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Zhou R, Qin X, Hou J, Liu Y. Research progress on Brassicaceae plants: a bibliometrics analysis. FRONTIERS IN PLANT SCIENCE 2024; 15:1285050. [PMID: 38357268 PMCID: PMC10864531 DOI: 10.3389/fpls.2024.1285050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 01/15/2024] [Indexed: 02/16/2024]
Abstract
The Brassicaceae is a worldwide family that produces ornamental flowers, edible vegetables, and oilseed plants, with high economic value in agriculture, horticulture, and landscaping. This study used the Web of Science core dataset and the CiteSpace bibliometric tool to quantitatively visualize the number of publications, authors, institutions, and countries of 3139 papers related to Brassicaceae plants from 2002 to 2022. The keywords and references were divided into two phases: Phase 1 (2002-2011) and Phase 2 (2012-2022) for quantitative and qualitative analysis. The results showed: An average annual publication volume of 149 articles, with an overall fluctuating upward trend; the research force was mainly led by Professor Ihsan A. Al-shehbaz from Missouri Botanical Garden; and the United States had the highest number of publications. In the first phase, research focused on the phylogeny of Brassicaceae plants, while the second phase delved into diverse research based on previous studies, research in areas such as polyploidy, molecular technique, physiology, and hyperaccumulator has been extended. Based on this research, we propounded some ideas for future studies on Brassicaceae plants and summarized the research gaps.
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Affiliation(s)
- Ruixue Zhou
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Xinsheng Qin
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Junjun Hou
- College of Horticultural Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Yining Liu
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
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2
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Karg CA, Taniguchi M, Lindsey JS, Moser S. Phyllobilins - Bioactive Natural Products Derived from Chlorophyll - Plant Origins, Structures, Absorption Spectra, and Biomedical Properties. PLANTA MEDICA 2023; 89:637-662. [PMID: 36198325 DOI: 10.1055/a-1955-4624] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Phyllobilins are open-chain products of the biological degradation of chlorophyll a in higher plants. Recent studies reveal that phyllobilins exert anti-oxidative and anti-inflammatory properties, as well as activities against cancer cells, that contribute to the human health benefits of numerous plants. In general, phyllobilins have been overlooked in phytochemical analyses, and - more importantly - in the analyses of medicinal plant extracts. Nevertheless, over the past three decades, > 70 phyllobilins have been identified upon examination of more than 30 plant species. Eight distinct chromophoric classes of phyllobilins are known: phyllolumibilins (PluBs), phylloleucobilins (PleBs), phylloxanthobilins (PxBs), and phylloroseobilins (PrBs)-each in type-I or type-II groups. Here, we present a database of absorption and fluorescence spectra that has been compiled of 73 phyllobilins to facilitate identification in phytochemical analyses. The spectra are provided in digital form and can be viewed and downloaded at www.photochemcad.com. The present review describes the plant origin, molecular structure, and absorption and fluorescence features of the 73 phyllobilins, along with an overview of key medicinal properties. The review should provide an enabling tool for the community for the straightforward identification of phyllobilins in plant extracts, and the foundation for deeper understanding of these ubiquitous but underexamined plant-derived micronutrients for human health.
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Affiliation(s)
- Cornelia A Karg
- Department of Pharmacy, Pharmaceutical Biology, Ludwig-Maximilian University of Munich, Germany
| | | | | | - Simone Moser
- Department of Pharmacy, Pharmaceutical Biology, Ludwig-Maximilian University of Munich, Germany
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3
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Ahmad F, Nadeem H. Mass Spectroscopy as an Analytical Tool to Harness the Production of Secondary Plant Metabolites: The Way Forward for Drug Discovery. Methods Mol Biol 2023; 2575:77-103. [PMID: 36301472 DOI: 10.1007/978-1-0716-2716-7_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The molecular map of diverse biological molecules linked with structure, function, signaling, and regulation within a cell can be elucidated using an analytically demanding omic approach. The latest trend of using "metabolomics" technologies has explained the natural phenomenon of opening a new avenue to understand and enhance bioactive compounds' production. Examination of sequenced plant genomes has revealed that a considerable portion of these encodes genes of secondary metabolism. In addition to genetic and molecular tools developed in the current era, the ever-increasing knowledge about plant metabolism's biochemistry has initiated an approach for wisely designed, more productive genetic engineering of plant secondary metabolism for improved defense systems and enhanced biosynthesis of beneficial metabolites. Secondary plant metabolites are natural products synthesized by plants that are not directly involved with their average growth and development but play a vital role in plant defense mechanisms. Plant secondary metabolites are classified into four major classes: terpenoids, phenolic compounds, alkaloids, and sulfur-containing compounds. More than 200,000 secondary metabolites are synthesized by plants having a unique and complex structure. Secondary plant metabolites are well characterized and quantified by omics approaches and therefore used by humans in different sectors such as agriculture, pharmaceuticals, chemical industries, and biofuel. The aim is to establish metabolomics as a comprehensive and dynamic model of diverse biological molecules for biomarkers and drug discovery. In this chapter, we aim to illustrate the role of metabolomic technology, precisely liquid chromatography-mass spectrometry, capillary electrophoresis mass spectrometry, gas chromatography-mass spectrometry, and nuclear magnetic resonance spectroscopy, specifically as a research tool in the production and identification of novel bioactive compounds for drug discovery and to obtain a unified insight of secondary metabolism in plants.
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Affiliation(s)
- Faheem Ahmad
- Department of Botany, Aligarh Muslim University, Aligarh, Uttar Pradesh, India.
| | - Hera Nadeem
- Department of Botany, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
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de Souza Araújo DM, de Almeida AAF, Pirovani CP, Mora-Ocampo IY, Lima Silva JP, Valle Meléndez RR. Molecular, biochemical and micromorphological responses of cacao seedlings of the Parinari series, carrying the lethal gene Luteus-Pa, in the presence and absence of cotyledons. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 194:550-569. [PMID: 36525937 DOI: 10.1016/j.plaphy.2022.11.009] [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: 05/29/2022] [Revised: 11/05/2022] [Accepted: 11/08/2022] [Indexed: 06/17/2023]
Abstract
Investigations of the compatibility between cacao genotypes of the population of the Parinari series (Pa), resulting from the reciprocal crossing of Pa 30 × Pa 169 and Pa 121 × Pa 169, allowed the verification of the occurrence of the recessive lethal single character called Luteus-Pa. These genotypes have this gene in heterozygosity, which when intercross or self-fertilize, segregate in a 3:1 ratio. Normal (NS) and mutant (MS) seedlings grow normally and, after a period of approximately 30 days of age, MS leaves begin to show a metallic yellow color, followed by necrotic spots, and death of the entire seedling, approximately 40 days after the emergency. The work evaluate the molecular, biochemical and micromorphological responses in NS and MS, with and without cotyledons, resulting from the crossing of the Pa 30 × Pa 169 cacao genotypes, aiming to elucidate the possible lethal mechanisms of the homozygous recessive Luteus-Pa. The presence of the lethal gene Luteus-Pa in the seedlings of the cacao genotypes of the population of the Parinari (Pa), with and without cotyledons, resulting from the crossing of Pa 30 × Pa 169, in addition to regulating the synthesis of proteins related to the photosynthetic and stress defense processes, promoted an increase in the synthesis of proteins involved in the glycolic pathway, induced oxidative stress, altered the mobilization of cotyledonary reserves, the integrity of cell membranes, leaf micromorphology and induced the death of seedlings, soon after depletion of protein and carbohydrate reserves, especially in the absence of cotyledons.
