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Gong J, Zhang H, Zeng Y, Cheng Y, Sun X, Wang P. Combining BN-PAGE and microscopy techniques to investigate pigment-protein complexes and plastid transitions in citrus fruit. PLANT METHODS 2022; 18:124. [PMID: 36403000 PMCID: PMC9675244 DOI: 10.1186/s13007-022-00956-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 11/10/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Chlorophyll and carotenoids, the most widely distributed lipophilic pigments in plants, contribute to fruit coloration during development and ripening. These pigments are assembled with pigment-protein complexes localized at plastid membrane. Pigment-protein complexes are essential for multiple cellular processes, however, their identity and composition in fruit have yet to be characterized. RESULTS By using BN-PAGE technique in combination with microscopy, we studied pigment-protein complexes and plastid transformation in the purified plastids from the exocarp of citrus fruit. The discontinuous sucrose gradient centrifugation was used to isolate total plastids from kumquat fruit, and the purity of isolated plastids was assessed by microscopy observation and western blot analysis. The isolated plastids at different coloring stages were subjected to pigment autofluorescence observation, western blot, two-dimensional electrophoresis analysis and BN-PAGE assessment. Our results demonstrated that (i) chloroplasts differentiate into chromoplasts during fruit coloring, and this differentiation is accompanied with a decrease in the chlorophyll/carotenoid ratio; (ii) BN-PAGE analysis reveals the profiles of macromolecular protein complexes among different types of plastids in citrus fruit; and (iii) the degradation rate of chlorophyll-protein complexes varies during the transition from chloroplasts to chromoplasts, with the stability generally following the order of LHCII > PS II core > LHC I > PS I core. CONCLUSIONS Our optimized methods for both plastid separation and BN-PAGE assessment provide an opportunity for developing a better understanding of pigment-protein complexes and plastid transitions in plant fruit. These attempts also have the potential for expanding our knowledge on the sub-cellular level synchronism of protein changes and pigment metabolism during the transition from chloroplasts to chromoplasts.
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Affiliation(s)
- Jinli Gong
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- National R&D Centre for Citrus Preservation, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Hang Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- National R&D Centre for Citrus Preservation, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yunliu Zeng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- National R&D Centre for Citrus Preservation, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yunjiang Cheng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- National R&D Centre for Citrus Preservation, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Xuepeng Sun
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China.
| | - Pengwei Wang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
- National R&D Centre for Citrus Preservation, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
- Hubei Hongshan Laboratory, Wuhan, 430070, China.
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Song J, Campbell L, Vinqvist-Tymchuk M. Application of quantitative proteomics to investigate fruit ripening and eating quality. JOURNAL OF PLANT PHYSIOLOGY 2022; 276:153766. [PMID: 35921768 DOI: 10.1016/j.jplph.2022.153766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 06/30/2022] [Accepted: 07/09/2022] [Indexed: 06/15/2023]
Abstract
The consumption of fruit and vegetables play an important role in human nutrition, dietary diversity and health. Fruit and vegetable industries impart significant impact on our society, economy, and environment, contributing towards sustainable development in both developing and developed countries. The eating quality of fruit is determined by its appearance, color, firmness, flavor, nutritional components, and the absence of defects from physiological disorders. However, all of these components are affected by many pre- and postharvest factors that influence fruit ripening and senescence. Significant efforts have been made to maintain and improve fruit eating quality by expanding our knowledge of fruit ripening and senescence, as well as by controlling and reducing losses. Innovative approaches are required to gain better understanding of the management of eating quality. With completion of the genome sequence for many horticultural products in recent years and development of the proteomic research technique, quantitative proteomic research on fruit is changing rapidly and represents a complementary research platform to address how genetics and environment influence the quality attributes of various produce. Quantiative proteomic research on fruit is advancing from protein abundance and protein quantitation to gene-protein interactions and post-translational modifications of proteins that occur during fruit development, ripening and in response to environmental influences. All of these techniques help to provide a comprehensive understanding of eating quality. This review focuses on current developments in the field as well as limitations and challenges, both in broad term and with specific examples. These examples include our own research experience in applying quantitative proteomic techniques to identify and quantify the protein changes in association with fruit ripening, quality and development of disorders, as well as possible control mechanisms.
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Affiliation(s)
- Jun Song
- Agriculture and Agri-Food Canada. KRDC, Kentville Research and Development Centre, Kentville, Nova Scotia, B4N 1J5, Canada.
| | - Leslie Campbell
- Agriculture and Agri-Food Canada. KRDC, Kentville Research and Development Centre, Kentville, Nova Scotia, B4N 1J5, Canada
| | - Melinda Vinqvist-Tymchuk
- Agriculture and Agri-Food Canada. KRDC, Kentville Research and Development Centre, Kentville, Nova Scotia, B4N 1J5, Canada
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Mathiazhagan M, Chidambara B, Hunashikatti LR, Ravishankar KV. Genomic Approaches for Improvement of Tropical Fruits: Fruit Quality, Shelf Life and Nutrient Content. Genes (Basel) 2021; 12:1881. [PMID: 34946829 PMCID: PMC8701245 DOI: 10.3390/genes12121881] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/23/2021] [Accepted: 11/16/2021] [Indexed: 12/17/2022] Open
Abstract
The breeding of tropical fruit trees for improving fruit traits is complicated, due to the long juvenile phase, generation cycle, parthenocarpy, polyploidy, polyembryony, heterozygosity and biotic and abiotic factors, as well as a lack of good genomic resources. Many molecular techniques have recently evolved to assist and hasten conventional breeding efforts. Molecular markers linked to fruit development and fruit quality traits such as fruit shape, size, texture, aroma, peel and pulp colour were identified in tropical fruit crops, facilitating Marker-assisted breeding (MAB). An increase in the availability of genome sequences of tropical fruits further aided in the discovery of SNP variants/Indels, QTLs and genes that can ascertain the genetic determinants of fruit characters. Through multi-omics approaches such as genomics, transcriptomics, metabolomics and proteomics, the identification and quantification of transcripts, including non-coding RNAs, involved in sugar metabolism, fruit development and ripening, shelf life, and the biotic and abiotic stress that impacts fruit quality were made possible. Utilizing genomic assisted breeding methods such as genome wide association (GWAS), genomic selection (GS) and genetic modifications using CRISPR/Cas9 and transgenics has paved the way to studying gene function and developing cultivars with desirable fruit traits by overcoming long breeding cycles. Such comprehensive multi-omics approaches related to fruit characters in tropical fruits and their applications in breeding strategies and crop improvement are reviewed, discussed and presented here.
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Affiliation(s)
| | | | | | - Kundapura V. Ravishankar
- Division of Basic Sciences, ICAR Indian Institute of Horticultural Research, Hessaraghatta Lake Post, Bengaluru 560089, India; (M.M.); (B.C.); (L.R.H.)
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4
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Huang X, Hou Z. Label-free quantitative proteomics analysis of jujube ( Ziziphus jujuba Mill.) during different growth stages. RSC Adv 2021; 11:22106-22119. [PMID: 35480818 PMCID: PMC9034241 DOI: 10.1039/d1ra02989d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 06/15/2021] [Indexed: 01/08/2023] Open
Abstract
Chinese jujube (Zizyphus jujuba Mill.), a member of the Rhamnaceae family with favorable nutritional and flavor quality, exhibited characteristic climacteric changes during its fruit growth stage. Therefore, fruit samples were harvested at four developmental stages on days 55 (young fruits), 76 (white-mature fruits), 96 (half-red fruits), and 116 (full-red fruits) after flowering (DAF). This study then investigated those four growth stage changes of the jujube proteome using label-free quantification proteomics. The results identified 4762 proteins in the samples, of which 3757 proteins were quantified. Compared with former stages, the stages examined were designated as "76 vs. 55 DAF" group, "96 vs. 76 DAF" group, and "116 vs. 96 DAF" group. Gene Ontology (GO) and KEGG annotation and enrichment analysis of the differentially expressed proteins (DEPs) showed that 76 vs. 55 DAF group pathways represented amino sugar, nucleotide sugar, ascorbate, and aldarate metabolic pathways. These pathways were associated with cell division and resistance. In the study, the jujube fruit puffing slowed down and attained a stable growth stage in the 76 vs. 55 DAF group. However, fatty acid biosynthesis and phenylalanine metabolism was mainly enriched in the 96 vs. 76 DAF group. Fatty acids are precursors of aromatic substances and fat-soluble pigments in fruit. The upregulation of differential proteins at this stage indicates that aromatic compounds were synthesized in large quantities at this stage and that fruit would enter the ripening stage. During the ripening stage, 55 DEPs were identified to be involved in photosynthesis and flavonoid biosynthesis in the 116 vs. 96 DAF group. Also, the fruit entered the mature stage, which showed that flavonoids were produced in large quantities. Furthermore, the color of jujube turned red, and photosynthesis was significantly reduced. Hence, a link was established between protein profiles and growth phenotypes, which will help improve our understanding of jujube fruit growth at the proteomic level.
