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Rajewski A, Carter-House D, Stajich J, Litt A. Datura genome reveals duplications of psychoactive alkaloid biosynthetic genes and high mutation rate following tissue culture. BMC Genomics 2021; 22:201. [PMID: 33752605 PMCID: PMC7986286 DOI: 10.1186/s12864-021-07489-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/26/2021] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Datura stramonium (Jimsonweed) is a medicinally and pharmaceutically important plant in the nightshade family (Solanaceae) known for its production of various toxic, hallucinogenic, and therapeutic tropane alkaloids. Recently, we published a tissue-culture based transformation protocol for D. stramonium that enables more thorough functional genomics studies of this plant. However, the tissue culture process can lead to undesirable phenotypic and genomic consequences independent of the transgene used. Here, we have assembled and annotated a draft genome of D. stramonium with a focus on tropane alkaloid biosynthetic genes. We then use mRNA sequencing and genome resequencing of transformants to characterize changes following tissue culture. RESULTS Our draft assembly conforms to the expected 2 gigabasepair haploid genome size of this plant and achieved a BUSCO score of 94.7% complete, single-copy genes. The repetitive content of the genome is 61%, with Gypsy-type retrotransposons accounting for half of this. Our gene annotation estimates the number of protein-coding genes at 52,149 and shows evidence of duplications in two key alkaloid biosynthetic genes, tropinone reductase I and hyoscyamine 6 β-hydroxylase. Following tissue culture, we detected only 186 differentially expressed genes, but were unable to correlate these changes in expression with either polymorphisms from resequencing or positional effects of transposons. CONCLUSIONS We have assembled, annotated, and characterized the first draft genome for this important model plant species. Using this resource, we show duplications of genes leading to the synthesis of the medicinally important alkaloid, scopolamine. Our results also demonstrate that following tissue culture, mutation rates of transformed plants are quite high (1.16 × 10- 3 mutations per site), but do not have a drastic impact on gene expression.
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Affiliation(s)
- Alex Rajewski
- Department of Botany and Plant Science, University of California, Riverside, California 92521 USA
| | - Derreck Carter-House
- Department of Microbiology and Plant Pathology, University of California, Riverside, California 92521 USA
| | - Jason Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, California 92521 USA
| | - Amy Litt
- Department of Botany and Plant Science, University of California, Riverside, California 92521 USA
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Generation of High Yielding and Fragrant Rice ( Oryza sativa L.) Lines by CRISPR/Cas9 Targeted Mutagenesis of Three Homoeologs of Cytochrome P450 Gene Family and OsBADH2 and Transcriptome and Proteome Profiling of Revealed Changes Triggered by Mutations. PLANTS 2020; 9:plants9060788. [PMID: 32586052 PMCID: PMC7355857 DOI: 10.3390/plants9060788] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/19/2020] [Accepted: 06/19/2020] [Indexed: 12/12/2022]
Abstract
The significant increase in grain yield and quality are often antagonistic but a constant demand for breeders and consumers. Some genes related to cytochrome P450 family are known for rice organ growth but their role in controlling grain yield is still unknown. Here, we generated new rice mutants with high yield and improved aroma by simultaneously editing three cytochrome P450 homoeologs (Os03g0603100, Os03g0568400, and GL3.2) and OsBADH2 with the CRISPR/Cas9 system, and RNA-sequencing and proteomic analysis were performed to unveil the subsequent changes. High mutation efficiency was achieved in both target sites of each gene and the mutations were predominantly only deletions, while insertions were rare, and no mutations were detected in the five most likely off-target sites against each sgRNA. Mutants exhibited increased grain size, 2-acetyl-1-pyrroline (2AP) content, and grain cell numbers while there was no change in other agronomic traits. Transgene-DNA-free mutant lines appeared with a frequency of 44.44% and homozygous mutations were stably transmitted, and bi-allelic and heterozygous mutations followed Mendelian inheritance, while the inheritance of chimeric mutations was unpredictable. Deep RNA sequencing and proteomic results revealed the regulation of genes and proteins related to cytochrome P450 family, grain size and development, and cell cycle. The KEGG and hub-gene and protein network analysis showed that the gene and proteins related to ribosomal and photosynthesis pathways were mainly enriched, respectively. Our findings provide a broad and detailed basis to understand the role of CRISPR/Cas9 in rice yield and quality improvement.
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Sheng X, Sun Z, Wang X, Tan Y, Yu D, Yuan G, Yuan D, Duan M. Improvement of the Rice "Easy-to-Shatter" Trait via CRISPR/Cas9-Mediated Mutagenesis of the qSH1 Gene. FRONTIERS IN PLANT SCIENCE 2020; 11:619. [PMID: 32528496 PMCID: PMC7262966 DOI: 10.3389/fpls.2020.00619] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/22/2020] [Indexed: 05/22/2023]
Abstract
"Easy-to-shatter" trait is a major cause of rice crop yield losses, emphasizing the economic value of developing elite rice cultivars with reduced seed shattering capable of achieving higher yields. In the present study, we describe the development of new indica rice lines that exhibit lower rates of seed shattering following the targeted CRISPR/Cas9-mediated editing of the qSH1 gene. We were able to identify qSH1 mutant T0 transgenic plants, with transgene-free homozygous mutants being obtained via segregation in the T1 generation. We then utilized two T2 transgene-free homozygous lines in order to assess the degree of seed shattering and major agronomic traits of these mutant lines and of wild-type rice plants (HR1128-WT). This approach revealed that qsh1 homozygous mutant lines exhibited significantly reduced seed shattering relative to HR1128-WT without any significant changes in other analyzed agronomic traits. We then used these mutant lines to develop new promising hybrid rice lines with intermediate seed shattering. Overall our results reveal that combining targeted gene editing via CRISPR/Cas9 with heterosis utilization approach can allow for the efficient development of novel promising hybrid rice cultivars that exhibit a intermediate of seed shattering, thereby ensuring better stability and improved rice yields.
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Affiliation(s)
- Xiabing Sheng
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
| | - Zhizhong Sun
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
| | - Xuefeng Wang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Yanning Tan
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
| | - Dong Yu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
| | - Guilong Yuan
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
| | - Dingyang Yuan
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
- Hunan Academy of Agricultural Sciences, Changsha, China
- *Correspondence: Dingyang Yuan,
| | - Meijuan Duan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
- Meijuan Duan,
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Zhang Y, Zhang Y, Yu J, Zhang H, Wang L, Wang S, Guo S, Miao Y, Chen S, Li Y, Dai S. NaCl-responsive ROS scavenging and energy supply in alkaligrass callus revealed from proteomic analysis. BMC Genomics 2019; 20:990. [PMID: 31847807 PMCID: PMC6918623 DOI: 10.1186/s12864-019-6325-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 11/22/2019] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Salinity has obvious effects on plant growth and crop productivity. The salinity-responsive mechanisms have been well-studied in differentiated organs (e.g., leaves, roots and stems), but not in unorganized cells such as callus. High-throughput quantitative proteomics approaches have been used to investigate callus development, somatic embryogenesis, organogenesis, and stress response in numbers of plant species. However, they have not been applied to callus from monocotyledonous halophyte alkaligrass (Puccinellia tenuifora). RESULTS The alkaligrass callus growth, viability and membrane integrity were perturbed by 50 mM and 150 mM NaCl treatments. Callus cells accumulated the proline, soluble sugar and glycine betaine for the maintenance of osmotic homeostasis. Importantly, the activities of ROS scavenging enzymes (e.g., SOD, APX, POD, GPX, MDHAR and GR) and antioxidants (e.g., ASA, DHA and GSH) were induced by salinity. The abundance patterns of 55 salt-responsive proteins indicate that salt signal transduction, cytoskeleton, ROS scavenging, energy supply, gene expression, protein synthesis and processing, as well as other basic metabolic processes were altered in callus to cope with the stress. CONCLUSIONS The undifferentiated callus exhibited unique salinity-responsive mechanisms for ROS scavenging and energy supply. Activation of the POD pathway and AsA-GSH cycle was universal in callus and differentiated organs, but salinity-induced SOD pathway and salinity-reduced CAT pathway in callus were different from those in leaves and roots. To cope with salinity, callus mainly relied on glycolysis, but not the TCA cycle, for energy supply.
