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Kowalik S, Groszyk J. Profiling of Barley, Wheat, and Rye FPG and OGG1 Genes during Grain Germination. Int J Mol Sci 2023; 24:12354. [PMID: 37569728 PMCID: PMC10418959 DOI: 10.3390/ijms241512354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/24/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023] Open
Abstract
This research is about the profiling of barley (Hordeum vulgare L.), wheat (Triticum aestivum L.), and rye (Secale cereale L.) FPG and OGG1 genes during grain germination. During seed germination, reactive oxygen species accumulate, which leads to DNA damage. In the base excision repair (BER) system, the enzymes formamidopyrimidine DNA glycosylase (FPG) and 8-oxoguanine DNA glycosylase (OGG1), among others, are responsible for repairing such damage. We decided to check how the expression of genes encoding these two enzymes changes in germinating grains. Spring varieties of barley, wheat, and rye from the previous growing season were used in the study. Expression level changes were checked using Real-Time PCR. After analyzing the obtained results, the maximum expression levels of FPG and OGG1 genes during germination were determined for barley, wheat, and rye. The results of the study show differences in expression levels specific to each species. The highest expression was observed at different time points for each of them. There were no differences in the highest expression for FPG and OGG1 within one species. In conclusion, the research provides information on how the level of FPG and OGG1 gene expression changes during the germination process in cereals. This is the first study looking at the expression levels of these two genes in cereals.
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Affiliation(s)
| | - Jolanta Groszyk
- Plant Breeding and Acclimatization Institute–National Research Institute, Radzików, 05-870 Błonie, Poland;
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2
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Pang X, Liu S, Suo J, Yang T, Hasan S, Hassan A, Xu J, Lu S, Mi S, Liu H, Yao J. Proteome Dynamics Analysis Reveals the Potential Mechanisms of Salinity and Drought Response during Seed Germination and Seedling Growth in Tamarix hispida. Genes (Basel) 2023; 14:genes14030656. [PMID: 36980928 PMCID: PMC10048391 DOI: 10.3390/genes14030656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 02/27/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Understanding the molecular mechanisms of seed germination and seedling growth is vital for mining functional genes for the improvement of plant drought in a desert. Tamarix hispida is extremely resistant to drought and soil salinity perennial shrubs or trees. This study was the first to investigate the protein abundance profile of the transition process during the processes of T. hispida seed germination and seedling growth using label-free proteomics approaches. Our data suggested that asynchronous regulation of transcriptomics and proteomics occurs upon short-term seed germination and seedling growth of T. hispida. Enrichment analysis revealed that the main differentially abundant proteins had significant enrichment in stimulus response, biosynthesis, and metabolism. Two delta-1-pyrroline-5-carboxylate synthetases (P5CS), one Ycf3-interacting protein (Y3IP), one low-temperature-induced 65 kDa protein-like molecule, and four peroxidases (PRX) were involved in both water deprivation and hyperosmotic salinity responses. Through a comparative analysis of transcriptomics and proteomics, we found that proteomics may be better at studying short-term developmental processes. Our results support the existence of several mechanisms that enhance tolerance to salinity and drought stress during seedling growth in T. hispida.
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Affiliation(s)
- Xin’an Pang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production and Construction Corps, College of Life Sciences, Tarim University, Alar 843300, China
| | - Shuo Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, China
| | - Jiangtao Suo
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, China
| | - Tiange Yang
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, China
| | - Samira Hasan
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, China
| | - Ali Hassan
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, China
| | - Jindong Xu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, China
| | - Sushuangqing Lu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, China
| | - Sisi Mi
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, China
| | - Hong Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, China
- Correspondence: (H.L.); (J.Y.)
| | - Jialing Yao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence: (H.L.); (J.Y.)