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Affiliation(s)
- D'avila Maria de Souza Araújo
- State University of Santa Cruz, Department of Biological Sciences, km 16 Jorge Amado Highway, 45662-900, Ilhéus, BA, Brazil
| | - Alex-Alan Furtado de Almeida
- State University of Santa Cruz, Department of Biological Sciences, km 16 Jorge Amado Highway, 45662-900, Ilhéus, BA, Brazil.
| | - Carlos Priminho Pirovani
- State University of Santa Cruz, Department of Biological Sciences, km 16 Jorge Amado Highway, 45662-900, Ilhéus, BA, Brazil
| | - Irma Yuliana Mora-Ocampo
- State University of Santa Cruz, Department of Biological Sciences, km 16 Jorge Amado Highway, 45662-900, Ilhéus, BA, Brazil
| | - João Paulo Lima Silva
- State University of Santa Cruz, Department of Biological Sciences, km 16 Jorge Amado Highway, 45662-900, Ilhéus, BA, Brazil
| | - Raúl René Valle Meléndez
- State University of Santa Cruz, Department of Biological Sciences, km 16 Jorge Amado Highway, 45662-900, Ilhéus, BA, Brazil; Executive Commission for the Cacao farming Plan, km 22 Jorge Amado Highway, 45650-780, Ilhéus, BA, Brazil
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Iqbal N, Czékus Z, Poór P, Ördög A. Plant defence mechanisms against mycotoxin Fumonisin B1. Chem Biol Interact 2021; 343:109494. [PMID: 33915161 DOI: 10.1016/j.cbi.2021.109494] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 03/30/2021] [Accepted: 04/21/2021] [Indexed: 10/21/2022]
Abstract
Fumonisin B1 (FB1) is the most harmful mycotoxin which prevails in several crops and affects the growth and yield as well. Hence, keeping the alarming consequences of FB1 under consideration, there is still a need to seek other more reliable approaches and scientific knowledge for FB1-induced cell death and a comprehensive understanding of the mechanisms of plant defence strategies. FB1-induced disturbance in sphingolipid metabolism initiates programmed cell death (PCD) through various modes such as the elevated generation of reactive oxygen species, lipid peroxidation, cytochrome c release from the mitochondria, and activation of specific proteases and nucleases causing DNA fragmentation. There is a close interaction between sphingolipids and defence phytohormones in response to FB1 exposure regulating PCD and defence. In this review, the model plant Arabidopsis and various crops have been presented with different levels of susceptibility and resistivity exposed to various concentration of FB1. In addition to this, regulation of PCD and defence mechanisms have been also demonstrated at the physiological, biochemical and molecular levels to help the understanding of the role and function of FB1-inducible molecules and genes and their expressions in plants against pathogen attacks which could provide molecular and biochemical markers for the detection of toxin exposure.
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Affiliation(s)
- Nadeem Iqbal
- Department of Plant Biology, University of Szeged, H-6726, Szeged, Közép fasor 52., Hungary; Doctoral School of Environmental Sciences, University of Szeged, Szeged, Hungary
| | - Zalán Czékus
- Department of Plant Biology, University of Szeged, H-6726, Szeged, Közép fasor 52., Hungary; Doctoral School of Biology, University of Szeged, Szeged, Hungary
| | - Péter Poór
- Department of Plant Biology, University of Szeged, H-6726, Szeged, Közép fasor 52., Hungary.
| | - Attila Ördög
- Department of Plant Biology, University of Szeged, H-6726, Szeged, Közép fasor 52., Hungary
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6
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Plant Proteomics and Systems Biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1346:51-66. [DOI: 10.1007/978-3-030-80352-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Baslam M, Mitsui T, Sueyoshi K, Ohyama T. Recent Advances in Carbon and Nitrogen Metabolism in C3 Plants. Int J Mol Sci 2020; 22:E318. [PMID: 33396811 PMCID: PMC7795015 DOI: 10.3390/ijms22010318] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/23/2020] [Accepted: 12/23/2020] [Indexed: 12/19/2022] Open
Abstract
C and N are the most important essential elements constituting organic compounds in plants. The shoots and roots depend on each other by exchanging C and N through the xylem and phloem transport systems. Complex mechanisms regulate C and N metabolism to optimize plant growth, agricultural crop production, and maintenance of the agroecosystem. In this paper, we cover the recent advances in understanding C and N metabolism, regulation, and transport in plants, as well as their underlying molecular mechanisms. Special emphasis is given to the mechanisms of starch metabolism in plastids and the changes in responses to environmental stress that were previously overlooked, since these changes provide an essential store of C that fuels plant metabolism and growth. We present general insights into the system biology approaches that have expanded our understanding of core biological questions related to C and N metabolism. Finally, this review synthesizes recent advances in our understanding of the trade-off concept that links C and N status to the plant's response to microorganisms.
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Affiliation(s)
- Marouane Baslam
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan; (M.B.); (T.M.)
| | - Toshiaki Mitsui
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan; (M.B.); (T.M.)
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan;
| | - Kuni Sueyoshi
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan;
| | - Takuji Ohyama
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan;
- Faculty of Applied Biosciences, Tokyo University of Agriculture, Tokyo 156-8502, Japan
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8
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Jin M, Wang H, Liu H, Xia Y, Ruan S, Huang Y, Qiu J, Du S, Xu L. Oxidative stress response and proteomic analysis reveal the mechanisms of toxicity of imidazolium-based ionic liquids against Arabidopsis thaliana. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 260:114013. [PMID: 32000025 DOI: 10.1016/j.envpol.2020.114013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 12/29/2019] [Accepted: 01/16/2020] [Indexed: 06/10/2023]
Abstract
Ionic liquids (ILs) are extensively used in various fields, posing a potential threat in the ecosystem because of their high stability, excellent solubility, and biological toxicity. In this study, the toxicity mechanism of three ILs, 1-octyl-3-methylimidazolium chloride ([C8MIM]Cl), 1-decyl-3-methylimidazolium chloride ([C10MIM]Cl), and 1-dodecyl-3-methylimidazolium chloride ([C12MIM]Cl) on Arabidopsis thaliana were revealed. Reactive oxygen species (ROS) level increased with higher concentration and longer carbon chain length of ILs, which led to the increase of malondialdehyde (MDA) content and antioxidase activity, including superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPX) and peroxidase (POD) activities. SOD, CAT, and GPX activities decreased in high ILs concentration due to the excessive ROS. Differentially expressed protein was analyzed based on Gene ontology (GO) and KEGG pathways analysis. 70, 45, 84 up-regulated proteins, and 72, 104, 79 down-regulated proteins were identified in [C8MIM]Cl, [C10MIM]Cl, and [C12MIM]Cl treatment, respectively (fold change ≥ 1.5 with ≥95% confidence). Cellular aldehyde metabolic process, mitochondrial and mitochondrial respiratory chains, glutathione transferase and oxidoreductase activity were enriched as up-regulated proteins as the defense mechanism of A. thaliana to resist external stresses. Chloroplast, photosynthetic membrane and thylakoid, structural constituent of ribosome, and transmembrane transport were enriched as the down-regulated protein. Compared with the control, 8 and 14 KEGG pathways were identified forup-regulated and down-regulated proteins, respectively, in three IL treatments. Metabolic pathways, carbon metabolism, biosynthesis of amino acids, porphyrin and chlorophyll metabolism were significantly down-regulated. The GO terms annotation demonstrated the oxidative stress response and effects on photosynthesis of A. thaliana in ILs treatment from biological process, cellular component, and molecular function categories.