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Affiliation(s)
- Xiaoli Huang
- College of Food Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences) No. 3501 Daxue Road, Changqing District Ji'nan Shandong Province 250353 P. R. China +86 531 89631191 +86 188 66151356
| | - Zhaohua Hou
- College of Food Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences) No. 3501 Daxue Road, Changqing District Ji'nan Shandong Province 250353 P. R. China +86 531 89631191 +86 188 66151356
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Ngashangva N, Mukherjee P, Sharma KC, Kalita MC, Indira S. Analysis of Antimicrobial Peptide Metabolome of Bacterial Endophyte Isolated From Traditionally Used Medicinal Plant Millettia pachycarpa Benth. Front Microbiol 2021; 12:656896. [PMID: 34149644 PMCID: PMC8208310 DOI: 10.3389/fmicb.2021.656896] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 04/21/2021] [Indexed: 12/13/2022] Open
Abstract
Increasing prevalence of antimicrobial resistance (AMR) has posed a major health concern worldwide, and the addition of new antimicrobial agents is diminishing due to overexploitation of plants and microbial resources. Inevitably, alternative sources and new strategies are needed to find novel biomolecules to counter AMR and pandemic circumstances. The association of plants with microorganisms is one basic natural interaction that involves the exchange of biomolecules. Such a symbiotic relationship might affect the respective bio-chemical properties and production of secondary metabolites in the host and microbes. Furthermore, the discovery of taxol and taxane from an endophytic fungus, Taxomyces andreanae from Taxus wallachiana, has stimulated much research on endophytes from medicinal plants. A gram-positive endophytic bacterium, Paenibacillus peoriae IBSD35, was isolated from the stem of Millettia pachycarpa Benth. It is a rod-shaped, motile, gram-positive, and endospore-forming bacteria. It is neutralophilic as per Joint Genome Institute’s (JGI) IMG system analysis. The plant was selected based on its ethnobotany history of traditional uses and highly insecticidal properties. Bioactive molecules were purified from P. peoriae IBSD35 culture broth using 70% ammonium sulfate and column chromatography techniques. The biomolecule was enriched to 151.72-fold and the yield percentage was 0.05. Peoriaerin II, a highly potent and broad-spectrum antimicrobial peptide against Staphylococcus aureus ATCC 25923, Escherichia coli ATCC 25922, and Candida albicans ATCC 10231 was isolated. LC-MS sequencing revealed that its N-terminal is methionine. It has four negatively charged residues (Asp + Glu) and a total number of two positively charged residues (Arg + Lys). Its molecular weight is 4,685.13 Da. It is linked to an LC-MS/MS inferred biosynthetic gene cluster with accession number A0A2S6P0H9, and blastp has shown it is 82.4% similar to fusaricidin synthetase of Paenibacillus polymyxa SC2. The 3D structure conformation of the BGC and AMP were predicted using SWISS MODEL homology modeling. Therefore, combining both genomic and proteomic results obtained from P. peoriae IBSD35, associated with M. pachycarpa Benth., will substantially increase the understanding of antimicrobial peptides and assist to uncover novel biological agents.
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Affiliation(s)
- Ng Ngashangva
- A National Institute of Department of Biotechnology, Institute of Bioresources and Sustainable Development (IBSD), Govt. of India, Imphal, India
| | - Pulok Mukherjee
- A National Institute of Department of Biotechnology, Institute of Bioresources and Sustainable Development (IBSD), Govt. of India, Imphal, India
| | - K Chandradev Sharma
- A National Institute of Department of Biotechnology, Institute of Bioresources and Sustainable Development (IBSD), Govt. of India, Imphal, India
| | - M C Kalita
- Department of Biotechnology, Gauhati University, Guwahati, India
| | - Sarangthem Indira
- A National Institute of Department of Biotechnology, Institute of Bioresources and Sustainable Development (IBSD), Govt. of India, Imphal, India
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Liu Z, Lv J, Zhang Z, Li H, Yang B, Chen W, Dai X, Li X, Yang S, Liu L, Ou L, Ma Y, Zou X. Integrative Transcriptome and Proteome Analysis Identifies Major Metabolic Pathways Involved in Pepper Fruit Development. J Proteome Res 2019; 18:982-994. [DOI: 10.1021/acs.jproteome.8b00673] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Zhoubin Liu
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China
- Vegetable Institution of Hunan Academy of Agricultural Science, Changsha 410125, China
| | - Junheng Lv
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China
- Vegetable Institution of Hunan Academy of Agricultural Science, Changsha 410125, China
| | - Zhuqing Zhang
- Vegetable Institution of Hunan Academy of Agricultural Science, Changsha 410125, China
| | - Heng Li
- Shanghai Applied Protein Technology Co. Ltd, Shanghai 200233, P.R. China
| | - Bozhi Yang
- Vegetable Institution of Hunan Academy of Agricultural Science, Changsha 410125, China
| | - Wenchao Chen
- Vegetable Institution of Hunan Academy of Agricultural Science, Changsha 410125, China
| | - Xiongze Dai
- Vegetable Institution of Hunan Academy of Agricultural Science, Changsha 410125, China
| | - Xuefeng Li
- Vegetable Institution of Hunan Academy of Agricultural Science, Changsha 410125, China
| | - Sha Yang
- Vegetable Institution of Hunan Academy of Agricultural Science, Changsha 410125, China
| | - Li Liu
- Shanghai Applied Protein Technology Co. Ltd, Shanghai 200233, P.R. China
| | - Lijun Ou
- Vegetable Institution of Hunan Academy of Agricultural Science, Changsha 410125, China
| | - Yanqing Ma
- Vegetable Institution of Hunan Academy of Agricultural Science, Changsha 410125, China
| | - Xuexiao Zou
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China
- Vegetable Institution of Hunan Academy of Agricultural Science, Changsha 410125, China
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7
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Sadka A, Shlizerman L, Kamara I, Blumwald E. Primary Metabolism in Citrus Fruit as Affected by Its Unique Structure. FRONTIERS IN PLANT SCIENCE 2019; 10:1167. [PMID: 31611894 PMCID: PMC6775482 DOI: 10.3389/fpls.2019.01167] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 08/26/2019] [Indexed: 05/18/2023]
Abstract
Citrus is one of the world's most important fruit crops, contributing essential nutrients, such as vitamin C and minerals, to the human diet. It is characterized by two important traits: first, its major edible part is composed of juice sacs, a unique structure among fruit, and second, relatively high levels of citric acid are accumulated in the vacuole of the juice sac cell. Although the major routes of primary metabolism are generally the same in citrus fruit and other plant systems, the fruit's unique structural features challenge our understanding of carbon flow into the fruit and its movement through all of its parts. In fact, acid metabolism and accumulation have only been summarized in a few reviews. Here we present a comprehensive view of sugar, acid and amino acid metabolism and their connections within the fruit, all in relation to the fruit's unique structure.