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3
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Fogeron ML, Lecoq L, Cole L, Montserret R, David G, Page A, Delolme F, Nassal M, Böckmann A. Phosphorylation of the Hepatitis B Virus Large Envelope Protein. Front Mol Biosci 2022; 8:821755. [PMID: 35282608 PMCID: PMC8904964 DOI: 10.3389/fmolb.2021.821755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/22/2021] [Indexed: 01/05/2023] Open
Abstract
We here establish the phosphorylation sites in the human hepatitis B virus (HBV) large envelope protein (L). L is involved in several functionally important interactions in the viral life cycle, including with the HBV cellular receptor, HBV capsid, Hsc70 chaperone, and cellular membranes during fusion. We have recently shown that cell-free synthesis of the homologous L protein of duck HBV in wheat germ extract results in very similar phosphorylation events to those previously observed in animal cells. Here, we used mass spectrometry and NMR to establish the phosphorylation patterns of human HBV L protein produced by both in vitro cell-free synthesis and in E. coli with the co-expression of the human MAPK14 kinase. While in the avian virus the phosphorylation of L has been shown to be dispensable for infectivity, the identified locations in the human virus protein, both in the PreS1 and PreS2 domains, raise the intriguing possibility that they might play a functional role, since they are found at strategic sites predicted to be involved in L interactions. This would warrant the further investigation of a possible function in virion formation or cell entry.
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Affiliation(s)
- Marie-Laure Fogeron
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Laura Cole
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Roland Montserret
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Guillaume David
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Adeline Page
- Protein Science Facility, SFR BioSciences CNRS UAR 3444, Inserm US8, UCBL, ENS de Lyon, Lyon, France
| | - Frédéric Delolme
- Protein Science Facility, SFR BioSciences CNRS UAR 3444, Inserm US8, UCBL, ENS de Lyon, Lyon, France
| | - Michael Nassal
- Department of Medicine II / Molecular Biology, Medical Center, University Hospital Freiburg, University of Freiburg, Freiburg im Breisgau, Germany
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
- *Correspondence: Anja Böckmann,
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4
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Comparative proteome analysis of matured dry and germinating Moringa oleifera seeds provides insights into protease activity during germination. Food Res Int 2020; 136:109332. [DOI: 10.1016/j.foodres.2020.109332] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 05/09/2020] [Accepted: 05/16/2020] [Indexed: 12/16/2022]
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5
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David G, Fogeron ML, Montserret R, Lecoq L, Page A, Delolme F, Nassal M, Böckmann A. Phosphorylation and Alternative Translation on Wheat Germ Cell-Free Protein Synthesis of the DHBV Large Envelope Protein. Front Mol Biosci 2019; 6:138. [PMID: 31850370 PMCID: PMC6902406 DOI: 10.3389/fmolb.2019.00138] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/18/2019] [Indexed: 12/13/2022] Open
Abstract
Wheat-germ cell-free protein synthesis (WG-CFPS) is a potent platform for the high-yield production of proteins. It is especially of interest for difficult-to-express eukaryotic proteins, such as toxic and transmembrane proteins, and presents an important tool in high-throughput protein screening. Until recently, an assumed drawback of WG-CFPS was a reduced capacity for post-translational modifications. Meanwhile, phosphorylation has been observed in WG-CFPS; yet, authenticity of the respective phosphorylation sites remained unclear. Here we show that a viral membrane protein, the duck hepatitis B virus (DHBV) large envelope protein (DHBs L), produced by WG-CFPS, is phosphorylated upon translation at the same sites as DHBs L produced during DHBV infection of primary hepatocytes. Furthermore, we show that alternative translation initiation of the L protein, previously identified in virus-producing hepatic cells, occurs on WG-CFPS as well. Together, these findings further strengthen the high potential of WG-CFPS to include the reproduction of specific modifications proteins experience in vivo.
