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Transcriptomic Insight into Underground Floral Differentiation in Erythronium japonicum. BIOMED RESEARCH INTERNATIONAL 2022; 2022:4447472. [PMID: 35087909 PMCID: PMC8789427 DOI: 10.1155/2022/4447472] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 11/23/2021] [Indexed: 12/18/2022]
Abstract
Erythronium japonicum Decne (Liliaceae) flowers in early spring after overwintering. Its sexual reproduction process includes an underground development process of floral organs, but the underlying molecular mechanisms are obscure. The present study is aimed at exploring the transcriptional changes and key genes involved at underground floral developmental stages, including flower primordium differentiation, perianth differentiation, stamen differentiation, and pistil differentiation in E. japonicum. Multistage high-quality transcriptomic data resulted in identifying putative candidate genes for underground floral differentiation in E. japonicum. A total of 174,408 unigenes were identified, 28,508 of which were differentially expressed genes (DEGs) at different floral developmental stages, while only 44 genes were identified with conserved regulation between different stages. Further annotation of DEGs resulted in the identification of 270 DEGs specific to floral differentiation. In addition, ELF3, PHD, cullin 1, SE14, ZSWIM3, GIGNATEA, and SERPIN B were identified as potential candidate genes involved in the regulation of floral differentiation. Besides, we explored transcription factors with differential regulation at different developmental stages and identified bHLH, FAR1, mTERF, MYB-related, NAC, Tify, and WRKY TFs for their potential involvement in the underground floral differentiation process. Together, these results laid the foundation for future molecular works to improve our understanding of the underground floral differentiation process and its genetic regulation in E. japonicum.
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Wijma M, Lembke CG, Diniz AL, Santini L, Zambotti-Villela L, Colepicolo P, Carneiro MS, Souza GM. Planting Season Impacts Sugarcane Stem Development, Secondary Metabolite Levels, and Natural Antisense Transcription. Cells 2021; 10:cells10123451. [PMID: 34943959 PMCID: PMC8700069 DOI: 10.3390/cells10123451] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/30/2021] [Accepted: 12/02/2021] [Indexed: 12/13/2022] Open
Abstract
To reduce the potentially irreversible environmental impacts caused by fossil fuels, the use of renewable energy sources must be increased on a global scale. One promising source of biomass and bioenergy is sugarcane. The study of this crop's development in different planting seasons can aid in successfully cultivating it in global climate change scenarios. The sugarcane variety SP80-3280 was field grown under two planting seasons with different climatic conditions. A systems biology approach was taken to study the changes on physiological, morphological, agrotechnological, transcriptomics, and metabolomics levels in the leaf +1, and immature, intermediate and mature internodes. Most of the variation found within the transcriptomics and metabolomics profiles is attributed to the differences among the distinct tissues. However, the integration of both transcriptomics and metabolomics data highlighted three main metabolic categories as the principal sources of variation across tissues: amino acid metabolism, biosynthesis of secondary metabolites, and xenobiotics biodegradation and metabolism. Differences in ripening and metabolite levels mainly in leaves and mature internodes may reflect the impact of contrasting environmental conditions on sugarcane development. In general, the same metabolites are found in mature internodes from both "one-year" and "one-and-a-half-year sugarcane", however, some metabolites (i.e., phenylpropanoids with economic value) and natural antisense transcript expression are only detected in the leaves of "one-year" sugarcane.
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Affiliation(s)
- Maryke Wijma
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-900, Brazil; (M.W.); (C.G.L.); (A.L.D.); (L.S.); (L.Z.-V.); (P.C.)
| | - Carolina Gimiliani Lembke
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-900, Brazil; (M.W.); (C.G.L.); (A.L.D.); (L.S.); (L.Z.-V.); (P.C.)
| | - Augusto Lima Diniz
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-900, Brazil; (M.W.); (C.G.L.); (A.L.D.); (L.S.); (L.Z.-V.); (P.C.)
| | - Luciane Santini
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-900, Brazil; (M.W.); (C.G.L.); (A.L.D.); (L.S.); (L.Z.-V.); (P.C.)