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Affiliation(s)
- Avi Sadka
- Department of Fruit Tree Sciences, Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
- *Correspondence: Avi Sadka,
| | - Lyudmila Shlizerman
- Department of Fruit Tree Sciences, Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Itzhak Kamara
- Department of Fruit Tree Sciences, Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Eduardo Blumwald
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
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Li L, Wu Q, Wang Y, Aghdam MS, Ban Z, Zhang X, Lu H, Li D, Yan J, Limwachiranon J, Luo Z. Systematically quantitative proteomics and metabolite profiles offer insight into fruit ripening behavior in Fragaria × ananassa. RSC Adv 2019; 9:14093-14108. [PMID: 35519301 PMCID: PMC9064045 DOI: 10.1039/c9ra00549h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 04/28/2019] [Indexed: 11/21/2022] Open
Abstract
Profound metabolic and proteomic changes involved in the primary and the secondary metabolism are required for the ripeness of fleshy fruit such as strawberries (Fragaria × ananassa). Here we present the quantitative proteomic profiling in parallel with metabolic and transcriptional profiling at five developmental stages of strawberry fruit ripening, and correlations between changes in representative metabolites and the abundance of related proteins were analyzed. Hierarchical clustering analysis of the quantitative proteomic profiling identified 143 proteins in strawberry fruit across five developmental stages. Meanwhile, both protein abundance and gene expression spanned a wide range of roles, such as the primary and the secondary metabolism, defense system, and response to stress stimuli. The decreased abundance of proteins contributed to the carbohydrate metabolism and the up-regulated expression of secondary biosynthetic proteins was found to be positively correlated with the accumulation of primary and secondary metabolites during strawberry development. Moreover, with the same annotations and high homology, the gene function of key genes involved in primary and secondary metabolism (FaTPI, FaPAL, FaMDH and FaME) was confirmed in Nicotiana via the transient expression assay, which provides further evidence for the role of those genes in metabolism of strawberry fruit. The results of the present study may serve as an important resource for the functional analysis of the proteome and offer new perspectives on regulation of fruit quality. Proteome and metabolite profiles of fruit ripening behavior in Fragaria × ananassa Duch. ‘Benihoppe’.![]()
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Wang JH, Liu JJ, Chen KL, Li HW, He J, Guan B, He L. Comparative transcriptome and proteome profiling of two Citrus sinensis cultivars during fruit development and ripening. BMC Genomics 2017; 18:984. [PMID: 29268697 PMCID: PMC5740884 DOI: 10.1186/s12864-017-4366-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 12/06/2017] [Indexed: 12/12/2022] Open
Abstract
Background Transcriptome and proteome analyses on fruit pulp from the blood orange ‘Zaohong’ and the navel orange ‘twenty-first century’ were performed to study Citrus sinensis quality-related molecular changes during consecutive developmental periods, including young fruit, fruit-coloring onset and fruit delayed-harvest for two months, during which fruit remained on the trees. Results The time-course analysis for the fruit developmental periods indicated a complex, dynamic gene expression pattern, with the numbers of differentially expressed genes (DEGs) between the two cultivars being 119, 426 and 904 at the three continuous stages tested during fruit development and ripening. The continuous increase in total soluble solids over the course of fruit development was correlated with up-regulated sucrose phosphate synthase (SPS) transcription levels in both cultivars. Eleven differentially expressed genes between the two cultivars involved in the flavonoid pathway were significantly enriched at the onset of the fruit-coloring stage when anthocyanins were detected in blood orange alone. Among 5185 proteins, 65 up-regulated and 29 down-regulated proteins were co-expressed with their cognate mRNAs with significant transcription and protein expression levels when the fruits from the two cultivars were compared at the fruit delayed-harvest stage. Additionally, important genes participating in the γ-aminobutyric acid (GABA) shunt were activated in blood orange at two significant expression levels in the fruit delayed-harvest stage. Thus, organic acids in fruit continuously decreased during this stage. Conclusions This research was the first to provide a more comprehensive understanding of the differentially expressed genes involved in anthocyanin, sucrose and citrate metabolism at the transcriptome and proteome levels in C. sinensis, especially during the fruit delayed-harvest stage. Electronic supplementary material The online version of this article (10.1186/s12864-017-4366-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jian-Hui Wang
- Horticulture Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China.,State-Sichuan Joint Engineering Laboratory of Citrus Breeding and Cultivation, Chengdu, 610066, China.,The Key Laboratory of Horticultural Crops Biology and Germplasm Enhancement in Southwest Regions, Ministry of Agriculture, Chengdu, 610066, China
| | - Jian-Jun Liu
- Horticulture Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China. .,State-Sichuan Joint Engineering Laboratory of Citrus Breeding and Cultivation, Chengdu, 610066, China. .,The Key Laboratory of Horticultural Crops Biology and Germplasm Enhancement in Southwest Regions, Ministry of Agriculture, Chengdu, 610066, China.
| | - Ke-Ling Chen
- Horticulture Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China.,State-Sichuan Joint Engineering Laboratory of Citrus Breeding and Cultivation, Chengdu, 610066, China.,The Key Laboratory of Horticultural Crops Biology and Germplasm Enhancement in Southwest Regions, Ministry of Agriculture, Chengdu, 610066, China
| | - Hong-Wen Li
- Horticulture Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China.,State-Sichuan Joint Engineering Laboratory of Citrus Breeding and Cultivation, Chengdu, 610066, China.,The Key Laboratory of Horticultural Crops Biology and Germplasm Enhancement in Southwest Regions, Ministry of Agriculture, Chengdu, 610066, China
| | - Jian He
- Horticulture Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China.,State-Sichuan Joint Engineering Laboratory of Citrus Breeding and Cultivation, Chengdu, 610066, China.,The Key Laboratory of Horticultural Crops Biology and Germplasm Enhancement in Southwest Regions, Ministry of Agriculture, Chengdu, 610066, China
| | - Bin Guan
- Horticulture Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China.,State-Sichuan Joint Engineering Laboratory of Citrus Breeding and Cultivation, Chengdu, 610066, China.,The Key Laboratory of Horticultural Crops Biology and Germplasm Enhancement in Southwest Regions, Ministry of Agriculture, Chengdu, 610066, China
| | - Li He
- Horticulture Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China.,State-Sichuan Joint Engineering Laboratory of Citrus Breeding and Cultivation, Chengdu, 610066, China.,The Key Laboratory of Horticultural Crops Biology and Germplasm Enhancement in Southwest Regions, Ministry of Agriculture, Chengdu, 610066, China
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Salzano AM, Sobolev A, Carbone V, Petriccione M, Renzone G, Capitani D, Vitale M, Minasi P, Pasquariello MS, Novi G, Zambrano N, Scortichini M, Mannina L, Scaloni A. A proteometabolomic study of Actinidia deliciosa fruit development. J Proteomics 2017; 172:11-24. [PMID: 29133123 DOI: 10.1016/j.jprot.2017.11.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 10/17/2017] [Accepted: 11/08/2017] [Indexed: 10/18/2022]
Affiliation(s)
- Anna Maria Salzano
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy
| | - Anatoly Sobolev
- Magnetic Resonance Laboratory "Annalaura Segre", Institute of Chemical Methodologies, National Research Council, 00015, Monterotondo, Rome, Italy
| | - Virginia Carbone
- Institute of Food Sciences, National Research Council, 83100 Avellino, Italy
| | - Milena Petriccione
- Centro di Ricerca per Olivicoltura, Frutticoltura e Agrumicoltura, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, 81100 Caserta, Italy
| | - Giovanni Renzone
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy
| | - Donatella Capitani
- Magnetic Resonance Laboratory "Annalaura Segre", Institute of Chemical Methodologies, National Research Council, 00015, Monterotondo, Rome, Italy
| | - Monica Vitale
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy; Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", 80131 Naples, Italy
| | - Paola Minasi
- Institute of Food Sciences, National Research Council, 83100 Avellino, Italy
| | - Maria Silvia Pasquariello
- Centro di Ricerca per Olivicoltura, Frutticoltura e Agrumicoltura, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, 81100 Caserta, Italy
| | - Gianfranco Novi
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy
| | - Nicola Zambrano
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", 80131 Naples, Italy; CEINGE Biotecnologie Avanzate, 80145 Naples, Italy
| | - Marco Scortichini
- Centro di Ricerca per Olivicoltura, Frutticoltura e Agrumicoltura, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, 81100 Caserta, Italy
| | - Luisa Mannina
- Magnetic Resonance Laboratory "Annalaura Segre", Institute of Chemical Methodologies, National Research Council, 00015, Monterotondo, Rome, Italy; Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, 00185 Rome, Italy.
| | - Andrea Scaloni
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy.