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Affiliation(s)
- Guillaume David
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, Lyon, France
| | - Marie-Laure Fogeron
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, Lyon, France
| | - Roland Montserret
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, Lyon, France
| | - Lauriane Lecoq
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, Lyon, France
| | - Adeline Page
- Protein Science Facility, SFR BioSciences CNRS UMS3444, Inserm US8, UCBL, ENS de Lyon, Lyon, France
| | - Frédéric Delolme
- Protein Science Facility, SFR BioSciences CNRS UMS3444, Inserm US8, UCBL, ENS de Lyon, Lyon, France
| | - Michael Nassal
- Internal Medicine II/Molecular Biology, University Hospital Freiburg, Freiburg, Germany
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, Lyon, France
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6
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Roldán-Arjona T, Ariza RR, Córdoba-Cañero D. DNA Base Excision Repair in Plants: An Unfolding Story With Familiar and Novel Characters. FRONTIERS IN PLANT SCIENCE 2019; 10:1055. [PMID: 31543887 PMCID: PMC6728418 DOI: 10.3389/fpls.2019.01055] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 07/30/2019] [Indexed: 05/05/2023]
Abstract
Base excision repair (BER) is a critical genome defense pathway that deals with a broad range of non-voluminous DNA lesions induced by endogenous or exogenous genotoxic agents. BER is a complex process initiated by the excision of the damaged base, proceeds through a sequence of reactions that generate various DNA intermediates, and culminates with restoration of the original DNA structure. BER has been extensively studied in microbial and animal systems, but knowledge in plants has lagged behind until recently. Results obtained so far indicate that plants share many BER factors with other organisms, but also possess some unique features and combinations. Plant BER plays an important role in preserving genome integrity through removal of damaged bases. However, it performs additional important functions, such as the replacement of the naturally modified base 5-methylcytosine with cytosine in a plant-specific pathway for active DNA demethylation.
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Affiliation(s)
- Teresa Roldán-Arjona
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Genetics, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Rafael R. Ariza
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Genetics, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Dolores Córdoba-Cañero
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Genetics, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
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7
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Probing early wheat grain development via transcriptomic and proteomic approaches. Funct Integr Genomics 2019; 20:63-74. [DOI: 10.1007/s10142-019-00698-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 06/20/2019] [Accepted: 06/24/2019] [Indexed: 12/20/2022]
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8
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Ancestor of land plants acquired the DNA-3-methyladenine glycosylase (MAG) gene from bacteria through horizontal gene transfer. Sci Rep 2017; 7:9324. [PMID: 28839126 PMCID: PMC5570899 DOI: 10.1038/s41598-017-05066-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 05/23/2017] [Indexed: 02/07/2023] Open
Abstract
The origin and evolution of land plants was an important event in the history of life and initiated the establishment of modern terrestrial ecosystems. From water to terrestrial environments, plants needed to overcome the enhanced ultraviolet (UV) radiation and many other DNA-damaging agents. Evolving new genes with the function of DNA repair is critical for the origin and radiation of land plants. In bacteria, the DNA-3-methyladenine glycosylase (MAG) recognizes of a variety of base lesions and initiates the process of the base excision repair for damaged DNA. The homologs of MAG gene are present in all major lineages of streptophytes, and both the phylogenic and sequence similarity analyses revealed that green plant MAG gene originated through an ancient horizontal gene transfer (HGT) event from bacteria. Experimental evidence demonstrated that the expression of the maize ZmMAG gene was induced by UV and zeocin, both of which are known as DNA-damaging agents. Further investigation revealed that Streptophyta MAG genes had undergone positive selection during the initial evolutionary period in the ancestor of land plants. Our findings demonstrated that the ancient HGT of MAG to the ancestor of land plants probably played an important role in preadaptation to DNA-damaging agents in terrestrial environments.
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9
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Wheat (Triticum aestivum L.) grain proteome response to elevated [CO2] varies between genotypes. J Cereal Sci 2017. [DOI: 10.1016/j.jcs.2017.03.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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10
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Naconsie M, Lertpanyasampatha M, Viboonjun U, Netrphan S, Kuwano M, Ogasawara N, Narangajavana J. Cassava root membrane proteome reveals activities during storage root maturation. JOURNAL OF PLANT RESEARCH 2016; 129:51-65. [PMID: 26547558 DOI: 10.1007/s10265-015-0761-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 07/13/2015] [Indexed: 06/05/2023]
Abstract
Cassava (Manihot esculenta Crantz) is one of the most important crops of Thailand. Its storage roots are used as food, feed, starch production, and be the important source for biofuel and biodegradable plastic production. Despite the importance of cassava storage roots, little is known about the mechanisms involved in their formation. This present study has focused on comparison of the expression profiles of cassava root proteome at various developmental stages using two-dimensional gel electrophoresis and LC-MS/MS. Based on an anatomical study using Toluidine Blue, the secondary growth was confirmed to be essential during the development of cassava storage root. To investigate biochemical processes occurring during storage root maturation, soluble and membrane proteins were isolated from storage roots harvested from 3-, 6-, 9-, and 12-month-old cassava plants. The proteins with differential expression pattern were analysed and identified to be associated with 8 functional groups: protein folding and degradation, energy, metabolism, secondary metabolism, stress response, transport facilitation, cytoskeleton, and unclassified function. The expression profiling of membrane proteins revealed the proteins involved in protein folding and degradation, energy, and cell structure were highly expressed during early stages of development. Integration of these data along with the information available in genome and transcriptome databases is critical to expand knowledge obtained solely from the field of proteomics. Possible role of identified proteins were discussed in relation with the activities during storage root maturation in cassava.