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Affiliation(s)
- Mingkang Jin
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310018, Zhejiang Province, China
| | - Huan Wang
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310018, Zhejiang Province, China
| | - Huijun Liu
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310018, Zhejiang Province, China; Instrumental Analysis Center of Zhejiang Gongshang University, Hangzhou, 310018, Zhejiang Province, China.
| | - Yilu Xia
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310018, Zhejiang Province, China
| | - Songlin Ruan
- Laboratory of Plant Molecular Biology & Proteomics, Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024, China
| | - Yuqing Huang
- Laboratory of Plant Molecular Biology & Proteomics, Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024, China
| | - Jieren Qiu
- Laboratory of Plant Molecular Biology & Proteomics, Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024, China
| | - Shaoting Du
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310018, Zhejiang Province, China; Instrumental Analysis Center of Zhejiang Gongshang University, Hangzhou, 310018, Zhejiang Province, China
| | - Linglin Xu
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310018, Zhejiang Province, China
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Zhang C, Liu P. The New Face of the Lipid Droplet: Lipid Droplet Proteins. Proteomics 2018; 19:e1700223. [DOI: 10.1002/pmic.201700223] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 08/13/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Congyan Zhang
- National Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences Beijing 100101 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Pingsheng Liu
- National Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences Beijing 100101 China
- University of Chinese Academy of Sciences Beijing 100049 China
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10
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Prathi NB, Palit P, Madhu P, M R, Laha GS, Balachandran SM, Madhav MS, Sundaram RM, Mangrauthia SK. Proteomic and transcriptomic approaches to identify resistance and susceptibility related proteins in contrasting rice genotypes infected with fungal pathogen Rhizoctonia solani. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 130:258-266. [PMID: 30029184 DOI: 10.1016/j.plaphy.2018.07.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 07/10/2018] [Accepted: 07/10/2018] [Indexed: 05/05/2023]
Abstract
The devastating sheath blight disease caused by Rhizoctonia solani Kuhn (teleomorph: Thanatephorus cucumeris) causes major yield loss in most rice growing regions of the world. In this study, two moderately tolerant and four susceptible genotypes of rice were selected for R. solani induced proteome analysis using two-dimensional polyacrylamide gel electrophoresis. Forty five differentially expressed proteins (DEPs) were identified and analyzed by Mass Spectrometry. Based on their functions, these proteins were classified into different groups, viz., photosynthesis, resistance and pathogenesis, stress, cell wall metabolism and cytoskeleton development associated proteins, and hypothetical or uncharacterized proteins. Expression of 14 genes encoding DEPs was analyzed by quantitative PCR which showed consistency in transcripts and genes expression pattern. Furthermore, the expression of 16 other genes involved in diverse biological functions was analyzed. Up-regulation of these genes in the tolerant genotype Pankaj during sheath blight disease suggested efficient genetic regulation of this cultivar under stress. Also, expression analysis of conserved microRNAs (miRNAs) and their target genes revealed important role of miRNAs in post-transcriptional gene regulation during development of rice sheath blight disease. Genome-wide discovery of miRNAs and further characterization of DEPs and genes will help in better understanding of the molecular events during sheath blight disease development in rice.
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Affiliation(s)
| | - Paramita Palit
- ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, 500030, India; International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India
| | - P Madhu
- ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, 500030, India
| | - Ramesh M
- ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, 500030, India
| | - G S Laha
- ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, 500030, India
| | - S M Balachandran
- ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, 500030, India
| | - M Sheshu Madhav
- ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, 500030, India
| | - R M Sundaram
- ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, 500030, India
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Sita K, Sehgal A, HanumanthaRao B, Nair RM, Vara Prasad PV, Kumar S, Gaur PM, Farooq M, Siddique KHM, Varshney RK, Nayyar H. Food Legumes and Rising Temperatures: Effects, Adaptive Functional Mechanisms Specific to Reproductive Growth Stage and Strategies to Improve Heat Tolerance. FRONTIERS IN PLANT SCIENCE 2017; 8:1658. [PMID: 29123532 PMCID: PMC5662899 DOI: 10.3389/fpls.2017.01658] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 09/08/2017] [Indexed: 05/20/2023]
Abstract
Ambient temperatures are predicted to rise in the future owing to several reasons associated with global climate changes. These temperature increases can result in heat stress- a severe threat to crop production in most countries. Legumes are well-known for their impact on agricultural sustainability as well as their nutritional and health benefits. Heat stress imposes challenges for legume crops and has deleterious effects on the morphology, physiology, and reproductive growth of plants. High-temperature stress at the time of the reproductive stage is becoming a severe limitation for production of grain legumes as their cultivation expands to warmer environments and temperature variability increases due to climate change. The reproductive period is vital in the life cycle of all plants and is susceptible to high-temperature stress as various metabolic processes are adversely impacted during this phase, which reduces crop yield. Food legumes exposed to high-temperature stress during reproduction show flower abortion, pollen and ovule infertility, impaired fertilization, and reduced seed filling, leading to smaller seeds and poor yields. Through various breeding techniques, heat tolerance in major legumes can be enhanced to improve performance in the field. Omics approaches unravel different mechanisms underlying thermotolerance, which is imperative to understand the processes of molecular responses toward high-temperature stress.
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Affiliation(s)
- Kumari Sita
- Department of Botany, Panjab University, Chandigarh, India
| | | | | | | | - P. V. Vara Prasad
- Sustainable Intensification Innovation Lab, Kansas State University, Manhattan, KS, United States
| | - Shiv Kumar
- International Center for Agricultural Research in the Dry Areas, Rabat, Morocco
| | - Pooran M. Gaur
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Muhammad Farooq
- Department of Agronomy, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | | | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
- The UWA Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh, India
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Ghatak A, Chaturvedi P, Paul P, Agrawal GK, Rakwal R, Kim ST, Weckwerth W, Gupta R. Proteomics survey of Solanaceae family: Current status and challenges ahead. J Proteomics 2017; 169:41-57. [PMID: 28528990 DOI: 10.1016/j.jprot.2017.05.016] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 03/19/2017] [Accepted: 05/16/2017] [Indexed: 10/25/2022]
Abstract
Solanaceae is one of the major economically important families of higher plants and has played a central role in human nutrition since the dawn of human civilization. Therefore, researchers have always been interested in understanding the complex behavior of Solanaceae members to identify key transcripts, proteins or metabolites, which are potentially associated with major traits. Proteomics studies have contributed significantly to understanding the physiology of Solanaceae members. A compilation of all the published reports showed that both gel-based (75%) and gel-free (25%) proteomic technologies have been utilized to establish the proteomes of different tissues, organs, and organelles under normal and adverse environmental conditions. Among the Solanaceae members, most of the research has been focused on tomato (42%) followed by potato (28%) and tobacco (20%), owing to their economic importance. This review comprehensively covers the progress made so far in the field of Solanaceae proteomics including novel methods developed to isolate the proteins from different tissues. Moreover, key proteins presented in this review can serve as a resource to select potential targets for crop improvement. We envisage that information presented in this review would enable us to design the stress tolerant plants with enhanced yields.
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Affiliation(s)
- Arindam Ghatak
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Palak Chaturvedi
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Puneet Paul
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, 68583-0915, USA
| | - Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO Box 13265, Kathmandu, Nepal; GRADE Academy Private Limited, Adarsh Nagar-13, Birgunj, Nepal
| | - Randeep Rakwal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO Box 13265, Kathmandu, Nepal; GRADE Academy Private Limited, Adarsh Nagar-13, Birgunj, Nepal; Faculty of Health and Sport Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan; Global Research Center for Innovative Life Science, Peptide Drug Innovation, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 4-41 Ebara 2-chome, Shinagawa, Tokyo 142-8501, Japan
| | - Sun Tae Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-707, Republic of Korea
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria; Vienna Metabolomics Center (VIME), University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Ravi Gupta
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-707, Republic of Korea.
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Sita K, Sehgal A, HanumanthaRao B, Nair RM, Vara Prasad PV, Kumar S, Gaur PM, Farooq M, Siddique KHM, Varshney RK, Nayyar H. Food Legumes and Rising Temperatures: Effects, Adaptive Functional Mechanisms Specific to Reproductive Growth Stage and Strategies to Improve Heat Tolerance. FRONTIERS IN PLANT SCIENCE 2017. [PMID: 29123532 DOI: 10.3389/flps.2017.01658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Ambient temperatures are predicted to rise in the future owing to several reasons associated with global climate changes. These temperature increases can result in heat stress- a severe threat to crop production in most countries. Legumes are well-known for their impact on agricultural sustainability as well as their nutritional and health benefits. Heat stress imposes challenges for legume crops and has deleterious effects on the morphology, physiology, and reproductive growth of plants. High-temperature stress at the time of the reproductive stage is becoming a severe limitation for production of grain legumes as their cultivation expands to warmer environments and temperature variability increases due to climate change. The reproductive period is vital in the life cycle of all plants and is susceptible to high-temperature stress as various metabolic processes are adversely impacted during this phase, which reduces crop yield. Food legumes exposed to high-temperature stress during reproduction show flower abortion, pollen and ovule infertility, impaired fertilization, and reduced seed filling, leading to smaller seeds and poor yields. Through various breeding techniques, heat tolerance in major legumes can be enhanced to improve performance in the field. Omics approaches unravel different mechanisms underlying thermotolerance, which is imperative to understand the processes of molecular responses toward high-temperature stress.