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Comparative proteomic analysis of membrane microdomains isolated from two hyperlipidemic animal models. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1061-1071. [DOI: 10.1016/j.bbapap.2016.05.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 04/28/2016] [Accepted: 05/24/2016] [Indexed: 11/22/2022]
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Uyy E, Suica VI, Boteanu RM, Manda D, Baciu AE, Badiu C, Antohe F. Endoplasmic Reticulum Chaperones Are Potential Active Factors in Thyroid Tumorigenesis. J Proteome Res 2016; 15:3377-87. [PMID: 27480176 DOI: 10.1021/acs.jproteome.6b00567] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The study aimed to evaluate the proteomic changes in benign follicular adenoma versus malignant follicular variant of papillary thyroid carcinoma. Tumor and nontumor adjacent samples were analyzed by liquid nanochromatography mass spectrometry, and protein abundance was evaluated by label-free quantification. Western blotting and quantitative real-time polymerase chain reaction were used to validate and complement the mass spectrometry data. The results demonstrated deregulated expression of four endoplasmic reticulum chaperones (78 kDa glucose-regulated protein, endoplasmin, calnexin, protein disulfide-isomerase A4), glutathione peroxidase 3 and thyroglobulin, all of them involved in thyroid hormone synthesis pathway. The altered tissue abundance of endoplasmic reticulum chaperones in thyroid cancer was correlated with serum expression levels. The identified proteins significantly discriminate between adenoma and carcinoma in both thyroid tissue and corresponding sera. Data are available via ProteomeXchange with identifier PXD004322.
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Affiliation(s)
- Elena Uyy
- Institute of Cellular Biology and Pathology "Nicolae Simionescu" , 8, B.P. Hasdeu Street, P.O. Box 35-14, 050568 Bucharest, Romania
| | - Viorel I Suica
- Institute of Cellular Biology and Pathology "Nicolae Simionescu" , 8, B.P. Hasdeu Street, P.O. Box 35-14, 050568 Bucharest, Romania
| | - Raluca M Boteanu
- Institute of Cellular Biology and Pathology "Nicolae Simionescu" , 8, B.P. Hasdeu Street, P.O. Box 35-14, 050568 Bucharest, Romania
| | - Dana Manda
- National Institute of Endocrinology "C.I. Parhon" , 34-36 Aviatorilor Boulevard, 011863 Bucharest, Romania
| | - Ancuta E Baciu
- National Institute of Endocrinology "C.I. Parhon" , 34-36 Aviatorilor Boulevard, 011863 Bucharest, Romania.,University of Bucharest, Faculty of Physics , 405 Atomiştilor Street, 077125 Magurele, Romania
| | - Corin Badiu
- National Institute of Endocrinology "C.I. Parhon" , 34-36 Aviatorilor Boulevard, 011863 Bucharest, Romania
| | - Felicia Antohe
- Institute of Cellular Biology and Pathology "Nicolae Simionescu" , 8, B.P. Hasdeu Street, P.O. Box 35-14, 050568 Bucharest, Romania
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Chapman JD, Edgar JS, Goodlett DR, Goo YA. Use of captive spray ionization to increase throughput of the data-independent acquisition technique PAcIFIC. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:1101-7. [PMID: 27060837 PMCID: PMC4830633 DOI: 10.1002/rcm.7544] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Revised: 01/30/2016] [Accepted: 02/21/2016] [Indexed: 05/05/2023]
Abstract
RATIONALE The Precursor Acquisition Independent From Ion Count (PAcIFIC) method is a data-independent acquisition technique capable of identifying proteins over eight orders of magnitude in a single analysis in human plasma. Widespread application of this technique in proteomic studies is hindered by its time-intensive nature. There exists a need to explore strategies to increase the throughput of the PAcIFIC method. METHODS The PAcIFIC acquisition technique was optimized for use with an Orbitrap mass spectrometer fitted with a captive spray ionization (CSI) source. Chromatographic methods, PAcIFIC acquisition parameters, for example, channels interrogated per chromatographic gradient, time span of chromatographic gradient, and sample loading amount, were investigated to achieve a maximum number of peptide and protein identifications on a yeast proteome where protein copy number had been previously determined. RESULTS A 24-hour CSI PAcIFIC method was developed with minimal reduction of peptide and protein identifications from the 4.2-day nano-electrospray ionization (nESI) PAcIFIC method. Analysis of a yeast cell lysate with the 4.2-day nESI PAcIFIC method resulted in 13,468 peptide and 2120 protein identifications. A 24-hour CSI PAcIFIC method resulted in 11,277 peptide and 1753 protein identifications. Increased sample loading of the CSI system allowed for an 8% increase in peptide and protein identifications. CONCLUSIONS A dramatic decrease in the overall analysis time of the PAcIFIC method (24 h with CSI versus 100.8 h with nESI) was achieved with minimal reduction of peptide and protein identifications. Furthermore, the CSI PAcIFIC method demonstrated a high degree of sensitivity and capability of identifying proteins across a large dynamic range observed with the nESI PAcIFIC method (CSI PAcIFIC identified proteins as low as 46 molecules per cell).
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Affiliation(s)
- John D Chapman
- Department of Medicinal Chemistry, School of Pharmacy, University of
Washington, Seattle, WA
| | - J. Scott Edgar
- Department of Medicinal Chemistry, School of Pharmacy, University of
Washington, Seattle, WA
| | - David R. Goodlett
- Department of Pharmaceutical Sciences, School of Pharmacy,
University of Maryland, Baltimore, MD
| | - Young Ah Goo
- Department of Pharmaceutical Sciences, School of Pharmacy,
University of Maryland, Baltimore, MD
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Shiratake K, Suzuki M. Omics studies of citrus, grape and rosaceae fruit trees. BREEDING SCIENCE 2016; 66:122-38. [PMID: 27069397 PMCID: PMC4780796 DOI: 10.1270/jsbbs.66.122] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 11/01/2015] [Indexed: 05/06/2023]
Abstract
Recent advance of bioinformatics and analytical apparatuses such as next generation DNA sequencer (NGS) and mass spectrometer (MS) has brought a big wave of comprehensive study to biology. Comprehensive study targeting all genes, transcripts (RNAs), proteins, metabolites, hormones, ions or phenotypes is called genomics, transcriptomics, proteomics, metabolomics, hormonomics, ionomics or phenomics, respectively. These omics are powerful approaches to identify key genes for important traits, to clarify events of physiological mechanisms and to reveal unknown metabolic pathways in crops. Recently, the use of omics approach has increased dramatically in fruit tree research. Although the most reported omics studies on fruit trees are transcriptomics, proteomics and metabolomics, and a few is reported on hormonomics and ionomics. In this article, we reviewed recent omics studies of major fruit trees, i.e. citrus, grapevine and rosaceae fruit trees. The effectiveness and prospects of omics in fruit tree research will as well be highlighted.