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Affiliation(s)
- Maliwan Naconsie
- Deparment of Biotechnology, Faculty of Science, Mahidol University, Rama 6 Rd.,Rajthewee, Phayathai, Bangkok, 10400, Thailand
| | - Manassawe Lertpanyasampatha
- Deparment of Biotechnology, Faculty of Science, Mahidol University, Rama 6 Rd.,Rajthewee, Phayathai, Bangkok, 10400, Thailand
| | - Unchera Viboonjun
- Deparment of Plant Science, Faculty of Science, Mahidol University, Phayathai, Bangkok, 10400, Thailand
| | - Supatcharee Netrphan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Rangsit, Pathumthani, 10210, Thailand
| | - Masayoshi Kuwano
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Naotake Ogasawara
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Jarunya Narangajavana
- Deparment of Biotechnology, Faculty of Science, Mahidol University, Rama 6 Rd.,Rajthewee, Phayathai, Bangkok, 10400, Thailand.
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11
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He M, Zhu C, Dong K, Zhang T, Cheng Z, Li J, Yan Y. Comparative proteome analysis of embryo and endosperm reveals central differential expression proteins involved in wheat seed germination. BMC PLANT BIOLOGY 2015; 15:97. [PMID: 25888100 PMCID: PMC4407426 DOI: 10.1186/s12870-015-0471-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 03/16/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND Wheat seeds provide a staple food and an important protein source for the world's population. Seed germination is vital to wheat growth and development and directly affects grain yield and quality. In this study, we performed the first comparative proteomic analysis of wheat embryo and endosperm during seed germination. RESULTS The proteomic changes in embryo and endosperm during the four different seed germination stages of elite Chinese bread wheat cultivar Zhengmai 9023 were first investigated. In total, 74 and 34 differentially expressed protein (DEP) spots representing 63 and 26 unique proteins were identified in embryo and endosperm, respectively. Eight common DEP were present in both tissues, and 55 and 18 DEP were specific to embryo and endosperm, respectively. These identified DEP spots could be sorted into 13 functional groups, in which the main group was involved in different metabolism pathways, particularly in the reserves necessary for mobilization in preparation for seed germination. The DEPs from the embryo were mainly related to carbohydrate metabolism, proteometabolism, amino acid metabolism, nucleic acid metabolism, and stress-related proteins, whereas those from the endosperm were mainly involved in protein storage, carbohydrate metabolism, inhibitors, stress response, and protein synthesis. During seed germination, both embryo and endosperm had a basic pattern of oxygen consumption, so the proteins related to respiration and energy metabolism were up-regulated or down-regulated along with respiration of wheat seeds. When germination was complete, most storage proteins from the endosperm began to be mobilized, but only a small amount was degraded during germination. Transcription expression of six representative DEP genes at the mRNA level was consistent with their protein expression changes. CONCLUSION Wheat seed germination is a complex process with imbibition, stirring, and germination stages, which involve a series of physiological, morphological, and proteomic changes. The first process is a rapid water uptake, in which the seed coat becomes softer and the physical state of storage materials change gradually. Then the germinated seed enters the second process (a plateau phase) and the third process (the embryonic axes elongation). Seed embryo and endosperm display distinct differentially expressed proteins, and their synergistic expression mechanisms provide a basis for the normal germination of wheat seeds.