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Affiliation(s)
- Yongxue Zhang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Yue Zhang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Juanjuan Yu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Heng Zhang
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Liyue Wang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Sining Wang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Siyi Guo
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng, 455000, China
| | - Yuchen Miao
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng, 455000, China
| | - Sixue Chen
- Department of Biology, Genetics Institute, Plant Molecular and Cellular Biology Program, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, 32610, USA
| | - Ying Li
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China.
| | - Shaojun Dai
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.
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Voillet V, San Cristobal M, Père MC, Billon Y, Canario L, Liaubet L, Lefaucheur L. Integrated Analysis of Proteomic and Transcriptomic Data Highlights Late Fetal Muscle Maturation Process. Mol Cell Proteomics 2018; 17:672-693. [PMID: 29311229 PMCID: PMC5880113 DOI: 10.1074/mcp.m116.066357] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 10/13/2017] [Indexed: 01/08/2023] Open
Abstract
In pigs, the perinatal period is the most critical time for survival. Piglet maturation, which occurs at the end of gestation, is an important determinant of early survival. Skeletal muscle plays a key role in adaptation to extra-uterine life, e.g. motor function and thermoregulation. Progeny from two breeds with extreme neonatal mortality rates were analyzed at 90 and 110 days of gestation (dg). The Large White breed is a highly selected breed for lean growth and exhibits a high rate of neonatal mortality, whereas the Meishan breed is fatter and more robust and has a low neonatal mortality. Our aim was to identify molecular signatures underlying late fetal longissimus muscle development. First, integrated analysis was used to explore relationships between co-expression network models built from a proteomic data set (bi-dimensional electrophoresis) and biological phenotypes. Second, correlations with a transcriptomic data set (microarrays) were investigated to combine different layers of expression with a focus on transcriptional regulation. Muscle glycogen content and myosin heavy chain polymorphism were good descriptors of muscle maturity and were used for further data integration analysis. Using 89 identified unique proteins, network inference, correlation with biological phenotypes and functional enrichment revealed that mitochondrial oxidative metabolism was a key determinant of neonatal muscle maturity. Some proteins, including ATP5A1 and CKMT2, were important nodes in the network related to muscle metabolism. Transcriptomic data suggest that overexpression of mitochondrial PCK2 was involved in the greater glycogen content of Meishan fetuses at 110 dg. GPD1, an enzyme involved in the mitochondrial oxidation of cytosolic NADH, was overexpressed in Meishan. Thirty-one proteins exhibited a positive correlation between mRNA and protein levels in both extreme fetal genotypes, suggesting transcriptional regulation. Gene ontology enrichment and Ingenuity analyses identified PPARGC1A and ESR1 as possible transcriptional factors positively involved in late fetal muscle maturation.
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Affiliation(s)
- Valentin Voillet
- From the ‡GenPhyse, Université de Toulouse, INRA, ENVT, F-31326 Castanet-Tolosan, France
| | - Magali San Cristobal
- From the ‡GenPhyse, Université de Toulouse, INRA, ENVT, F-31326 Castanet-Tolosan, France
| | | | - Yvon Billon
- ¶INRA, UE1372, GenESI, F-17700 Surgères, France
| | - Laurianne Canario
- From the ‡GenPhyse, Université de Toulouse, INRA, ENVT, F-31326 Castanet-Tolosan, France
| | - Laurence Liaubet
- From the ‡GenPhyse, Université de Toulouse, INRA, ENVT, F-31326 Castanet-Tolosan, France
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Heringer AS, Santa-Catarina C, Silveira V. Insights from Proteomic Studies into Plant Somatic Embryogenesis. Proteomics 2018; 18:e1700265. [DOI: 10.1002/pmic.201700265] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 01/08/2018] [Indexed: 12/24/2022]
Affiliation(s)
- Angelo Schuabb Heringer
- Laboratório de Biotecnologia; Centro de Biociências e Biotecnologia; Universidade Estadual do Norte Fluminense Darcy Ribeiro; Rio de Janeiro Brazil
- Unidade de Biologia Integrativa; Setor de Genômica e Proteômica; Universidade Estadual do Norte Fluminense Darcy Ribeiro; Rio de Janeiro Brazil
| | - Claudete Santa-Catarina
- Laboratório de Biologia Celular e Tecidual; Centro de Biociências e Biotecnologia; Universidade Estadual do Norte Fluminense Darcy Ribeiro; Rio de Janeiro Brazil
| | - Vanildo Silveira
- Laboratório de Biotecnologia; Centro de Biociências e Biotecnologia; Universidade Estadual do Norte Fluminense Darcy Ribeiro; Rio de Janeiro Brazil
- Unidade de Biologia Integrativa; Setor de Genômica e Proteômica; Universidade Estadual do Norte Fluminense Darcy Ribeiro; Rio de Janeiro Brazil
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Aguilar-Hernández V, Loyola-Vargas VM. Advanced Proteomic Approaches to Elucidate Somatic Embryogenesis. FRONTIERS IN PLANT SCIENCE 2018; 9:1658. [PMID: 30524454 PMCID: PMC6262180 DOI: 10.3389/fpls.2018.01658] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 10/25/2018] [Indexed: 05/06/2023]
Abstract
Somatic embryogenesis (SE) is a cell differentiation process by which a somatic cell changes its genetic program and develops into an embryonic cell. Investigating this process with various explant sources in vitro has allowed us to trace somatic embryo development from germination to plantlets and has led to the generation of new technologies, including genetic transformation, endangered species conservation, and synthetic seed production. A transcriptome data comparison from different stages of the developing somatic embryo has revealed a complex network controlling the somatic cell's fate, suggesting that an interconnected network acts at the protein level. Here, we discuss the current progress on SE using proteomic-based data, focusing on changing patterns of proteins during the establishment of the somatic embryo. Despite the advanced proteomic approaches available so far, deciphering how the somatic embryo is induced is still in its infancy. The new proteomics techniques that lead to the quantification of proteins with different abundances during the induction of SE are opening this area of study for the first time. These quantitative differences can elucidate the different pathways involved in SE induction. We envisage that the application of these proteomic technologies can be pivotal to identifying proteins critical to the process of SE, demonstrating the cellular localization, posttranslational modifications, and turnover protein events required to switch from a somatic cell to a somatic embryo cell and providing new insights into the molecular mechanisms underlying SE. This work will help to develop biotechnological strategies for mass production of quality crop material.
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Affiliation(s)
- Victor Aguilar-Hernández
- Catedrático CONACYT, Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Mexico
- *Correspondence: Victor Aguilar-Hernández, orcid.org/0000-0001-8239-4047
| | - Víctor M. Loyola-Vargas
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Mexico
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Dressler FF, Bodi I, Menza M, Moss R, Bugger H, Bode C, Behrends JC, Seemann G, Odening KE. Interregional electro-mechanical heterogeneity in the rabbit myocardium. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 130:344-355. [PMID: 28655649 DOI: 10.1016/j.pbiomolbio.2017.06.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 06/21/2017] [Accepted: 06/22/2017] [Indexed: 12/28/2022]
Abstract
BACKGROUND Increased electrical heterogeneity has been causatively linked to arrhythmic disorders, yet the knowledge about physiological heterogeneity remains incomplete. This study investigates regional electro-mechanical heterogeneities in rabbits, one of the key animal models for arrhythmic disorders. METHODS AND FINDINGS 7 wild-type rabbits were examined by phase-contrast magnetic resonance imaging in vivo to assess cardiac wall movement velocities. Using a novel data-processing algorithm regional contraction-like profiles were calculated. Contraction started earlier and was longer in left ventricular (LV) apex than base. Patch clamp recordings showed longer action potentials (AP) in LV apex compared to the base of LV, septum, and right ventricle. Western blots of cardiac ion channels and calcium handling proteins showed lower expression of Cav1.2, KvLQT1, Kv1.4, NCX and Phospholamban in LV apex vs. base. A single-cell in silico model integrating the quantitative regional differences in ion channels reproduced a longer contraction and longer AP in apex vs. base. CONCLUSIONS Apico-basal electro-mechanical heterogeneity is physiologically present in the healthy rabbit heart. An apico-basal electro-mechanical gradient exists with longer APD and contraction duration in the apex and associated regionally heterogeneous expression of five key proteins. This pattern of apical mechanical dominance probably serves to increase pumping efficiency.