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Affiliation(s)
- Kumari Sita
- Department of Botany, Panjab University, Chandigarh, India
| | | | | | | | - P V Vara Prasad
- Sustainable Intensification Innovation Lab, Kansas State University, Manhattan, KS, United States
| | - Shiv Kumar
- International Center for Agricultural Research in the Dry Areas, Rabat, Morocco
| | - Pooran M Gaur
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Muhammad Farooq
- Department of Agronomy, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
- The UWA Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh, India
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Metabolomics, a Powerful Tool for Agricultural Research. Int J Mol Sci 2016; 17:ijms17111871. [PMID: 27869667 PMCID: PMC5133871 DOI: 10.3390/ijms17111871] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Revised: 11/02/2016] [Accepted: 11/03/2016] [Indexed: 11/17/2022] Open
Abstract
Metabolomics, which is based mainly on nuclear magnetic resonance (NMR), gas-chromatography (GC) or liquid-chromatography (LC) coupled to mass spectrometry (MS) analytical technologies to systematically acquire the qualitative and quantitative information of low-molecular-mass endogenous metabolites, provides a direct snapshot of the physiological condition in biological samples. As complements to transcriptomics and proteomics, it has played pivotal roles in agricultural and food science research. In this review, we discuss the capacities of NMR, GC/LC-MS in the acquisition of plant metabolome, and address the potential promise and diverse applications of metabolomics, particularly lipidomics, to investigate the responses of Arabidopsis thaliana, a primary plant model for agricultural research, to environmental stressors including heat, freezing, drought, and salinity.
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15
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Ramalingam A, Kudapa H, Pazhamala LT, Weckwerth W, Varshney RK. Proteomics and Metabolomics: Two Emerging Areas for Legume Improvement. FRONTIERS IN PLANT SCIENCE 2015; 6:1116. [PMID: 26734026 PMCID: PMC4689856 DOI: 10.3389/fpls.2015.01116] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 11/25/2015] [Indexed: 05/19/2023]
Abstract
The crop legumes such as chickpea, common bean, cowpea, peanut, pigeonpea, soybean, etc. are important sources of nutrition and contribute to a significant amount of biological nitrogen fixation (>20 million tons of fixed nitrogen) in agriculture. However, the production of legumes is constrained due to abiotic and biotic stresses. It is therefore imperative to understand the molecular mechanisms of plant response to different stresses and identify key candidate genes regulating tolerance which can be deployed in breeding programs. The information obtained from transcriptomics has facilitated the identification of candidate genes for the given trait of interest and utilizing them in crop breeding programs to improve stress tolerance. However, the mechanisms of stress tolerance are complex due to the influence of multi-genes and post-transcriptional regulations. Furthermore, stress conditions greatly affect gene expression which in turn causes modifications in the composition of plant proteomes and metabolomes. Therefore, functional genomics involving various proteomics and metabolomics approaches have been obligatory for understanding plant stress tolerance. These approaches have also been found useful to unravel different pathways related to plant and seed development as well as symbiosis. Proteome and metabolome profiling using high-throughput based systems have been extensively applied in the model legume species, Medicago truncatula and Lotus japonicus, as well as in the model crop legume, soybean, to examine stress signaling pathways, cellular and developmental processes and nodule symbiosis. Moreover, the availability of protein reference maps as well as proteomics and metabolomics databases greatly support research and understanding of various biological processes in legumes. Protein-protein interaction techniques, particularly the yeast two-hybrid system have been advantageous for studying symbiosis and stress signaling in legumes. In this review, several studies on proteomics and metabolomics in model and crop legumes have been discussed. Additionally, applications of advanced proteomics and metabolomics approaches have also been included in this review for future applications in legume research. The integration of these "omics" approaches will greatly support the identification of accurate biomarkers in legume smart breeding programs.
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Affiliation(s)
- Abirami Ramalingam
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Hyderabad, India
| | - Himabindu Kudapa
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Hyderabad, India
| | - Lekha T Pazhamala
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Hyderabad, India
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna Vienna, Austria
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India; School of Plant Biology and Institute of Agriculture, The University of Western AustraliaCrawley, WA, Australia
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Rea G, Cristofaro F, Pani G, Pascucci B, Ghuge SA, Corsetto PA, Imbriani M, Visai L, Rizzo AM. Microgravity-driven remodeling of the proteome reveals insights into molecular mechanisms and signal networks involved in response to the space flight environment. J Proteomics 2015; 137:3-18. [PMID: 26571091 DOI: 10.1016/j.jprot.2015.11.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 11/02/2015] [Accepted: 11/04/2015] [Indexed: 12/21/2022]
Abstract
UNLABELLED Space is a hostile environment characterized by high vacuum, extreme temperatures, meteoroids, space debris, ionospheric plasma, microgravity and space radiation, which all represent risks for human health. A deep understanding of the biological consequences of exposure to the space environment is required to design efficient countermeasures to minimize their negative impact on human health. Recently, proteomic approaches have received a significant amount of attention in the effort to further study microgravity-induced physiological changes. In this review, we summarize the current knowledge about the effects of microgravity on microorganisms (in particular Cupriavidus metallidurans CH34, Bacillus cereus and Rhodospirillum rubrum S1H), plants (whole plants, organs, and cell cultures), mammalian cells (endothelial cells, bone cells, chondrocytes, muscle cells, thyroid cancer cells, immune system cells) and animals (invertebrates, vertebrates and mammals). Herein, we describe their proteome's response to microgravity, focusing on proteomic discoveries and their future potential applications in space research. BIOLOGICAL SIGNIFICANCE Space experiments and operational flight experience have identified detrimental effects on human health and performance because of exposure to weightlessness, even when currently available countermeasures are implemented. Many experimental tools and methods have been developed to study microgravity induced physiological changes. Recently, genomic and proteomic approaches have received a significant amount of attention. This review summarizes the recent research studies of the proteome response to microgravity inmicroorganisms, plants, mammalians cells and animals. Current proteomic tools allow large-scale, high-throughput analyses for the detection, identification, and functional investigation of all proteomes. Understanding gene and/or protein expression is the key to unlocking the mechanisms behind microgravity-induced problems and to finding effective countermeasures to spaceflight-induced alterations but also for the study of diseases on earth. Future perspectives are also highlighted.
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Affiliation(s)
- Giuseppina Rea
- Institute of Crystallography, National Research Council of Italy (CNR), Via Salaria km 29.300, 00015 Monterotondo Scalo, Rome, Italy
| | - Francesco Cristofaro
- Department of Molecular Medicine, Center for Health Technologies (CHT), University of Pavia, Via Taramelli 3/b, 27100 Pavia, Italy
| | - Giuseppe Pani
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Via D. Trentacoste 2, 20134 Milan, Italy
| | - Barbara Pascucci
- Institute of Crystallography, National Research Council of Italy (CNR), Via Salaria km 29.300, 00015 Monterotondo Scalo, Rome, Italy
| | - Sandip A Ghuge
- Institute of Crystallography, National Research Council of Italy (CNR), Via Salaria km 29.300, 00015 Monterotondo Scalo, Rome, Italy
| | - Paola Antonia Corsetto
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Via D. Trentacoste 2, 20134 Milan, Italy
| | - Marcello Imbriani
- Department of Public Health, Experimental Medicine and Forensics, University of Pavia, V.le Forlanini 8, Pavia, Italy; Department of Occupational Medicine, Toxicology and Environmental Risks, S. Maugeri Foundation, IRCCS, Via S. Boezio 28, 27100 Pavia, Italy
| | - Livia Visai
- Department of Molecular Medicine, Center for Health Technologies (CHT), University of Pavia, Via Taramelli 3/b, 27100 Pavia, Italy; Department of Occupational Medicine, Toxicology and Environmental Risks, S. Maugeri Foundation, IRCCS, Via S. Boezio 28, 27100 Pavia, Italy.