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Affiliation(s)
- Miao He
- College of Life Science, Capital Normal University, Beijing, 100048, China.
| | - Chong Zhu
- College of Life Science, Capital Normal University, Beijing, 100048, China.
| | - Kun Dong
- College of Life Science, Capital Normal University, Beijing, 100048, China.
| | - Ting Zhang
- College of Life Science, Capital Normal University, Beijing, 100048, China.
| | - Zhiwei Cheng
- College of Life Science, Capital Normal University, Beijing, 100048, China.
| | - Jiarui Li
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA.
| | - Yueming Yan
- College of Life Science, Capital Normal University, Beijing, 100048, China.
- Hubei Collaborative Innovation Center for Grain Industry, 434025, Jingzhou, China.
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Thakur A, Bhatla SC. Proteomic analysis of oil body membrane proteins accompanying the onset of desiccation phase during sunflower seed development. PLANT SIGNALING & BEHAVIOR 2015; 10:e1030100. [PMID: 26786011 PMCID: PMC4854339 DOI: 10.1080/15592324.2015.1030100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 03/10/2015] [Accepted: 03/11/2015] [Indexed: 05/20/2023]
Abstract
A noteworthy metabolic signature accompanying oil body (OB) biogenesis during oilseed development is associated with the modulation of the oil body membranes proteins. Present work focuses on 2-dimensional polyacrylamide gel electrophoresis (2-D PAGE)-based analysis of the temporal changes in the OB membrane proteins analyzed by LC-MS/MS accompanying the onset of desiccation (20-30 d after anthesis; DAA) in the developing seeds of sunflower (Helianthus annuus L.). Protein spots unique to 20-30 DAA stages were picked up from 2-D gels for identification and the identified proteins were categorized into 7 functional classes. These include proteins involved in energy metabolism, reactive oxygen scavenging, proteolysis and protein turnover, signaling, oleosin and oil body biogenesis-associated proteins, desiccation and cytoskeleton. At 30 DAA stage, exclusive expressions of enzymes belonging to energy metabolism, desiccation and cytoskeleton were evident which indicated an increase in the metabolic and enzymatic activity in the cells at this stage of seed development (seed filling). Increased expression of cruciferina-like protein and dehydrin at 30 DAA stage marks the onset of desiccation. The data has been analyzed and discussed to highlight desiccation stage-associated metabolic events during oilseed development.
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Affiliation(s)
- Anita Thakur
- Laboratory of Plant Physiology and Biochemistry; Department of Botany; University of Delhi; Delhi, India
| | - Satish C Bhatla
- Laboratory of Plant Physiology and Biochemistry; Department of Botany; University of Delhi; Delhi, India
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Cunsolo V, Muccilli V, Saletti R, Foti S. Mass spectrometry in the proteome analysis of mature cereal kernels. MASS SPECTROMETRY REVIEWS 2012; 31:448-465. [PMID: 22711440 DOI: 10.1002/mas.20347] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 07/07/2011] [Accepted: 07/07/2011] [Indexed: 06/01/2023]
Abstract
In the last decade, the improved performance and versatility of the mass spectrometers together with the increasing availability of gene and genomic sequence database, led the mass spectrometry to become an indispensable tool for either protein and proteome analyses in cereals. Mass spectrometric works on prolamins have rapidly evolved from the determination of the molecular masses of proteins to the proteomic approaches aimed to a large-scale protein identification and study of functional and regulatory aspects of proteins. Mass spectrometry coupled with electrophoresis, chromatographic methods, and bioinformatics tools is currently making significant contributions to a better knowledge of the composition and structure of the cereal proteins and their structure-function relationships. Results obtained using mass spectrometry, including characterization of prolamins, investigation of the gluten toxicity for coeliac patients, identification of proteins responsible of cereal allergies, determination of the protein pattern and its modification under environmental or stress effects, investigation of genetically modified varieties by proteomic approaches, are summarized here, to illustrate current trends, analytical troubles and challenges, and suggest possible future perspectives.
