1
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Fedoreyeva LI, Baranova EN, Chaban IA, Dilovarova TA, Vanyushin BF, Kononenko NV. Elongating Effect of the Peptide AEDL on the Root of Nicotiana tabacum under Salinity. PLANTS 2022; 11:plants11101352. [PMID: 35631778 PMCID: PMC9147445 DOI: 10.3390/plants11101352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 11/18/2022]
Abstract
The overall survival of a plant depends on the development, growth, and functioning of the roots. Root development and growth are not only genetically programmed but are constantly influenced by environmental factors, with the roots adapting to such changes. The peptide AEDL (alanine–glutamine acid–asparagine acid–leucine) at a concentration of 10−7 M had an elongating effect on the root cells of Nicotiana tabacum seedlings. The action of this peptide at such a low concentration is similar to that of peptide phytohormones. In the presence of 150 mM NaCl, a strong distortion in the development and architecture of the tobacco roots was observed. However, the combined presence of AEDL and NaCl resulted in normal root development. In the presence of AEDL, reactive oxygen species (ROS) were detected in the elongation and root hair zones of the roots. The ROS marker fluorescence intensity in plant cells grown with AEDL was much lower than that of plant cells grown without the peptide. Thus, AEDL protected the root tissue from damage by oxidative stress caused by the toxic effects of NaCl. Localization and accumulation of AEDL at the root were tissue-specific. Fluorescence microscopy showed that FITC-AEDL predominantly localized in the zones of elongation and root hairs, with insignificant localization in the meristem zone. AEDL induced a change in the structural organization of chromatin. Structural changes in chromatin caused significant changes in the expression of numerous genes associated with the development and differentiation of the root system. In the roots of tobacco seedlings grown in the presence of AEDL, the expression of WOX family genes decreased, and differentiation of stem cells increased, which led to root elongation. However, in the presence of NaCl, elongation of the tobacco root occurred via a different mechanism involving genes of the expansin family that weaken the cell wall in the elongation zone. Root elongation of plants is of fundamental importance in biology and is especially relevant to crop production as it can affect crop yields.
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Affiliation(s)
- Larisa I. Fedoreyeva
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya 42, 127550 Moscow, Russia; (E.N.B.); (I.A.C.); (T.A.D.); (B.F.V.); (N.V.K.)
- Correspondence:
| | - Ekaterina N. Baranova
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya 42, 127550 Moscow, Russia; (E.N.B.); (I.A.C.); (T.A.D.); (B.F.V.); (N.V.K.)
- N.V. Tsitsin Main Botanical Garden of Russian Academy of Sciences, Botanicheskaya 4, 127276 Moscow, Russia
| | - Inn A. Chaban
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya 42, 127550 Moscow, Russia; (E.N.B.); (I.A.C.); (T.A.D.); (B.F.V.); (N.V.K.)
| | - Tatyana A. Dilovarova
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya 42, 127550 Moscow, Russia; (E.N.B.); (I.A.C.); (T.A.D.); (B.F.V.); (N.V.K.)
| | - Boris F. Vanyushin
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya 42, 127550 Moscow, Russia; (E.N.B.); (I.A.C.); (T.A.D.); (B.F.V.); (N.V.K.)
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
| | - Neonila V. Kononenko
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya 42, 127550 Moscow, Russia; (E.N.B.); (I.A.C.); (T.A.D.); (B.F.V.); (N.V.K.)
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Moisseyev G, Park K, Cui A, Freitas D, Rajagopal D, Konda AR, Martin-Olenski M, Mcham M, Liu K, Du Q, Schnable JC, Moriyama EN, Cahoon EB, Zhang C. RGPDB: database of root-associated genes and promoters in maize, soybean, and sorghum. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2020:5851117. [PMID: 32500918 PMCID: PMC7273057 DOI: 10.1093/database/baaa038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 03/02/2020] [Accepted: 05/06/2020] [Indexed: 12/21/2022]
Abstract
Root-associated genes play an important role in plants. Despite the fact that there have been studies on root biology, information on genes that are specifically expressed or upregulated in roots is poorly collected. There exist very few databases dedicated to genes and promoters associated with root biology, preventing effective root-related studies. Therefore, we analyzed multiple types of omics data to identify root-associated genes in maize, soybean, and sorghum and constructed a comprehensive online database of these genes and their promoter sequences. This database creates a pivotal platform capable of stimulating and facilitating further studies on manipulating root growth and development.
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Affiliation(s)
- Gleb Moisseyev
- Young Nebraska Scientists Program, University of Nebraska (EPSCoR), Lincoln, NE 68588, USA
| | - Kiyoul Park
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588 USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
| | - Alix Cui
- Young Nebraska Scientists Program, University of Nebraska (EPSCoR), Lincoln, NE 68588, USA
| | - Daniel Freitas
- Young Nebraska Scientists Program, University of Nebraska (EPSCoR), Lincoln, NE 68588, USA
| | - Divith Rajagopal
- Young Nebraska Scientists Program, University of Nebraska (EPSCoR), Lincoln, NE 68588, USA
| | - Anji Reddy Konda
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588 USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
| | | | - Mackenzie Mcham
- Young Nebraska Scientists Program, University of Nebraska (EPSCoR), Lincoln, NE 68588, USA
| | - Kan Liu
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588 USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
| | - Qian Du
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588 USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
| | - James C Schnable
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583 USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
| | - Etsuko N Moriyama
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588 USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
| | - Edgar B Cahoon
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588 USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
| | - Chi Zhang
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588 USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
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3
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Qu CP, Xu ZR, Hu YB, Lu Y, Yang CJ, Sun GY, Liu GJ. RNA-SEQ Reveals Transcriptional Level Changes of Poplar Roots in Different Forms of Nitrogen Treatments. FRONTIERS IN PLANT SCIENCE 2016; 7:51. [PMID: 26870068 PMCID: PMC4735414 DOI: 10.3389/fpls.2016.00051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 01/13/2016] [Indexed: 05/07/2023]
Abstract
Poplar has emerged as a model plant for better understanding cellular and molecular changes accompanying tree growth, development, and response to environment. Long-term application of different forms of nitrogen (such as [Formula: see text]-N and [Formula: see text]-N) may cause morphological changes of poplar roots; however, the molecular level changes are still not well-known. In this study, we analyzed the expression profiling of poplar roots treated by three forms of nitrogen: S1 ([Formula: see text]), S2 (NH4NO3), and S3 ([Formula: see text]) by using RNA-SEQ technique. We found 463 genes significantly differentially expressed in roots by different N treatments, of which a total of 112 genes were found to differentially express between S1 and S2, 171 genes between S2 and S3, and 319 genes between S1 and S3. A cluster analysis shows significant difference in many transcription factor families and functional genes family under different N forms. Through an analysis of Mapman metabolic pathway, we found that the significantly differentially expressed genes are associated with fermentation, glycolysis, and tricarboxylic acid cycle (TCA), secondary metabolism, hormone metabolism, and transport processing. Interestingly, we did not find significantly differentially expressed genes in N metabolism pathway, mitochondrial electron transport/ATP synthesis and mineral nutrition. We also found abundant candidate genes (20 transcription factors and 30 functional genes) regulating morphology changes of poplar roots under the three N forms. The results obtained are beneficial to a better understanding of the potential molecular and cellular mechanisms regulating root morphology changes under different N treatments.
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Affiliation(s)
- Chun-Pu Qu
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry UniversityHarbin, China
| | - Zhi-Ru Xu
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry UniversityHarbin, China
- College of Life Science, Northeast Forestry UniversityHarbin, China
| | - Yan-Bo Hu
- College of Life Science, Northeast Forestry UniversityHarbin, China
| | - Yao Lu
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry UniversityHarbin, China
| | - Cheng-Jun Yang
- School of Forestry, Northeast Forestry UniversityHarbin, China
| | - Guang-Yu Sun
- College of Life Science, Northeast Forestry UniversityHarbin, China
| | - Guan-Jun Liu
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry UniversityHarbin, China
- *Correspondence: Guan-Jun Liu
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Vatter T, Neuhäuser B, Stetter M, Ludewig U. Regulation of length and density of Arabidopsis root hairs by ammonium and nitrate. JOURNAL OF PLANT RESEARCH 2015; 128:839-848. [PMID: 26008190 DOI: 10.1007/s10265-015-0733-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 04/25/2015] [Indexed: 06/04/2023]
Abstract
Root hairs expand the effective root surface to increase the uptake of nutrients and water from the soil. Here the local effects of the two major nitrogen sources, ammonium and nitrate, on root hairs were investigated using split plates. In three contrasting accessions of A. thaliana, namely Col-0, Tsu-0 and Sha, root hairs were differentially affected by the nitrogen forms and their concentration. Root hairs in Sha were short in the absence of nitrate. In Col-0, hair length was moderately decreased with increasing nitrate or ammonium. In all accessions, the root hair density was insensitive to 1,000-fold changes in the ammonium concentrations, when supplied locally as the exclusive nitrogen form. In contrast, the root hair density generally increased with nitrate as the exclusive local nitrogen source. The nitrate sensitivity was reduced at mM concentrations in a loss-of-function mutant of the nitrate transporter and sensor gene NRT1;1 (NPF6.3). Little differences with respect to ammonium were found in a mutant lacking four high affinity AMT-type ammonium transporters, but interestingly, the response to high nitrate was reduced and may indicate a general defect in nitrogen signaling in that mutant. Genetic diversity and the presence of the nitrogen transceptor NRT1;1 explain heterogeneity in the responses of root hairs to different nitrogen forms in Arabidopsis accessions.
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Affiliation(s)
- Thomas Vatter
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Fruwirthstr. 20, 70593, Stuttgart, Germany
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5
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Ibarra-Laclette E, Méndez-Bravo A, Pérez-Torres CA, Albert VA, Mockaitis K, Kilaru A, López-Gómez R, Cervantes-Luevano JI, Herrera-Estrella L. Deep sequencing of the Mexican avocado transcriptome, an ancient angiosperm with a high content of fatty acids. BMC Genomics 2015; 16:599. [PMID: 26268848 PMCID: PMC4533766 DOI: 10.1186/s12864-015-1775-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 07/14/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Avocado (Persea americana) is an economically important tropical fruit considered to be a good source of fatty acids. Despite its importance, the molecular and cellular characterization of biochemical and developmental processes in avocado is limited due to the lack of transcriptome and genomic information. RESULTS The transcriptomes of seeds, roots, stems, leaves, aerial buds and flowers were determined using different sequencing platforms. Additionally, the transcriptomes of three different stages of fruit ripening (pre-climacteric, climacteric and post-climacteric) were also analyzed. The analysis of the RNAseqatlas presented here reveals strong differences in gene expression patterns between different organs, especially between root and flower, but also reveals similarities among the gene expression patterns in other organs, such as stem, leaves and aerial buds (vegetative organs) or seed and fruit (storage organs). Important regulators, functional categories, and differentially expressed genes involved in avocado fruit ripening were identified. Additionally, to demonstrate the utility of the avocado gene expression atlas, we investigated the expression patterns of genes implicated in fatty acid metabolism and fruit ripening. CONCLUSIONS A description of transcriptomic changes occurring during fruit ripening was obtained in Mexican avocado, contributing to a dynamic view of the expression patterns of genes involved in fatty acid biosynthesis and the fruit ripening process.