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Affiliation(s)
- Franz F Dressler
- Department of Cardiology and Angiology I, Heart Center University of Freiburg, Hugstetter Strasse 55, 79106 Freiburg, Germany; Faculty of Medicine, University of Freiburg, Breisacher Strasse 153, 79110 Freiburg, Germany
| | - Ilona Bodi
- Department of Cardiology and Angiology I, Heart Center University of Freiburg, Hugstetter Strasse 55, 79106 Freiburg, Germany; Faculty of Medicine, University of Freiburg, Breisacher Strasse 153, 79110 Freiburg, Germany
| | - Marius Menza
- Faculty of Medicine, University of Freiburg, Breisacher Strasse 153, 79110 Freiburg, Germany; Department of Medical Physics, Medical Center - University of Freiburg, Breisacher Straße 60a, 79106 Freiburg, Germany
| | - Robin Moss
- Faculty of Medicine, University of Freiburg, Breisacher Strasse 153, 79110 Freiburg, Germany; Institute of Biomedical Engineering, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76128 Karlsruhe, Germany; Institute for Experimental Cardiovascular Medicine, Heart Center University of Freiburg, Medical Center - University of Freiburg, Elsaesserstrasse 2q, 79110 Freiburg, Germany
| | - Heiko Bugger
- Department of Cardiology and Angiology I, Heart Center University of Freiburg, Hugstetter Strasse 55, 79106 Freiburg, Germany; Faculty of Medicine, University of Freiburg, Breisacher Strasse 153, 79110 Freiburg, Germany
| | - Christoph Bode
- Department of Cardiology and Angiology I, Heart Center University of Freiburg, Hugstetter Strasse 55, 79106 Freiburg, Germany; Faculty of Medicine, University of Freiburg, Breisacher Strasse 153, 79110 Freiburg, Germany
| | - Jan C Behrends
- Faculty of Medicine, University of Freiburg, Breisacher Strasse 153, 79110 Freiburg, Germany; Department of Physiology, Laboratory for Membrane Physiology and -Technology, University of Freiburg, Hermann-Herder-Strasse 7, 79104 Freiburg, Germany
| | - Gunnar Seemann
- Faculty of Medicine, University of Freiburg, Breisacher Strasse 153, 79110 Freiburg, Germany; Institute of Biomedical Engineering, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76128 Karlsruhe, Germany; Institute for Experimental Cardiovascular Medicine, Heart Center University of Freiburg, Medical Center - University of Freiburg, Elsaesserstrasse 2q, 79110 Freiburg, Germany
| | - Katja E Odening
- Department of Cardiology and Angiology I, Heart Center University of Freiburg, Hugstetter Strasse 55, 79106 Freiburg, Germany; Faculty of Medicine, University of Freiburg, Breisacher Strasse 153, 79110 Freiburg, Germany; Institute for Experimental Cardiovascular Medicine, Heart Center University of Freiburg, Medical Center - University of Freiburg, Elsaesserstrasse 2q, 79110 Freiburg, Germany.
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Ge F, Hu H, Huang X, Zhang Y, Wang Y, Li Z, Zou C, Peng H, Li L, Gao S, Pan G, Shen Y. Metabolomic and Proteomic Analysis of Maize Embryonic Callus induced from immature embryo. Sci Rep 2017; 7:1004. [PMID: 28432333 PMCID: PMC5430770 DOI: 10.1038/s41598-017-01280-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 03/27/2017] [Indexed: 11/09/2022] Open
Abstract
The low ratio of embryonic callus (EC) induction has inhibited the rapid development of maize genetic engineering. Still, little is known to explain the genotype-dependence of EC induction. Here, we performed a large-scale, quantitative analysis of the maize EC metabolome and proteome at three typical induction stages in two inbred lines with a range of EC induction capabilities. Comparison of the metabolomes and proteomes suggests that the differential molecular responses begin at an early stage of development and continue throughout the process of EC formation. The two inbred lines show different responses under various conditions, such as metal ion binding, cell enlargement, stem cell formation, meristematic activity maintenance, somatic embryogenesis, cell wall synthesis, and hormone signal transduction. Furthermore, the differences in hormone (auxin, cytokinin, gibberellin, salicylic acid, jasmonic acid, brassinosteroid and ethylene) synthesis and transduction ability could partially explain the higher EC induction ratio in the inbred line 18-599R. During EC formation, repression of the "histone deacetylase 2 and ERF transcription factors" complex in 18-599R activated the expression of downstream genes, which further promoted EC induction. Together, our data provide new insights into the molecular regulatory mechanism responsible for efficient EC induction in maize.
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Affiliation(s)
- Fei Ge
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hongmei Hu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xing Huang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yanling Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yanli Wang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhaoling Li
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chaoying Zou
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Huanwei Peng
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, 611130, China
| | - Lujiang Li
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shibin Gao
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangtang Pan
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yaou Shen
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
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Lin Z, Wang Z, Zhang X, Liu Z, Li G, Wang S, Ding Y. Complementary Proteome and Transcriptome Profiling in Developing Grains of a Notched-Belly Rice Mutant Reveals Key Pathways Involved in Chalkiness Formation. PLANT & CELL PHYSIOLOGY 2017; 58:560-573. [PMID: 28158863 PMCID: PMC5444571 DOI: 10.1093/pcp/pcx001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 01/02/2017] [Indexed: 05/03/2023]
Abstract
Rice grain chalkiness is a highly complex trait involved in multiple metabolic pathways and controlled by polygenes and growth conditions. To uncover novel aspects of chalkiness formation, we performed an integrated profiling of gene activity in the developing grains of a notched-belly rice mutant. Using exhaustive tandem mass spectrometry-based shotgun proteomics and whole-genome RNA sequencing to generate a nearly complete catalog of expressed mRNAs and proteins, we reliably identified 38,476 transcripts and 3,840 proteins. Comparison between the translucent part and chalky part of the notched-belly grains resulted in only a few differently express genes (240) and differently express proteins (363), thus making it possible to focus on 'core' genes or common pathways. Several novel key pathways were identified as of relevance to chalkiness formation, in particular the shift of C and N metabolism, the down-regulation of ribosomal proteins and the resulting low abundance of storage proteins especially the 13 kDa prolamin subunit, and the suppressed photosynthetic capacity in the pericarp of the chalky part. Further, genes and proteins as transporters for carbohydrates, amino acid/peptides, proteins, lipids and inorganic ions showed an increasing expression pattern in the chalky part of the notched-belly grains. Similarly, transcripts and proteins of receptors for auxin, ABA, ethylene and brassinosteroid were also up-regulated. In summary, this joint analysis of transcript and protein profiles provides a comprehensive reference map of gene activity regarding the physiological state in the chalky endosperm.
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Affiliation(s)
- Zhaomiao Lin
- College of Agronomy, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Zunxin Wang
- College of Agronomy, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Xincheng Zhang
- College of Agronomy, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Zhenghui Liu
- College of Agronomy, Nanjing Agricultural University, Nanjing 210095, PR China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing 210095, PR China
- Corresponding author: E-mail, ; Fax, +86-25-84395313
| | - Ganghua Li
- College of Agronomy, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Shaohua Wang
- College of Agronomy, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Yanfeng Ding
- College of Agronomy, Nanjing Agricultural University, Nanjing 210095, PR China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing 210095, PR China
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Budzinski IGF, Moon DH, Morosini JS, Lindén P, Bragatto J, Moritz T, Labate CA. Integrated analysis of gene expression from carbon metabolism, proteome and metabolome, reveals altered primary metabolism in Eucalyptus grandis bark, in response to seasonal variation. BMC PLANT BIOLOGY 2016; 16:149. [PMID: 27364638 PMCID: PMC4929727 DOI: 10.1186/s12870-016-0839-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 06/22/2016] [Indexed: 05/09/2023]
Abstract
BACKGROUND Seasonal variation is presumed to play an important role in the regulation of tree growth, especially for Eucalyptus grandis, a fast-growing tree. This variation may induce changes in the whole tree at transcriptional, protein and metabolite levels. Bark represents an important group of tissues that protect trees from desiccation and pathogen attack, and it has been identified as potential feedstock for lignocellulosic derived biofuels. Despite the growing interest, little is known about the molecular mechanisms that regulates bark metabolism, particularly in tropical countries. RESULTS In this study we report the changes observed in the primary metabolism of E. grandis bark during two contrasting seasons in Brazil, summer (wet) and winter (dry), through the combination of transcripts (RT-qPCR), proteome (2-DE gels) and metabolome (GC-MS) analysis, in an integrated manner. Twenty-four genes, involved in carbon metabolism, were analyzed in the two seasons. Eleven were up-regulated in summer, three were up-regulated in winter and ten did not show statistical differences in the expression pattern. The proteomic analysis using 2-DE gels showed 77 proteins expressing differences in abundance, with 38 spots up-regulated in summer and 37 in winter. Different metabolites significantly accumulated during winter. CONCLUSIONS This study revealed a metabolic reconfiguration in the primary metabolism of E. grandis bark, triggered by seasonal variation. Transcripts and protein data suggests that during winter carbohydrate formation seems to be favored by tree metabolism. Glucose, fructose and sucrose accumulated at significant levels during the winter.