| | - Angela M Rizzo
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Via D. Trentacoste 2, 20134 Milan, Italy
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Hu J, Rampitsch C, Bykova NV. Advances in plant proteomics toward improvement of crop productivity and stress resistancex. FRONTIERS IN PLANT SCIENCE 2015; 6:209. [PMID: 25926838 PMCID: PMC4396383 DOI: 10.3389/fpls.2015.00209] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 03/16/2015] [Indexed: 05/14/2023]
Abstract
Abiotic and biotic stresses constrain plant growth and development negatively impacting crop production. Plants have developed stress-specific adaptations as well as simultaneous responses to a combination of various abiotic stresses with pathogen infection. The efficiency of stress-induced adaptive responses is dependent on activation of molecular signaling pathways and intracellular networks by modulating expression, or abundance, and/or post-translational modification (PTM) of proteins primarily associated with defense mechanisms. In this review, we summarize and evaluate the contribution of proteomic studies to our understanding of stress response mechanisms in different plant organs and tissues. Advanced quantitative proteomic techniques have improved the coverage of total proteomes and sub-proteomes from small amounts of starting material, and characterized PTMs as well as protein-protein interactions at the cellular level, providing detailed information on organ- and tissue-specific regulatory mechanisms responding to a variety of individual stresses or stress combinations during plant life cycle. In particular, we address the tissue-specific signaling networks localized to various organelles that participate in stress-related physiological plasticity and adaptive mechanisms, such as photosynthetic efficiency, symbiotic nitrogen fixation, plant growth, tolerance and common responses to environmental stresses. We also provide an update on the progress of proteomics with major crop species and discuss the current challenges and limitations inherent to proteomics techniques and data interpretation for non-model organisms. Future directions in proteomics research toward crop improvement are further discussed.
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Affiliation(s)
- Junjie Hu
- Department of Biology, Memorial University of Newfoundland, St. John’sNL, Canada
- Cereal Proteomics, Cereal Research Centre, Agriculture and Agri-Food Canada, MordenMB, Canada
| | - Christof Rampitsch
- Cereal Proteomics, Cereal Research Centre, Agriculture and Agri-Food Canada, MordenMB, Canada
| | - Natalia V. Bykova
- Cereal Proteomics, Cereal Research Centre, Agriculture and Agri-Food Canada, MordenMB, Canada
- *Correspondence: Natalia V. Bykova, Cereal Proteomics, Cereal Research Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB R6M 1Y5, Canada
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18
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Rydahl MG, Fangel JU, Mikkelsen MD, Johansen IE, Andreas A, Harholt J, Ulvskov P, Jørgensen B, Domozych DS, Willats WGT. Penium margaritaceum as a model organism for cell wall analysis of expanding plant cells. Methods Mol Biol 2015; 1242:1-21. [PMID: 25408439 DOI: 10.1007/978-1-4939-1902-4_1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The growth of a plant cell encompasses a complex set of subcellular components interacting in a highly coordinated fashion. Ultimately, these activities create specific cell wall structural domains that regulate the prime force of expansion, internally generated turgor pressure. The precise organization of the polymeric networks of the cell wall around the protoplast also contributes to the direction of growth, the shape of the cell, and the proper positioning of the cell in a tissue. In essence, plant cell expansion represents the foundation of development. Most studies of plant cell expansion have focused primarily upon late divergent multicellular land plants and specialized cell types (e.g., pollen tubes, root hairs). Here, we describe a unicellular green alga, Penium margaritaceum (Penium), which can serve as a valuable model organism for understanding cell expansion and the underlying mechanics of the cell wall in a single plant cell.
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Affiliation(s)
- Maja G Rydahl
- Department of Plant and Environmental Sciences, Faculty ofScience, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Copenhagen, Denmark
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19
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Ngara R, Ndimba BK. Model plant systems in salinity and drought stress proteomics studies: a perspective on Arabidopsis and Sorghum. PLANT BIOLOGY (STUTTGART, GERMANY) 2014; 16:1029-32. [PMID: 25258177 DOI: 10.1111/plb.12247] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 08/04/2014] [Indexed: 05/27/2023]
Abstract
More than a decade after the sequencing of its genome, Arabidopsis still stands as the epitome of a model system in plant biology. Arabidopsis proteomics has also taught us great lessons on different aspects of plant growth, development and physiology. Without doubt our understanding of basic principles of plant biology would not have been this advanced if it were not for knowledge gained using Arabidopsis as a model system. However, with the projections of global climate change and rapid population growth, it is high time we evaluate the applicability of this model system in studies aimed at understanding abiotic stress tolerance and adaptation, with a particular emphasis on maintaining yield under hot and dry environmental conditions. Because of the innate nature of sorghum's tolerance to drought and moderate tolerance to salinity stresses, we believe sorghum is the next logical model system in such studies amongst cereals. In this acute view, we highlight the importance of Arabidopsis as a model system, briefly discuss its potential limitations in drought and salt stress studies, and present our views on the potential usefulness of sorghum as a model system for cereals in drought and salinity stress proteomic studies.
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Affiliation(s)
- R Ngara
- Department of Plant Sciences, University of the Free State, Phuthaditjhaba, South Africa
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20
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Vaahtera L, Brosché M, Wrzaczek M, Kangasjärvi J. Specificity in ROS signaling and transcript signatures. Antioxid Redox Signal 2014; 21:1422-41. [PMID: 24180661 PMCID: PMC4158988 DOI: 10.1089/ars.2013.5662] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
SIGNIFICANCE Reactive oxygen species (ROS), important signaling molecules in plants, are involved in developmental control and stress adaptation. ROS production can trigger broad transcriptional changes; however, it is not clear how specificity in transcriptional regulation is achieved. RECENT ADVANCES A large collection of public transcriptome data from the model plant Arabidopsis thaliana is available for analysis. These data can be used for the analysis of biological processes that are associated with ROS signaling and for the identification of suitable transcriptional indicators. Several online tools, such as Genevestigator and Expression Angler, have simplified the task to analyze, interpret, and visualize this wealth of data. CRITICAL ISSUES The analysis of the exact transcriptional responses to ROS requires the production of specific ROS in distinct subcellular compartments with precise timing, which is experimentally difficult. Analyses are further complicated by the effect of ROS production in one subcellular location on the ROS accumulation in other compartments. In addition, even subtle differences in the method of ROS production or treatment can lead to significantly different outcomes when various stimuli are compared. FUTURE DIRECTIONS Due to the difficulty of inducing ROS production specifically with regard to ROS type, subcellular localization, and timing, we propose that the concept of a "ROS marker gene" should be re-evaluated. We suggest guidelines for the analysis of transcriptional data in ROS signaling. The use of "ROS signatures," which consist of a set of genes that together can show characteristic and indicative responses, should be preferred over the use of individual marker genes.
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Affiliation(s)
- Lauri Vaahtera
- 1 Division of Plant Biology, Department of Biosciences, University of Helsinki , Helsinki, Finland
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21
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Qiu H, Price DC, Weber APM, Facchinelli F, Yoon HS, Bhattacharya D. Assessing the bacterial contribution to the plastid proteome. TRENDS IN PLANT SCIENCE 2013; 18:680-7. [PMID: 24139901 DOI: 10.1016/j.tplants.2013.09.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 09/11/2013] [Accepted: 09/18/2013] [Indexed: 05/08/2023]
Abstract
Plastids fulfill a variety of different functions (e.g., photosynthesis and amino acid biosynthesis) that rely on proteins of cyanobacterial (i.e., endosymbiont), noncyanobacterial, and 'host' (eukaryotic) origins. Analysis of plastid proteome data from glaucophytes and green algae allows robust inference of protein origins and organelle protein sharing across the >1 billion years of Archaeplastida evolution. Here, we show that more than one-third of genes encoding plastid proteins lack detectable homologs in Cyanobacteria, underlining the taxonomically broad contributions to plastid functions. Chlamydiae and Proteobacteria are the most significant other bacterial sources of plastid proteins. Mapping of plastid proteins to metabolic pathways shows a core set of anciently derived proteins in Archaeplastida, with many others being lineage specific and derived from independent horizontal gene transfer (HGT) events.