| | - Leonardo Zambotti-Villela
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-900, Brazil; (M.W.); (C.G.L.); (A.L.D.); (L.S.); (L.Z.-V.); (P.C.)
| | - Pio Colepicolo
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-900, Brazil; (M.W.); (C.G.L.); (A.L.D.); (L.S.); (L.Z.-V.); (P.C.)
| | - Monalisa Sampaio Carneiro
- Centro de Ciências Agrárias, Departamento de Biotecnologia e Produção Vegetal e Animal, Universidade Federal de São Carlos, São Paulo 13600-970, Brazil;
| | - Glaucia Mendes Souza
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-900, Brazil; (M.W.); (C.G.L.); (A.L.D.); (L.S.); (L.Z.-V.); (P.C.)
- Correspondence:
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NMR spectroscopy analysis reveals differential metabolic responses in arabidopsis roots and leaves treated with a cytokinesis inhibitor. PLoS One 2020; 15:e0241627. [PMID: 33156865 PMCID: PMC7647083 DOI: 10.1371/journal.pone.0241627] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/16/2020] [Indexed: 12/26/2022] Open
Abstract
In plant cytokinesis, de novo formation of a cell plate evolving into the new cell wall partitions the cytoplasm of the dividing cell. In our earlier chemical genomics studies, we identified and characterized the small molecule endosidin-7, that specifically inhibits callose deposition at the cell plate, arresting late-stage cytokinesis in arabidopsis. Endosidin-7 has emerged as a very valuable tool for dissecting this essential plant process. To gain insights regarding its mode of action and the effects of cytokinesis inhibition on the overall plant response, we investigated the effect of endosidin-7 through a nuclear magnetic resonance spectroscopy (NMR) metabolomics approach. In this case study, metabolomics profiles of arabidopsis leaf and root tissues were analyzed at different growth stages and endosidin-7 exposure levels. The results show leaf and root-specific metabolic profile changes and the effects of endosidin-7 treatment on these metabolomes. Statistical analyses indicated that the effect of endosidin-7 treatment was more significant than the developmental impact. The endosidin-7 induced metabolic profiles suggest compensations for cytokinesis inhibition in central metabolism pathways. This study further shows that long-term treatment of endosidin-7 profoundly changes, likely via alteration of hormonal regulation, the primary metabolism of arabidopsis seedlings. Hormonal pathway-changes are likely reflecting the plant’s responses, compensating for the arrested cell division, which in turn are leading to global metabolite modulation. The presented NMR spectral data are made available through the Metabolomics Workbench, providing a reference resource for the scientific community.
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Recent Advances in MS-Based Plant Proteomics: Proteomics Data Validation Through Integration with Other Classic and -Omics Approaches. PROGRESS IN BOTANY 2019. [DOI: 10.1007/124_2019_32] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Ma G, Shi X, Zou Q, Tian D, An X, Zhu K. iTRAQ-based quantitative proteomic analysis reveals dynamic changes during daylily flower senescence. PLANTA 2018; 248:859-873. [PMID: 29943113 DOI: 10.1007/s00425-018-2943-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 06/18/2018] [Indexed: 05/12/2023]
Abstract
Sugar-related metabolic biological processes and metabolic pathways as well as invertase, protease, and ribosomal proteins may be critical regulators controlling the circadian rhythm and ephemeral properties of daylily flowers. Daylily is a familiar perennial flower. The daylily flower opens at dawn and withers away at night. Flower longevity in almost all daylily varieties from opening to fading is less than 24 h. In the past decades, the physiological changes and genetic responses to senescence in daylily flowers have been reported. However, the main metabolic pathways and biological processes involved in daylily flower senescence and the proteins involved in premature senility of daylily flowers are poorly understood. Herein, we identified differences between the proteomes of four developmental stages (s1-s4) of daylily flowers using iTRAQ-based quantitative proteomic methods. A total of 445 proteins (containing at least two unique peptides) were identified, and differentially expressed proteins (upregulation ≥ 1.5 or downregulation ≤ 0.67, P value ≤ 0.05) were detected between these stages in the following numbers: 58 (s2/s1), 59 (s3/s1), 31 (s3/s2), 64 (s4/s1), 52 (s4/s2), and 29 (s4/s3). Protein functions and classifications were analyzed based on GO, KEGG, and COG, and expressive hierarchical cluster analysis and functional enrichment analysis for differentially expressed proteins were carried out. A comparison of the late stages (s3 and s4) with the early stage (s1) revealed that the sugar (hexose, monosaccharide, and glucose) metabolic process GO category was the most enriched, and sugar (galactose, pentose, starch, and sucrose) metabolism pathways constituted the most enriched KEGG category. Finally, the potential research value of invertase, protease, and ribosomal proteins for revealing the mechanism underlying the circadian rhythm and ephemeral properties of daylily flowers are discussed. These data and analyses provide new insight into the senescence mechanism of daylily flowers.