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Affiliation(s)
- Enrique Ibarra-Laclette
- Laboratorio Nacional de Genómica para la Biodiversidad-Langebio/Unidad de Genómica Avanzada UGA, Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, Mexico.,Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., 91070, Xalapa, Veracruz, Mexico
| | - Alfonso Méndez-Bravo
- Laboratorio Nacional de Genómica para la Biodiversidad-Langebio/Unidad de Genómica Avanzada UGA, Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, Mexico.,Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., 91070, Xalapa, Veracruz, Mexico
| | - Claudia Anahí Pérez-Torres
- Laboratorio Nacional de Genómica para la Biodiversidad-Langebio/Unidad de Genómica Avanzada UGA, Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, Mexico.,Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., 91070, Xalapa, Veracruz, Mexico.,Investigador Cátedra CONACyT en el Instituto de Ecología A.C., Veracruz, Mexico
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA
| | - Keithanne Mockaitis
- Department of Biology and Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, 47405, USA
| | - Aruna Kilaru
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, 37614, USA.,Department of Biomedical Sciences, East Tennessee State University, Johnson City, TN, 37614, USA
| | - Rodolfo López-Gómez
- Instituto de Investigaciones Químico-Biológicas (IIQB), Universidad Michoacana de San Nicolás de Hidalgo, 58030, Morelia, Michoacán, Mexico
| | - Jacob Israel Cervantes-Luevano
- Laboratorio Nacional de Genómica para la Biodiversidad-Langebio/Unidad de Genómica Avanzada UGA, Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, Mexico
| | - Luis Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad-Langebio/Unidad de Genómica Avanzada UGA, Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, Mexico.
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6
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Transcriptome-wide identification of the genes responding to replanting disease in Rehmannia glutinosa L. roots. Mol Biol Rep 2014; 42:881-92. [DOI: 10.1007/s11033-014-3825-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 11/10/2014] [Indexed: 01/22/2023]
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7
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Generation and analysis of expressed sequence tags (ESTs) from halophyte Atriplex canescens to explore salt-responsive related genes. Int J Mol Sci 2014; 15:11172-89. [PMID: 24960361 PMCID: PMC4100206 DOI: 10.3390/ijms150611172] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 06/11/2014] [Accepted: 06/12/2014] [Indexed: 11/24/2022] Open
Abstract
Little information is available on gene expression profiling of halophyte A. canescens. To elucidate the molecular mechanism for stress tolerance in A. canescens, a full-length complementary DNA library was generated from A. canescens exposed to 400 mM NaCl, and provided 343 high-quality ESTs. In an evaluation of 343 valid EST sequences in the cDNA library, 197 unigenes were assembled, among which 190 unigenes (83.1% ESTs) were identified according to their significant similarities with proteins of known functions. All the 343 EST sequences have been deposited in the dbEST GenBank under accession numbers JZ535802 to JZ536144. According to Arabidopsis MIPS functional category and GO classifications, we identified 193 unigenes of the 311 annotations EST, representing 72 non-redundant unigenes sharing similarities with genes related to the defense response. The sets of ESTs obtained provide a rich genetic resource and 17 up-regulated genes related to salt stress resistance were identified by qRT-PCR. Six of these genes may contribute crucially to earlier and later stage salt stress resistance. Additionally, among the 343 unigenes sequences, 22 simple sequence repeats (SSRs) were also identified contributing to the study of A. canescens resources.
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Li R, Han Y, Lv P, Du R, Liu G. Molecular mapping of the brace root traits in sorghum (Sorghum bicolor L. Moench). BREEDING SCIENCE 2014; 64:193-8. [PMID: 24987306 PMCID: PMC4065327 DOI: 10.1270/jsbbs.64.193] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 02/16/2014] [Indexed: 05/23/2023]
Abstract
The presence and morphology of plant brace roots are important root architecture traits. Brace roots contribute significantly to effective anchorage and water and nutrient uptake during late growth and development, and more importantly, have a substantial influence on grain yield under soil flooding or water limited conditions. However, little is known about the genetic mechanisms that underlie brace root traits. In this study, quantitative trait loci (QTLs) for presence of brace roots from the sorghum landrace "Sansui" were mapped and associated molecular markers were identified. A linkage map was constructed with 109 assigned simple sequence repeat markers using a F2 mapping population derived from the cross Sansui/Jiliang 2. Two QTLs associated with presence of brace roots were localized on chromosomes 6 and 7. The major QTL on chromosome 7 between markers Dsenhsbm7 and Xcup 70 explained about 52.5% of the phenotypic variation, and the minor QTL on chromosome 6 was flanked by Xtxp127 and Xtxp6 and accounted for 7.0% of phenotypic variation. These results will provide information for the improvement of sorghum root architecture associated with brace roots.
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Affiliation(s)
- Ronggai Li
- Institute of Millet Crops, Hebei Academy of Agricultural & Forestry Sciences,
Shijiazhuang 050031,
China
- School of Biological Sciences, University of Aberdeen,
Zoology Building, Tillydrone Avenue, Aberdeen AB24 2TZ,
UK
| | - Yucui Han
- Institute of Millet Crops, Hebei Academy of Agricultural & Forestry Sciences,
Shijiazhuang 050031,
China
| | - Peng Lv
- Institute of Millet Crops, Hebei Academy of Agricultural & Forestry Sciences,
Shijiazhuang 050031,
China
| | - Ruiheng Du
- Institute of Millet Crops, Hebei Academy of Agricultural & Forestry Sciences,
Shijiazhuang 050031,
China
| | - Guoqing Liu
- Institute of Millet Crops, Hebei Academy of Agricultural & Forestry Sciences,
Shijiazhuang 050031,
China
- Corresponding author (e-mail: )
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Peng Z, Zhang C, Zhang Y, Hu T, Mu S, Li X, Gao J. Transcriptome sequencing and analysis of the fast growing shoots of moso bamboo (Phyllostachys edulis). PLoS One 2013; 8:e78944. [PMID: 24244391 PMCID: PMC3820679 DOI: 10.1371/journal.pone.0078944] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 09/17/2013] [Indexed: 01/23/2023] Open
Abstract
Background The moso bamboo, a large woody bamboo with the highest ecological, economic, and cultural value of all bamboos, has one of the highest growth speeds in the world. Genetic research into moso bamboo has been scarce, partly because of the lack of previous genomic resources. In the present study, for the first time, we performed de novo transcriptome sequencing and mapped to the moso bamboo genomic resources (reference genome and genes) to produce a comprehensive dataset for the fast growing shoots of moso bamboo. Results The fast growing shoots mixed with six different heights and culms after leaf expansion of moso bamboo transcriptome were sequenced using the Illumina HiSeq™ 2000 sequencing platform, respectively. More than 80 million reads including 65,045,670 and 68,431,884 clean reads were produced in the two libraries. More than 81% of the reads were matched to the reference genome, and nearly 50% of the reads were matched to the reference genes. The genes with log 2 ratio > 2 or < −2 (P<0.001) were characterized as the most differentially expressed genes. 6,076 up-regulated and 4,613 down-regulated genes were classified into functional categories. Candidate genes which mainly involved transcript factors, plant hormones, cell cycle regulation, cell wall metabolism and cell morphogenesis genes were further analyzed and they may form a network that regulates the fast growth of moso bamboo shoots. Conclusion Firstly, our data provides the most comprehensive transcriptomic resource for moso bamboo to date. Candidate genes have been identified and they are potentially involved in the growth and development of moso bamboo. The results give a better insight into the mechanisms of moso bamboo shoots rapid growth and provide gene resources for improving plant growth.
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Affiliation(s)
- Zhenhua Peng
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, People's Republic of China
| | - Chunling Zhang
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, People's Republic of China
| | - Ying Zhang
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, People's Republic of China
| | - Tao Hu
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, People's Republic of China
| | - Shaohua Mu
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, People's Republic of China
| | - Xueping Li
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, People's Republic of China
| | - Jian Gao
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, People's Republic of China
- * E-mail:
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10
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Smandi S, Guerfali FZ, Farhat M, Ben-Aissa K, Laouini D, Guizani-Tabbane L, Dellagi K, Benkahla A. Methodology optimizing SAGE library tag-to-gene mapping: application to Leishmania. BMC Res Notes 2012; 5:74. [PMID: 22283878 PMCID: PMC3292834 DOI: 10.1186/1756-0500-5-74] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Accepted: 01/27/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Leishmaniasis are widespread parasitic-diseases with an urgent need for more active and less toxic drugs and for effective vaccines. Understanding the biology of the parasite especially in the context of host parasite interaction is a crucial step towards such improvements in therapy and control. Several experimental approaches including SAGE (Serial analysis of gene expression) have been developed in order to investigate the parasite transcriptome organisation and plasticity. Usual SAGE tag-to-gene mapping techniques are inadequate because almost all tags are normally located in the 3'-UTR outside the CDS, whereas most information available for Leishmania transcripts is restricted to the CDS predictions. The aim of this work is to optimize a SAGE libraries tag-to-gene mapping technique and to show how this development improves the understanding of Leishmania transcriptome. FINDINGS The in silico method implemented herein was based on mapping the tags to Leishmania genome using BLAST then mapping the tags to their gene using a data-driven probability distribution. This optimized tag-to-gene mappings improved the knowledge of Leishmania genome structure and transcription. It allowed analyzing the expression of a maximal number of Leishmania genes, the delimitation of the 3' UTR of 478 genes and the identification of biological processes that are differentially modulated during the promastigote to amastigote differentiation. CONCLUSION The developed method optimizes the assignment of SAGE tags in trypanosomatidae genomes as well as in any genome having polycistronic transcription and small intergenic regions.
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Affiliation(s)
- Sondos Smandi
- Laboratoire d'Immuno-Pathologie, Vaccinologie et Génétique Moléculaire (LIVGM), WHO Collaborating Center for Research and Training in Leishmaniasis, Institut Pasteur de Tunis, 13 place Pasteur BP74 1002, Tunis, Tunisia.
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11
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Acosta-Muñiz CH, Escobar-Tovar L, Valdes-Rodríguez S, Fernández-Pavia S, Arias-Saucedo LJ, de la Cruz Espindola Barquera M, Gómez Lim MÁ. Identification of avocado (Persea americana) root proteins induced by infection with the oomycete Phytophthora cinnamomi using a proteomic approach. PHYSIOLOGIA PLANTARUM 2012; 144:59-72. [PMID: 21916897 DOI: 10.1111/j.1399-3054.2011.01522.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Avocado root rot, caused by Phytophthora cinnamomi, is the most important disease that limits avocado production. A proteomic approach was employed to identify proteins that are upregulated by infection with P. cinnamomi. Different proteins were shown to be differentially expressed after challenge with the pathogen by two-dimensional (2-D) gel electrophoresis. A densitometric evaluation of protein expression indicated differential regulation during the time-course analyzed. Some proteins induced in response to the infection were identified by standard peptide mass fingerprinting using matrix-assisted laser desorption/ionization-time of flight-mass spectrometry and sequencing by MALDI LIFT-TOF/TOF tandem mass spectrometry. Of the 400 protein spots detected on 2-D gels, 21 seemed to change in abundance by 3 hours after infection. Sixteen proteins were upregulated, 5 of these were only detected in infected roots and 11 showed an increased abundance. Among the differentially expressed proteins identified are homologs to isoflavone reductase, glutathione S-transferase, several abscisic acid stress-ripening proteins, cinnamyl alcohol dehydrogenase, cinnamoyl-CoA reductase, cysteine synthase and quinone reductase. A 17.3-kDa small heat-shock protein and a glycine-rich RNA-binding protein were identified as downregulated. Our group is the first to report on gene induction in response to oomycete infection in roots from avocado, using proteomic techniques.