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Affiliation(s)
- Ilara Gabriela Frasson Budzinski
- />Laboratório Max Feffer de Genética de Plantas, Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP 13418-900 Brasil
| | - David H. Moon
- />Laboratório Max Feffer de Genética de Plantas, Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP 13418-900 Brasil
| | - Júlia Silva Morosini
- />Laboratório Max Feffer de Genética de Plantas, Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP 13418-900 Brasil
| | - Pernilla Lindén
- />Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, SE-901 83 Sweden
| | - Juliano Bragatto
- />Laboratório Max Feffer de Genética de Plantas, Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP 13418-900 Brasil
| | - Thomaz Moritz
- />Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, SE-901 83 Sweden
| | - Carlos Alberto Labate
- />Laboratório Max Feffer de Genética de Plantas, Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP 13418-900 Brasil
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12
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Induction and quantitative proteomic analysis of cell dedifferentiation during callus formation of lotus (Nelumbo nucifera Gaertn.spp. baijianlian). J Proteomics 2016; 131:61-70. [DOI: 10.1016/j.jprot.2015.10.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 09/29/2015] [Accepted: 10/08/2015] [Indexed: 11/23/2022]
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13
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Varhaníková M, Uvackova L, Skultety L, Pretova A, Obert B, Hajduch M. Comparative quantitative proteomic analysis of embryogenic and non-embryogenic calli in maize suggests the role of oxylipins in plant totipotency. J Proteomics 2014; 104:57-65. [PMID: 24530378 DOI: 10.1016/j.jprot.2014.02.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 01/31/2014] [Accepted: 02/02/2014] [Indexed: 01/08/2023]
Abstract
UNLABELLED Totipotency, the ability of somatic plant cell to generate whole plant through somatic embryogenesis, is still not well understood. In this study, maize immature zygotic embryos were used to generate embryogenic (EC) and non-embryogenic (NEC) calli. In order to compare proteomes of EC and NEC, two-dimensional electrophoresis (2-DE) in combination with mass spectrometry was used. This approach resulted into 361 quantified 2-DE spots out of which 44 were found statistically significantly differentially abundant between EC and NEC. Mass spectrometry provided the identity for 23 proteins that were classified into 8 metabolic categories. The most abundant were proteins associated with energy followed by proteins associated with disease and defense. Based on the abundances of identified proteins in this and other studies, working model for plant totipotency was proposed. One aspect of this working model suggests that increased abundances of proteins associated with pyruvate biosynthesis and suppression of embryogenic genes might be responsible for differences between EC and NEC cells. Furthermore we speculate that the increased abundance of lipoxygenase in the NEC cells results in changes in the equilibrium levels of one or more signaling molecules and is at least partly responsible for somatic cell reprogramming during totipotency. BIOLOGICAL SIGNIFICANCE Totipotency, the ability of somatic plant cell to generate whole plant through somatic embryogenesis, is still not well understood. In order to further advance understanding of this biological phenomenon, proteomes of embryogenic and non-embryogenic callus, derived from immature zygotic embryos of inbred maize line A19, were compared using 2-DE based proteomic technology. Based on the abundances of identified proteins in this and other studies, working model for plant totipotency was proposed. One aspect of this working model suggests that increased abundances of proteins associated with pyruvate biosynthesis and suppression of embryogenic genes might be responsible for differences between EC and NEC cells. Furthermore we speculate that the increased abundance of lipoxygenase in the NEC cells results in changes in the equilibrium levels of one or more signaling molecules and is at least partly responsible for somatic cell reprogramming during totipotency. This article is part of a Special Issue entitled: Environmental and structural proteomics.
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Affiliation(s)
- Miroslava Varhaníková
- Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences, Nitra, Slovakia
| | - Lubica Uvackova
- Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences, Nitra, Slovakia
| | - Ludovit Skultety
- Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia; Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Anna Pretova
- Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences, Nitra, Slovakia; University of Cyril and Method, Trnava, Slovakia
| | - Bohuš Obert
- Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences, Nitra, Slovakia
| | - Martin Hajduch
- Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences, Nitra, Slovakia; Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia.
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Zhang M, Shen S. Effective protein extraction protocol for proteomics studies of Jerusalem artichoke leaves. J Sep Sci 2013; 36:2203-9. [PMID: 23630184 DOI: 10.1002/jssc.201300199] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 04/16/2013] [Accepted: 04/16/2013] [Indexed: 11/11/2022]
Abstract
Protein extraction is a crucial step for proteomics studies. To establish an effective protein extraction protocol suitable for two-dimensional electrophoresis (2DE) analysis in Jerusalem artichoke (Helianthus tuberosus L.), three different protein extraction methods-trichloroacetic acid/acetone, Mg/NP-40, and phenol/ammonium acetate-were evaluated using Jerusalem artichoke leaves as source materials. Of the three methods, trichloroacetic acid/acetone yielded the best protein separation pattern and highest number of protein spots in 2DE analysis. Proteins highly abundant in leaves, such as Rubisco, are typically problematic during leaf 2DE analysis, however, and this disadvantage was evident using trichloroacetic acid/acetone. To reduce the influence of abundant proteins on the detection of low-abundance proteins, we optimized the trichloroacetic acid/acetone method by incorporating a PEG fractionation approach. After optimization, 363 additional (36.2%) protein spots were detected on the 2DE gel. Our results suggest that trichloroacetic acid/acetone method is a better protein extraction technique than Mg/NP-40 and phenol/ammonium acetate in Jerusalem artichoke leaf 2DE analysis, and that trichloroacetic acid/acetone method combined with PEG fractionation procedure is the most effective approach for leaf 2DE analysis of Jerusalem artichoke.
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Affiliation(s)
- Meide Zhang
- Institute of Chinese Herbal Medicine, Hubei Academy of Agricultural Sciences, Enshi, China.
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Bernardo L, Prinsi B, Negri AS, Cattivelli L, Espen L, Valè G. Proteomic characterization of the Rph15 barley resistance gene-mediated defence responses to leaf rust. BMC Genomics 2012; 13:642. [PMID: 23167439 PMCID: PMC3541957 DOI: 10.1186/1471-2164-13-642] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 11/09/2012] [Indexed: 11/28/2022] Open
Abstract
Background Leaf rust, caused by the biotrophic fungal pathogen Puccinia hordei, is one of the most important foliar disease of barley (Hordeum vulgare) and represents a serious threat in many production regions of the world. The leaf rust resistance gene Rph15 is of outstanding interest for resistance breeding because it confers resistance to over 350 Puccinia hordei isolates collected from around the world. Molecular and biochemical mechanisms responsible for the Rph15 effectiveness are currently not investigated. The aim of the present work was to study the Rph15-based defence responses using a proteomic approach. Results Protein pattern changes in response to the leaf rust pathogen infection were investigated in two barley near isogenic lines (NILs), Bowman (leaf rust susceptible) and Bowman-Rph15 (leaf rust resistant), differing for the introgression of the leaf rust resistance gene Rph15. Two infection time points, 24 hours and four days post inoculation (dpi), were analysed. No statistically significant differences were identified at the early time point, while at 4 dpi eighteen protein spots were significantly up or down regulated with a fold-change equal or higher than two in response to pathogen infection. Almost all the pathogen-responsive proteins were identified in the Bowman-Rph15 resistant NIL. Protein spots were characterized by LC-MS/MS analysis and found to be involved in photosynthesis and energy metabolism, carbohydrate metabolism, protein degradation and defence. Proteomic data were complemented by transcriptional analysis of the respective genes. The identified proteins can be related to modulation of the photosynthetic apparatus components, re-direction of the metabolism to sustain defence responses and deployment of defence proteins. Conclusions The identification of leaf rust infection-modulated defence responses restricted to the resistant NIL support the hypothesis that basal defence responses of Bowman, but not the Rph15 resistance gene-based ones, are suppressed or delayed by pathogen effectors to levels below the detection power of the adopted proteomic approach. Additionally, Rph15-mediated resistance processes identified mainly resides on a modulation of primary metabolism, affecting photosyntesis and carbohydrate pool.
