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Chen H, Chou M, Wang X, Liu S, Zhang F, Wei G. Profiling of differentially expressed genes in roots of Robinia pseudoacacia during nodule development using suppressive subtractive hybridization. PLoS One 2013; 8:e63930. [PMID: 23776436 PMCID: PMC3679122 DOI: 10.1371/journal.pone.0063930] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 04/09/2013] [Indexed: 11/23/2022] Open
Abstract
Background Legume-rhizobium symbiosis is a complex process that is regulated in the host plant cell through gene expression network. Many nodulin genes that are upregulated during different stages of nodulation have been identified in leguminous herbs. However, no nodulin genes in woody legume trees, such as black locust (Robinia pseudoacacia), have yet been reported. Methodology/Principal findings To identify the nodulin genes involved in R. pseudoacacia-Mesorhizobium amorphae CCNWGS0123 symbiosis, a suppressive subtractive hybridization approach was applied to reveal profiling of differentially expressed genes and two subtracted cDNA libraries each containing 600 clones were constructed. Then, 114 unigenes were identified from forward SSH library by differential screening and the putative functions of these translational products were classified into 13 categories. With a particular interest in regulatory genes, twenty-one upregulated genes encoding potential regulatory proteins were selected based on the result of reverse transcription-polymerase chain reaction (RT-PCR) analysis. They included nine putative transcription genes, eight putative post-translational regulator genes and four membrane protein genes. The expression patterns of these genes were further analyzed by quantitative RT-PCR at different stages of nodule development. Conclusions The data presented here offer the first insights into the molecular foundation underlying R. pseudoacacia–M. amorphae symbiosis. A number of regulatory genes screened in the present study revealed a high level of regulatory complexity (transcriptional, post-transcriptional, translational and post-translational) that is likely essential to develop symbiosis. In addition, the possible roles of these genes in black locust nodulation are discussed.
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Affiliation(s)
- Hongyan Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi, China
| | - Minxia Chou
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi, China
| | - Xinye Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi, China
| | - Sisi Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi, China
| | - Feilong Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi, China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi, China
- * E-mail:
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Takanashi K, Sugiyama A, Yazaki K. Involvement of auxin distribution in root nodule development of Lotus japonicus. PLANTA 2011; 234:73-81. [PMID: 21369920 DOI: 10.1007/s00425-011-1385-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2010] [Accepted: 02/11/2011] [Indexed: 05/23/2023]
Abstract
The symbiosis between legume plants and rhizobia causes the development of new organs, nodules which function as an apparatus for nitrogen fixation. In this study, the roles of auxin in nodule development in Lotus japonicus have been demonstrated using molecular genetic tools and auxin inhibitors. The expression of an auxin-reporter GH3 fused to β-glucuronidase (GUS) was analyzed in L. japonicus roots, and showed a strong signal in the central cylinder of the root, whereas upon rhizobium infection, generation of GUS signal was observed at the dividing outer cortical cells during the first nodule cell divisions. When nodules were developed to maturity, strong GUS staining was detected in vascular tissues of nodules, suggesting distinct auxin involvement in the determinate nodule development. Numbers and the development of nodules were affected by auxin transport inhibitors (1-naphthylphthalamic acid, NPA and triindobenzoic acid, TIBA), and by a newly synthesized auxin antagonist, α-(phenyl ethyl-2-one)-indole-3-acetic acid (PEO-IAA). The common phenotypical alteration by these auxin inhibitors was the inhibition in forming lenticel which is normally developed on the nodule surface from the root outer cortex. The inhibition of lenticel formation was correlated with the inhibition of nodule vascular bundle development. These results indicate that auxin is required for the normal development of determinate nodules in a multidirectional manner.