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Affiliation(s)
- Carlos H Acosta-Muñiz
- Centro de Investigación en alimentación y desarrollo A C, Av. Rio Conchos s/n, Parque Industrial Cuauhtémoc, CP. 31570, Cuauhtémoc, Chihuahua, México
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Molina C, Zaman-Allah M, Khan F, Fatnassi N, Horres R, Rotter B, Steinhauer D, Amenc L, Drevon JJ, Winter P, Kahl G. The salt-responsive transcriptome of chickpea roots and nodules via deepSuperSAGE. BMC PLANT BIOLOGY 2011; 11:31. [PMID: 21320317 PMCID: PMC3045889 DOI: 10.1186/1471-2229-11-31] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Accepted: 02/14/2011] [Indexed: 05/20/2023]
Abstract
BACKGROUND The combination of high-throughput transcript profiling and next-generation sequencing technologies is a prerequisite for genome-wide comprehensive transcriptome analysis. Our recent innovation of deepSuperSAGE is based on an advanced SuperSAGE protocol and its combination with massively parallel pyrosequencing on Roche's 454 sequencing platform. As a demonstration of the power of this combination, we have chosen the salt stress transcriptomes of roots and nodules of the third most important legume crop chickpea (Cicer arietinum L.). While our report is more technology-oriented, it nevertheless addresses a major world-wide problem for crops generally: high salinity. Together with low temperatures and water stress, high salinity is responsible for crop losses of millions of tons of various legume (and other) crops. Continuously deteriorating environmental conditions will combine with salinity stress to further compromise crop yields. As a good example for such stress-exposed crop plants, we started to characterize salt stress responses of chickpeas on the transcriptome level. RESULTS We used deepSuperSAGE to detect early global transcriptome changes in salt-stressed chickpea. The salt stress responses of 86,919 transcripts representing 17,918 unique 26 bp deepSuperSAGE tags (UniTags) from roots of the salt-tolerant variety INRAT-93 two hours after treatment with 25 mM NaCl were characterized. Additionally, the expression of 57,281 transcripts representing 13,115 UniTags was monitored in nodules of the same plants. From a total of 144,200 analyzed 26 bp tags in roots and nodules together, 21,401 unique transcripts were identified. Of these, only 363 and 106 specific transcripts, respectively, were commonly up- or down-regulated (>3.0-fold) under salt stress in both organs, witnessing a differential organ-specific response to stress.Profiting from recent pioneer works on massive cDNA sequencing in chickpea, more than 9,400 UniTags were able to be linked to UniProt entries. Additionally, gene ontology (GO) categories over-representation analysis enabled to filter out enriched biological processes among the differentially expressed UniTags. Subsequently, the gathered information was further cross-checked with stress-related pathways. From several filtered pathways, here we focus exemplarily on transcripts associated with the generation and scavenging of reactive oxygen species (ROS), as well as on transcripts involved in Na+ homeostasis. Although both processes are already very well characterized in other plants, the information generated in the present work is of high value. Information on expression profiles and sequence similarity for several hundreds of transcripts of potential interest is now available. CONCLUSIONS This report demonstrates, that the combination of the high-throughput transcriptome profiling technology SuperSAGE with one of the next-generation sequencing platforms allows deep insights into the first molecular reactions of a plant exposed to salinity. Cross validation with recent reports enriched the information about the salt stress dynamics of more than 9,000 chickpea ESTs, and enlarged their pool of alternative transcripts isoforms. As an example for the high resolution of the employed technology that we coin deepSuperSAGE, we demonstrate that ROS-scavenging and -generating pathways undergo strong global transcriptome changes in chickpea roots and nodules already 2 hours after onset of moderate salt stress (25 mM NaCl). Additionally, a set of more than 15 candidate transcripts are proposed to be potential components of the salt overly sensitive (SOS) pathway in chickpea. Newly identified transcript isoforms are potential targets for breeding novel cultivars with high salinity tolerance. We demonstrate that these targets can be integrated into breeding schemes by micro-arrays and RT-PCR assays downstream of the generation of 26 bp tags by SuperSAGE.
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Affiliation(s)
- Carlos Molina
- Molecular BioSciences, Biocenter, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, D-60439 Frankfurt am Main, Germany
- Unité de Recherche en Légumineuses, INRA-URLEG, 17 Rue Sully, 21000 Dijon, France
| | | | - Faheema Khan
- Molecular BioSciences, Biocenter, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, D-60439 Frankfurt am Main, Germany
- Molecular Ecology Laboratory, Department of Botany, Jamia Hamdard University, New Delhi, India
| | - Nadia Fatnassi
- Estación Experimental del Zaidín, CSIC, C/Profesor Albareda, 1, 18008-Granada, Spain
| | - Ralf Horres
- Molecular BioSciences, Biocenter, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, D-60439 Frankfurt am Main, Germany
| | - Björn Rotter
- GenXPro GmbH, Frankfurt Innovation Center FIZ Biotechnology, Altendörferallee 3, D-60438 Frankfurt am Main, Germany
| | - Diana Steinhauer
- GenXPro GmbH, Frankfurt Innovation Center FIZ Biotechnology, Altendörferallee 3, D-60438 Frankfurt am Main, Germany
| | - Laurie Amenc
- Soil Symbiosis and Environment, INRA, 1 place Viala, 34060 Montpellier-Cedex, France
| | - Jean-Jacques Drevon
- Soil Symbiosis and Environment, INRA, 1 place Viala, 34060 Montpellier-Cedex, France
| | - Peter Winter
- GenXPro GmbH, Frankfurt Innovation Center FIZ Biotechnology, Altendörferallee 3, D-60438 Frankfurt am Main, Germany
| | - Günter Kahl
- Molecular BioSciences, Biocenter, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, D-60439 Frankfurt am Main, Germany
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Kim HJ, Baek KH, Lee BW, Choi D, Hur CG. In silico identification and characterization of microRNAs and their putative target genes in Solanaceae plants. Genome 2011; 54:91-8. [PMID: 21326365 DOI: 10.1139/g10-104] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
MicroRNAs (miRNAs) are a class of small, single-stranded, noncoding RNAs ranging from 19 to 25 nucleotides. The miRNA control various cellular functions by negatively regulating gene expression at the post-transcriptional level. The miRNA regulation over their target genes has a central role in regulating plant growth and development; however, only a few reports have been published on the function of miRNAs in the family Solanaceae. We identified Solanaceae miRNAs and their target genes by analyzing expressed sequence tag (EST) data from five different Solanaceae species. A comprehensive bioinformatic analysis of EST data of Solanaceae species revealed the presence of at least 11 miRNAs and 54 target genes in pepper (Capsicum annuum L.), 22 miRNAs and 221 target genes in potato (Solanum tuberosum L.), 12 miRNAs and 417 target genes in tomato (Solanum lycopersicum L.), 46 miRNAs and 60 target genes in tobacco (Nicotiana tabacum L.), and 7 miRNAs and 28 target genes in Nicotiana benthamiana. The identified Solanaceae miRNAs and their target genes were deposited in the SolmiRNA database, which is freely available for academic research only at http://genepool.kribb.re.kr/SolmiRNA. Our data indicate that the Solanaceae family has both conserved and specific miRNAs and that their target genes may play important roles in growth and development of Solanaceae plants.
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Affiliation(s)
- Hyun-Jin Kim
- Bioinformatics Research Center, Korea Research Institute of Bioscience and Biotechnology, 111 Gwahangno, Yuseong-gu, Daejeon 305-806, Korea
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Swarbreck SM, Lindquist EA, Ackerly DD, Andersen GL. Analysis of leaf and root transcriptomes of soil-grown Avena barbata plants. PLANT & CELL PHYSIOLOGY 2011; 52:317-32. [PMID: 21310848 DOI: 10.1093/pcp/pcq188] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Slender wild oat (Avena barbata) is an annual grass dominant in many grassland ecosystems in Mediterranean climate. This species has been the subject of ecological studies aimed at understanding the effect of global climate change on grassland ecosystems and the genetic basis for adaptation under varying environmental conditions. We present the sequencing and analysis of cDNA libraries constructed from leaf and root samples collected from A. barbata grown on natural soil and under varying rainfall patterns. More than 1 million expressed sequence tags (ESTs) were generated using both GS 454-FLX pyrosequencing and Sanger sequencing, and these tags were assembled into consensus sequences. We identified numerous candidate polymorphic markers in the data set, providing possibilities for linking the genomic and the existing genetic information for A. barbata. Using the digital Northern method, we showed that genes involved in photosynthesis were down-regulated under high rainfall while stress-related genes were up-regulated. We also identified a number of genes unique to the root library with unknown function. Real-time reverse transcription-PCR was used to confirm the root specificity of some of these transcripts such as two genes encoding O-methyl transferase. Also we showed differential expression of five root-specific genes under three water levels and two developmental stages. Through a combination of Sanger and 454-based sequencing technologies, we were able to generate a large set of transcribed sequences for A. barbata. This data set provides a platform for further studies of this important wild grass species.
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Affiliation(s)
- Stéphanie M Swarbreck
- Earth Sciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA.
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Li YJ, Fu YR, Huang JG, Wu CA, Zheng CC. Transcript profiling during the early development of the maize brace root via Solexa sequencing. FEBS J 2010; 278:156-66. [PMID: 21122072 DOI: 10.1111/j.1742-4658.2010.07941.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Currently, the molecular regulation mechanisms involved in the early development of maize brace root are poorly known. To gain insight into the transcriptome dynamics that are associated with its development, genome-wide gene expression profiling was conducted by Solexa sequencing (Illumina Inc., San Diego, CA, USA). More than five million tags were generated from the stem node tissues without and with just-emerged brace roots, including 149,524 and 178,131 clean tags in the two libraries, respectively. Of these, 82,864 (55.4%) and 91,678 (51.5%) tags were matched to the reference genes. The most differentially expressed tags with a log(2) ratio > 2 or < -2 (P < 0.001) were analyzed further, representing 143 up-regulated and 152 down-regulated genes, except for unknown transcripts, which were classified into 11 functional categories. The most enriched categories were those of metabolism, signal transduction and cellular transport. Many genes or biological pathways were found to be commonly shared between brace root and lateral or adventitious root development, such as genes participating in cell wall degradation and synthesis, auxin transport and signaling, ethylene signaling, etc. Next, the expression patterns of 20 genes were assessed by quantitative real-time PCR, and the results obtained showed general agreement with the Solexa analysis. Furthermore, a comparison of the brace root transcriptome with that of maize primary root revealed substantial differences in the categories and abundances of expressed transcripts. In conclusion, we first reveal the complex changes in the transcriptome during the early development of maize brace root and provide a comprehensive set of data that are essential for understanding its molecular regulation.