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Affiliation(s)
- Letizia Bernardo
- CRA-Consiglio per la ricerca e la sperimentazione in agricoltura, Genomics Research Centre, Via S. Protaso 302, Fiorenzuola d'Arda, PC I-29017, Italy
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Transcriptome Analysis of Age-Related Gain of Callus-Forming Capacity in Arabidopsis Hypocotyls. ACTA ACUST UNITED AC 2012; 53:1457-69. [DOI: 10.1093/pcp/pcs090] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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17
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Corrado G, Alagna F, Rocco M, Renzone G, Varricchio P, Coppola V, Coppola M, Garonna A, Baldoni L, Scaloni A, Rao R. Molecular interactions between the olive and the fruit fly Bactrocera oleae. BMC PLANT BIOLOGY 2012; 12:86. [PMID: 22694925 PMCID: PMC3733423 DOI: 10.1186/1471-2229-12-86] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Accepted: 05/22/2012] [Indexed: 05/20/2023]
Abstract
BACKGROUND The fruit fly Bactrocera oleae is the primary biotic stressor of cultivated olives, causing direct and indirect damages that significantly reduce both the yield and the quality of olive oil. To study the olive-B. oleae interaction, we conducted transcriptomic and proteomic investigations of the molecular response of the drupe. The identifications of genes and proteins involved in the fruit response were performed using a Suppression Subtractive Hybridisation technique and a combined bi-dimensional electrophoresis/nanoLC-ESI-LIT-MS/MS approach, respectively. RESULTS We identified 196 ESTs and 26 protein spots as differentially expressed in olives with larval feeding tunnels. A bioinformatic analysis of the identified non-redundant EST and protein collection indicated that different molecular processes were affected, such as stress response, phytohormone signalling, transcriptional control and primary metabolism, and that a considerable proportion of the ESTs could not be classified. The altered expression of 20 transcripts was also analysed by real-time PCR, and the most striking differences were further confirmed in the fruit of a different olive variety. We also cloned the full-length coding sequences of two genes, Oe-chitinase I and Oe-PR27, and showed that these are wound-inducible genes and activated by B. oleae punctures. CONCLUSIONS This study represents the first report that reveals the molecular players and signalling pathways involved in the interaction between the olive fruit and its most damaging biotic stressor. Drupe response is complex, involving genes and proteins involved in photosynthesis as well as in the production of ROS, the activation of different stress response pathways and the production of compounds involved in direct defence against phytophagous larvae. Among the latter, trypsin inhibitors should play a major role in drupe resistance reaction.
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Affiliation(s)
- Giandomenico Corrado
- Dipartimento di Scienze del Suolo, Pianta, Ambiente e Produzioni Animali, Universita’ degli Studi di Napoli Federico II, Via Università 100, Portici, Napoli, 80055, Italy
| | - Fiammetta Alagna
- Istituto di Genetica Vegetale, Consiglio Nazionale delle Ricerche, Via della Madonna Alta 130, Perugia, 06128, Italy
| | - Mariapina Rocco
- Dipartimento di Scienze per la Biologia, la Geologia e l’Ambiente, Universita’ del Sannio, Via dei Mulini 59/A, Benevento, 82100, Italy
| | - Giovanni Renzone
- Istituto per il Sistema Produzione Animale in Ambiente Mediterraneo, Consiglio Nazionale delle Ricerche, Via Argine 1085, Napoli, 80147, Italy
| | - Paola Varricchio
- Dipartimento di Scienze del Suolo, Pianta, Ambiente e Produzioni Animali, Universita’ degli Studi di Napoli Federico II, Via Università 100, Portici, Napoli, 80055, Italy
| | - Valentina Coppola
- Dipartimento di Scienze del Suolo, Pianta, Ambiente e Produzioni Animali, Universita’ degli Studi di Napoli Federico II, Via Università 100, Portici, Napoli, 80055, Italy
| | - Mariangela Coppola
- Dipartimento di Scienze del Suolo, Pianta, Ambiente e Produzioni Animali, Universita’ degli Studi di Napoli Federico II, Via Università 100, Portici, Napoli, 80055, Italy
| | - Antonio Garonna
- Dipartimento di Entomologia e Zoologia Agraria “F. Silvestri”, Universita’ degli Studi di Napoli Federico II, Via Università 100, Portici, 80055, Italy
| | - Luciana Baldoni
- Istituto di Genetica Vegetale, Consiglio Nazionale delle Ricerche, Via della Madonna Alta 130, Perugia, 06128, Italy
| | - Andrea Scaloni
- Istituto per il Sistema Produzione Animale in Ambiente Mediterraneo, Consiglio Nazionale delle Ricerche, Via Argine 1085, Napoli, 80147, Italy
| | - Rosa Rao
- Dipartimento di Scienze del Suolo, Pianta, Ambiente e Produzioni Animali, Universita’ degli Studi di Napoli Federico II, Via Università 100, Portici, Napoli, 80055, Italy
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A proteomic analysis of storage stress responses in Ipomoea batatas (L.) Lam. tuberous root. Mol Biol Rep 2012; 39:8015-25. [DOI: 10.1007/s11033-012-1648-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Accepted: 04/16/2012] [Indexed: 02/06/2023]
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19
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Neelakandan AK, Wang K. Recent progress in the understanding of tissue culture-induced genome level changes in plants and potential applications. PLANT CELL REPORTS 2012; 31:597-620. [PMID: 22179259 DOI: 10.1007/s00299-011-1202-z] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Revised: 11/30/2011] [Accepted: 12/01/2011] [Indexed: 05/23/2023]
Abstract
In vitro cell and tissue-based systems have tremendous potential in fundamental research and for commercial applications such as clonal propagation, genetic engineering and production of valuable metabolites. Since the invention of plant cell and tissue culture techniques more than half a century ago, scientists have been trying to understand the morphological, physiological, biochemical and molecular changes associated with tissue culture responses. Establishment of de novo developmental cell fate in vitro is governed by factors such as genetic make-up, stress and plant growth regulators. In vitro culture is believed to destabilize the genetic and epigenetic program of intact plant tissue and can lead to chromosomal and DNA sequence variations, methylation changes, transposon activation, and generation of somaclonal variants. In this review, we discuss the current status of understanding the genomic and epigenomic changes that take place under in vitro conditions. It is hoped that a precise and comprehensive knowledge of the molecular basis of these variations and acquisition of developmental cell fate would help to devise strategies to improve the totipotency and embryogenic capability in recalcitrant species and genotypes, and to address bottlenecks associated with clonal propagation.
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20
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Li X, Bai H, Wang X, Li L, Cao Y, Wei J, Liu Y, Liu L, Gong X, Wu L, Liu S, Liu G. Identification and validation of rice reference proteins for western blotting. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:4763-72. [PMID: 21705388 PMCID: PMC3192993 DOI: 10.1093/jxb/err084] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Studies of rice protein expression have increased considerably with the development of rice functional genomics. In order to obtain reliable expression results in western blotting, information on appropriate reference proteins is necessary for data normalization. To date, no published study has identified and systematically validated reference proteins suitable for the investigation of rice protein expression. In this study, nine candidate proteins were selected and their specific antibodies were obtained through immunization of rabbits with either recombinant proteins expressed in Escherichia coli or synthesized peptides. Western blotting was carried out to detect the expression of target proteins in a set of 10 rice samples representing different rice tissues/organs at different developmental stages. The expression stability of the proteins was analysed using geNorm and Microcal Origin 6.0 software. The results indicated that heat shock protein (HSP) and elongation factor 1-α (eEF-1α) were the most constantly expressed among all rice proteins tested throughout all developmental stages, while the proteins encoded by conventional internal reference genes fluctuated in amount. Comparison among the profiling of translation and transcription [expressed sequence tags (EST) and massively parallel signature sequencing (MPSS)] revealed that a correlation existed. Based on the standard curves derived from the antigen-antibody reaction, the concentrations of HSP and eEF-1α proteins in rice leaves were ∼0.12%. Under the present experimental conditions, the lower limits of detection for HSP and eEF-1α proteins in rice were 0.24 ng and 0.06 ng, respectively. In conclusion, the reference proteins selected in this study, and the corresponding antibodies, can be used in qualitative and quantitative analysis of rice proteins.