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Affiliation(s)
- Huan Qiu
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ 08540, USA
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22
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Proteomics of model and crop plant species: Status, current limitations and strategic advances for crop improvement. J Proteomics 2013; 93:5-19. [DOI: 10.1016/j.jprot.2013.05.036] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 05/20/2013] [Accepted: 05/29/2013] [Indexed: 12/22/2022]
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Affiliation(s)
- Jesús Jorrín-Novo
- Agricultural and Plant Proteomics, Biochemistry and Molecular Biology, University of Córdoba, Cordoba, Spain.
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24
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Agrawal GK, Sarkar A, Righetti PG, Pedreschi R, Carpentier S, Wang T, Barkla BJ, Kohli A, Ndimba BK, Bykova NV, Rampitsch C, Zolla L, Rafudeen MS, Cramer R, Bindschedler LV, Tsakirpaloglou N, Ndimba RJ, Farrant JM, Renaut J, Job D, Kikuchi S, Rakwal R. A decade of plant proteomics and mass spectrometry: translation of technical advancements to food security and safety issues. MASS SPECTROMETRY REVIEWS 2013; 32:335-65. [PMID: 23315723 DOI: 10.1002/mas.21365] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 09/10/2012] [Accepted: 09/10/2012] [Indexed: 05/21/2023]
Abstract
Tremendous progress in plant proteomics driven by mass spectrometry (MS) techniques has been made since 2000 when few proteomics reports were published and plant proteomics was in its infancy. These achievements include the refinement of existing techniques and the search for new techniques to address food security, safety, and health issues. It is projected that in 2050, the world's population will reach 9-12 billion people demanding a food production increase of 34-70% (FAO, 2009) from today's food production. Provision of food in a sustainable and environmentally committed manner for such a demand without threatening natural resources, requires that agricultural production increases significantly and that postharvest handling and food manufacturing systems become more efficient requiring lower energy expenditure, a decrease in postharvest losses, less waste generation and food with longer shelf life. There is also a need to look for alternative protein sources to animal based (i.e., plant based) to be able to fulfill the increase in protein demands by 2050. Thus, plant biology has a critical role to play as a science capable of addressing such challenges. In this review, we discuss proteomics especially MS, as a platform, being utilized in plant biology research for the past 10 years having the potential to expedite the process of understanding plant biology for human benefits. The increasing application of proteomics technologies in food security, analysis, and safety is emphasized in this review. But, we are aware that no unique approach/technology is capable to address the global food issues. Proteomics-generated information/resources must be integrated and correlated with other omics-based approaches, information, and conventional programs to ensure sufficient food and resources for human development now and in the future.
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Affiliation(s)
- Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry, PO Box 13265, Kathmandu, Nepal.
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Nacir H, Bréhélin C. When proteomics reveals unsuspected roles: the plastoglobule example. FRONTIERS IN PLANT SCIENCE 2013; 4:114. [PMID: 23630540 PMCID: PMC3635846 DOI: 10.3389/fpls.2013.00114] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 04/11/2013] [Indexed: 05/18/2023]
Abstract
Plastoglobules are globular compartments found in plastids. Before initial proteomic studies were published, these particles were often viewed as passive lipid droplets whose unique role was to store lipids coming from the thylakoid turn-over, or to accumulate carotenoids in the chromoplasts. Yet, two proteomic studies, published concomitantly, suggested for the first time that plastoglobules are more than "junk cupboards" for lipids. Indeed, both studies demonstrated that plastoglobules do not only include structural proteins belonging to the plastoglobulin/fibrillin family, but also contain active enzymes. The specific plastoglobule localization of these enzymes has been confirmed by different approaches such as immunogold localization and GFP protein fusions, thus providing evidence that plastoglobules actively participate in diverse pathways of plastid metabolism. These proteomic studies have been the basis for numerous recent works investigating plastoglobule function. However, a lot still needs to be discovered about the molecular composition and the role of plastoglobules. In this chapter, we will describe how the proteomic approaches have launched new perspectives on plastoglobule functions.
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Affiliation(s)
- Houda Nacir
- Laboratoire de Biogenèse Membranaire, CNRSVillenave d’Ornon, France
- Laboratoire de Biogenèse Membranaire, Université de BordeauxVillenave d’Ornon, France
| | - Claire Bréhélin
- Laboratoire de Biogenèse Membranaire, CNRSVillenave d’Ornon, France
- Laboratoire de Biogenèse Membranaire, Université de BordeauxVillenave d’Ornon, France
- *Correspondence: Claire Bréhélin, Laboratoire de Biogenèse Membranaire, CNRS – Université de Bordeaux, UMR5200, Campus INRA de Bordeaux, 71 Avenue E. Bourlaux, BP 81, F-33883 Villenave d’Ornon Cedex, France. e-mail:
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Capron A, Chang XF, Hall H, Ellis B, Beatson RP, Berleth T. Identification of quantitative trait loci controlling fibre length and lignin content in Arabidopsis thaliana stems. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:185-97. [PMID: 23136168 PMCID: PMC3528028 DOI: 10.1093/jxb/ers319] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Fibre properties and the biochemical composition of cell walls are important traits in many applications. For example, the lengths of fibres define the strength and quality of paper, and lignin content is a critical parameter for the use of biomass in biofuel production. Identifying genes controlling these traits is comparatively difficult in woody species, because of long generation times and limited amenability to high-resolution genetic mapping. To address this problem, this study mapped quantitative trait loci (QTLs) defining fibre length and lignin content in the Arabidopsis recombinant inbred line population Col-4 × Ler-0. Adapting high-throughput phenotyping techniques for both traits for measurements in Arabidopsis inflorescence stems identified significant QTLs for fibre length on chromosomes 2 and 5, as well as one significant QTL affecting lignin content on chromosome 2. For fibre length, total variation within the population was 208% higher than between parental lines and the identified QTLs explained 50.58% of the observed variation. For lignin content, the values were 261 and 26.51%, respectively. Bioinformatics analysis of the associated intervals identified a number of candidate genes for fibre length and lignin content. This study demonstrates that molecular mapping of QTLs pertaining to wood and fibre properties is possible in Arabidopsis, which substantially broadens the use of Arabidopsis as a model species for the functional characterization of plant genes.
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Affiliation(s)
- Arnaud Capron
- University of Toronto-CSB, 25 Willcocks Street, Toronto, ON, Canada, M5S 3B2
| | - Xue Feng Chang
- British Columbia Institute of Technology, 3700 Willingdon Avenue, Burnaby, BC, Canada, V5G 3H2
| | - Hardy Hall
- University of British Columbia – Michael Smith Laboratories, #301–2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Brian Ellis
- University of British Columbia – Michael Smith Laboratories, #301–2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Rodger P. Beatson
- British Columbia Institute of Technology, 3700 Willingdon Avenue, Burnaby, BC, Canada, V5G 3H2
| | - Thomas Berleth
- University of Toronto-CSB, 25 Willcocks Street, Toronto, ON, Canada, M5S 3B2
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WANG X, LIN Y, LIU D, XU H, LIU T, ZHAO F. Cerium toxicity, uptake and translocation in Arabidopsis thaliana seedlings. J RARE EARTH 2012. [DOI: 10.1016/s1002-0721(12)60094-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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28
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Translational plant proteomics: a perspective. J Proteomics 2012; 75:4588-601. [PMID: 22516432 DOI: 10.1016/j.jprot.2012.03.055] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2011] [Revised: 02/25/2012] [Accepted: 03/25/2012] [Indexed: 11/21/2022]
Abstract
Translational proteomics is an emerging sub-discipline of the proteomics field in the biological sciences. Translational plant proteomics aims to integrate knowledge from basic sciences to translate it into field applications to solve issues related but not limited to the recreational and economic values of plants, food security and safety, and energy sustainability. In this review, we highlight the substantial progress reached in plant proteomics during the past decade which has paved the way for translational plant proteomics. Increasing proteomics knowledge in plants is not limited to model and non-model plants, proteogenomics, crop improvement, and food analysis, safety, and nutrition but to many more potential applications. Given the wealth of information generated and to some extent applied, there is the need for more efficient and broader channels to freely disseminate the information to the scientific community. This article is part of a Special Issue entitled: Translational Proteomics.