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Affiliation(s)
- Guangying Ma
- Floriculture Research and Development Center of Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China.
| | - Xiaohua Shi
- Floriculture Research and Development Center of Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Qingcheng Zou
- Floriculture Research and Development Center of Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Danqing Tian
- Floriculture Research and Development Center of Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Xia An
- Floriculture Research and Development Center of Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Kaiyuan Zhu
- Floriculture Research and Development Center of Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
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Volpicella M, Fanizza I, Leoni C, Gadaleta A, Nigro D, Gattulli B, Mangini G, Blanco A, Ceci LR. Identification and Characterization of the Sucrose Synthase 2 Gene (Sus2) in Durum Wheat. FRONTIERS IN PLANT SCIENCE 2016; 7:266. [PMID: 27014292 PMCID: PMC4785679 DOI: 10.3389/fpls.2016.00266] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 02/19/2016] [Indexed: 05/14/2023]
Abstract
Sucrose transport is the central system for the allocation of carbon resources in vascular plants. Sucrose synthase (SUS), which reversibly catalyzes sucrose synthesis and cleavage, represents a key enzyme in the control of the flow of carbon into starch biosynthesis. In the present study the genomic identification and characterization of the Sus2-2A and Sus2-2B genes coding for SUS in durum wheat (cultivars Ciccio and Svevo) is reported. The genes were analyzed for their expression in different tissues and at different seed maturation stages, in four tetraploid wheat genotypes (Svevo, Ciccio, Primadur, and 5-BIL42). The activity of the encoded proteins was evaluated by specific activity assays on endosperm extracts and their structure established by modeling approaches. The combined results of sucrose synthase 2 expression and activity levels were then considered in the light of their possible involvement in starch yield.
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Affiliation(s)
- Mariateresa Volpicella
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari “A. Moro”Bari, Italy
- *Correspondence: Mariateresa Volpicella,
| | - Immacolata Fanizza
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari “A. Moro”Bari, Italy
| | - Claudia Leoni
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari “A. Moro”Bari, Italy
| | - Agata Gadaleta
- Department of Agricultural and Environmental Sciences, University of Bari “A. Moro”Bari, Italy
| | - Domenica Nigro
- Department of Soil, Plant and Food Sciences Section Genetics and Plant Breeding, University of Bari “A. Moro”Bari, Italy
| | - Bruno Gattulli
- Institute of Biomembranes and Bioenergetics – National Research CouncilBari, Italy
| | - Giacomo Mangini
- Department of Soil, Plant and Food Sciences Section Genetics and Plant Breeding, University of Bari “A. Moro”Bari, Italy
| | - Antonio Blanco
- Department of Soil, Plant and Food Sciences Section Genetics and Plant Breeding, University of Bari “A. Moro”Bari, Italy
| | - Luigi R. Ceci
- Institute of Biomembranes and Bioenergetics – National Research CouncilBari, Italy
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Puzanskiy RK, Shavarda AL, Tarakhovskaya ER, Shishova MF. Analysis of metabolic profile of Chlamydomonas reinhardtii cultivated under autotrophic conditions. APPL BIOCHEM MICRO+ 2014. [DOI: 10.1134/s0003683815010135] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Toubiana D, Fernie AR, Nikoloski Z, Fait A. Network analysis: tackling complex data to study plant metabolism. Trends Biotechnol 2012; 31:29-36. [PMID: 23245943 DOI: 10.1016/j.tibtech.2012.10.011] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2012] [Revised: 10/18/2012] [Accepted: 10/24/2012] [Indexed: 11/18/2022]
Abstract
Incomplete knowledge of biochemical pathways makes the holistic description of plant metabolism a non-trivial undertaking. Sensitive analytical platforms, which are capable of accurately quantifying the levels of the various molecular entities of the cell, can assist in tackling this task. However, the ever-increasing amount of high-throughput data, often from multiple technologies, requires significant computational efforts for integrative analysis. Here we introduce the application of network analysis to study plant metabolism and describe the construction and analysis of correlation-based networks from (time-resolved) metabolomics data. By investigating the interactions between metabolites, network analysis can help to interpret complex datasets through the identification of key network components. The relationship between structural and biological roles of network components can be evaluated and employed to aid metabolic engineering.