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Affiliation(s)
- Xiaoming Li
- College of Life Sciences, Agricultural University of Hebei, Baoding, 071001, China
| | - Hui Bai
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 101318, China
| | - Xianyun Wang
- College of Life Sciences, Agricultural University of Hebei, Baoding, 071001, China
| | - Liyun Li
- College of Life Sciences, Agricultural University of Hebei, Baoding, 071001, China
| | - Yinghao Cao
- College of Life Sciences, Agricultural University of Hebei, Baoding, 071001, China
| | - Jian Wei
- College of Life Sciences, Agricultural University of Hebei, Baoding, 071001, China
| | - Yumeng Liu
- College of Life Sciences, Agricultural University of Hebei, Baoding, 071001, China
| | - Lijuan Liu
- College of Life Sciences, Agricultural University of Hebei, Baoding, 071001, China
| | - Xiaodong Gong
- College of Life Sciences, Agricultural University of Hebei, Baoding, 071001, China
| | - Lin Wu
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 101318, China
| | - Siqi Liu
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 101318, China
| | - Guozhen Liu
- College of Life Sciences, Agricultural University of Hebei, Baoding, 071001, China
- To whom correspondence should be addressed. E-mail:
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Shi Q, Zhang BY, Gao C, Han J, Wang GR, Chen C, Tian C, Dong XP. The diversities of PrP(Sc) distributions and pathologic changes in various brain regions from a Chinese patient with G114V genetic CJD. Neuropathology 2011; 32:51-9. [PMID: 21732990 DOI: 10.1111/j.1440-1789.2011.01237.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human genetic Creutzfeldt-Jakob disease (gCJD; one of the prion diseases) is caused by point mutations and insertions in the prion protein gene (PRNP). Previously we have reported a Chinese gCJD case with a substitution of valine (V) for glycine (G) at codon 114. To investigate the detailed pathogenic and pathologic characteristics of G114V gCJD, 10 different brain regions were thoroughly analyzed. PrP-specific Western blots and immunohistochemical (IHC) assays identified larger amounts of PrP(Sc) in the regions of brain cortex. Assays of the transcriptions of PrP-specific mRNA by RT-PCR and real-time PCR showed comparable levels in 10 brain regions. In line with the distribution of PrP(Sc) , typical vacuolations in brains, markedly in four cortex regions, were detected. Contrast to the distributing features of spongiform and of PrP(Sc) , massive gliosis was detected in all brain regions by GFAP-specific IHC tests. Moreover, two-dimensional gel immunoblots found three major sets of PrP(Sc) spots, indicating that PrP(Sc) in brain tissues was a mixture of molecules with different biochemical properties. The data here provide the pathogenic and neuropathological features of G114V gCJD.
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Affiliation(s)
- Qi Shi
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China
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Fan W, Cui W, Li X, Chen S, Liu G, Shen S. Proteomics analysis of rice seedling responses to ovine saliva. JOURNAL OF PLANT PHYSIOLOGY 2011; 168:500-509. [PMID: 20950890 DOI: 10.1016/j.jplph.2010.08.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Revised: 07/29/2010] [Accepted: 08/03/2010] [Indexed: 05/30/2023]
Abstract
Grazing is accompanied by a multitude of processes including wounding, saliva deposition, and defoliation. Previous studies have focused on the effects of the grazing or clipping intensity on plant regrowth, survival, and composition in the grassland. However, the impact of saliva deposition on plants is poorly understood. In this study, rice was used as a model plant to study the differentially expressed proteins after ovine saliva treatment. The shoots of 2-week-old seedlings were crosscut and the lower parts were daubed with ovine saliva at the cut surface. After 2, 6, 12 and 24h, proteomics analysis was performed using proteins extracted from the saliva-treated shoots. The results showed that proteins involved in multiple pathways were differentially expressed in response to ovine saliva, including catalase (CAT), peroxiredoxin (Prx), ATP synthase, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). Moreover, real-time quantitative reverse-transcription-PCR (RT-PCR) data showed that most of the genes were also regulated at the transcript level. Our results indicate the ovine saliva induces an early response in the rice seedling by stress-related pathways. This study provides information about the response of rice seedlings to ovine saliva at the protein level.
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Affiliation(s)
- Weihong Fan
- Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, PR China
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Valledor L, Jorrín JV, Rodríguez JL, Lenz C, Meijón M, Rodríguez R, Cañal MJ. Combined proteomic and transcriptomic analysis identifies differentially expressed pathways associated to Pinus radiata needle maturation. J Proteome Res 2010; 9:3954-79. [PMID: 20509709 DOI: 10.1021/pr1001669] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Needle differentiation is a very complex process that leads to the formation of a mature photosynthetic organ from pluripotent needle primordia. The proteome and transcriptome of immature and fully developed needles of Pinus radiata D. Don were compared to described changes in mRNA and protein species that characterize the needle maturation developmental process. A total of 856 protein spots were analyzed, defining a total of 280 spots as differential between developmental stages, from which 127 were confidently identified. A suppressive subtractive library (2048 clones, 274 non redundant contigs) was built, and 176 genes showed to be differentially expressed. The Joint data analysis of proteomic and transcriptomic results provided a broad overview of differentially expressed pathways associated with needle maturation and stress-related pathways. Proteins and genes related to energy metabolism pathways, photosynthesis, and oxidative phosphorylation were overexpressed in mature needles. Amino acid metabolism, transcription, and translation pathways were overexpressed in immature needles. Interestingly, stress related proteins were characteristic of immature tissues, a fact that may be linked to defense mechanisms and the higher growth rate and morphogenetic competence exhibited by these needles. Thus, this work provides an overview of the molecular changes affecting proteomes and transcriptomes during P. radiata needle maturation, having an integrative vision of the functioning and physiology of this process.
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Affiliation(s)
- Luis Valledor
- EPIPHYSAGE Research Group, Area de Fisiología Vegetal, Departamento B.O.S., Instituto Universitario de Biotecnología de Asturias (IUBA), Universidad de Oviedo, Oviedo, Spain.