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Affiliation(s)
- Yan-Jie Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China
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Murphy JP, Kong F, Pinto DM, Wang-Pruski G. Relative quantitative proteomic analysis reveals wound response proteins correlated with after-cooking darkening. Proteomics 2010; 10:4258-69. [DOI: 10.1002/pmic.200900718] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Patterson K, Cakmak T, Cooper A, Lager I, Rasmusson AG, Escobar MA. Distinct signalling pathways and transcriptome response signatures differentiate ammonium- and nitrate-supplied plants. PLANT, CELL & ENVIRONMENT 2010; 33:1486-501. [PMID: 20444219 PMCID: PMC2920365 DOI: 10.1111/j.1365-3040.2010.02158.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Nitrogen is the only macronutrient that is commonly available to plants in both oxidized and reduced forms, mainly nitrate and ammonium. The physiological and molecular effects of nitrate supply have been well studied, but comparatively little is known about ammonium nutrition and its differential effects on cell function and gene expression. We have used a physiologically realistic hydroponic growth system to compare the transcriptomes and redox status of the roots of ammonium- and nitrate-supplied Arabidopsis thaliana plants. While approximately 60% of nitrogen-regulated genes displayed common responses to both ammonium and nitrate, significant 'nitrate-specific' and 'ammonium-specific' gene sets were identified. Pathways involved in cytokinin response and reductant generation/distribution were specifically altered by nitrate, while a complex biotic stress response and changes in nodulin gene expression were characteristic of ammonium-supplied plants. Nitrate supply was associated with a rapid decrease in H(2)O(2) production, potentially because of an increased export of reductant from the mitochondrial matrix. The underlying basis of the nitrate- and ammonium-specific patterns of gene expression appears to be different signals elaborated from each nitrogen source, including alterations in extracellular pH that are associated with ammonium uptake, downstream metabolites in the ammonium assimilation pathway, and the presence or absence of the nitrate ion.
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Affiliation(s)
- Kurt Patterson
- Department of Biological Sciences, California State University San Marcos, San Marcos, California 92096, USA (K.P., T.C., A.C., M.A.E.); Department of Biology, Lund University, SE-22362, Lund, Sweden (I.L., A.G.R.)
| | | | - Andrew Cooper
- Department of Biological Sciences, California State University San Marcos, San Marcos, California 92096, USA (K.P., T.C., A.C., M.A.E.); Department of Biology, Lund University, SE-22362, Lund, Sweden (I.L., A.G.R.)
| | - Ida Lager
- Department of Biological Sciences, California State University San Marcos, San Marcos, California 92096, USA (K.P., T.C., A.C., M.A.E.); Department of Biology, Lund University, SE-22362, Lund, Sweden (I.L., A.G.R.)
| | - Allan G. Rasmusson
- Department of Biological Sciences, California State University San Marcos, San Marcos, California 92096, USA (K.P., T.C., A.C., M.A.E.); Department of Biology, Lund University, SE-22362, Lund, Sweden (I.L., A.G.R.)
| | - Matthew A. Escobar
- Department of Biological Sciences, California State University San Marcos, San Marcos, California 92096, USA (K.P., T.C., A.C., M.A.E.); Department of Biology, Lund University, SE-22362, Lund, Sweden (I.L., A.G.R.)
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Eswaran N, Parameswaran S, Sathram B, Anantharaman B, Kumar G RK, Tangirala SJ. Yeast functional screen to identify genetic determinants capable of conferring abiotic stress tolerance in Jatropha curcas. BMC Biotechnol 2010; 10:23. [PMID: 20302659 PMCID: PMC2851662 DOI: 10.1186/1472-6750-10-23] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Accepted: 03/20/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Environmentally inflicted stresses such as salinity and drought limit the plant productivity both in natural and agricultural system. Increasing emphasis has been directed to molecular breeding strategies to enhance the intrinsic ability of plant to survive stress conditions. Functional screens in microorganisms with heterologous genes are a rapid, effective and powerful tool to identify stress tolerant genes in plants. Jatropha curcas (Physic nut) has been identified as a potential source of biodiesel plant. In order to improve its productivity under stress conditions to benefit commercial plantations, we initiated prospecting of novel genes expressed during stress in J. curcas that can be utilized to enhance stress tolerance ability of plant. RESULTS To identify genes expressed during salt tolerance, cDNA expression libraries were constructed from salt-stressed roots of J. curcas, regulated under the control of the yeast GAL1 system. Using a replica based screening, twenty thousand yeast transformants were screened to identify transformants expressing heterologous gene sequences from J. curcas with enhanced ability to tolerate stress. From the screen we obtained 32 full length genes from J. curcas [GenBank accession numbers FJ489601-FJ489611, FJ619041-FJ619057 and FJ623457-FJ623460] that can confer abiotic stress tolerance. As a part of this screen, we optimized conditions for salt stress in J. curcas, defined parameters for salt stress in yeast, as well as isolated three salt hypersensitive yeast strains shs-2, shs-6 and shs-8 generated through a process of random mutagenesis, and exhibited growth retardation beyond 750 mM NaCl. Further, we demonstrated complementation of the salt sensitive phenotypes in the shs mutants, and analyzed the expression patterns for selected J. curcas genes obtained from the screen in both leaf and root tissues after salt stress treatments. CONCLUSIONS The approach described in this report provides a rapid and universal assay system for large scale screening of genes for varied abiotic stress tolerance within a short span of time. Using this screening strategy we could isolate both genes with previously known function in stress tolerance as well as novel sequences with yet unknown function in salt stress tolerance from J. curcas. The isolated genes could be over-expressed using plant expression system to generate and evaluate transgenic plants for stress tolerance as well as be used as markers for breeding salt stress tolerance in plants.
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Affiliation(s)
- Nalini Eswaran
- Plant Metabolic Engineering Group, Reliance Life Sciences Pvt Ltd, Dhirubhai Ambani Life Sciences Center, R-282, Thane- Belapur Road, Rabale, Navi Mumbai- 400 701, India
| | - Sriram Parameswaran
- Plant Metabolic Engineering Group, Reliance Life Sciences Pvt Ltd, Dhirubhai Ambani Life Sciences Center, R-282, Thane- Belapur Road, Rabale, Navi Mumbai- 400 701, India
- DuPont Knowledge Centre, ICICI Knowledge Park, Genome Valley, Turkapalli, Shamirpet, Hyderabad 500 078, India
| | - Balaji Sathram
- Plant Metabolic Engineering Group, Reliance Life Sciences Pvt Ltd, Dhirubhai Ambani Life Sciences Center, R-282, Thane- Belapur Road, Rabale, Navi Mumbai- 400 701, India
| | - Bhagyam Anantharaman
- Plant Metabolic Engineering Group, Reliance Life Sciences Pvt Ltd, Dhirubhai Ambani Life Sciences Center, R-282, Thane- Belapur Road, Rabale, Navi Mumbai- 400 701, India
| | - Raja Krishna Kumar G
- Plant Metabolic Engineering Group, Reliance Life Sciences Pvt Ltd, Dhirubhai Ambani Life Sciences Center, R-282, Thane- Belapur Road, Rabale, Navi Mumbai- 400 701, India
| | - Sudhakar Johnson Tangirala
- Plant Metabolic Engineering Group, Reliance Life Sciences Pvt Ltd, Dhirubhai Ambani Life Sciences Center, R-282, Thane- Belapur Road, Rabale, Navi Mumbai- 400 701, India
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White PJ, Wiesel L, Broadley MR. Cation Channels and the Uptake of Radiocaesium by Plants. ION CHANNELS AND PLANT STRESS RESPONSES 2010. [DOI: 10.1007/978-3-642-10494-7_3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Vega-Arreguín JC, Ibarra-Laclette E, Jiménez-Moraila B, Martínez O, Vielle-Calzada JP, Herrera-Estrella L, Herrera-Estrella A. Deep sampling of the Palomero maize transcriptome by a high throughput strategy of pyrosequencing. BMC Genomics 2009; 10:299. [PMID: 19580677 PMCID: PMC2714558 DOI: 10.1186/1471-2164-10-299] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2008] [Accepted: 07/06/2009] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND In-depth sequencing analysis has not been able to determine the overall complexity of transcriptional activity of a plant organ or tissue sample. In some cases, deep parallel sequencing of Expressed Sequence Tags (ESTs), although not yet optimized for the sequencing of cDNAs, has represented an efficient procedure for validating gene prediction and estimating overall gene coverage. This approach could be very valuable for complex plant genomes. In addition, little emphasis has been given to efforts aiming at an estimation of the overall transcriptional universe found in a multicellular organism at a specific developmental stage. RESULTS To explore, in depth, the transcriptional diversity in an ancient maize landrace, we developed a protocol to optimize the sequencing of cDNAs and performed 4 consecutive GS20-454 pyrosequencing runs of a cDNA library obtained from 2 week-old Palomero Toluqueño maize plants. The protocol reported here allowed obtaining over 90% of informative sequences. These GS20-454 runs generated over 1.5 Million reads, representing the largest amount of sequences reported from a single plant cDNA library. A collection of 367,391 quality-filtered reads (30.09 Mb) from a single run was sufficient to identify transcripts corresponding to 34% of public maize ESTs databases; total sequences generated after 4 filtered runs increased this coverage to 50%. Comparisons of all 1.5 Million reads to the Maize Assembled Genomic Islands (MAGIs) provided evidence for the transcriptional activity of 11% of MAGIs. We estimate that 5.67% (86,069 sequences) do not align with public ESTs or annotated genes, potentially representing new maize transcripts. Following the assembly of 74.4% of the reads in 65,493 contigs, real-time PCR of selected genes confirmed a predicted correlation between the abundance of GS20-454 sequences and corresponding levels of gene expression. CONCLUSION A protocol was developed that significantly increases the number, length and quality of cDNA reads using massive 454 parallel sequencing. We show that recurrent 454 pyrosequencing of a single cDNA sample is necessary to attain a thorough representation of the transcriptional universe present in maize, that can also be used to estimate transcript abundance of specific genes. This data suggests that the molecular and functional diversity contained in the vast native landraces remains to be explored, and that large-scale transcriptional sequencing of a presumed ancestor of the modern maize varieties represents a valuable approach to characterize the functional diversity of maize for future agricultural and evolutionary studies.
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Affiliation(s)
- Julio C Vega-Arreguín
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Campus Guanajuato, Carretera Irapuato-León, Irapuato, Gto, Mexico.
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Rouached H, Secco D, Arpat AB. Getting the most sulfate from soil: Regulation of sulfate uptake transporters in Arabidopsis. JOURNAL OF PLANT PHYSIOLOGY 2009; 166:893-902. [PMID: 19375816 DOI: 10.1016/j.jplph.2009.02.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2009] [Accepted: 02/25/2009] [Indexed: 05/20/2023]
Abstract
Sulfur (S) is an essential macronutrient for all living organisms. Plants require large amounts of sulfate for growth and development, and this serves as a major entry point of sulfate into the food web. Plants acquire S in its ionic form from the soil; they have evolved tightly controlled mechanisms for the regulation of sulfate uptake in response to its external and internal availability. In the model plant Arabidopsis thaliana, the first key step in sulfate uptake is presumed to be carried out exclusively by only two high-affinity sulfate transporters: SULTR1;1 and SULTR1;2. A better understanding of the mode of regulation for these two transporters is crucial because they constitute the first determinative step in balancing sulfate in respect to its supply and demand. Here, we review the recent progress achieved in our comprehension of (i) mechanisms that regulate these two high-affinity sulfate transporters at the transcriptional and post-transcriptional levels, and (ii) their structure-function relationship. Such progress is important to enable biotechnological and agronomic strategies aimed at enhancing sulfate uptake and improving crop yield in S-deficient soils.
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Affiliation(s)
- Hatem Rouached
- Department of Plant Molecular Biology, University of Lausanne, Lausanne CH-1015, Switzerland.
