hainan, China.
| | - Guohua Ding
- Key Laboratory for Ecology of Tropical Islands, Ministry of Education, College of Life Sciences, Hainan Normal University, Haikou 571158, Hainan, China.
| | - Liping Zhu
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, College of Life Sciences, Shihezi University, Shihezi 832003, China.
- Key Laboratory for Ecology of Tropical Islands, Ministry of Education, College of Life Sciences, Hainan Normal University, Haikou 571158, Hainan, China.
| | - Li Yu
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, College of Life Sciences, Shihezi University, Shihezi 832003, China.
- Key Laboratory for Ecology of Tropical Islands, Ministry of Education, College of Life Sciences, Hainan Normal University, Haikou 571158, Hainan, China.
| | - Boxuan Yuan
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, College of Life Sciences, Shihezi University, Shihezi 832003, China.
- Key Laboratory for Ecology of Tropical Islands, Ministry of Education, College of Life Sciences, Hainan Normal University, Haikou 571158, Hainan, China.
| | - Xuan Gao
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, College of Life Sciences, Shihezi University, Shihezi 832003, China.
| | - Dan Wang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, Hainan, China.
| | - Yong Sun
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, Hainan, China.
| | - Yang Liu
- Key Laboratory for Ecology of Tropical Islands, Ministry of Education, College of Life Sciences, Hainan Normal University, Haikou 571158, Hainan, China.
| | - Hongbin Li
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, College of Life Sciences, Shihezi University, Shihezi 832003, China.
| | - Xuchu Wang
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, College of Life Sciences, Shihezi University, Shihezi 832003, China.
- Key Laboratory for Ecology of Tropical Islands, Ministry of Education, College of Life Sciences, Hainan Normal University, Haikou 571158, Hainan, China.
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Jin X, Zhu L, Tao C, Xie Q, Xu X, Chang L, Tan Y, Ding G, Li H, Wang X. An improved protein extraction method applied to cotton leaves is compatible with 2-DE and LC-MS. BMC Genomics 2019; 20:285. [PMID: 30975097 PMCID: PMC6458646 DOI: 10.1186/s12864-019-5658-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 03/29/2019] [Indexed: 12/16/2022] Open
Abstract
Background Two-dimensional electrophoresis (2-DE) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) are widely used in plant proteomics research. However, these two techniques cannot be simultaneously satisfied by traditional protein extraction methods when investigate cotton leaf proteome. Results Here, we evaluated the efficiency of three different protein extraction methods for 2-DE and LC-MS/MS analyses of total proteins obtained from cotton leaves. The protein yield of the borax/PVPP/phenol (BPP) method (0.14%) was significantly lower than the yields of the trichloroacetic acid/acetone (TCA) precipitation method (1.42%) and optimized TCA combined with BPP (TCA-B) method (0.47%). The BPP method was failed to get a clear 2-DE electrophoretogram. Fifty pairs of protein spots were randomly selected from the 2-DE gels of TCA- and TCA-B-extracted proteins for identification by MALDI TOF/TOF, and the results of 42 pairs were consistent. High-throughput proteomic analysis showed that 6339, 9282 and 9697 unique proteins were identified from the total cotton leaf proteins extracted by the TCA, BPP and TCA-B methods, respectively. Gene Ontology (GO) analysis revealed that the proteins specifically identified by TCA method were primarily distributed in the plasma membrane, while BPP and TCA-B methods specific proteins distributed in the cytosol, indicating the sub-cellular preference of different protein extraction methods. Further, ATP-dependent zinc metalloprotease FTSH 8 could be observed in the 2-DE gels of TCA and TCA-B methods, and could only be detected in the LC-MS/MS results of the BPP and TCA-B methods, showing that TCA-B method might be the optimized choice for both 2-DE and LC-MS/MS. Conclusion Our data provided an improved TCA-B method for protein extraction that is compatible with 2-DE and LC-MS/MS for cotton leaves and similar plant tissues which is rich in polysaccharides and polyphenols. Electronic supplementary material The online version of this article (10.1186/s12864-019-5658-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiang Jin
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, 571158, China.,College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi, 832003, China
| | - Liping Zhu
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi, 832003, China
| | - Chengcheng Tao
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi, 832003, China
| | - Quanliang Xie
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi, 832003, China
| | - Xinyang Xu
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, 571158, China
| | - Lili Chang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Yanhua Tan
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Guohua Ding
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, 571158, China
| | - Hongbin Li
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi, 832003, China.
| | - Xuchu Wang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, 571158, China. .,College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi, 832003, China. .,Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China.