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Liberman LM, Sozzani R, Benfey PN. Integrative systems biology: an attempt to describe a simple weed. CURRENT OPINION IN PLANT BIOLOGY 2012; 15:162-7. [PMID: 22277598 PMCID: PMC3435099 DOI: 10.1016/j.pbi.2012.01.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Revised: 12/22/2011] [Accepted: 01/03/2012] [Indexed: 05/19/2023]
Abstract
Genome-scale studies hold great promise for revealing novel plant biology. Because of the complexity of these techniques, numerous considerations need to be made before embarking on a study. Here we focus on the Arabidopsis model system because of the wealth of available genome-scale data. Many approaches are available that provide genome-scale information regarding the state of a given organism (e.g. genomics, epigenomics, transcriptomics, proteomics, metabolomics interactomics, ionomics, phenomics, etc.). Integration of all of these types of data will be necessary for a comprehensive description of Arabidopsis. In this review we propose that 'triangulation' among transcriptomics, proteomics and metabolomics is a meaningful approach for beginning this integrative analysis and uncovering a systems level perspective of Arabidopsis biology.
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Affiliation(s)
- Louisa M Liberman
- Department of Biology and Duke Center for Systems Biology, Duke University, Durham, NC, USA
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Geisler-Lee J, Wang Q, Yao Y, Zhang W, Geisler M, Li K, Huang Y, Chen Y, Kolmakov A, Ma X. Phytotoxicity, accumulation and transport of silver nanoparticles byArabidopsis thaliana. Nanotoxicology 2012; 7:323-37. [DOI: 10.3109/17435390.2012.658094] [Citation(s) in RCA: 209] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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31
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Bayarri S, Gracia MJ, Pérez-Arquillué C, Lázaro R, Herrera A. Toxoplasma gondii in commercially available pork meat and cured ham: a contribution to risk assessment for consumers. J Food Prot 2012; 75:597-600. [PMID: 22410238 DOI: 10.4315/0362-028x.jfp-11-350] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Toxoplasmosis is an infection caused by Toxoplasma gondii, whose transmission has usually been attributed to ingestion of undercooked or raw meat. Dry-cured ham is a high-quality meat product of increasing economic relevance, and epidemiological studies point to cured meat products as a risk factor for acquiring toxoplasmosis. With the aim of contributing to the risk assessment process, 50 samples of fresh pork meat and commercial cured ham were collected in the city of Zaragoza (northeastern Spain), and the presence of viable forms of T. gondii was analyzed. A mouse concentration bioassay technique was used, and the presence of the parasite in mice was determined by indirect immunofluorescence assay. T. gondii was detected in two samples of rib, reflecting a frequency of 8% positive fresh pork meat (4% positivity of total samples analyzed). Brains of seropositive mice were analyzed by histology and PCR, although the parasite was not isolated in the seroconverted mice. No viable forms were detected either in other types of fresh meat or in the samples of cured ham.
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Affiliation(s)
- Susana Bayarri
- Departamento de Producción Animal y Ciencia de los Alimentos, Universidad de Zaragoza, Facultad de Veterinaria, c/ Miguel Servet 177, 50013 Spain.
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Jones AME, Aebersold R, Ahrens CH, Apweiler R, Baerenfaller K, Baker M, Bendixen E, Briggs S, Brownridge P, Brunner E, Daube M, Deutsch EW, Grossniklaus U, Heazlewood J, Hengartner MO, Hermjakob H, Jovanovic M, Lawless C, Lochnit G, Martens L, Ravnsborg C, Schrimpf SP, Shim YH, Subasic D, Tholey A, van Wijk K, von Mering C, Weiss M, Zheng X. The HUPO initiative on Model Organism Proteomes, iMOP. Proteomics 2012; 12:340-5. [DOI: 10.1002/pmic.201290014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Falvo S, Di Carli M, Desiderio A, Benvenuto E, Moglia A, America T, Lanteri S, Acquadro A. 2-D DIGE analysis of UV-C radiation-responsive proteins in globe artichoke leaves. Proteomics 2012; 12:448-60. [PMID: 22162389 DOI: 10.1002/pmic.201100337] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Revised: 11/22/2011] [Accepted: 11/24/2011] [Indexed: 01/08/2023]
Abstract
Plants respond to ultraviolet stress inducing a self-defence through the regulation of specific gene family members. The UV acclimation is the result of biochemical and physiological processes, such as enhancement of the antioxidant enzymatic system and accumulation of UV-absorbing phenolic compounds (e.g. flavonoids). Globe artichoke is an attractive species for studying the protein network involved in UV stress response, being characterized by remarkable levels of inducible antioxidants. Proteomic tools can assist the evaluation of the expression patterns of UV-responsive proteins and we applied the difference in-gel electrophoresis (DIGE) technology for monitoring the globe artichoke proteome variation at four time points following an acute UV-C exposure. A total of 145 UV-C-modulated proteins were observed and 119 were identified by LC-MS/MS using a ∼144,000 customized Compositae protein database, which included about 19,000 globe artichoke unigenes. Proteins were Gene Ontology (GO) categorized, visualized on their pathways and their behaviour was discussed. A predicted protein interaction network was produced and highly connected hub-like proteins were highlighted. Most of the proteins differentially modulated were chloroplast located, involved in photosynthesis, sugar metabolisms, protein folding and abiotic stress. The identification of UV-C-responsive proteins may contribute to shed light on the molecular mechanisms underlying plant responses to UV stress.
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Affiliation(s)
- Sara Falvo
- DIVAPRA, University of Turin, Grugliasco, Torino, Italy
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34
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Singh D, Singh PK, Chaudhary S, Mehla K, Kumar S. Exome sequencing and advances in crop improvement. ADVANCES IN GENETICS 2012; 79:87-121. [PMID: 22989766 DOI: 10.1016/b978-0-12-394395-8.00003-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Next-generation sequencing strategies have opened new vistas for molecular plant breeding. The sequence information obtained by the advent of next-generation sequencing provides a valuable tool not only for improving domesticated crops but also for investigating the natural evolution of crops. Such information provides an enormous potential for sustainable agriculture. In this review, we discuss how such sequencing approaches have transformed exome sequencing into a practical utility that has enormous potential for crop improvement in agriculture. Furthermore, we also describe the future of crop improvement beyond the exome sequencing strategies.
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Affiliation(s)
- Devi Singh
- Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, UP, India
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Doroshenk KA, Crofts AJ, Morris RT, Wyrick JJ, Okita TW. RiceRBP: A Resource for Experimentally Identified RNA Binding Proteins in Oryza sativa. FRONTIERS IN PLANT SCIENCE 2012; 3:90. [PMID: 22645600 PMCID: PMC3355793 DOI: 10.3389/fpls.2012.00090] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Accepted: 04/20/2012] [Indexed: 05/05/2023]
Abstract
RNA binding proteins (RBPs) play an important role not only in nuclear gene expression, but also in cytosolic events, including RNA transport, localization, translation, and stability. Although over 200 RBPs are predicted from the Arabidopsis genome alone, relatively little is known about these proteins in plants as many exhibit no homology to known RBPs in other eukaryotes. Furthermore, RBPs likely have low expression levels making them difficult to identify and study. As part of our continuing efforts to understand plant cytosolic gene expression and the factors involved, we employed a combination of affinity chromatography and proteomic techniques to enrich for low abundance RBPs in developing rice seed. Our results have been compiled into RiceRBP (http://www.bioinformatics2.wsu.edu/RiceRBP), a database that contains 257 experimentally identified proteins, many of which have not previously been predicted to be RBPs. For each of the identified proteins, RiceRBP provides information on transcript and protein sequence, predicted protein domains, details of the experimental identification, and whether antibodies have been generated for public use. In addition, tools are available to analyze expression patterns for the identified genes, view phylogentic relationships and search for orthologous proteins. RiceRBP is a valuable tool for the community in the study of plant RBPs.