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Abstract
The role of sex chromosomes in sex determination has been well studied in diverse groups of organisms. However, the role of the genes on the sex chromosomes in conferring sexual dimorphism is still being experimentally evaluated. An unequal complement of sex chromosomes between two sexes makes them amenable to sex-specific evolutionary forces. Sex-linked genes preferentially expressed in one sex over the other offer a potential means of addressing the role of sex chromosomes in sexual dimorphism. We examined the testis transcriptome of the silkworm, Bombyx mori, which has a ZW chromosome constitution in the female and ZZ in the male, and show that the Z chromosome harbors a significantly higher number of genes expressed preferentially in testis compared to the autosomes. We hypothesize that sexual antagonism and absence of dosage compensation have possibly led to the accumulation of many male-specific genes on the Z chromosome. Further, our analysis of testis-specific paralogous genes suggests that the accumulation on the Z chromosome of genes advantageous to males has occurred primarily by translocation or tandem duplication.
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Skinner DJ, Gasser CS. Expression-based discovery of candidate ovule development regulators through transcriptional profiling of ovule mutants. BMC PLANT BIOLOGY 2009; 9:29. [PMID: 19291320 PMCID: PMC2664812 DOI: 10.1186/1471-2229-9-29] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2008] [Accepted: 03/16/2009] [Indexed: 05/05/2023]
Abstract
BACKGROUND Arabidopsis ovules comprise four morphologically distinct parts: the nucellus, which contains the embryo sac, two integuments that become the seed coat, and the funiculus that anchors the ovule within the carpel. Analysis of developmental mutants has shown that ovule morphogenesis relies on tightly regulated genetic interactions that can serve as a model for developmental regulation. Redundancy, pleiotropic effects and subtle phenotypes may preclude identification of mutants affecting some processes in screens for phenotypic changes. Expression-based gene discovery can be used access such obscured genes. RESULTS Affymetrix microarrays were used for expression-based gene discovery to identify sets of genes expressed in either or both integuments. The genes were identified by comparison of pistil mRNA from wild type with mRNA from two mutants; inner no outer (ino, which lacks the outer integument), and aintegumenta (ant, which lacks both integuments). Pools of pistils representing early and late stages of ovule development were evaluated and data from the three genotypes were used to designate genes that were predominantly expressed in the integuments using pair-wise and cluster analyses. Approximately two hundred genes were found to have a high probability of preferential expression in these structures, and the predictive nature of the expression classes was confirmed with reverse transcriptase polymerase chain reaction and in situ hybridization. CONCLUSION The results showed that it was possible to use a mutant, ant, with broad effects on plant phenotype to identify genes expressed specifically in ovules, when coupled with predictions from known gene expression patterns, or in combination with a more specific mutant, ino. Robust microarray averaging (RMA) analysis of array data provided the most reliable comparisons, especially for weakly expressed genes. The studies yielded an over-abundance of transcriptional regulators in the identified genes, and these form a set of candidate genes for evaluation of roles in ovule development using reverse genetics.
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Affiliation(s)
- Debra J Skinner
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
- Department of Crop Science, University of Illinois, Urbana, IL 61801, USA
| | - Charles S Gasser
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
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Faunes F, Sánchez N, Castellanos J, Vergara IA, Melo F, Larraín J. Identification of novel transcripts with differential dorso-ventral expression in Xenopus gastrula using serial analysis of gene expression. Genome Biol 2009; 10:R15. [PMID: 19210784 PMCID: PMC2688288 DOI: 10.1186/gb-2009-10-2-r15] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2008] [Revised: 11/25/2008] [Accepted: 02/11/2009] [Indexed: 11/12/2022] Open
Abstract
Comparison of dorsal and ventral transcriptomes of Xenopus tropicalis gastrulae using serial analysis of gene expression provides at least 86 novel differentially expressed transcripts. Background Recent evidence from global studies of gene expression indicates that transcriptomes are more complex than expected. Xenopus has been typically used as a model organism to study early embryonic development, particularly dorso-ventral patterning. In order to identify novel transcripts involved in dorso-ventral patterning, we compared dorsal and ventral transcriptomes of Xenopus tropicalis at the gastrula stage using serial analysis of gene expression (SAGE). Results Of the experimental tags, 54.5% were confidently mapped to transcripts and 125 showed a significant difference in their frequency of occurrence between dorsal and ventral libraries. We selected 20 differentially expressed tags and assigned them to specific transcripts using bioinformatics and reverse SAGE. Five mapped to transcripts with known dorso-ventral expression and the frequency of appearance for these tags in each library is in agreement with the expression described by other methods. The other 15 tags mapped to transcripts with no previously described asymmetric expression along the dorso-ventral axis. The differential expression of ten of these novel transcripts was validated by in situ hybridization and/or RT-PCR. We can estimate that this SAGE experiment provides a list of at least 86 novel transcripts with differential expression along the dorso-ventral axis. Interestingly, the expression of some novel transcripts was independent of β-catenin. Conclusions Our SAGE analysis provides a list of novel transcripts with differential expression in the dorso-ventral axis and a large number of orphan tags that can be used to identify novel transcripts and to improve the current annotation of the X. tropicalis genome.
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Affiliation(s)
- Fernando Faunes
- Center for Cell Regulation and Pathology and Center for Aging and Regeneration, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, 8331150, Chile
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Kim HJ, Baek KH, Lee SW, Kim J, Lee BW, Cho HS, Kim WT, Choi D, Hur CG. Pepper EST database: comprehensive in silico tool for analyzing the chili pepper (Capsicum annuum) transcriptome. BMC PLANT BIOLOGY 2008; 8:101. [PMID: 18844979 PMCID: PMC2575210 DOI: 10.1186/1471-2229-8-101] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2008] [Accepted: 10/09/2008] [Indexed: 05/19/2023]
Abstract
BACKGROUND There is no dedicated database available for Expressed Sequence Tags (EST) of the chili pepper (Capsicum annuum), although the interest in a chili pepper EST database is increasing internationally due to the nutritional, economic, and pharmaceutical value of the plant. Recent advances in high-throughput sequencing of the ESTs of chili pepper cv. Bukang have produced hundreds of thousands of complementary DNA (cDNA) sequences. Therefore, a chili pepper EST database was designed and constructed to enable comprehensive analysis of chili pepper gene expression in response to biotic and abiotic stresses. RESULTS We built the Pepper EST database to mine the complexity of chili pepper ESTs. The database was built on 122,582 sequenced ESTs and 116,412 refined ESTs from 21 pepper EST libraries. The ESTs were clustered and assembled into virtual consensus cDNAs and the cDNAs were assigned to metabolic pathway, Gene Ontology (GO), and MIPS Functional Catalogue (FunCat). The Pepper EST database is designed to provide a workbench for (i) identifying unigenes in pepper plants, (ii) analyzing expression patterns in different developmental tissues and under conditions of stress, and (iii) comparing the ESTs with those of other members of the Solanaceae family. The Pepper EST database is freely available at http://genepool.kribb.re.kr/pepper/. CONCLUSION The Pepper EST database is expected to provide a high-quality resource, which will contribute to gaining a systemic understanding of plant diseases and facilitate genetics-based population studies. The database is also expected to contribute to analysis of gene synteny as part of the chili pepper sequencing project by mapping ESTs to the genome.
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Affiliation(s)
- Hyun-Jin Kim
- Omics Integration Research Center, KRIBB, 111 Gwahangno, Yuseong-gu, Daejeon 305-806, Korea
| | - Kwang-Hyun Baek
- School of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Korea
| | - Seung-Won Lee
- Omics Integration Research Center, KRIBB, 111 Gwahangno, Yuseong-gu, Daejeon 305-806, Korea
| | - JungEun Kim
- Omics Integration Research Center, KRIBB, 111 Gwahangno, Yuseong-gu, Daejeon 305-806, Korea
| | - Bong-Woo Lee
- Omics Integration Research Center, KRIBB, 111 Gwahangno, Yuseong-gu, Daejeon 305-806, Korea
| | - Hye-Sun Cho
- Plant Genome Research Center, KRIBB, 111 Gwahangno, Yuseong-gu, Daejeon 305-806, Korea
| | - Woo Taek Kim
- Department of Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Doil Choi
- Department of Plant Science, Seoul National University, Seoul 151-921, Korea
| | - Cheol-Goo Hur
- Omics Integration Research Center, KRIBB, 111 Gwahangno, Yuseong-gu, Daejeon 305-806, Korea
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Rouached H, Wirtz M, Alary R, Hell R, Arpat AB, Davidian JC, Fourcroy P, Berthomieu P. Differential regulation of the expression of two high-affinity sulfate transporters, SULTR1.1 and SULTR1.2, in Arabidopsis. PLANT PHYSIOLOGY 2008; 147:897-911. [PMID: 18400935 PMCID: PMC2409035 DOI: 10.1104/pp.108.118612] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2008] [Accepted: 04/02/2008] [Indexed: 05/18/2023]
Abstract
The molecular mechanisms regulating the initial uptake of inorganic sulfate in plants are still largely unknown. The current model for the regulation of sulfate uptake and assimilation attributes positive and negative regulatory roles to O-acetyl-serine (O-acetyl-Ser) and glutathione, respectively. This model seems to suffer from exceptions and it has not yet been clearly validated whether intracellular O-acetyl-Ser and glutathione levels have impacts on regulation. The transcript level of the two high-affinity sulfate transporters SULTR1.1 and SULTR1.2 responsible for sulfate uptake from the soil solution was compared to the intracellular contents of O-acetyl-Ser, glutathione, and sulfate in roots of plants submitted to a wide diversity of experimental conditions. SULTR1.1 and SULTR1.2 were differentially expressed and neither of the genes was regulated in accordance with the current model. The SULTR1.1 transcript level was mainly altered in response to the sulfur-related treatments. Split-root experiments show that the expression of SULTR1.1 is locally regulated in response to sulfate starvation. In contrast, accumulation of SULTR1.2 transcripts appeared to be mainly related to metabolic demand and is controlled by photoperiod. On the basis of the new molecular insights provided in this study, we suggest that the expression of the two transporters depends on different regulatory networks. We hypothesize that interplay between SULTR1.1 and SULTR1.2 transporters could be an important mechanism to regulate sulfate content in the roots.
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Affiliation(s)
- Hatem Rouached
- Biochimie et Physiologie Moléculaire des Plantes , Unité Mixte de Recherche, Montpellier SupAgro/CNRS/INRA, Université Montpellier II, 34060 Montpellier cedex 1, France.
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Barberon M, Berthomieu P, Clairotte M, Shibagaki N, Davidian JC, Gosti F. Unequal functional redundancy between the two Arabidopsis thaliana high-affinity sulphate transporters SULTR1;1 and SULTR1;2. THE NEW PHYTOLOGIST 2008; 180:608-619. [PMID: 18761637 DOI: 10.1111/j.1469-8137.2008.02604.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
* In Arabidopsis, SULTR1;1 and SULTR1;2 are two genes proposed to be involved in high-affinity sulphate uptake from the soil solution. We address here the specific issue of their functional redundancy for the uptake of sulphate and for the accumulation of its toxic analogue selenate with regard to plant growth and selenate tolerance. * Using the complete set of genotypes, including the wild-type, each one of the single sultr1;1 and sultr1;2 mutants and the resulting double sultr1;1-sultr1;2 mutant, we performed a detailed phenotypic analysis of root length, shoot biomass, sulphate uptake, sulphate and selenate accumulation and selenate tolerance. * The results all ordered the four different genotypes according to the same functional hierarchy. Wild-type and sultr1;1 mutant plants displayed similar phenotypes. By contrast, sultr1;1-sultr1;2 double-mutant plants showed the most extreme phenotype and the sultr1;2 mutant displayed intermediate performances. Additionally, the degree of selenate tolerance was directly related to the seedling selenate content according to a single sigmoid regression curve common to all the genotypes. * The SULTR1;1 and SULTR1;2 genes display unequal functional redundancy, which leaves open for SULTR1;1 the possibility of displaying an additional function besides its role in sulphate membrane transport.