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Affiliation(s)
- Katsuhiro Shiratake
- Graduate School of Bioagricultural Sciences, Nagoya University,
Chikusa, Nagoya, Aichi 464-8601,
Japan
- Corresponding author (e-mail: )
| | - Mami Suzuki
- Graduate School of Bioagricultural Sciences, Nagoya University,
Chikusa, Nagoya, Aichi 464-8601,
Japan
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15
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Suica VI, Uyy E, Boteanu RM, Ivan L, Antohe F. Alteration of actin dependent signaling pathways associated with membrane microdomains in hyperlipidemia. Proteome Sci 2015; 13:30. [PMID: 26628893 PMCID: PMC4666118 DOI: 10.1186/s12953-015-0087-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 11/24/2015] [Indexed: 01/05/2023] Open
Abstract
Background Membrane microdomains represent dynamic membrane nano-assemblies enriched in signaling molecules suggesting their active involvement in not only physiological but also pathological molecular processes. The hyperlipidemic stress is a major risk factor of atherosclerosis, but its exact mechanisms of action at the membrane microdomains level remain elusive. The aim of the present study was to determine whether membrane-cytoskeleton proteome in the pulmonary tissue could be modulated by the hyperlipidemic stress, a major risk factor of atherosclerosis. Results High resolution mass spectrometry based proteomics analysis was performed for detergent resistant membrane microdomains isolated from lung homogenates of control, ApoE deficient and statin treated ApoE deficient mice. The findings of the study allowed the identification with high confidence of 1925 proteins, 291 of which were found significantly altered by the modified genetic background, by the statin treatment or both conditions. Principal component analysis revealed a proximal partitioning of the biological replicates, but also a distinct spatial scattering of the sample groups, highlighting different quantitative profiles. The statistical significant over-representation of Regulation of actin cytoskeleton, Focal adhesion and Adherens junction Kyoto Encyclopedia of Genes and Genomes signaling pathways was demonstrated through bioinformatics analysis. The three inter-relation maps comprised 29 of regulated proteins, proving membrane-cytoskeleton coupling targeting and alteration by hyperlipidemia and/or statin treatment. Conclusions The findings of the study allowed the identification with high confidence of the main proteins modulated by the hyperlipidemic stress involved in the actin-dependent pathways. Our study provides the basis for future work probing how the protein activities at the membrane-cytoskeleton interface are dependent upon genetic induced hyperlipidemia. Electronic supplementary material The online version of this article (doi:10.1186/s12953-015-0087-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Viorel-Iulian Suica
- Institute of Cellular Biology and Pathology "Nicolae Simionescu", 8 BP Hasdeu Street, PO Box 35-14, 050568 Bucharest, Romania
| | - Elena Uyy
- Institute of Cellular Biology and Pathology "Nicolae Simionescu", 8 BP Hasdeu Street, PO Box 35-14, 050568 Bucharest, Romania
| | - Raluca Maria Boteanu
- Institute of Cellular Biology and Pathology "Nicolae Simionescu", 8 BP Hasdeu Street, PO Box 35-14, 050568 Bucharest, Romania
| | - Luminita Ivan
- Institute of Cellular Biology and Pathology "Nicolae Simionescu", 8 BP Hasdeu Street, PO Box 35-14, 050568 Bucharest, Romania
| | - Felicia Antohe
- Institute of Cellular Biology and Pathology "Nicolae Simionescu", 8 BP Hasdeu Street, PO Box 35-14, 050568 Bucharest, Romania
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16
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Kamal AHM, Komatsu S. Involvement of Reactive Oxygen Species and Mitochondrial Proteins in Biophoton Emission in Roots of Soybean Plants under Flooding Stress. J Proteome Res 2015; 14:2219-36. [PMID: 25806999 DOI: 10.1021/acs.jproteome.5b00007] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
To understand the mechanism of biophoton emission, ROS and mitochondrial proteins were analyzed in soybean plants under flooding stress. Enzyme activity and biophoton emission were increased in the flooding stress samples when assayed in reaction mixes specific for antioxidant enzymes and reactive oxygen species; although the level of the hydroxyl radicals was increased at day 4 (2 days of flooding) compared to nonflooding at day 4, the emission of biophotons did not change. Mitochondria were isolated and purified from the roots of soybean plants grown under flooding stress by using a Percoll gradient, and proteins were analyzed by a gel-free proteomic technique. Out of the 98 mitochondrial proteins that significantly changed abundance under flooding stress, 47 increased and 51 decreased at day 4. The mitochondrial enzymes fumarase, glutathione-S-transferase, and aldehyde dehydrogenase increased at day 4 in protein abundance and enzyme activity. Enzyme activity and biophoton emission decreased at day 4 by the assay of lipoxygenase under stress. Aconitase, acyl CoA oxidase, succinate dehydrogenase, and NADH ubiquinone dehydrogenase were up-regulated at the transcription level. These results indicate that oxidation and peroxide scavenging might lead to biophoton emission and oxidative damage in the roots of soybean plants under flooding stress.
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Affiliation(s)
- Abu Hena Mostafa Kamal
- National Institute of Crop Science, National Agriculture and Food Research Organization, Kannondai 2-1-18, Tsukuba 305-8518, Japan
| | - Setsuko Komatsu
- National Institute of Crop Science, National Agriculture and Food Research Organization, Kannondai 2-1-18, Tsukuba 305-8518, Japan
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17
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Bioactive peptides released from in vitro digestion of human milk with or without pasteurization. Pediatr Res 2015; 77:546-53. [PMID: 25580741 DOI: 10.1038/pr.2015.10] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 10/08/2014] [Indexed: 11/08/2022]
Abstract
BACKGROUND Pasteurized donor human milk (HM) serves as the best alternative for breast-feeding when availability of mother's milk is limited. Pasteurization is also applied to mother's own milk for very low birth weight infants, who are vulnerable to microbial infection. Whether pasteurization affects protein digestibility and therefore modulates the profile of bioactive peptides released from HM proteins by gastrointestinal digestion, has not been examined to date. METHODS HM with and without pasteurization (62.5 °C for 30 min) were subjected to in vitro gastrointestinal digestion, followed by peptidomic analysis to compare the formation of bioactive peptides. RESULTS Some of the bioactive peptides, such as caseinophosphopeptide homologues, a possible opioid peptide (or propeptide), and an antibacterial peptide, were present in undigested HM and showed resistance to in vitro digestion, suggesting that these peptides are likely to exert their bioactivities in the gastrointestinal lumen, or be stably transported to target organs. In vitro digestion of HM released a large variety of bioactive peptides such as angiotensin I-converting enzyme-inhibitory, antioxidative, and immunomodulatory peptides. Bioactive peptides were released largely in the same manner with and without pasteurization. CONCLUSION Provision of pasteurized HM may be as beneficial as breast-feeding in terms of milk protein-derived bioactive peptides.
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Yu Q, Plotto A, Baldwin EA, Bai J, Huang M, Yu Y, Dhaliwal HS, Gmitter FG. Proteomic and metabolomic analyses provide insight into production of volatile and non-volatile flavor components in mandarin hybrid fruit. BMC PLANT BIOLOGY 2015; 15:76. [PMID: 25848837 PMCID: PMC4356138 DOI: 10.1186/s12870-015-0466-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 02/20/2015] [Indexed: 05/11/2023]
Abstract
BACKGROUND Although many of the volatile constituents of flavor and aroma in citrus have been identified, the knowledge of molecular mechanisms and regulation of volatile production are very limited. Our aim was to understand mechanisms of flavor volatile production and regulation in mandarin fruit. RESULT Fruits of two mandarin hybrids, Temple and Murcott with contrasting volatile and non- volatile profiles, were collected at three developmental stages. A combination of methods, including the isobaric tags for relative and absolute quantification (iTRAQ), quantitative real-time polymerase chain reaction, gas chromatography, and high-performance liquid chromatography, was used to identify proteins, measure gene expression levels, volatiles, sugars, organic acids and carotenoids. Two thirds of differentially expressed proteins were identified in the pathways of glycolysis, citric acid cycle, amino acid, sugar and starch metabolism. An enzyme encoding valencene synthase gene (Cstps1) was more abundant in Temple than in Murcott. Valencene accounted for 9.4% of total volatile content in Temple, whereas no valencene was detected in Murcott fruit. Murcott expression of Cstps1 is severely reduced. CONCLUSION We showed that the diversion of valencene and other sesquiterpenes into the terpenoid pathway together with high production of apocarotenoid volatiles might have resulted in the lower concentration of carotenoids in Temple fruit.
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Affiliation(s)
- Qibin Yu
- />University of Florida, Institute of Food and Agricultural Sciences, Citrus Research and Education Center, Lake Alfred, FL 33850 USA
| | - Anne Plotto
- />USDA-ARS Horticultural Research Laboratory, Fort Pierce, FL 34945 USA
| | | | - Jinhe Bai
- />USDA-ARS Horticultural Research Laboratory, Fort Pierce, FL 34945 USA
| | - Ming Huang
- />University of Florida, Institute of Food and Agricultural Sciences, Citrus Research and Education Center, Lake Alfred, FL 33850 USA
| | - Yuan Yu
- />University of Florida, Institute of Food and Agricultural Sciences, Citrus Research and Education Center, Lake Alfred, FL 33850 USA
| | - Harvinder S Dhaliwal
- />College of Agriculture, Punjab Agricultural University, Ludhiana, Punjab 141004 India
| | - Frederick G Gmitter
- />University of Florida, Institute of Food and Agricultural Sciences, Citrus Research and Education Center, Lake Alfred, FL 33850 USA
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Yao C, Yu J, Taylor L, Polgar P, McComb ME, Costello CE. Protein Expression by Human Pulmonary Artery Smooth Muscle Cells Containing a BMPR2 Mutation and the Action of ET-1 as Determined by Proteomic Mass Spectrometry. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2015; 378:347-359. [PMID: 25866469 PMCID: PMC4387548 DOI: 10.1016/j.ijms.2014.10.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Pulmonary arterial hypertension (PAH) is a disease characterized by increased pulmonary vascular resistance and remodeling. Increase in the population of vascular smooth muscle cells is among the key events contributing to the remodeling. Endothelin-1 (ET-1), a potent vasoconstrictor, is linked to the etiology and progression of PAH. Here we analyze changes in protein expressions in response to ET-1 in pulmonary arterial smooth muscle cells (PASMC) from a healthy Control (non-PAH) and a PAH subject presenting a bone morphogenetic protein type II receptor (BMPR2) mutation with exon 1-8 deletion. Protein expressions were analyzed by proteomic mass spectrometry using label-free quantitation and the correlations were subjected to Ingenuity™ Pathway Analysis. The results point to eIF2/mTOR/p70S6K, RhoA/actin cytoskeleton/integrin and protein unbiquitination as canonical pathways whose protein expressions increase with the development of PAH. These pathways have an intimal function in the PAH-related physiology of smooth muscle proliferation, apoptosis, contraction and cellular stress. Exposure of the cells to ET-1 further increases protein expression within these pathways. Thus our results show changes in signaling pathways as a consequence of PAH and the effect of ET-1 interference on Control and PAH-affected cells.