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Affiliation(s)
- David Toubiana
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
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10
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Agrawal GK, Job D, Zivy M, Agrawal VP, Bradshaw RA, Dunn MJ, Haynes PA, van Wijk KJ, Kikuchi S, Renaut J, Weckwerth W, Rakwal R. Time to articulate a vision for the future of plant proteomics - A global perspective: An initiative for establishing the International Plant Proteomics Organization (INPPO). Proteomics 2011; 11:1559-68. [DOI: 10.1002/pmic.201000608] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2010] [Revised: 11/23/2010] [Accepted: 12/27/2010] [Indexed: 01/11/2023]
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11
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Kaspar S, Weier D, Weschke W, Mock HP, Matros A. Protein analysis of laser capture micro-dissected tissues revealed cell-type specific biological functions in developing barley grains. Anal Bioanal Chem 2010; 398:2883-93. [PMID: 20798931 DOI: 10.1007/s00216-010-4120-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Revised: 08/09/2010] [Accepted: 08/10/2010] [Indexed: 02/06/2023]
Abstract
Both the nucellar projection (NP) and endosperm transfer cells (ETC) of the developing barley grain (harvested 8 days after flowering) were isolated by laser capture micro-dissection combined with pressure catapulting. Protein extracts were analyzed by nanoUPLC separation combined with ESI-Q-TOF mass spectrometry. The majority of the ~160 proteins identified were involved in translation, protein synthesis, or protein destination. The NP proteome was enriched for stress defense molecules, while proteins involved in assimilate transport and the mobilization of nutrients were common to both the NP and the ETC. The combined qualitative and quantitative protein profiling allowed for the identification of several proteins showing tissue specificity in their expression, which underlines the distinct biological functions of these two tissues within the developing barley grain.
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Affiliation(s)
- Stephanie Kaspar
- Applied Biochemistry Group, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany
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12
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Génard M, Bertin N, Gautier H, Lescourret F, Quilot B. Virtual profiling: a new way to analyse phenotypes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 62:344-55. [PMID: 20113443 DOI: 10.1111/j.1365-313x.2010.04152.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Simulation models can be used to perform virtual profiling in order to analyse eco-physiological processes controlling plant phenotype. To illustrate this, an eco-physiological model has been used to compare and contrast the status of a virtual fruit system under two situations of carbon supply. The model simulates fruit growth, accumulation of sugar, citric acid and water, transpiration, respiration and ethylene emission, and was successfully tested on peach (Prunus persica L. Batsch) for two leaf-to-fruit ratios (6 and 18 leaves per fruit). The development stage and the variation in leaf number had large effects of the fruit model variables dealing with growth, metabolism and fruit quality. A sensitivity analysis showed that changing a single parameter value, which could correspond to a genotypic change induced by a mutation, either strongly affects most of the processes, or affects a specific process or none. Correlation analysis showed that, in a complex system such as fruit, the intensity of many physiological processes and quality traits co-varies. It also showed unexpected co-variations resulting from emergent properties of the system. This virtual profiling approach opens a new route to explore the impact of mutations, or naturally occurring genetic variations, under differing environmental conditions.