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Affiliation(s)
- Marie Barberon
- UMR de Biochimie et Physiologie Moléculaire des Plantes, Centre International d'Etudes Supérieures en Sciences Agronomiques, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Montpellier II, 2 Place Pierre Viala, 34060 Montpellier cedex 1, France
| | - Pierre Berthomieu
- UMR de Biochimie et Physiologie Moléculaire des Plantes, Centre International d'Etudes Supérieures en Sciences Agronomiques, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Montpellier II, 2 Place Pierre Viala, 34060 Montpellier cedex 1, France
| | - Michael Clairotte
- UMR de Biogéochimie du Sol et de la Rhizosphère, Centre International d'Etudes Supérieures en Sciences Agronomiques, Institut National de la Recherche Agronomique, 2 Place Pierre Viala, 34060 Montpellier cedex 1, France
| | - Nakako Shibagaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Jean-Claude Davidian
- UMR de Biochimie et Physiologie Moléculaire des Plantes, Centre International d'Etudes Supérieures en Sciences Agronomiques, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Montpellier II, 2 Place Pierre Viala, 34060 Montpellier cedex 1, France
| | - Françoise Gosti
- UMR de Biochimie et Physiologie Moléculaire des Plantes, Centre International d'Etudes Supérieures en Sciences Agronomiques, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Montpellier II, 2 Place Pierre Viala, 34060 Montpellier cedex 1, France
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Wang R, Xing X, Crawford N. Nitrite acts as a transcriptome signal at micromolar concentrations in Arabidopsis roots. PLANT PHYSIOLOGY 2007; 145:1735-45. [PMID: 17951451 PMCID: PMC2151675 DOI: 10.1104/pp.107.108944] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Nitrate serves as a potent signal to control gene expression in plants and algae, but little is known about the signaling role of nitrite, the direct product of nitrate reduction. Analysis of several nitrate-induced genes showed that nitrite increases mRNA levels as rapidly as nitrate in nitrogen-starved Arabidopsis (Arabidopsis thaliana) roots. Both nitrite and nitrate induction are apparent at concentrations as low as 100 nm. The response at low nitrite concentrations was not due to contaminating nitrate, which was present at <1% of the nitrite concentration. High levels of ammonium (20 mm) in the growth medium suppressed induction of several genes by nitrate, but had varied effects on the nitrite response. Transcriptome analysis using 250 or 5 microm nitrate or nitrite showed that over one-half of the nitrate-induced genes, which included genes involved in nitrate and ammonium assimilation, energy production, and carbon and nitrogen metabolism responded equivalently to nitrite; however, the nitrite response was more robust and there were many genes that responded specifically to nitrite. Thus, nitrite can serve as a signal as well as if not better than nitrate.
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Affiliation(s)
- Rongchen Wang
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, La Jolla, California 92093-0116, USA
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30
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Irian S, Xu P, Dai X, Zhao PX, Roossinck MJ. Regulation of a virus-induced lethal disease in tomato revealed by LongSAGE analysis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2007; 20:1477-1488. [PMID: 17990955 DOI: 10.1094/mpmi-20-12-1477] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Infection of Cucumber mosaic virus (CMV) and D satellite RNA (satRNA) in tomato plants induces rapid plant death, which has caused catastrophic crop losses. We conducted long serial analysis of gene expression (LongSAGE) in control and virus-infected plants to identify the genes that may be involved in the development of this lethal tomato disease. The transcriptomes were compared between mock-inoculated plants and plants infected with CMV, CMV/D satRNA, or CMV/Dm satRNA (a nonnecrogenic mutant of D satRNA with three mutated nucleotides). The analysis revealed both general and specific changes in the tomato transcriptome after infection with these viruses. A massive transcriptional difference of approximately 400 genes was found between the transcriptomes of CMV/D and CMV/Dm satRNA-infected plants. Particularly, the Long-SAGE data indicated the activation of ethylene synthesis and signaling by CMV/D satRNA infection. Results from inoculation tests with an ethylene-insensitive mutant and treatments with an ethylene action inhibitor further confirmed the role of ethylene in mediating the epinastic leaf symptoms and the secondary cell death in the stem. Results from Northern blot analysis demonstrated the partial contribution of ethylene in the induced defense responses in CMV/D satRNA-infected plants.
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Affiliation(s)
- Saeed Irian
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73401, USA
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31
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Song S, Qu H, Chen C, Hu S, Yu J. Differential gene expression in an elite hybrid rice cultivar (Oryza sativa, L) and its parental lines based on SAGE data. BMC PLANT BIOLOGY 2007; 7:49. [PMID: 17877838 PMCID: PMC2077334 DOI: 10.1186/1471-2229-7-49] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2007] [Accepted: 09/19/2007] [Indexed: 05/17/2023]
Abstract
BACKGROUND It was proposed that differentially-expressed genes, aside from genetic variations affecting protein processing and functioning, between hybrid and its parents provide essential candidates for studying heterosis or hybrid vigor. Based our serial analysis of gene expression (SAGE) data from an elite Chinese super-hybrid rice (LYP9) and its parental cultivars (93-11 and PA64s) in three major tissue types (leaves, roots and panicles) at different developmental stages, we analyzed the transcriptome and looked for candidate genes related to rice heterosis. RESULTS By using an improved strategy of tag-to-gene mapping and two recently annotated genome assemblies (93-11 and PA64s), we identified 10,268 additional high-quality tags, reaching a grand total of 20,595 together with our previous result. We further detected 8.5% and 5.9% physically-mapped genes that are differentially-expressed among the triad (in at least one of the three stages) with P-values less than 0.05 and 0.01, respectively. These genes distributed in 12 major gene expression patterns; among them, 406 up-regulated and 469 down-regulated genes (P < 0.05) were observed. Functional annotations on the identified genes highlighted the conclusion that up-regulated genes (some of them are known enzymes) in hybrid are mostly related to enhancing carbon assimilation in leaves and roots. In addition, we detected a group of up-regulated genes related to male sterility and 442 down-regulated genes related to signal transduction and protein processing, which may be responsible for rice heterosis. CONCLUSION We improved tag-to-gene mapping strategy by combining information from transcript sequences and rice genome annotation, and obtained a more comprehensive view on genes that related to rice heterosis. The candidates for heterosis-related genes among different genotypes provided new avenue for exploring the molecular mechanism underlying heterosis.
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Affiliation(s)
- Shuhui Song
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China
- Department of Biology, Graduate University of the Chinese Academy of Sciences, Beijing 100094, China
| | - Hongzhu Qu
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China
- Department of Biology, Graduate University of the Chinese Academy of Sciences, Beijing 100094, China
| | - Chen Chen
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China
- Department of Biology, Graduate University of the Chinese Academy of Sciences, Beijing 100094, China
| | - Songnian Hu
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China
| | - Jun Yu
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China
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32
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Song X, Ni Z, Yao Y, Xie C, Li Z, Wu H, Zhang Y, Sun Q. Wheat (Triticum aestivumL.) root proteome and differentially expressed root proteins between hybrid and parents. Proteomics 2007; 7:3538-57. [PMID: 17722204 DOI: 10.1002/pmic.200700147] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
To better understand the development of wheat roots, a reference map of the major soluble proteins of wheat roots was established using a combination of 2-DE and MALDI TOF MS and MS/MS, and a total of 450 protein spots were detected with silver staining in a pH ranges of 4-7, of which 282 spots corresponding to 240 proteins were identified. These identified proteins were grouped into diverse functional categories. In comparison with a wheat leave proteome, in root, proteins involved in metabolism and transport were over-represented, whereas proteins involved in energy, disease and defense, transcription, and signal transduction were under-represented. To further get an insight into the molecular basis of wheat heterosis, differential proteome analysis between hybrid and parents were performed. A total of 45 differentially expressed protein spots were detected, and both quantitative and qualitative differences could be observed. Moreover, 25 of the 45 differentially expressed protein spots were identified, which were involved in metabolism, signal transduction, energy, cell growth and division, disease and defense, secondary metabolism. These results indicated that hybridization between two parental lines can cause expression differences between wheat hybrid and its parents not only at mRNA levels but also at protein abundances.
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Affiliation(s)
- Xiao Song
- Key Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing, China
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33
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Hennig L. Patterns of beauty--omics meets plant development. TRENDS IN PLANT SCIENCE 2007; 12:287-93. [PMID: 17580122 DOI: 10.1016/j.tplants.2007.05.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2007] [Revised: 04/17/2007] [Accepted: 05/31/2007] [Indexed: 05/15/2023]
Abstract
Developmental biology aims to identify mechanisms that govern cell proliferation and differentiation in the body plan formation of multicellular organisms. In the past, developmental biologists described how anatomy and morphology are established during ontogenesis, and developmental geneticists identified many developmental regulators. In contrast to the traditional approaches that mostly focus on one or a few genes at a time, highly parallel profiling technologies have been developed for use in biological research over the past decade. Such parallel profiling technologies probe many genes, transcripts, proteins or metabolites at once. In this review, I discuss the growing impact of transcriptomics, proteomics, metabolomics and modelling on plant developmental biology. Novel profiling technologies will not make traditional gene-centred approaches obsolete but should instead complement forward developmental genetics.
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Affiliation(s)
- Lars Hennig
- Institute of Plant Sciences & Zurich-Basel Plant Science Center, ETH Zurich, LFW E17, CH-8092 Zurich, Switzerland.
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34
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Calsa T, Figueira A. Serial analysis of gene expression in sugarcane (Saccharum spp.) leaves revealed alternative C4 metabolism and putative antisense transcripts. PLANT MOLECULAR BIOLOGY 2007; 63:745-62. [PMID: 17211512 DOI: 10.1007/s11103-006-9121-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2006] [Accepted: 11/25/2006] [Indexed: 05/07/2023]
Abstract
Sugarcane (Saccharum spp.) is a highly efficient biomass and sugar producing crop. Leaf reactions have been considered as potential rate-limiting step for sucrose accumulation in sugarcane stalks. To characterize the sugarcane leaf transcriptome, field-grown mature leaves from cultivar "SP80-3280" were analyzed using Serial Analysis of Gene Expression (SAGE). From 480 sequenced clones, 9,482 valid tags were extracted, with 5,227 unique sequences, from which 3,659 (70%) matched at least a sugarcane assembled sequence (SAS) with putative function; while 872 tags (16.7%) matched SAS with unknown function; 523 (10%) matched SAS without a putative annotation; and only 173 (3.3%) did not match any sugarcane ESTs. Based on gene ontology (GO), photosystem (PS) I reaction center was identified as the most frequent gene product location, followed by the remaining sites of PS I, PS II and thylakoid complexes. For metabolic processes, photosynthesis light harvesting complexes; carbon fixation; and chlorophyll biosynthesis were the most enriched GO-terms. Considering the alternative photosynthetic C(4) cycles, tag frequencies related to phosphoenolpyruvate carboxykinase (PEPCK) and aspartate aminotransferase compared to those for NADP(+)-malic enzyme (NADP-ME) and NADP-malate dehydrogenase, suggested that PEPCK-type decarboxylation appeared to predominate over NADP-ME in mature leaves, although both may occur, opposite to currently assumed in sugarcane. From the unique tag set, 894 tags (17.1%) were assigned as potentially derived from antisense transcripts, while 73 tags (1.4%) were assigned to more than one SAS, suggesting the occurrence of alternative processing. The occurrence of antisense was validated by quantitative reverse transcription amplification. Sugarcane leaf transcriptome provided new insights for functional studies associated with sucrose synthesis and accumulation.