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Palama TL, Menard P, Fock I, Choi YH, Bourdon E, Govinden-Soulange J, Bahut M, Payet B, Verpoorte R, Kodja H. Shoot differentiation from protocorm callus cultures of Vanilla planifolia (Orchidaceae): proteomic and metabolic responses at early stage. BMC PLANT BIOLOGY 2010; 10:82. [PMID: 20444255 PMCID: PMC3095354 DOI: 10.1186/1471-2229-10-82] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Accepted: 05/05/2010] [Indexed: 05/05/2023]
Abstract
BACKGROUND Vanilla planifolia is an important Orchid commercially cultivated for the production of natural vanilla flavour. Vanilla plants are conventionally propagated by stem cuttings and thus causing injury to the mother plants. Regeneration and in vitro mass multiplication are proposed as an alternative to minimize damage to mother plants. Because mass production of V. planifolia through indirect shoot differentiation from callus culture is rare and may be a successful use of in vitro techniques for producing somaclonal variants, we have established a novel protocol for the regeneration of vanilla plants and investigated the initial biochemical and molecular mechanisms that trigger shoot organogenesis from embryogenic/organogenic callus. RESULTS For embryogenic callus induction, seeds obtained from 7-month-old green pods of V. planifolia were inoculated on MS basal medium (BM) containing TDZ (0.5 mg l(-1)). Germination of unorganized mass callus such as protocorm -like structure (PLS) arising from each seed has been observed. The primary embryogenic calli have been formed after transferring on BM containing IAA (0.5 mg l(-1)) and TDZ (0.5 mg l(-1)). These calli were maintained by subculturing on BM containing IAA (0.5 mg l(-1)) and TDZ (0.3 mg l(-1)) during 6 months and formed embryogenic/organogenic calli. Histological analysis showed that shoot organogenesis was induced between 15 and 20 days after embryogenic/organogenic calli were transferred onto MS basal medium with NAA (0.5 mg l(-1)). By associating proteomics and metabolomics analyses, the biochemical and molecular markers responsible for shoot induction have been studied in 15-day-old calli at the stage where no differentiating part was visible on organogenic calli. Two-dimensional electrophoresis followed by matrix-assisted laser desorption ionization time-of-flight-tandem mass spectrometry (MALDI-TOF-TOF-MS) analysis revealed that 15 protein spots are significantly expressed (P < 0.05) at earlier stages of shoot differentiation. The majority of these proteins are involved in amino acid-protein metabolism and photosynthetic activity. In accordance with proteomic analysis, metabolic profiling using 1D and 2D NMR techniques showed the importance of numerous compounds related with sugar mobilization and nitrogen metabolism. NMR analysis techniques also allowed the identification of some secondary metabolites such as phenolic compounds whose accumulation was enhanced during shoot differentiation. CONCLUSION The subculture of embryogenic/organogenic calli onto shoot differentiation medium triggers the stimulation of cell metabolism principally at three levels namely (i) initiation of photosynthesis, glycolysis and phenolic compounds synthesis; (ii) amino acid-protein synthesis, and protein stabilization; (iii) sugar degradation. These biochemical mechanisms associated with the initiation of shoot formation during protocorm-like body (PLB) organogenesis could be coordinated by the removal of TDZ in callus maintenance medium. These results might contribute to elucidate the complex mechanism that leads to vanilla callus differentiation and subsequent shoot formation into PLB organogenesis. Moreover, our results highlight an early intermediate metabolic event in vanillin biosynthetic pathway with respect to secondary metabolism. Indeed, for the first time in vanilla tissue culture, phenolic compounds such as glucoside A and glucoside B were identified. The degradation of these compounds in specialized tissue (i.e. young green beans) probably contributes to the biosynthesis of glucovanillin, the parent compound of vanillin.
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Affiliation(s)
- Tony L Palama
- UMR "Peuplement végétaux et Bioagresseurs en Milieu Tropical" Faculté des Sciences et Technologies, Université de La Réunion, 15 Avenue René Cassin, Saint-Denis, La Réunion, France
- Division of Pharmacognosy, Section Metabolomics, Institute Biology, Leiden University, Leiden, The Netherlands
| | - Patrice Menard
- UMR "Peuplement végétaux et Bioagresseurs en Milieu Tropical" Faculté des Sciences et Technologies, Université de La Réunion, 15 Avenue René Cassin, Saint-Denis, La Réunion, France
| | - Isabelle Fock
- UMR "Peuplement végétaux et Bioagresseurs en Milieu Tropical" Faculté des Sciences et Technologies, Université de La Réunion, 15 Avenue René Cassin, Saint-Denis, La Réunion, France
| | - Young H Choi
- Division of Pharmacognosy, Section Metabolomics, Institute Biology, Leiden University, Leiden, The Netherlands
| | - Emmanuel Bourdon
- Laboratoire de Biochimie et Génétique Moléculaire, Faculté des Sciences et Technologies, Université de La Réunion, 15 Avenue René Cassin, Saint-Denis, La Réunion
| | - Joyce Govinden-Soulange
- UMR "Peuplement végétaux et Bioagresseurs en Milieu Tropical" Faculté des Sciences et Technologies, Université de La Réunion, 15 Avenue René Cassin, Saint-Denis, La Réunion, France
- Faculty of Agriculture, University of Mauritius, Réduit, Mauritius
| | - Muriel Bahut
- Plate Forme de Biotechnologies moléculaires, Faculté des Sciences, Université d'Angers, 22, rue Roger Amsler, 49100 Angers, France
| | - Bertrand Payet
- Laboratoire de Chimie des Substances Naturelles et des Sciences des Aliments, Faculté des Sciences et Technologies, Université de La Réunion, 15 Avenue René Cassin, Saint-Denis, La Réunion, France
| | - Robert Verpoorte
- Division of Pharmacognosy, Section Metabolomics, Institute Biology, Leiden University, Leiden, The Netherlands
| | - Hippolyte Kodja
- UMR "Peuplement végétaux et Bioagresseurs en Milieu Tropical" Faculté des Sciences et Technologies, Université de La Réunion, 15 Avenue René Cassin, Saint-Denis, La Réunion, France
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Agrawal GK, Jwa NS, Rakwal R. Rice proteomics: ending phase I and the beginning of phase II. Proteomics 2009; 9:935-63. [PMID: 19212951 DOI: 10.1002/pmic.200800594] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Rice is a critically important food crop plant on our planet. It is also an excellent model plant for cereal crops, and now in position to serve as a reference plant for biofuel production. Proteomics study of rice therefore is crucial to better understand "rice" as a whole. Rice proteomics has moved well beyond the initial proteome analysis in the early to late 1990s. Since the year 2000, numerous proteomic studies have been performed in rice during growth and development and against a wide variety of environmental factors. These proteomic investigations have established the high-resolution 2-D reference gels of rice tissues, organs, and organelle under normal and adverse (stressed) conditions by optimizing suitable, reproducible systems for gel, and MS-based proteomic techniques, which "rejuvenated" the rice proteome field. This constituted the "phase I" in rice proteomics, and resulted in rice being labeled as the "cornerstone" of cereal food crop proteomes. Now, we are in position to state that rice proteomics today marks the "beginning of phase II". This is due to the fact that rice researchers are capable of digging deeper into the rice proteome, mapping PTMs (in particular reversible protein phosphorylation), performing inter- and intra-species comparisons, integrating proteomics data with other "omic" technologies-generated data, and probing the functional aspect of individual proteins. These advancements and their impact on the future of rice proteomics are the focus of this review.
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Jorrín-Novo JV, Maldonado AM, Echevarría-Zomeño S, Valledor L, Castillejo MA, Curto M, Valero J, Sghaier B, Donoso G, Redondo I. Plant proteomics update (2007–2008): Second-generation proteomic techniques, an appropriate experimental design, and data analysis to fulfill MIAPE standards, increase plant proteome coverage and expand biological knowledge. J Proteomics 2009; 72:285-314. [DOI: 10.1016/j.jprot.2009.01.026] [Citation(s) in RCA: 174] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Bousette N, Kislinger T, Fong V, Isserlin R, Hewel JA, Emili A, Gramolini AO. Large-Scale Characterization and Analysis of the Murine Cardiac Proteome. J Proteome Res 2009; 8:1887-901. [DOI: 10.1021/pr800845a] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nicolas Bousette
- Department of Physiology, University of Toronto, Heart and Stroke/Richard Lewar Centre of Cardiovascular Excellence, Department of Medical Biophysics, University of Toronto, and University Health Network, Toronto, Ontario, Canada, Banting and Best Department of Medical Research, and Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, M5G 1L6, Canada
| | - Thomas Kislinger
- Department of Physiology, University of Toronto, Heart and Stroke/Richard Lewar Centre of Cardiovascular Excellence, Department of Medical Biophysics, University of Toronto, and University Health Network, Toronto, Ontario, Canada, Banting and Best Department of Medical Research, and Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, M5G 1L6, Canada
| | - Vincent Fong
- Department of Physiology, University of Toronto, Heart and Stroke/Richard Lewar Centre of Cardiovascular Excellence, Department of Medical Biophysics, University of Toronto, and University Health Network, Toronto, Ontario, Canada, Banting and Best Department of Medical Research, and Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, M5G 1L6, Canada
| | - Ruth Isserlin
- Department of Physiology, University of Toronto, Heart and Stroke/Richard Lewar Centre of Cardiovascular Excellence, Department of Medical Biophysics, University of Toronto, and University Health Network, Toronto, Ontario, Canada, Banting and Best Department of Medical Research, and Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, M5G 1L6, Canada
| | - Johannes A. Hewel
- Department of Physiology, University of Toronto, Heart and Stroke/Richard Lewar Centre of Cardiovascular Excellence, Department of Medical Biophysics, University of Toronto, and University Health Network, Toronto, Ontario, Canada, Banting and Best Department of Medical Research, and Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, M5G 1L6, Canada
| | - Andrew Emili
- Department of Physiology, University of Toronto, Heart and Stroke/Richard Lewar Centre of Cardiovascular Excellence, Department of Medical Biophysics, University of Toronto, and University Health Network, Toronto, Ontario, Canada, Banting and Best Department of Medical Research, and Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, M5G 1L6, Canada
| | - Anthony O. Gramolini
- Department of Physiology, University of Toronto, Heart and Stroke/Richard Lewar Centre of Cardiovascular Excellence, Department of Medical Biophysics, University of Toronto, and University Health Network, Toronto, Ontario, Canada, Banting and Best Department of Medical Research, and Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, M5G 1L6, Canada
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Yin L, Lan Y, Zhu L. Analysis of the protein expression profiling during rice callus differentiation under different plant hormone conditions. PLANT MOLECULAR BIOLOGY 2008; 68:597-617. [PMID: 18815891 DOI: 10.1007/s11103-008-9395-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2008] [Accepted: 08/27/2008] [Indexed: 05/21/2023]
Abstract
Plant hormones function to coordinate plant growth and development. While the plant hormones, mainly auxin and cytokinin, are exogenously added to various plant tissue cultures, their effects on the organogenesis are apparent, but little is known concerning the molecular mechanisms by which they function in cultured cells. Rice, as a model plant in monocots, is also suitable to tissue culture studies. Here, we used four types of regeneration mediums with different relative concentrations of cytokinin and auxin for rice callus differentiation, the calli at different differentiation stages were collected for proteomic analysis. 2-dimensional electrophoresis revealed that 213 protein spots significantly differentially expressed during callus differentiation under different hormone conditions. By using mass spectrometry, 183 differentially expressed protein spots were identified to match 157 unique proteins. Most of these differential proteins were cellular/metabolic process-related proteins, whose different expression patterns may be correlated with the cytokinin and auxin regulation. Several hormone-related proteins were prominently featured in differentiated calli as compared with the initiated calli, such as alpha-amylase isoforms, mannose-binding rice lectin, putative dehydration stress-induced protein, cysteine endopeptidase and cystatin. All these results provide a novel insight into how the two plant hormones effect the callus differentiation in rice on the proteomic level.