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Gao L, Sun Y, Wu M, Wang D, Wei J, Wu B, Wang G, Wu W, Jin X, Wang X, He P. Physiological and Proteomic Analyses of Molybdenum- and Ethylene-Responsive Mechanisms in Rubber Latex. FRONTIERS IN PLANT SCIENCE 2018; 9:621. [PMID: 29868077 PMCID: PMC5962772 DOI: 10.3389/fpls.2018.00621] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 04/19/2018] [Indexed: 06/08/2023]
Abstract
Molybdenum (Mo) is an essential micronutrient in many plants. In the rubber tree Hevea brasiliensis, Mo application can reduce the shrinkage of the tapping line, decrease tapping panel dryness, and finally increase rubber latex yield. After combined Mo with ethylene (Eth), these effects become more obvious. However, the molecular mechanism remains unclear. Here, we compared the changed patterns of physiological parameters and protein accumulation in rubber latex after treated with Mo and/or Eth. Our results demonstrated that both Eth and Mo can improve the contents of thiol, sucrose, and dry yield in rubber latex. However, lutoid bursting is significantly inhibited by Mo. Comparative proteomics identified 169 differentially expressed proteins, including 114 unique proteins, which are mainly involved in posttranslational modification, carbohydrate metabolism, and energy production. The abundances of several proteins involved in rubber particle aggregation are decreased upon Mo stimulation, while many enzymes related to natural rubber biosynthesis are increased. Comparison of the accumulation patterns of 25 proteins revealed that a large portion of proteins have different changed patterns with their gene expression levels. Activity assays of six enzymes revealed that Mo stimulation can increase latex yield by improving the activity of some Mo-responsive enzymes. These results not only deepen our understanding of the rubber latex proteome but also provide new insights into the molecular mechanism of Mo-stimulated rubber latex yield.
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Affiliation(s)
- Le Gao
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- College of Life Sciences, Key Laboratory for Ecology of Tropical Islands, Ministry of Education, Hainan Normal University, Haikou, China
| | - Yong Sun
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- College of Life Sciences, Key Laboratory for Ecology of Tropical Islands, Ministry of Education, Hainan Normal University, Haikou, China
| | - Min Wu
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Dan Wang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jiashao Wei
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Bingsun Wu
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Guihua Wang
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Wenguan Wu
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xiang Jin
- College of Life Sciences, Key Laboratory for Ecology of Tropical Islands, Ministry of Education, Hainan Normal University, Haikou, China
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xuchu Wang
- College of Life Sciences, Key Laboratory for Ecology of Tropical Islands, Ministry of Education, Hainan Normal University, Haikou, China
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Peng He
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- College of Life Sciences, Key Laboratory for Ecology of Tropical Islands, Ministry of Education, Hainan Normal University, Haikou, China
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Wang D, Sun Y, Chang L, Tong Z, Xie Q, Jin X, Zhu L, He P, Li H, Wang X. Subcellular proteome profiles of different latex fractions revealed washed solutions from rubber particles contain crucial enzymes for natural rubber biosynthesis. J Proteomics 2018; 182:53-64. [PMID: 29729991 DOI: 10.1016/j.jprot.2018.05.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 04/30/2018] [Accepted: 05/02/2018] [Indexed: 01/20/2023]
Abstract
Rubber particle (RP) is a specific organelle for natural rubber biosynthesis (NRB) and storage in rubber tree Hevea brasiliensis. NRB is processed by RP membrane-localized proteins, which were traditionally purified by repeated washing. However, we noticed many proteins in the discarded washing solutions (WS) from RP. Here, we compared the proteome profiles of WS, C-serum (CS) and RP by 2-DE, and identified 233 abundant proteins from WS by mass spectrometry. Many spots on 2-DE gels were identified as different protein species. We further performed shotgun analysis of CS, WS and RP and identified 1837, 1799 and 1020 unique proteins, respectively. Together with 2-DE, we finally identified 1825 proteins from WS, 246 were WS-specific. These WS-specific proteins were annotated in Gene Ontology, indicating most abundant pathways are organic substance metabolic process, protein degradation, primary metabolic process, and energy metabolism. Protein-protein interaction analysis revealed these WS-specific proteins are mainly involved in ribosomal metabolism, proteasome system, vacuolar protein sorting and endocytosis. Label free and Western blotting revealed many WS-specific proteins and protein complexes are crucial for NRB initiation. These findings not only deepen our understanding of WS proteome, but also provide new evidences on the roles of RP membrane proteins in NRB. SIGNIFICANCE Natural rubber is stored in rubber particle from the rubber tree. Rubber particles were traditionally purified by repeated washing, but many proteins were identified from the washing solutions (WS). We obtained the first visualization proteome profiles with 1825 proteins from WS, including 246 WS-specific ones. These WS proteins contain almost all enzymes for polyisoprene initiation and may play important roles in rubber biosynthesis.