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Affiliation(s)
- Vincenzo Cunsolo
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Italy
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14
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New insights into the effects of high temperature, drought and post-anthesis fertilizer on wheat grain development. J Cereal Sci 2012. [DOI: 10.1016/j.jcs.2011.12.012] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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15
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16
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A novel hardness-related and starch granule-associated protein marker in wheat: LMW-GS-‘S’. J Cereal Sci 2012. [DOI: 10.1016/j.jcs.2011.10.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Seed proteomics. J Proteomics 2011; 74:389-400. [DOI: 10.1016/j.jprot.2010.12.004] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Revised: 12/08/2010] [Accepted: 12/10/2010] [Indexed: 12/29/2022]
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18
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Miernyk JA, Preťová A, Olmedilla A, Klubicová K, Obert B, Hajduch M. Using proteomics to study sexual reproduction in angiosperms. ACTA ACUST UNITED AC 2010; 24:9-22. [PMID: 20830489 DOI: 10.1007/s00497-010-0149-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Accepted: 08/21/2010] [Indexed: 12/18/2022]
Abstract
While a relative latecomer to the postgenomics era of functional biology, the application of mass spectrometry-based proteomic analysis has increased exponentially over the past 10 years. Some of this increase is the result of transition of chemists, physicists, and mathematicians to the study of biology, and some is due to improved methods, increased instrument sensitivity, and better techniques of bioinformatics-based data analysis. Proteomic Biological processes are typically studied in isolation, and seldom are efforts made to coordinate results obtained using structural, biochemical, and molecular-genetic strategies. Mass spectrometry-based proteomic analysis can serve as a platform to bridge these disparate results and to additionally incorporate both temporal and anatomical considerations. Recently, proteomic analyses have transcended their initial purely descriptive applications and are being employed extensively in studies of posttranslational protein modifications, protein interactions, and control of metabolic networks. Herein, we provide a brief introduction to sample preparation, comparison of gel-based versus gel-free methods, and explanation of data analysis emphasizing plant reproductive applications. We critically review the results from the relatively small number of extant proteomics-based analyses of angiosperm reproduction, from flowers to seedlings, and speculate on the utility of this strategy for future developments and directions.
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Affiliation(s)
- Ján A Miernyk
- Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences, Nitra, Slovak Republic
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Proteomic analysis of wheat embryos with 2-DE and liquid-phase chromatography (ProteomeLab PF-2D) — A wider perspective of the proteome. J Proteomics 2010; 73:1707-21. [DOI: 10.1016/j.jprot.2010.05.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Revised: 05/07/2010] [Accepted: 05/07/2010] [Indexed: 01/03/2023]
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Jerkovic A, Kriegel AM, Bradner JR, Atwell BJ, Roberts TH, Willows RD. Strategic distribution of protective proteins within bran layers of wheat protects the nutrient-rich endosperm. PLANT PHYSIOLOGY 2010; 152:1459-70. [PMID: 20061449 PMCID: PMC2832279 DOI: 10.1104/pp.109.149864] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Accepted: 01/05/2010] [Indexed: 05/13/2023]
Abstract
Bran from bread wheat (Triticum aestivum 'Babbler') grain is composed of many outer layers of dead maternal tissues that overlie living aleurone cells. The dead cell layers function as a barrier resistant to degradation, whereas the aleurone layer is involved in mobilizing organic substrates in the endosperm during germination. We microdissected three defined bran fractions, outer layers (epidermis and hypodermis), intermediate fraction (cross cells, tube cells, testa, and nucellar tissue), and inner layer (aleurone cells), and used proteomics to identify their individual protein complements. All proteins of the outer layers were enzymes, whose function is to provide direct protection against pathogens or improve tissue strength. The more complex proteome of the intermediate layers suggests a greater diversity of function, including the inhibition of enzymes secreted by pathogens. The inner layer contains proteins involved in metabolism, as would be expected from live aleurone cells, but this layer also includes defense enzymes and inhibitors as well as 7S globulin (specific to this layer). Using immunofluorescence microscopy, oxalate oxidase was localized predominantly to the outer layers, xylanase inhibitor protein I to the xylan-rich nucellar layer of the intermediate fraction and pathogenesis-related protein 4 mainly to the aleurone. Activities of the water-extractable enzymes oxalate oxidase, peroxidase, and polyphenol oxidase were highest in the outer layers, whereas chitinase activity was found only in assays of whole grains. We conclude that the differential protein complements of each bran layer in wheat provide distinct lines of defense in protecting the embryo and nutrient-rich endosperm.