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Affiliation(s)
- Tercilio Calsa
- Laboratório de Melhoramento de Plantas, Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, Brazil
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Robinson SJ, Guenther JD, Lewis CT, Links MG, Parkin IAP. Reaping the Benefits of SAGE. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2007; 406:365-86. [PMID: 18287703 DOI: 10.1007/978-1-59745-535-0_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Serial analysis of gene expression (SAGE) is a powerful technique which yields a digital measure of gene expression through the sequencing of libraries of specific mRNA-derived fragments, namely SAGE tags. This chapter introduces the methods and software tools that are available for researchers to analyze gene expression through SAGE analysis. A detailed examination of SAGE analysis in Arabidopsis thaliana using the publicly available analysis tool, SaskSAGE, is provided. The use of this software allows the user to maximize the information gained from SAGE experiments in a model system with a fully sequenced genome.
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Affiliation(s)
- Stephen J Robinson
- Agriculture and Agri-Food, Saskatoon Research Centre, Saskatoon, Saskatchewan, Canada
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McIntosh S, Watson L, Bundock P, Crawford A, White J, Cordeiro G, Barbary D, Rooke L, Henry R. SAGE of the developing wheat caryopsis. PLANT BIOTECHNOLOGY JOURNAL 2007; 5:69-83. [PMID: 17207258 DOI: 10.1111/j.1467-7652.2006.00218.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Understanding the development of the cereal caryopsis holds the future for metabolic engineering in the interests of enhancing global food production. We have developed a Serial Analysis of Gene Expression (SAGE) data platform to investigate the developing wheat (Triticum aestivum) caryopsis. LongSAGE libraries have been constructed at five time-points post-anthesis to coincide with key processes in caryopsis development. More than 90,000 LongSAGE tags have been sequenced generating 29,261 unique tag sequences across all five libraries. Tag abundance, generated from cumulative tag counts, provides insight into the redundancy and diversity of each library. Annotation of the 500 most abundant tags spanning development highlights the array of functional groups being expressed. The relative frequency of these more abundant transcripts allows quantitative analysis of patterns of expression during grain development. We have identified activities of cellular proliferation/differentiation, the accumulation of storage proteins and starch biosynthesis. The abundance of calcium-dependent protein kinases indicate their importance in signalling across development. Acquisition of a broad array of defence coincides with storage accumulation and is dominated by inhibitors of amylase activity. Differential expression profiles of abundant tags from each library reveal the coordinated expression of genes responsible for the cellular events constituting caryopsis development. This SAGE platform has also provided a resource of novel sequence and expression information including the identification of potentially useful promoter activities. Further investigations into both the abundant and low expressing transcripts will provide greater insight into wheat caryopsis development and assist in wheat improvement programmes.
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Affiliation(s)
- Shane McIntosh
- Grain Foods CRC, Centre for Plant Conservation Genetics, Southern Cross University, PO Box 157, Lismore, NSW 2480 Australia.
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37
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Affiliation(s)
- Siobhan M Brady
- Department of Biology and Institute for Genome Sciences and Policy Duke University Durham, NC 27708, USA
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Alonso JM, Ecker JR. Moving forward in reverse: genetic technologies to enable genome-wide phenomic screens in Arabidopsis. Nat Rev Genet 2006; 7:524-36. [PMID: 16755288 DOI: 10.1038/nrg1893] [Citation(s) in RCA: 186] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Genome sequencing, in combination with various computational and empirical approaches to sequence annotation, has made possible the identification of more than 30,000 genes in Arabidopsis thaliana. Increasingly sophisticated genetic tools are being developed with the long-term goal of understanding how the coordinated activity of these genes gives rise to a complex organism. The combination of classical forward genetics with recently developed genome-wide, gene-indexed mutant collections is beginning to revolutionize the way in which gene functions are studied in plants. High-throughput screens using these mutant populations should provide a means to analyse plant gene functions--the phenome--on a genomic scale.
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Affiliation(s)
- Jose M Alonso
- North Carolina State University, Department of Genetics, Raleigh, North Carolina 27695-7614, USA.
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39
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Neill JD, Ridpath JF, Liebler-Tenorio E. Global gene expression profiling of Bovine immature B cells using serial analysis of gene expression. Anim Biotechnol 2006; 17:21-31. [PMID: 16621757 DOI: 10.1080/10495390500460957] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The Peyer's patches of the small intestine are important sites of antigen processing. The follicles of the Peyer's patches receive the antigen transported by the M cells at the mucosal surface and then play a major role in development of both protective humoral and mucosal immune responses. Serial analysis of gene expression (SAGE) was employed to derive the global gene expression profile of B lymphocytes isolated from the IPPF. Analysis of the SAGE data revealed the identity of genes and the level to which they are expressed by IPPF B lymphocytes. This analysis indicated that they were metabolically active and that the transcripts encoding proteins necessary for a response to antigen presentation were expressed. These transcripts included the B cell receptor components CD76a and b (Ig-alpha and Ig-beta) and accessory c-Src family kinases Lyn and Blk. Furthermore, many of the positive and negative regulators, and accessory proteins that are necessary for B cell antigen receptor signaling were identified. Also present were transcripts encoding interleukins and their cognate receptors. Overall, this SAGE analysis yielded a global picture of gene expression in IPPF B lymphocytes and provides a starting point for the comparison of gene expression in further functional studies.
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Affiliation(s)
- John D Neill
- Virus and Prion Diseases of Livestock Research Unit, USDA, ARS, National Animal Disease Center, Ames, Iowa 50010, USA.
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40
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Abstract
Systems theory has been applied to process analysis in a variety of scientific disciplines from engineering to evolutionary biology. In the recent postgenomic era, the accumulation of an enormous amount of data gained from a variety of technologies has led to a revisiting of systems theory concepts. This systems biology approach has been integral in understanding a variety of processes in a number of model organisms. This review gives an overview of systems biology approaches, from component identification to modeling of networks. Various features of the root, including its development and the availability of high resolution gene expression data sets that describe root development, make the root amenable to a systems approach. The current status of systems approaches to understanding root development is reviewed.
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White J, Pacey-Miller T, Crawford A, Cordeiro G, Barbary D, Bundock P, Henry R. Abundant transcripts of malting barley identified by serial analysis of gene expression (SAGE). PLANT BIOTECHNOLOGY JOURNAL 2006; 4:289-301. [PMID: 17147635 DOI: 10.1111/j.1467-7652.2006.00181.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Serial analysis of gene expression (SAGE) was applied to the major cereal crop barley (Hordeum vulgare) to characterize the transcriptional profile of grain during the malting process. Seven SAGE libraries were generated from seed at different time points during malting, in addition to one library from dry mature seed. A total of 155,206 LongSAGE tags, representing 41,909 unique sequences, was generated. This study reports an in-depth analysis of the most abundant transcripts from each of eight specific time points in a malting barley time course. The 100 most abundant tags from each library were analysed to identify the putative functional role of highly abundant transcripts. The largest functional groups included transcripts coding for stress response and cell defence, ribosomal proteins and storage proteins. The most abundant tag represented B22EL8, a barley metallothionein, which showed significant up-regulation across the malting time course. Considerable changes in the abundance profiles of some of the highly abundant tags occurred at 24 h post-steeping, indicating that it may be an important time point for gene expression changes associated with barley seed germination.
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Affiliation(s)
- Jessica White
- Grain Foods CRC, Centre for Plant Conservation Genetics, Southern Cross University, PO Box 157, Lismore, NSW 2480, Australia
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Knoll-Gellida A, André M, Gattegno T, Forgue J, Admon A, Babin PJ. Molecular phenotype of zebrafish ovarian follicle by serial analysis of gene expression and proteomic profiling, and comparison with the transcriptomes of other animals. BMC Genomics 2006; 7:46. [PMID: 16526958 PMCID: PMC1488847 DOI: 10.1186/1471-2164-7-46] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2005] [Accepted: 03/09/2006] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The ability of an oocyte to develop into a viable embryo depends on the accumulation of specific maternal information and molecules, such as RNAs and proteins. A serial analysis of gene expression (SAGE) was carried out in parallel with proteomic analysis on fully-grown ovarian follicles from zebrafish (Danio rerio). The data obtained were compared with ovary/follicle/egg molecular phenotypes of other animals, published or available in public sequence databases. RESULTS Sequencing of 27,486 SAGE tags identified 11,399 different ones, including 3,329 tags with an occurrence superior to one. Fifty-eight genes were expressed at over 0.15% of the total population and represented 17.34% of the mRNA population identified. The three most expressed transcripts were a rhamnose-binding lectin, beta-actin 2, and a transcribed locus similar to the H2B histone family. Comparison with the large-scale expressed sequence tags sequencing approach revealed highly expressed transcripts that were not previously known to be expressed at high levels in fish ovaries, like the short-sized polarized metallothionein 2 transcript. A higher sensitivity for the detection of transcripts with a characterized maternal genetic contribution was also demonstrated compared to large-scale sequencing of cDNA libraries. Ferritin heavy polypeptide 1, heat shock protein 90-beta, lactate dehydrogenase B4, beta-actin isoforms, tubulin beta 2, ATP synthase subunit 9, together with 40 S ribosomal protein S27a, were common highly-expressed transcripts of vertebrate ovary/unfertilized egg. Comparison of transcriptome and proteome data revealed that transcript levels provide little predictive value with respect to the extent of protein abundance. All the proteins identified by proteomic analysis of fully-grown zebrafish follicles had at least one transcript counterpart, with two exceptions: eosinophil chemotactic cytokine and nothepsin. CONCLUSION This study provides a complete sequence data set of maternal mRNA stored in zebrafish germ cells at the end of oogenesis. This catalogue contains highly-expressed transcripts that are part of a vertebrate ovarian expressed gene signature. Comparison of transcriptome and proteome data identified downregulated transcripts or proteins potentially incorporated in the oocyte by endocytosis. The molecular phenotype described provides groundwork for future experimental approaches aimed at identifying functionally important stored maternal transcripts and proteins involved in oogenesis and early stages of embryo development.