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Affiliation(s)
- Chunxiang Yao
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, 670 Albany St., Boston, MA 02118 USA
| | - Jun Yu
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118 USA
| | - Linda Taylor
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118 USA
| | - Peter Polgar
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118 USA
| | - Mark E. McComb
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, 670 Albany St., Boston, MA 02118 USA
| | - Catherine E. Costello
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, 670 Albany St., Boston, MA 02118 USA
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118 USA
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20
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Kamal AHM, Rashid H, Sakata K, Komatsu S. Gel-free quantitative proteomic approach to identify cotyledon proteins in soybean under flooding stress. J Proteomics 2015; 112:1-13. [PMID: 25201076 DOI: 10.1016/j.jprot.2014.08.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Revised: 08/22/2014] [Accepted: 08/27/2014] [Indexed: 01/10/2023]
Abstract
Flooding stress causes growth inhibition and ultimately death in most crop species by limiting of energy production. To better understand plant responses to flooding stress, here, flooding-responsive proteins in the cotyledons of soybean were identified using a gel-free quantitative proteomic approach. One hundred forty six proteins were commonly observed in both control and flooding-stressed plants, and 19 were identified under only flooding stress conditions. The main functional categories were protein and development-related proteins. Protein-protein interaction analysis revealed that zincin-like metalloprotease and cupin family proteins were found to highly interact with other proteins under flooding stress. Plant stearoyl acyl-carrier protein, ascorbate peroxidase 1, and secretion-associated RAS superfamily 2 were down-regulated, whereas ferretin 1 was up-regulated at the transcription level. Notably, the levels of all corresponding proteins were decreased, indicating that mRNA translation to proteins is impaired under flooding conditions. Decreased levels of ferritin may lead to a strong deregulation of the expression of several metal transporter genes and over-accumulation of iron, which led to increased levels of reactive oxygen species, resulting to detoxification of these reactive species. Taken together, these results suggest that ferritin might have an essential role in protecting plant cells against oxidative damage under flooding conditions. BIOLOGICAL SIGNIFICANCE This study reported the comparative proteomic analysis of cotyledon of soybean plants between non-flooding and flooding conditions using the gel-free quantitative techniques. Mass spectrometry analysis of the proteins from cotyledon resulted in the identification of a total of 165 proteins under flooding stress. These proteins were assigned to different functional categories, such as protein, development, stress, redox, and glycolysis. Therefore, this study provides not only the comparative proteomic analysis but also the molecular mechanism underlying the flooding responsive protein functions in the cotyledon.
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Affiliation(s)
| | - Hamid Rashid
- Mohammad Ali Jinnah University, Islamabad, Pakistan
| | - Katsumi Sakata
- Maebashi Institute of Technology, Maebashi 371-0816, Japan
| | - Setsuko Komatsu
- National Institute of Crop Science, NARO, Tsukuba 305-8518, Japan.
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Wong SY, Chen YC. Droplet-based electrospray ionization mass spectrometry for qualitative and quantitative analysis. JOURNAL OF MASS SPECTROMETRY : JMS 2014; 49:432-436. [PMID: 24809906 DOI: 10.1002/jms.3355] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 02/20/2014] [Accepted: 03/03/2014] [Indexed: 06/03/2023]
Affiliation(s)
- Song-Yi Wong
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu, 300, Taiwan
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22
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Molassiotis A, Tanou G, Filippou P, Fotopoulos V. Proteomics in the fruit tree science arena: new insights into fruit defense, development, and ripening. Proteomics 2014; 13:1871-84. [PMID: 23986917 DOI: 10.1002/pmic.201200428] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Fruit tree crops are agricultural commodities of high economic importance, while fruits also represent one of the most vital components of the human diet. Therefore, a great effort has been made to understand the molecular mechanisms covering fundamental biological processes in fruit tree physiology and fruit biology. Thanks to the development of cutting-edge "omics" technologies such as proteomic analysis, scientists now have powerful tools to support traditional fruit tree research. Such proteomic analyses are establishing high-density 2DE reference maps and peptide mass fingerprint databases that can lead fruit science into a new postgenomic research era. Here, an overview of the application of proteomics in key aspects of fruit tree physiology as well as in fruit biology, including defense responses to abiotic and biotic stress factors, is presented. A panoramic view of ripening-related proteins is also discussed, as an example of proteomic application in fruit science.
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Liao H, Li S, Wei Z, Shen Q, Xu Y. Insights into high-efficiency lignocellulolytic enzyme production by Penicillium oxalicum GZ-2 induced by a complex substrate. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:162. [PMID: 25419234 PMCID: PMC4239378 DOI: 10.1186/s13068-014-0162-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 10/21/2014] [Indexed: 05/15/2023]
Abstract
BACKGROUND Agricultural residue is more efficient than purified cellulose at inducing lignocellulolytic enzyme production in Penicillium oxalicum GZ-2, but in Trichoderma reesei RUT-C30, cellulose induces a more efficient response. To understand the reasons, we designed an artificially simulated plant biomass (cellulose plus xylan) to study the roles and relationships of each component in the production of lignocellulolytic enzymes by P. oxalicum GZ-2. RESULTS The changes in lignocellulolytic enzyme activity, gene expression involving (hemi)cellulolytic enzymes, and the secretome of cultures grown on Avicel (A), xylan (X), or a mixture of both (AX) were studied. The addition of xylan to the cellulose culture did not affect fungal growth but significantly increased the activity of cellulase and hemicellulase. In the AX treatment, the transcripts of cellulase genes (egl1, egl2, egl3, sow, and cbh2) and hemicellulase genes (xyl3 and xyl4) were significantly upregulated (P <0.05). The proportion of biomass-degrading proteins in the secretome was altered; in particular, the percentage of cellulases and hemicellulases was increased. The percentage of cellulases and hemicellulases in the AX secretome increased from 4.5% and 7.6% to 10.3% and 21.8%, respectively, compared to the secretome of the A treatment. Cellobiohydrolase II (encoded by cbh2) and xylanase II (encoded by xyl2) were the main proteins in the secretome, and their corresponding genes (cbh2 and xyl2) were transcripted at the highest levels among the cellulolytic and xylanolytic genes. Several important proteins such as swollenin, cellobiohydrolase, and endo-beta-1,4-xylanase were only induced by AX. Bray-Curtis similarity indices, a dendrogram analysis, and a diversity index all demonstrated that the secretome produced by P. oxalicum GZ-2 depended on the substrate and that strain GZ-2 directionally adjusted the compositions of lignocellulolytic enzymes in its secretome to preferably degrade a complex substrate. CONCLUSION The addition of xylan to the cellulose medium not only induces more hemicellulases but also strongly activates cellulase production. The proportion of the biomass-degrading proteins in the secretome was altered significantly, with the proportion of cellulases and hemicellulases especially increased. Xylan and cellulose have positively synergistic effects, and they play a key role in the induction of highly efficient lignocellulolytic enzymes.