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Affiliation(s)
- Dan Wang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China; College of Life Sciences, Ministry of Education Key Laboratory for Ecology of Tropical Islands, Hainan Normal University, Haikou, Hainan 571158, China
| | - Yong Sun
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China; Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan 571737, China
| | - Lili Chang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China
| | - Zheng Tong
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China
| | - Quanliang Xie
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China; College of Life Sciences, Key Laboratory of Agrobiotechnology, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Xiang Jin
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China; College of Life Sciences, Ministry of Education Key Laboratory for Ecology of Tropical Islands, Hainan Normal University, Haikou, Hainan 571158, China
| | - Liping Zhu
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China; College of Life Sciences, Key Laboratory of Agrobiotechnology, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Peng He
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan 571737, China
| | - Hongbin Li
- College of Life Sciences, Key Laboratory of Agrobiotechnology, Shihezi University, Shihezi, Xinjiang 832003, China.
| | - Xuchu Wang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China; College of Life Sciences, Ministry of Education Key Laboratory for Ecology of Tropical Islands, Hainan Normal University, Haikou, Hainan 571158, China; College of Life Sciences, Key Laboratory of Agrobiotechnology, Shihezi University, Shihezi, Xinjiang 832003, China.
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Jiang Z, Kumar M, Padula MP, Pernice M, Kahlke T, Kim M, Ralph PJ. Development of an Efficient Protein Extraction Method Compatible with LC-MS/MS for Proteome Mapping in Two Australian Seagrasses Zostera muelleri and Posidonia australis. FRONTIERS IN PLANT SCIENCE 2017; 8:1416. [PMID: 28861098 PMCID: PMC5559503 DOI: 10.3389/fpls.2017.01416] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/31/2017] [Indexed: 05/31/2023]
Abstract
The availability of the first complete genome sequence of the marine flowering plant Zostera marina (commonly known as seagrass) in early 2016, is expected to significantly raise the impact of seagrass proteomics. Seagrasses are marine ecosystem engineers that are currently declining worldwide at an alarming rate due to both natural and anthropogenic disturbances. Seagrasses (especially species of the genus Zostera) are compromised for proteomic studies primarily due to the lack of efficient protein extraction methods because of their recalcitrant cell wall which is rich in complex polysaccharides and a high abundance of secondary metabolites in their cells. In the present study, three protein extraction methods that are commonly used in plant proteomics i.e., phenol (P); trichloroacetic acid/acetone/SDS/phenol (TASP); and borax/polyvinyl-polypyrrolidone/phenol (BPP) extraction, were evaluated quantitatively and qualitatively based on two dimensional isoelectric focusing (2D-IEF) maps and LC-MS/MS analysis using the two most abundant Australian seagrass species, namely Zostera muelleri and Posidonia australis. All three tested methods produced high quality protein extracts with excellent 2D-IEF maps in P. australis. However, the BPP method produces better results in Z. muelleri compared to TASP and P. Therefore, we further modified the BPP method (M-BPP) by homogenizing the tissue in a modified protein extraction buffer containing both ionic and non-ionic detergents (0.5% SDS; 1.5% Triton X-100), 2% PVPP and protease inhibitors. Further, the extracted proteins were solubilized in 0.5% of zwitterionic detergent (C7BzO) instead of 4% CHAPS. This slight modification to the BPP method resulted in a higher protein yield, and good quality 2-DE maps with a higher number of protein spots in both the tested seagrasses. Further, the M-BPP method was successfully utilized in western-blot analysis of phosphoenolpyruvate carboxylase (PEPC-a key enzyme for carbon metabolism). This optimized protein extraction method will be a significant stride toward seagrass proteome mining and identifying the protein biomarkers to stress response of seagrasses under the scenario of global climate change and anthropogenic perturbations.
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Affiliation(s)
- Zhijian Jiang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of SciencesGuangzhou, China
- Climate Change Cluster (C3), Faculty of Science, University of Technology Sydney (UTS)Sydney, NSW, Australia
| | - Manoj Kumar
- Climate Change Cluster (C3), Faculty of Science, University of Technology Sydney (UTS)Sydney, NSW, Australia
| | - Matthew P. Padula
- Proteomics Core Facility, University of Technology Sydney (UTS)Sydney, NSW, Australia
| | - Mathieu Pernice
- Climate Change Cluster (C3), Faculty of Science, University of Technology Sydney (UTS)Sydney, NSW, Australia
| | - Tim Kahlke
- Climate Change Cluster (C3), Faculty of Science, University of Technology Sydney (UTS)Sydney, NSW, Australia
| | - Mikael Kim
- Climate Change Cluster (C3), Faculty of Science, University of Technology Sydney (UTS)Sydney, NSW, Australia
| | - Peter J. Ralph
- Climate Change Cluster (C3), Faculty of Science, University of Technology Sydney (UTS)Sydney, NSW, Australia
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