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Affiliation(s)
| | | | | | | | | | - Robert D. Willows
- Department of Chemistry and Biomolecular Sciences (A.J., A.M.K., J.R.B., T.H.R., R.D.W.) and Department of Biological Sciences (B.J.A.), Macquarie University, Sydney, New South Wales 2109, Australia; and Grain Foods Cooperative Research Centre Ltd., North Ryde, New South Wales 2113, Australia (A.J., A.M.K., J.R.B., B.J.A., T.H.R., R.D.W.)
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Zörb C, Steinfurth D, Seling S, Langenkämper G, Koehler P, Wieser H, Lindhauer MG, Mühling KH. Quantitative protein composition and baking quality of winter wheat as affected by late sulfur fertilization. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2009; 57:3877-3885. [PMID: 19326868 DOI: 10.1021/jf8038988] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Increasing prices for wheat products and fertilizers, as well as reduced sulfur (S) contributions from the atmosphere, call for an improvement of product quality and agricultural management. To detect the impact of a time-dependent S fertilization, the quantitative protein composition and the baking quality of two different wheat cultivars, Batis and Turkis, were evaluated. The glutathione concentration in grains serves as a reliable marker of the need for added S fertilizer. The quantitation of gliadins and glutenin subunits by reversed-phase high-performance liquid chromatography confirmed that S-rich proteins significantly increased with S fertilization, whereas the S-poor proteins significantly decreased. Proteome analysis by means of high-resolution protein profiles detected 55 and 37 proteins from Batis and Turkis changed by late S fertilization. A microscale baking test using wholemeal flour was implemented for the evaluation of baking quality, and late S fertilization was found to improve the composition of gluten proteins and baking quality.
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Affiliation(s)
- Christian Zörb
- Institute of Plant Nutrition and Soil Science, Christian Albrechts University Kiel, Hermann-Rodewald-Strasse 2, D-24118 Kiel, Germany.
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Mak Y, Willows RD, Roberts TH, Wrigley CW, Sharp PJ, Copeland L. Germination of Wheat: A Functional Proteomics Analysis of the Embryo. Cereal Chem 2009. [DOI: 10.1094/cchem-86-3-0281] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Yunxian Mak
- Faculty of Agriculture, Food and Natural Resources, University of Sydney, NSW 2006, Australia
| | - Robert D. Willows
- Department of Chemistry and Biomolecular Sciences, Macquarie University, NSW 2109, Australia
| | - Thomas H. Roberts
- Department of Chemistry and Biomolecular Sciences, Macquarie University, NSW 2109, Australia
| | | | - Peter J. Sharp
- Faculty of Agriculture, Food and Natural Resources, University of Sydney, NSW 2006, Australia
- Plant Breeding Institute, University of Sydney, Camden, NSW 2570, Australia
| | - Les Copeland
- Faculty of Agriculture, Food and Natural Resources, University of Sydney, NSW 2006, Australia
- Corresponding author. Fax: +61-2-9351 2945. E-mail:
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Manickavasagan A, Jayas DS, White NDG, Paliwal J. Wheat Class Identification Using Thermal Imaging. FOOD BIOPROCESS TECH 2008. [DOI: 10.1007/s11947-008-0110-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Abstract
The advent of proteomics has made it possible to identify a broad spectrum of proteins in living systems. This capability is especially useful for crops as it may give clues not only about nutritional value, but also about yield and how these factors are affected by adverse conditions. In this review, we describe the recent progress in crop proteomics and highlight the achievements made in understanding the proteomes of major crops. The major emphasis will be on crop responses to abiotic stresses. Rigorous genetic testing of the role of possibly important proteins can be conducted. The increasing ease with the DNA, mRNA and protein levels can be conducted and connected suggests that proteomics data will not be difficult to apply to practical crop breeding.
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