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Affiliation(s)
- Kelly A. Doroshenk
- Institute of Biological Chemistry, Washington State UniversityPullman, WA, USA
| | | | - Robert T. Morris
- School of Molecular Biosciences, Center for Reproductive Biology, Washington State UniversityPullman, WA, USA
| | - John J. Wyrick
- School of Molecular Biosciences, Center for Reproductive Biology, Washington State UniversityPullman, WA, USA
| | - Thomas W. Okita
- Institute of Biological Chemistry, Washington State UniversityPullman, WA, USA
- *Correspondence: Thomas W. Okita, Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA. e-mail:
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Cox J, M.A.Heeren R, James P, Jorrin-Novo JV, Kolker E, Levander F, Morrice N, Picotti P, Righetti PG, Sánchez JC, Turck CW, Zubarev R, Alexandre BM, Corrales FJ, Marko-Varga G, O'Donovan S, O'Neil S, Prechl J, Simões T, Weckwerth W, Penque D. Facing challenges in Proteomics today and in the coming decade: Report of Roundtable Discussions at the 4th EuPA Scientific Meeting, Portugal, Estoril 2010. J Proteomics 2011; 75:4-17. [DOI: 10.1016/j.jprot.2011.04.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Accepted: 04/22/2011] [Indexed: 12/17/2022]
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Remmerie N, De Vijlder T, Laukens K, Dang TH, Lemière F, Mertens I, Valkenborg D, Blust R, Witters E. Next generation functional proteomics in non-model plants: A survey on techniques and applications for the analysis of protein complexes and post-translational modifications. PHYTOCHEMISTRY 2011; 72:1192-218. [PMID: 21345472 DOI: 10.1016/j.phytochem.2011.01.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Revised: 11/21/2010] [Accepted: 01/03/2011] [Indexed: 05/11/2023]
Abstract
The congruent development of computational technology, bioinformatics and analytical instrumentation makes proteomics ready for the next leap. Present-day state of the art proteomics grew from a descriptive method towards a full stake holder in systems biology. High throughput and genome wide studies are now made at the functional level. These include quantitative aspects, functional aspects with respect to protein interactions as well as post translational modifications and advanced computational methods that aid in predicting protein function and mapping these functionalities across the species border. In this review an overview is given of the current status of these aspects in plant studies with special attention to non-genomic model plants.
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Affiliation(s)
- Noor Remmerie
- Center for Proteomics, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
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Terashima M, Specht M, Hippler M. The chloroplast proteome: a survey from the Chlamydomonas reinhardtii perspective with a focus on distinctive features. Curr Genet 2011; 57:151-68. [PMID: 21533645 DOI: 10.1007/s00294-011-0339-1] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Revised: 04/05/2011] [Accepted: 04/07/2011] [Indexed: 01/12/2023]
Abstract
The unicellular green alga Chlamydomonas reinhardtii has emerged to be an important model organism for the study of oxygenic eukaryotic photosynthesis as well as other processes occurring in the chloroplast. However, the chloroplast proteome in C. reinhardtii has only recently been comprehensively characterized, made possible by proteomics emerging as an accessible and powerful tool over the last decade. In this review, we introduce a compiled list of 996 experimentally chloroplast-localized proteins for C. reinhardtii, stemming largely from our previous proteomic dataset comparing chloroplasts and mitochondria samples to localize proteins. In order to get a taste of some cellular functions taking place in the C. reinhardtii chloroplast, we will focus this review particularly on metabolic differences between chloroplasts of C. reinhardtii and higher plants. Areas that will be covered are photosynthesis, chlorophyll biosynthesis, carbon metabolism, fermentative metabolism, ferredoxins and ferredoxin-interacting proteins.
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Affiliation(s)
- Mia Terashima
- Department of Biology, Institute of Plant Biology and Biotechnology, University of Münster, Hindenburgplatz 55, 48143, Münster, Germany
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39
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Reumann S. Toward a definition of the complete proteome of plant peroxisomes: Where experimental proteomics must be complemented by bioinformatics. Proteomics 2011; 11:1764-79. [PMID: 21472859 DOI: 10.1002/pmic.201000681] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Revised: 02/06/2011] [Accepted: 02/11/2011] [Indexed: 12/23/2022]
Abstract
In the past few years, proteome analysis of Arabidopsis peroxisomes has been established by the complementary efforts of four research groups and has emerged as the major unbiased approach to identify new peroxisomal proteins on a large scale. Collectively, more than 100 new candidate proteins from plant peroxisomes have been identified, including long-awaited low-abundance proteins. More than 50 proteins have been validated as peroxisome targeted, nearly doubling the number of established plant peroxisomal proteins. Sequence homologies of the new proteins predict unexpected enzyme activities, novel metabolic pathways and unknown non-metabolic peroxisome functions. Despite this remarkable success, proteome analyses of plant peroxisomes remain highly material intensive and require major preparative efforts. Characterization of the membrane proteome or post-translational protein modifications poses major technical challenges. New strategies, including quantitative mass spectrometry methods, need to be applied to allow further identifications of plant peroxisomal proteins, such as of stress-inducible proteins. In the long process of defining the complete proteome of plant peroxisomes, the prediction of peroxisome-targeted proteins from plant genome sequences emerges as an essential complementary approach to identify additional peroxisomal proteins that are, for instance, specific to peroxisome variants from minor tissues and organs or to abiotically stressed model and crop plants.
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Affiliation(s)
- Sigrun Reumann
- Centre for Organelle Research, University of Stavanger, Stavanger, Norway.
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40
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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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41
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Ryngajllo M, Childs L, Lohse M, Giorgi FM, Lude A, Selbig J, Usadel B. SLocX: Predicting Subcellular Localization of Arabidopsis Proteins Leveraging Gene Expression Data. FRONTIERS IN PLANT SCIENCE 2011; 2:43. [PMID: 22639594 PMCID: PMC3355584 DOI: 10.3389/fpls.2011.00043] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Accepted: 08/12/2011] [Indexed: 05/08/2023]
Abstract
Despite the growing volume of experimentally validated knowledge about the subcellular localization of plant proteins, a well performing in silico prediction tool is still a necessity. Existing tools, which employ information derived from protein sequence alone, offer limited accuracy and/or rely on full sequence availability. We explored whether gene expression profiling data can be harnessed to enhance prediction performance. To achieve this, we trained several support vector machines to predict the subcellular localization of Arabidopsis thaliana proteins using sequence derived information, expression behavior, or a combination of these data and compared their predictive performance through a cross-validation test. We show that gene expression carries information about the subcellular localization not available in sequence information, yielding dramatic benefits for plastid localization prediction, and some notable improvements for other compartments such as the mitochondrion, the Golgi, and the plasma membrane. Based on these results, we constructed a novel subcellular localization prediction engine, SLocX, combining gene expression profiling data with protein sequence-based information. We then validated the results of this engine using an independent test set of annotated proteins and a transient expression of GFP fusion proteins. Here, we present the prediction framework and a website of predicted localizations for Arabidopsis. The relatively good accuracy of our prediction engine, even in cases where only partial protein sequence is available (e.g., in sequences lacking the N-terminal region), offers a promising opportunity for similar application to non-sequenced or poorly annotated plant species. Although the prediction scope of our method is currently limited by the availability of expression information on the ATH1 array, we believe that the advances in measuring gene expression technology will make our method applicable for all Arabidopsis proteins.
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Affiliation(s)
| | - Liam Childs
- Max Planck Institute of Molecular Plant PhysiologyPotsdam, Germany
| | - Marc Lohse
- Max Planck Institute of Molecular Plant PhysiologyPotsdam, Germany
| | | | - Anja Lude
- Max Planck Institute of Molecular Plant PhysiologyPotsdam, Germany
| | - Joachim Selbig
- Department of Bioinformatics, Institute of Biochemistry and Biology, University of PotsdamPotsdam, Germany
| | - Björn Usadel
- Max Planck Institute of Molecular Plant PhysiologyPotsdam, Germany
- *Correspondence: Björn Usadel, Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, Golm, 14476 Potsdam, Germany. e-mail:
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