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Affiliation(s)
- Hanpeng Liao
- National Enginnering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095 China
| | - Shuixian Li
- National Enginnering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095 China
| | - Zhong Wei
- National Enginnering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095 China
| | - Qirong Shen
- National Enginnering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yangchun Xu
- National Enginnering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095 China
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Li L, Song J, Kalt W, Forney C, Tsao R, Pinto D, Chisholm K, Campbell L, Fillmore S, Li X. Quantitative proteomic investigation employing stable isotope labeling by peptide dimethylation on proteins of strawberry fruit at different ripening stages. J Proteomics 2013; 94:219-39. [DOI: 10.1016/j.jprot.2013.09.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 08/27/2013] [Accepted: 09/12/2013] [Indexed: 02/01/2023]
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25
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Racchi ML. Antioxidant Defenses in Plants with Attention to Prunus and Citrus spp. Antioxidants (Basel) 2013; 2:340-69. [PMID: 26784469 PMCID: PMC4665512 DOI: 10.3390/antiox2040340] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Revised: 10/08/2013] [Accepted: 10/28/2013] [Indexed: 12/13/2022] Open
Abstract
This short review briefly introduces the formation of reactive oxygen species (ROS) as by-products of oxidation/reduction (redox) reactions, and the ways in which the antioxidant defense machinery is involved directly or indirectly in ROS scavenging. Major antioxidants, both enzymatic and non enzymatic, that protect higher plant cells from oxidative stress damage are described. Biochemical and molecular features of the antioxidant enzymes superoxide dismutase (SOD), catalase (CAT), and ascorbate peroxidase (APX) are discussed because they play crucial roles in scavenging ROS in the different cell compartments and in response to stress conditions. Among the non enzymatic defenses, particular attention is paid to ascorbic acid, glutathione, flavonoids, carotenoids, and tocopherols. The operation of ROS scavenging systems during the seasonal cycle and specific developmental events, such as fruit ripening and senescence, are discussed in relation to the intense ROS formation during these processes that impact fruit quality. Particular attention is paid to Prunus and Citrus species because of the nutritional and antioxidant properties contained in these commonly consumed fruits.
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Affiliation(s)
- Milvia Luisa Racchi
- Department of Agri-Food Production and Environmental Sciences, Section of Agricultural Genetics-DISPAA, University of Florence, via Maragliano 77, Firenze 50144, Italy.
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Vu K, Eigenheer RA, Phinney BS, Gelli A. Cryptococcus neoformans promotes its transmigration into the central nervous system by inducing molecular and cellular changes in brain endothelial cells. Infect Immun 2013; 81:3139-47. [PMID: 23774597 PMCID: PMC3754227 DOI: 10.1128/iai.00554-13] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 06/07/2013] [Indexed: 12/31/2022] Open
Abstract
Cryptococcus spp. cause fungal meningitis, a life-threatening infection that occurs predominately in immunocompromised individuals. In order for Cryptococcus neoformans to invade the central nervous system (CNS), it must first penetrate the brain endothelium, also known as the blood-brain barrier (BBB). Despite the importance of the interrelation between C. neoformans and the brain endothelium in establishing CNS infection, very little is known about this microenvironment. Here we sought to resolve the cellular and molecular basis that defines the fungal-BBB interface during cryptococcal attachment to, and internalization by, the human brain endothelium. In order to accomplish this by a systems-wide approach, the proteomic profile of human brain endothelial cells challenged with C. neoformans was resolved using a label-free differential quantitative mass spectrometry method known as spectral counting (SC). Here, we demonstrate that as brain endothelial cells associate with, and internalize, cryptococci, they upregulate the expression of several proteins involved with cytoskeleton, metabolism, signaling, and inflammation, suggesting that they are actively signaling and undergoing cytoskeleton remodeling via annexin A2, S100A10, transgelin, and myosin. Transmission electronic microscopy (TEM) analysis demonstrates dramatic structural changes in nuclei, mitochondria, the endoplasmic reticulum (ER), and the plasma membrane that are indicative of cell stress and cell damage. The translocation of HMGB1, a marker of cell injury, the downregulation of proteins that function in transcription, energy production, protein processing, and the upregulation of cyclophilin A further support the notion that C. neoformans elicits changes in brain endothelial cells that facilitate the migration of cryptococci across the BBB and ultimately induce endothelial cell necrosis.
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Affiliation(s)
- Kiem Vu
- Department of Pharmacology, School of Medicine, University of California, Genome and Biomedical Sciences Facility, Davis, California, USA
| | - Richard A. Eigenheer
- Proteomics Core Facility, University of California, Genome Center, Davis, California, USA
| | - Brett S. Phinney
- Proteomics Core Facility, University of California, Genome Center, Davis, California, USA
| | - Angie Gelli
- Department of Pharmacology, School of Medicine, University of California, Genome and Biomedical Sciences Facility, Davis, California, USA
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Kim JH, Inerowicz D, Hedrick V, Regnier F. Integrated Sample Preparation Methodology for Proteomics: Analysis of Native Proteins. Anal Chem 2013; 85:8039-45. [PMID: 23937592 DOI: 10.1021/ac401477w] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Jin-Hee Kim
- Department of Chemistry and ‡Bindley Bioscience Center at Discovery Park, Purdue University, West Lafayette, Indiana
47906, United States
| | - Dorota Inerowicz
- Department of Chemistry and ‡Bindley Bioscience Center at Discovery Park, Purdue University, West Lafayette, Indiana
47906, United States
| | - Vicki Hedrick
- Department of Chemistry and ‡Bindley Bioscience Center at Discovery Park, Purdue University, West Lafayette, Indiana
47906, United States
| | - Fred Regnier
- Department of Chemistry and ‡Bindley Bioscience Center at Discovery Park, Purdue University, West Lafayette, Indiana
47906, United States
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Pedreschi R, Lurie S, Hertog M, Nicolaï B, Mes J, Woltering E. Post-harvest proteomics and food security. Proteomics 2013; 13:1772-83. [PMID: 23483703 DOI: 10.1002/pmic.201200387] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 10/27/2012] [Accepted: 11/11/2012] [Indexed: 12/12/2022]
Abstract
To guarantee sufficient food supply for a growing world population, efforts towards improving crop yield and plant resistance should be complemented with efforts to reduce post-harvest losses. Post-harvest losses are substantial and occur at different stages of the food chain in developed and developing countries. In recent years, a substantially increasing interest can be seen in the application of proteomics to understand post-harvest events. In the near future post-harvest proteomics will be poised to move from fundamental research to aiding the reduction of food losses. Proteomics research can help in reducing food losses through (i) identification and validation of gene products associated to specific quality traits supporting marker-assisted crop improvement programmes, (ii) delivering markers of initial quality that allow optimisation of distribution conditions and prediction of remaining shelf-life for decision support systems and (iii) delivering early detection tools of physiological or pathogen-related post-harvest problems. In this manuscript, recent proteomics studies on post-harvest and stress physiology are reviewed and discussed. Perspectives on future directions of post-harvest proteomics studies aiming to reduce food losses are presented.
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Affiliation(s)
- Romina Pedreschi
- Food & Biobased Research Centre, Wageningen University, Wageningen, The Netherlands.
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29
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Song J, Sun R, Li D, Tan F, Li X, Jiang P, Huang X, Lin L, Deng Z, Zhang Y. An improvement of shotgun proteomics analysis by adding next-generation sequencing transcriptome data in orange. PLoS One 2012; 7:e39494. [PMID: 22768084 PMCID: PMC3387166 DOI: 10.1371/journal.pone.0039494] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 05/22/2012] [Indexed: 11/24/2022] Open
Abstract
Background Shotgun proteomics data analysis usually relies on database search. Because commonly employed protein sequence databases of most species do not contain sufficient protein information, the application of shotgun proteomics to the research of protein sequence profile remains a big challenge, especially to the species whose genome has not been sequenced yet. Methodology/Principal Findings In this paper, we present a workflow with integrated database to partly address this problem. First, we downloaded the homologous species database. Next, we identified the transcriptome of the sample, created a protein sequence database based on the transcriptome data, and integtrated it with homologous species database. Lastly, we developed a workflow for identifying peptides simultaneously from shotgun proteomics data. Conclusions/Significance We used datasets from orange leaves samples to demonstrate our workflow. The results showed that the integrated database had great advantage on orange shotgun proteomics data analysis compared to the homologous species database, an 18.5% increase in number of proteins identification.