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Affiliation(s)
- Michel Génard
- UR1115, Plantes et Systèmes de Culture Horticoles, INRA, F-84000 Avignon, France.
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13
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Rehrauer H, Aquino C, Gruissem W, Henz SR, Hilson P, Laubinger S, Naouar N, Patrignani A, Rombauts S, Shu H, Van de Peer Y, Vuylsteke M, Weigel D, Zeller G, Hennig L. AGRONOMICS1: a new resource for Arabidopsis transcriptome profiling. PLANT PHYSIOLOGY 2010; 152:487-99. [PMID: 20032078 PMCID: PMC2815891 DOI: 10.1104/pp.109.150185] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2009] [Accepted: 12/17/2009] [Indexed: 05/20/2023]
Abstract
Transcriptome profiling has become a routine tool in biology. For Arabidopsis (Arabidopsis thaliana), the Affymetrix ATH1 expression array is most commonly used, but it lacks about one-third of all annotated genes present in the reference strain. An alternative are tiling arrays, but previous designs have not allowed the simultaneous analysis of both strands on a single array. We introduce AGRONOMICS1, a new Affymetrix Arabidopsis microarray that contains the complete paths of both genome strands, with on average one 25mer probe per 35-bp genome sequence window. In addition, the new AGRONOMICS1 array contains all perfect match probes from the original ATH1 array, allowing for seamless integration of the very large existing ATH1 knowledge base. The AGRONOMICS1 array can be used for diverse functional genomics applications such as reliable expression profiling of more than 30,000 genes, detection of alternative splicing, and chromatin immunoprecipitation coupled to microarrays (ChIP-chip). Here, we describe the design of the array and compare its performance with that of the ATH1 array. We find results from both microarrays to be of similar quality, but AGRONOMICS1 arrays yield robust expression information for many more genes, as expected. Analysis of the ATH1 probes on AGRONOMICS1 arrays produces results that closely mirror those of ATH1 arrays. Finally, the AGRONOMICS1 array is shown to be useful for ChIP-chip experiments. We show that heterochromatic H3K9me2 is strongly confined to the gene body of target genes in euchromatic chromosome regions, suggesting that spreading of heterochromatin is limited outside of pericentromeric regions.
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Baginsky S, Hennig L, Zimmermann P, Gruissem W. Gene expression analysis, proteomics, and network discovery. PLANT PHYSIOLOGY 2010; 152:402-10. [PMID: 20018595 PMCID: PMC2815903 DOI: 10.1104/pp.109.150433] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Accepted: 12/06/2009] [Indexed: 05/21/2023]
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15
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Omelyanchuk NA, Mironova VV, Kolchanov NA. Plant developmental genetics: Integrating data from different experiments in databases. RUSS J GENET+ 2009. [DOI: 10.1134/s1022795409110052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Chen M, Mooney BP, Hajduch M, Joshi T, Zhou M, Xu D, Thelen JJ. System analysis of an Arabidopsis mutant altered in de novo fatty acid synthesis reveals diverse changes in seed composition and metabolism. PLANT PHYSIOLOGY 2009; 150:27-41. [PMID: 19279196 PMCID: PMC2675738 DOI: 10.1104/pp.108.134882] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2008] [Accepted: 02/27/2009] [Indexed: 05/18/2023]
Abstract
Embryo-specific overexpression of biotin carboxyl carrier protein 2 (BCCP2) inhibited plastid acetyl-coenzyme A carboxylase (ACCase), resulting in altered oil, protein, and carbohydrate composition in mature Arabidopsis (Arabidopsis thaliana) seed. To characterize gene and protein regulatory consequences of this mutation, global microarray, two-dimensional difference gel electrophoresis, iTRAQ, and quantitative immunoblotting were performed in parallel. These analyses revealed that (1) transgenic overexpression of BCCP2 did not affect the expression of three other ACCase subunits; (2) four subunits to plastid pyruvate dehydrogenase complex were 25% to 70% down-regulated at protein but not transcript levels; (3) key glycolysis and de novo fatty acid/lipid synthesis enzymes were induced; (4) multiple storage proteins, but not cognate transcripts, were up-regulated; and (5) the biotin synthesis pathway was up-regulated at both transcript and protein levels. Biotin production appears closely matched to endogenous BCCP levels, since overexpression of BCCP2 produced mostly apo-BCCP2 and the resulting ACCase-compromised, low-oil phenotype. Differential expression of glycolysis, plastid pyruvate dehydrogenase complex, fatty acid, and lipid synthesis activities indicate multiple, complex regulatory responses including feedback as well as futile "feed-forward" elicitation in the case of fatty acid and lipid biosynthetic enzymes. Induction of storage proteins reveals that oil and protein synthesis share carbon intermediate(s) and that reducing malonyl-coenzyme A flow into fatty acids diverts carbon into amino acid and protein synthesis.