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Affiliation(s)
- Lan Yin
- National Plant Gene Research Centre, Chinese Academy of Sciences, Beijing, 100101, China
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Yi Z, Bowen BP, Hwang H, Jenkinson CP, Coletta DK, Lefort N, Bajaj M, Kashyap S, Berria R, De Filippis EA, Mandarino LJ. Global relationship between the proteome and transcriptome of human skeletal muscle. J Proteome Res 2008; 7:3230-41. [PMID: 18613714 DOI: 10.1021/pr800064s] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Skeletal muscle is one of the largest tissues in the human body. Changes in mRNA and protein abundance in this tissue are central to a large number of metabolic and other disorders, including, commonly, insulin resistance. Proteomic and microarray analyses are important approaches for gaining insight into the molecular and biochemical basis for normal and pathophysiological conditions. With the use of vastus lateralis muscle obtained from two groups of healthy, nonobese subjects, we performed a detailed comparison of the muscle proteome, obtained by HPLC-ESI-MS/MS, with the muscle transcriptome, obtained using oligonucleotide microarrays. HPLC-ESI-MS/MS analysis identified 507 unique proteins as present in four out of six subjects, while 5193 distinct transcripts were called present by oligonucleotide microarrays from four out of six subjects. The majority of the proteins identified by mass spectrometry also had their corresponding transcripts detected by microarray analysis, although 73 proteins were only identified in the proteomic analysis. Reflecting the high abundance of mitochondria in skeletal muscle, 30% of proteins detected were attributed to the mitochondrion, as compared to only 9% of transcripts. On the basis of Gene Ontology annotations, proteins assigned to mitochondrial inner membrane, mitochondrial envelope, structural molecule activity, electron transport, as well as generation of precursor metabolites and energy, had more corresponding transcripts detected than would be expected by chance. On the contrary, proteins assigned to Golgi apparatus, extracellular region, lyase activity, kinase activity, and protein modification process had fewer corresponding transcripts detected than would be expected by chance. In conclusion, these results provide the first global comparison of the human skeletal muscle proteome and transcriptome to date. These data show that a combination of proteomic and transcriptic analyses will provide data that can be used to test hypotheses regarding the pathogenesis of muscle disorders as well as to generate observational data that can be used to form novel hypotheses.
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Affiliation(s)
- Zhengping Yi
- Center for Metabolic Biology, Arizona State University, Tempe, AZ 85287, USA
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Ritz MF, Ratajczak P, Curin Y, Cam E, Mendelowitsch A, Pinet F, Andriantsitohaina R. Chronic treatment with red wine polyphenol compounds mediates neuroprotection in a rat model of ischemic cerebral stroke. J Nutr 2008; 138:519-25. [PMID: 18287360 DOI: 10.1093/jn/138.3.519] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
In this study, we investigated the in vivo effects of red wine polyphenol compounds (RWPC) in rats that were submitted to middle cerebral occlusion as an experimental model of stroke. Male Wistar rats were given RWPC [30 mg/(kg x d) dissolved in drinking water] or water for 1 wk before being subjected to transient middle cerebral artery occlusion followed by reperfusion. Sham-operated rats were subjected to transient occlusion in which the filament was not completely introduced. The release of amino acids and energy metabolites were monitored by intracerebral microdialysis. The volume of the ischemic lesion was assessed 24 h after reperfusion. Proteomic analysis of brain tissue was performed to study the effects of ischemia and RWPC on specific protein expression. Treatment with RWPC completely prevented the burst of excitatory amino acids that occurred in response to ischemia in untreated rats and significantly reduced brain infarct volumes. Rats chronically treated with RWPC, however, had lower basal concentrations of energy metabolites, including glucose and lactate in the brain parenchyma, compared with untreated rats. Chronic RWPC treatment significantly enhanced the residual cerebral blood flow during occlusion and reperfusion in rats subjected to transient occlusion compared with untreated rats. This effect resulted from arterial vasodilatation, as the internal diameters of several arteries were significantly enlarged after RWPC treatment. Proteomic studies revealed the modulation by RWPC of the expression of proteins involved in the maintenance of neuronal caliber and axon formation, in the protection against oxidative stress, and in energy metabolism. These findings provide an experimental basis for the beneficial effects of RWPC on the neurovascular unit during stroke.
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Affiliation(s)
- Marie-Françoise Ritz
- Neurosurgery Laboratory, Department of Research, University Hospital, Basel 4056, Switzerland
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Qi SW, Chaudhry MT, Zhang Y, Meng B, Huang Y, Zhao KX, Poetsch A, Jiang CY, Liu S, Liu SJ. Comparative proteomes of Corynebacterium glutamicum grown on aromatic compounds revealed novel proteins involved in aromatic degradation and a clear link between aromatic catabolism and gluconeogenesis via fructose-1,6-bisphosphatase. Proteomics 2007; 7:3775-87. [PMID: 17880007 DOI: 10.1002/pmic.200700481] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The current study examined the aromatic degradation and central metabolism in Corynebacterium glutamicum by proteomic and molecular methods. Comparative analysis of proteomes from cells grown on gentisate and on glucose revealed that 30% of the proteins of which their abundance changed were involved in aromatic degradation and central carbon metabolism. Similar results were obtained from cells grown on benzoate, 4-cresol, phenol, and resorcinol. Results from these experiments revealed that (i) enzymes involved in degradation of benzoate, 4-cresol, gentisate, phenol, and resorcinol were specifically synthesized and (ii) that the abundance of enzymes involved in central carbon metabolism of glycolysis/gluconeogenesis, pentose phosphate pathway, and TCA cycles were significantly changed on various aromatic compounds. Significantly, three novel proteins, NCgl0524, NCgl0525, and NCgl0527, were identified on 4-cresol. The genes encoding NCgl0525 and NCgl0527 were confirmed to be necessary for assimilation of 4-cresol with C. glutamicum. The abundance of fructose-1,6-bisphosphatase (Fbp) was universally increased on all the tested aromatic compounds. This Fbp gene was disrupted and the mutant WT(Deltafbp) lost the ability to grow on aromatic compounds. Genetic complementation by the Fbp gene restored this ability. We concluded that gluconeogenesis is a necessary process for C. glutamicum growing on various aromatic compounds.
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Affiliation(s)
- Su-Wei Qi
- State Key Laboratory of Microbial Resource, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
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