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Affiliation(s)
- Jiaping Song
- The Shenzhen Proteome Engineering Laboratory, BGI Shenzhen, Shenzhen, P. R. China
| | - Renjie Sun
- The Shenzhen Proteome Engineering Laboratory, BGI Shenzhen, Shenzhen, P. R. China
| | - Dazhi Li
- National Center for Citrus Improvement, Hunan Agricultural University, Changsha, Hunan, P. R. China
| | - Fengji Tan
- The Shenzhen Proteome Engineering Laboratory, BGI Shenzhen, Shenzhen, P. R. China
| | - Xin Li
- The Shenzhen Proteome Engineering Laboratory, BGI Shenzhen, Shenzhen, P. R. China
| | - Pingping Jiang
- The Shenzhen Proteome Engineering Laboratory, BGI Shenzhen, Shenzhen, P. R. China
| | - Xinjie Huang
- The Shenzhen Proteome Engineering Laboratory, BGI Shenzhen, Shenzhen, P. R. China
| | - Liang Lin
- The Shenzhen Proteome Engineering Laboratory, BGI Shenzhen, Shenzhen, P. R. China
| | - Ziniu Deng
- National Center for Citrus Improvement, Hunan Agricultural University, Changsha, Hunan, P. R. China
| | - Yong Zhang
- The Shenzhen Proteome Engineering Laboratory, BGI Shenzhen, Shenzhen, P. R. China
- * E-mail:
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30
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Pan Z, Zeng Y, An J, Ye J, Xu Q, Deng X. An integrative analysis of transcriptome and proteome provides new insights into carotenoid biosynthesis and regulation in sweet orange fruits. J Proteomics 2012; 75:2670-84. [DOI: 10.1016/j.jprot.2012.03.016] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Revised: 02/21/2012] [Accepted: 03/14/2012] [Indexed: 12/23/2022]
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31
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Do plasma proteins distinguish between liposomes of varying charge density? J Proteomics 2012; 75:1924-32. [DOI: 10.1016/j.jprot.2012.01.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Revised: 12/09/2011] [Accepted: 01/04/2012] [Indexed: 11/20/2022]
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32
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Label-free quantitative analysis for studying the interactions between nanoparticles and plasma proteins. Anal Bioanal Chem 2012; 405:635-45. [PMID: 22274284 DOI: 10.1007/s00216-011-5691-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 12/19/2011] [Accepted: 12/21/2011] [Indexed: 12/12/2022]
Abstract
A shotgun proteomics approach was used to compare human plasma protein binding capability with cationic liposomes, DNA-cationic lipid complexes (lipoplexes), and lipid-polycation-DNA (LPD) complexes. Nano-high-performance liquid chromatography coupled with a high-resolution LTQ Orbitrap XL mass spectrometer was used to characterize and compare their protein corona. Spectral counting and area under curve methods were used to perform label-free quantification. Substantial qualitative and quantitative differences were found among proteins bound to the three different systems investigated. Protein variety found on lipoplexes and LPD complexes was richer than that found on cationic liposomes. There were also significant differences between the amounts of protein. Such results could help in the design of gene-delivery systems, because some proteins could be more selectively bound rather than others, and their bio-distribution could be driven in vivo for more efficient and effective gene therapy.
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33
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Zeng Y, Pan Z, Ding Y, Zhu A, Cao H, Xu Q, Deng X. A proteomic analysis of the chromoplasts isolated from sweet orange fruits [Citrus sinensis (L.) Osbeck]. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:5297-309. [PMID: 21841170 PMCID: PMC3223033 DOI: 10.1093/jxb/err140] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2010] [Revised: 03/28/2011] [Accepted: 03/29/2011] [Indexed: 05/18/2023]
Abstract
Here, a comprehensive proteomic analysis of the chromoplasts purified from sweet orange using Nycodenz density gradient centrifugation is reported. A GeLC-MS/MS shotgun approach was used to identify the proteins of pooled chromoplast samples. A total of 493 proteins were identified from purified chromoplasts, of which 418 are putative plastid proteins based on in silico sequence homology and functional analyses. Based on the predicted functions of these identified plastid proteins, a large proportion (∼60%) of the chromoplast proteome of sweet orange is constituted by proteins involved in carbohydrate metabolism, amino acid/protein synthesis, and secondary metabolism. Of note, HDS (hydroxymethylbutenyl 4-diphosphate synthase), PAP (plastid-lipid-associated protein), and psHSPs (plastid small heat shock proteins) involved in the synthesis or storage of carotenoid and stress response are among the most abundant proteins identified. A comparison of chromoplast proteomes between sweet orange and tomato suggested a high level of conservation in a broad range of metabolic pathways. However, the citrus chromoplast was characterized by more extensive carotenoid synthesis, extensive amino acid synthesis without nitrogen assimilation, and evidence for lipid metabolism concerning jasmonic acid synthesis. In conclusion, this study provides an insight into the major metabolic pathways as well as some unique characteristics of the sweet orange chromoplasts at the whole proteome level.
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Affiliation(s)
| | | | | | | | | | | | - Xiuxin Deng
- To whom correspondence should be addressed. E-mail:
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34
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Katz E, Boo KH, Kim HY, Eigenheer RA, Phinney BS, Shulaev V, Negre-Zakharov F, Sadka A, Blumwald E. Label-free shotgun proteomics and metabolite analysis reveal a significant metabolic shift during citrus fruit development. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:5367-84. [PMID: 21841177 PMCID: PMC3223037 DOI: 10.1093/jxb/err197] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Revised: 05/17/2011] [Accepted: 05/20/2011] [Indexed: 05/18/2023]
Abstract
Label-free LC-MS/MS-based shot-gun proteomics was used to quantify the differential protein synthesis and metabolite profiling in order to assess metabolic changes during the development of citrus fruits. Our results suggested the occurrence of a metabolic change during citrus fruit maturation, where the organic acid and amino acid accumulation seen during the early stages of development shifted into sugar synthesis during the later stage of citrus fruit development. The expression of invertases remained unchanged, while an invertase inhibitor was up-regulated towards maturation. The increased expression of sucrose-phosphate synthase and sucrose-6-phosphate phosphatase and the rapid sugar accumulation suggest that sucrose is also being synthesized in citrus juice sac cells during the later stage of fruit development.
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Affiliation(s)
- Ehud Katz
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Kyung Hwan Boo
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Ho Youn Kim
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Richard A. Eigenheer
- Genome Center, Proteomics Core Facility, University of California, Davis, CA 95616, USA
| | - Brett S. Phinney
- Genome Center, Proteomics Core Facility, University of California, Davis, CA 95616, USA
| | - Vladimir Shulaev
- Department of Biological Sciences, University of North Texas, TX 76203-5017, USA
| | | | - Avi Sadka
- Department of Fruit Tree Species, ARO, The Volcani Center, 50250 Bet Dagan, Israel
| | - Eduardo Blumwald
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
- To whom correspondence should be addressed. E-mail:
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35
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Palma JM, Corpas FJ, del Río LA. Proteomics as an approach to the understanding of the molecular physiology of fruit development and ripening. J Proteomics 2011; 74:1230-43. [PMID: 21524723 DOI: 10.1016/j.jprot.2011.04.010] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 04/05/2011] [Accepted: 04/11/2011] [Indexed: 11/24/2022]
Abstract
Fruit ripening is a developmental complex process which occurs in higher plants and involves a number of stages displayed from immature to mature fruits that depend on the plant species and the environmental conditions. Nowadays, the importance of fruit ripening comes mainly from the link between this physiological process in plants and the economic repercussions as a result of one of the human activities, the agricultural industry. In most cases, fruit ripening is accompanied by colour changes due to different pigment content and increases in sugar levels, among others. Major physiological modifications that affect colour, texture, flavour, and aroma are under the control of both external (light and temperature) and internal (developmental gene regulation and hormonal control) factors. Due to the huge amount of metabolic changes that take place during ripening in fruits from higher plants, the accomplishment of new throughput methods which can provide a global evaluation of this process would be desirable. Differential proteomics of immature and mature fruits would be a useful tool to gain information on the molecular changes which occur during ripening, but also the investigation of fruits at different ripening stages will provide a dynamic picture of the whole transformation of fruits. This subject is furthermore of great interest as many fruits are essential for human nutrition. Thus far different maturation profiles have been reported specific for each crop species. In this work, a thorough review of the proteomic database from fruit development and maturation of important crop species will be updated to understand the molecular physiology of fruits at ripening stages.
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Affiliation(s)
- José M Palma
- Departmento de Bioquímica, Biología Celular y Molecular de Plantas, Estación Experimental del Zaidín, CSIC, Apartado 419, 18080 Granada, Spain.
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