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Affiliation(s)
- Mingjie Chen
- Interdisciplinary Plant Group and Division of Biochemistry , Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA
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Nelson T, Gandotra N, Tausta SL. Plant cell types: reporting and sampling with new technologies. CURRENT OPINION IN PLANT BIOLOGY 2008; 11:567-73. [PMID: 18653377 DOI: 10.1016/j.pbi.2008.06.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2008] [Revised: 06/12/2008] [Accepted: 06/12/2008] [Indexed: 05/21/2023]
Abstract
Plants have relatively few cell types, but their specialized functions and their interactions are essential for physiology, development, and defense. The contributions of individual cells have been distinguished by methods including in situ reporting, cell sampling, and cell separation, thus far mostly limited to measurement of single transcripts, proteins, or metabolites. Advances in transcriptomics, proteomics, metabolomics, and activity assays with small samples and in the modeling of these data into networks of expression, regulation, interaction, and metabolism make it possible to evaluate the roles of cell types at system levels. Recent analyses include cell types of developing roots, bundle sheath and mesophyll cells of C4-type leaves, xylem and phloem cells of vascular systems, and specialized regions of embryos and shoot apices.
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Affiliation(s)
- Timothy Nelson
- Department of Molecular, Cellular and Developmental Biology, Yale University, P.O. Box 208104, New Haven, CT 06520-8104, USA.
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18
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Zybailov B, Rutschow H, Friso G, Rudella A, Emanuelsson O, Sun Q, van Wijk KJ. Sorting signals, N-terminal modifications and abundance of the chloroplast proteome. PLoS One 2008; 3:e1994. [PMID: 18431481 PMCID: PMC2291561 DOI: 10.1371/journal.pone.0001994] [Citation(s) in RCA: 501] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2008] [Accepted: 03/06/2008] [Indexed: 01/24/2023] Open
Abstract
Characterization of the chloroplast proteome is needed to understand the essential contribution of the chloroplast to plant growth and development. Here we present a large scale analysis by nanoLC-Q-TOF and nanoLC-LTQ-Orbitrap mass spectrometry (MS) of ten independent chloroplast preparations from Arabidopsis thaliana which unambiguously identified 1325 proteins. Novel proteins include various kinases and putative nucleotide binding proteins. Based on repeated and independent MS based protein identifications requiring multiple matched peptide sequences, as well as literature, 916 nuclear-encoded proteins were assigned with high confidence to the plastid, of which 86% had a predicted chloroplast transit peptide (cTP). The protein abundance of soluble stromal proteins was calculated from normalized spectral counts from LTQ-Obitrap analysis and was found to cover four orders of magnitude. Comparison to gel-based quantification demonstrates that ‘spectral counting’ can provide large scale protein quantification for Arabidopsis. This quantitative information was used to determine possible biases for protein targeting prediction by TargetP and also to understand the significance of protein contaminants. The abundance data for 550 stromal proteins was used to understand abundance of metabolic pathways and chloroplast processes. We highlight the abundance of 48 stromal proteins involved in post-translational proteome homeostasis (including aminopeptidases, proteases, deformylases, chaperones, protein sorting components) and discuss the biological implications. N-terminal modifications were identified for a subset of nuclear- and chloroplast-encoded proteins and a novel N-terminal acetylation motif was discovered. Analysis of cTPs and their cleavage sites of Arabidopsis chloroplast proteins, as well as their predicted rice homologues, identified new species-dependent features, which will facilitate improved subcellular localization prediction. No evidence was found for suggested targeting via the secretory system. This study provides the most comprehensive chloroplast proteome analysis to date and an expanded Plant Proteome Database (PPDB) in which all MS data are projected on identified gene models.