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Affiliation(s)
- Anja Knoll-Gellida
- Génomique et Physiologie des Poissons, UMR NUAGE, Université Bordeaux 1, 33405 Talence cedex, France
| | - Michèle André
- Génomique et Physiologie des Poissons, UMR NUAGE, Université Bordeaux 1, 33405 Talence cedex, France
| | - Tamar Gattegno
- Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Jean Forgue
- Génomique et Physiologie des Poissons, UMR NUAGE, Université Bordeaux 1, 33405 Talence cedex, France
| | - Arie Admon
- Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Patrick J Babin
- Génomique et Physiologie des Poissons, UMR NUAGE, Université Bordeaux 1, 33405 Talence cedex, France
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Escobar MA, Geisler DA, Rasmusson AG. Reorganization of the alternative pathways of the Arabidopsis respiratory chain by nitrogen supply: opposing effects of ammonium and nitrate. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2006; 45:775-88. [PMID: 16460511 DOI: 10.1111/j.1365-313x.2005.02640.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The mitochondrial oxidative phosphorylation system in plants possesses a variety of alternative pathways that decrease respiratory ATP production. These alternative pathways are mediated by three classes of bypass proteins: the type II NAD(P)H dehydrogenases (which circumvent complex I of the electron transport chain), the alternative oxidases (AOXs; which circumvent complexes III and IV) and the uncoupling proteins (which circumvent ATP synthase). We have monitored the expression of all genes encoding respiratory bypass proteins in Arabidopsis thaliana growing with different sources of inorganic nitrogen (N). Resupply of nitrate (NO) to N-limited seedling cultures caused a decrease in the transcript abundance of several type II NAD(P)H dehydrogenase and AOX genes, while resupply of ammonium (NH) led to broad increases in expression in the same gene families. Similar results were observed upon switching between nitrate and ammonium in the absence of N stress. Nitrate signalling was found to be mediated primarily by the nitrate ion itself, whereas ammonium regulation was dependent upon assimilation and affected by changes in apoplastic pH. Corresponding alterations in alternative respiratory pathway capacities were apparent in seedlings supplied with either nitrate or ammonium as an N source and in mitochondria purified from the seedlings. Specifically, AOX capacity and protein abundance, as well as calcium-dependent external NADH oxidation, were substantially elevated after growth on ammonium. The increased capacity of respiratory bypass pathways after switching from nitrate to ammonium was correlated to an overall respiratory increase.
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Affiliation(s)
- Matthew A Escobar
- Department of Cell and Organism Biology, Lund University, Sölvegatan 35B, SE-223 62 Lund, Sweden
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Coemans B, Matsumura H, Terauchi R, Remy S, Swennen R, Sági L. SuperSAGE combined with PCR walking allows global gene expression profiling of banana (Musa acuminata), a non-model organism. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 111:1118-26. [PMID: 16133315 DOI: 10.1007/s00122-005-0039-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2005] [Accepted: 07/04/2005] [Indexed: 05/04/2023]
Abstract
Super-serial analysis of gene expression (SuperSAGE) was used to characterize, for the first time, the global gene expression pattern in banana (Musa acuminata). A total of 10,196 tags were generated from leaf tissue, representing 5,292 expressed genes. Forty-nine tags of the top 100 most abundantly expressed transcripts were annotated by homology to cDNA or EST sequences. Typically for leaf tissue, analysis of the transcript profiles showed that the majority of the abundant transcripts are involved in energy production, mainly photosynthesis. However, the most abundant tag was derived from a type 3 metallothionein transcript, which accounted for nearly 3% of total transcripts analysed. Furthermore, the 26-bp long SuperSAGE tags were applied in 3'-rapid amplification of cDNA ends (3'RACE) for the identification of unknown tags. In combination with thermal asymmetric interlaced PCR (TAIL-PCR), this allowed the recovery of a full gene sequence of a novel NADPH:protochlorophyllide oxidoreductase, the key enzyme in chlorophyll biosynthesis. SuperSAGE in conjunction with 3'RACE and TAIL-PCR will be a powerful tool for transcriptomics of non-model, but otherwise important organisms.
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Affiliation(s)
- Bert Coemans
- Laboratory of Tropical Crop Improvement, Katholieke Universiteit Leuven, Kasteelpark Arenberg 13, 3001 Leuven, Belgium.
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Poroyko V, Hejlek LG, Spollen WG, Springer GK, Nguyen HT, Sharp RE, Bohnert HJ. The maize root transcriptome by serial analysis of gene expression. PLANT PHYSIOLOGY 2005; 138:1700-10. [PMID: 15965024 PMCID: PMC1176439 DOI: 10.1104/pp.104.057638] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Serial Analysis of Gene Expression was used to define number and relative abundance of transcripts in the root tip of well-watered maize seedlings (Zea mays cv FR697). In total, 161,320 tags represented a minimum of 14,850 genes, based on at least two tags detected per transcript. The root transcriptome has been sampled to an estimated copy number of approximately five transcripts per cell. An extrapolation from the data and testing of single-tag identifiers by reverse transcription-PCR indicated that the maize root transcriptome should amount to at least 22,000 expressed genes. Frequency ranged from low copy number (2-5, 68.8%) to highly abundant transcripts (100-->1,200; 1%). Quantitative reverse transcription-PCR for selected transcripts indicated high correlation with tag frequency. Computational analysis compared this set with known maize transcripts and other root transcriptome models. Among the 14,850 tags, 7,010 (47%) were found for which no maize cDNA or gene model existed. Comparing the maize root transcriptome with that in other plants indicated that highly expressed transcripts differed substantially; less than 5% of the most abundant transcripts were shared between maize and Arabidopsis (Arabidopsis thaliana). Transcript categories highlight functions of the maize root tip. Significant variation in abundance characterizes transcripts derived from isoforms of individual enzymes in biochemical pathways.
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Affiliation(s)
- V Poroyko
- Department of Plant Biology , University of Illinois, Urbana, Illinois 61801, USA
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Bao J, Lee S, Chen C, Zhang X, Zhang Y, Liu S, Clark T, Wang J, Cao M, Yang H, Wang SM, Yu J. Serial analysis of gene expression study of a hybrid rice strain (LYP9) and its parental cultivars. PLANT PHYSIOLOGY 2005; 138:1216-31. [PMID: 16009997 PMCID: PMC1176396 DOI: 10.1104/pp.105.060988] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Using the serial analysis of gene expression technique, we surveyed transcriptomes of three major tissues (panicles, leaves, and roots) of a super-hybrid rice (Oryza sativa) strain, LYP9, in comparison to its parental cultivars, 93-11 (indica) and PA64s (japonica). We acquired 465,679 tags from the serial analysis of gene expression libraries, which were consolidated into 68,483 unique tags. Focusing our initial functional analyses on a subset of the data that are supported by full-length cDNAs and the tags (genes) differentially expressed in the hybrid at a significant level (P<0.01), we identified 595 up-regulated (22 tags in panicles, 228 in leaves, and 345 in roots) and 25 down-regulated (seven tags in panicles, 15 in leaves, and three in roots) in LYP9. Most of the tag-identified and up-regulated genes were found related to enhancing carbon- and nitrogen-assimilation, including photosynthesis in leaves, nitrogen uptake in roots, and rapid growth in both roots and panicles. Among the down-regulated genes in LYP9, there is an essential enzyme in photorespiration, alanine:glyoxylate aminotransferase 1. Our study adds a new set of data crucial for the understanding of molecular mechanisms of heterosis and gene regulation networks of the cultivated rice.
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Affiliation(s)
- JingYue Bao
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
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Asamizu E, Nakamura Y, Sato S, Tabata S. Comparison of the transcript profiles from the root and the nodulating root of the model legume Lotus japonicus by serial analysis of gene expression. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2005; 18:487-98. [PMID: 15915647 DOI: 10.1094/mpmi-18-0487] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
We performed a comprehensive transcript analysis on the early stage of root nodulation in the model legume Lotus japonicus by serial analysis of gene expression (SAGE). SAGE libraries were made from uninfected roots and nodulating roots abundant in nodule primordia, and 85,482 and 80,233 SAGE tags were recovered, respectively. Comparison of the tag frequency identified 407 tag species that appeared in significantly greater numbers in the nodulating root than in the uninfected root, and the converse was found for 428 tag species. Gene identification of the tags was performed by matching them to L. japonicus expressed sequence tag sequences. We made several novel findings by applying SAGE to transcript analysis of legume root nodulation. A gene that showed the most significant increase in tag number upon nodulation has not been described previously. Different levels of transcription induction among leghemoglobin gene paralogs were found, indicating the effectiveness of SAGE in discriminating different gene family members. We identified genes for 44 unknown tags by means of reverse SAGE. We found 11 antisense tags that increased during nodulation, indicating that regulation of gene expression by antisense transcripts may occur in an organ-dependent manner.
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Affiliation(s)
- Erika Asamizu
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan.
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48
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Rouached H, Berthomieu P, El Kassis E, Cathala N, Catherinot V, Labesse G, Davidian JC, Fourcroy P. Structural and Functional Analysis of the C-terminal STAS (Sulfate Transporter and Anti-sigma Antagonist) Domain of the Arabidopsis thaliana Sulfate Transporter SULTR1.2. J Biol Chem 2005; 280:15976-83. [PMID: 15718229 DOI: 10.1074/jbc.m501635200] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The C-terminal region of sulfate transporters from plants and animals belonging to the SLC26 family members shares a weak but significant similarity with the Bacillus sp. anti-anti-sigma protein SpoIIAA, thus defining the STAS domain (sulfate transporter and anti-sigma antagonist). The present study is a structure/function analysis of the STAS domain of SULTR1.2, an Arabidopsis thaliana sulfate transporter. A three-dimensional model of the SULTR1.2 STAS domain was built which indicated that it shares the SpoIIAA folds. Moreover, the phosphorylation site, which is necessary for SpoIIAA activity, is conserved in the SULTR1.2 STAS domain. The model was used to direct mutagenesis studies using a yeast mutant defective for sulfate transport. Truncation of the whole SULTR1.2 STAS domain resulted in the loss of sulfate transport function. Analyses of small deletions and mutations showed that the C-terminal tail of the SULTR1.2 STAS domain and particularly two cysteine residues plays an important role in sulfate transport by SULTR1.2. All the substitutions made at the putative phosphorylation site Thr-587 led to a complete loss of the sulfate transport function of SULTR1.2. The reduction or suppression of sulfate transport of the SULTR1.2 mutants in yeast was not due to an incorrect targeting to the plasma membrane. Both our three-dimensional modeling and mutational analyses strengthen the hypothesis that the SULTR1.2 STAS domain is involved in protein-protein interactions that could control sulfate transport.
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Affiliation(s)
- Hatem Rouached
- Biochimie et Physiologie Moléculaire des Plantes, CNRS (UMR 5004), Université Montpellier 2, Institut National de la Recherche Agronomique, Ecole Nationale Supérieure Agronomique, Montpellier, 34060 France
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Ibrahim AFM, Hedley PE, Cardle L, Kruger W, Marshall DF, Muehlbauer GJ, Waugh R. A comparative analysis of transcript abundance using SAGE and Affymetrix arrays. Funct Integr Genomics 2005; 5:163-74. [PMID: 15714318 DOI: 10.1007/s10142-005-0135-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2004] [Revised: 12/13/2004] [Accepted: 12/22/2004] [Indexed: 12/18/2022]
Abstract
A number of methods are currently used for gene expression profiling. They differ in scale, economy and sensitivity. We present the results of a direct comparison between serial analysis of gene expression (SAGE) and the Barley1 Affymetrix GeneChip. Both technology platforms were used to obtain quantitative measurements of transcript abundance using identical RNA samples and assessed for their ability to quantify differential gene expression. For SAGE, a total of 82,122 tags were generated from two independent libraries representing whole developing barley caryopsis and dissected embryos. The Barley1 GeneChip contains 22,791 probe sets. Results obtained from both methods are generally comparable, indicating that both will lead to similar conclusions regarding transcript levels and differential gene expression. However, excluding singletons, 24.4% of the unique SAGE tags had no corresponding probe set on the Barley1 array indicating that a broader snapshot of gene expression was obtained by SAGE. Discrepancies were observed for a number of "genes" and these are discussed.
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Affiliation(s)
- Adel F M Ibrahim
- Genome Dynamics, Scottish Crop Research Institute, Invergowrie, Dundee, UK.
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