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Affiliation(s)
- Boris Zybailov
- Department of Plant Biology, Cornell University, Ithaca, New York, United States of America
| | - Heidi Rutschow
- Department of Plant Biology, Cornell University, Ithaca, New York, United States of America
| | - Giulia Friso
- Department of Plant Biology, Cornell University, Ithaca, New York, United States of America
| | - Andrea Rudella
- Department of Plant Biology, Cornell University, Ithaca, New York, United States of America
| | - Olof Emanuelsson
- Stockholm Bioinformatics Center, AlbaNova, Stockholm University, Stockholm, Sweden
| | - Qi Sun
- Computation Biology Service Unit, Cornell Theory Center, Cornell University, Ithaca, New York, United States of America
| | - Klaas J. van Wijk
- Department of Plant Biology, Cornell University, Ithaca, New York, United States of America
- * To whom correspondence should be addressed. E-mail:
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Exner V, Hennig L. Chromatin rearrangements in development. CURRENT OPINION IN PLANT BIOLOGY 2008; 11:64-9. [PMID: 18024147 DOI: 10.1016/j.pbi.2007.10.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2007] [Revised: 10/02/2007] [Accepted: 10/03/2007] [Indexed: 05/22/2023]
Abstract
Chromatin states change dramatically during plant development. Globally, cytologically defined heterochromatin increases during cell differentiation and organ maturation, while it decreases during callus formation and protoplastization. Interestingly, around the time of bolting, heterochromatin content of leaf nuclei decreases transiently. Locally, chromatin compactness of the regulatory gene GLABRA2 is controlled by positional cues and correlates with transcriptional activity. In the case of the flowering time regulator FLC, chromatin compactness and histone modifications are controlled by environmental cues and ensure faithful maintenance of gene repression after vernalization. The combination of cytological studies, locus-specific analyses, and novel genome-wide profiling techniques should soon lead to a more detailed understanding of the mechanisms coupling intranuclear architecture and development.
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Affiliation(s)
- Vivien Exner
- Institute of Plant Sciences & Zurich-Basel Plant Science Center, ETH Zurich, CH-8092 Zurich, Switzerland.
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20
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Fait A, Fromm H, Walter D, Galili G, Fernie AR. Highway or byway: the metabolic role of the GABA shunt in plants. TRENDS IN PLANT SCIENCE 2008; 13:14-9. [PMID: 18155636 DOI: 10.1016/j.tplants.2007.10.005] [Citation(s) in RCA: 390] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2007] [Revised: 10/19/2007] [Accepted: 10/31/2007] [Indexed: 05/18/2023]
Abstract
Much of the recent work on the gamma-aminobutyrate (GABA) shunt in plants has concentrated on stress/pest-associated and signalling roles. However, fifty years after the structural elucidation of the pathway, aspects of its regulation and even of its biological significance remain largely obscure. Here, we assess the importance of GABA metabolism in plants, reviewing relevant biological circumstances and taking advantage of high-throughput data accessibility and computational approaches. We discuss the premise that GABA metabolism plays a major role in carbon and nitrogen primary metabolism. We further evaluate technological developments that will likely allow us to address the quantitative importance of this shunt within the biological processes to which it contributes.
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Affiliation(s)
- Aaron Fait
- Department Willmitzer, Max Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
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