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Affiliation(s)
- Kojiro Takanashi
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji 611-0011, Japan
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Wang Y, Li P, Cao X, Wang X, Zhang A, Li X. Identification and expression analysis of miRNAs from nitrogen-fixing soybean nodules. Biochem Biophys Res Commun 2009; 378:799-803. [PMID: 19084500 DOI: 10.1016/j.bbrc.2008.11.140] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2008] [Accepted: 11/25/2008] [Indexed: 12/28/2022]
Abstract
miRNAs are approximately 21nt non-coding RNAs and play important roles in plant development and response to stress. Symbiotic nitrogen fixation (SNF) is agronomically important for reducing the need of nitrogen fertilizers. The soybean root nodule is the place where SNF takes place. To identify miRNAs that are possibly involved in nitrogen fixation in soybean functional nitrogen-fixing nodules, a small library of RNAs was constructed from the functional nodules harvested 28 days after inoculation with rhizobium. Thirty-two small RNA sequences were identified as belonging to 11 miRNA families. Eight miRNAs are conserved across plant species, twenty are specific to soybean, and the four remaining miRNAs are novel. Expression analysis revealed that miRNAs were differentially expressed in the different tissues. Combinatorial miRNA target prediction identified genes that are involved in multiple biological processes. The results suggest that miRNAs play critical and diverse roles in SNF, nutrient acquisition, and plant development.
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Affiliation(s)
- Yanwei Wang
- The State Key Laboratory of Plant Cell & Chromosome Engineering, Center of Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, PR China
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Kakar K, Wandrey M, Czechowski T, Gaertner T, Scheible WR, Stitt M, Torres-Jerez I, Xiao Y, Redman JC, Wu HC, Cheung F, Town CD, Udvardi MK. A community resource for high-throughput quantitative RT-PCR analysis of transcription factor gene expression in Medicago truncatula. PLANT METHODS 2008; 4:18. [PMID: 18611268 PMCID: PMC2490690 DOI: 10.1186/1746-4811-4-18] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2008] [Accepted: 07/08/2008] [Indexed: 05/18/2023]
Abstract
BACKGROUND Medicago truncatula is a model legume species that is currently the focus of an international genome sequencing effort. Although several different oligonucleotide and cDNA arrays have been produced for genome-wide transcript analysis of this species, intrinsic limitations in the sensitivity of hybridization-based technologies mean that transcripts of genes expressed at low-levels cannot be measured accurately with these tools. Amongst such genes are many encoding transcription factors (TFs), which are arguably the most important class of regulatory proteins. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) is the most sensitive method currently available for transcript quantification, and one that can be scaled up to analyze transcripts of thousands of genes in parallel. Thus, qRT-PCR is an ideal method to tackle the problem of TF transcript quantification in Medicago and other plants. RESULTS We established a bioinformatics pipeline to identify putative TF genes in Medicago truncatula and to design gene-specific oligonucleotide primers for qRT-PCR analysis of TF transcripts. We validated the efficacy and gene-specificity of over 1000 TF primer pairs and utilized these to identify sets of organ-enhanced TF genes that may play important roles in organ development or differentiation in this species. This community resource will be developed further as more genome sequence becomes available, with the ultimate goal of producing validated, gene-specific primers for all Medicago TF genes. CONCLUSION High-throughput qRT-PCR using a 384-well plate format enables rapid, flexible, and sensitive quantification of all predicted Medicago transcription factor mRNAs. This resource has been utilized recently by several groups in Europe, Australia, and the USA, and we expect that it will become the 'gold-standard' for TF transcript profiling in Medicago truncatula.
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Affiliation(s)
- Klementina Kakar
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Maren Wandrey
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Tomasz Czechowski
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Tanja Gaertner
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Wolf-Rüdiger Scheible
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Mark Stitt
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Ivone Torres-Jerez
- The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Yongli Xiao
- The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, 20850, USA
| | - Julia C Redman
- The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, 20850, USA
| | - Hank C Wu
- The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, 20850, USA
| | - Foo Cheung
- The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, 20850, USA
| | - Christopher D Town
- The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, 20850, USA
| | - Michael K Udvardi
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
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Udvardi MK, Kakar K, Wandrey M, Montanari O, Murray J, Andriankaja A, Zhang JY, Benedito V, Hofer JMI, Chueng F, Town CD. Legume transcription factors: global regulators of plant development and response to the environment. PLANT PHYSIOLOGY 2007; 144:538-49. [PMID: 17556517 PMCID: PMC1914172 DOI: 10.1104/pp.107.098061] [Citation(s) in RCA: 162] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2007] [Accepted: 03/24/2007] [Indexed: 05/15/2023]
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Manthey K, Krajinski F, Hohnjec N, Firnhaber C, Pühler A, Perlick AM, Küster H. Transcriptome profiling in root nodules and arbuscular mycorrhiza identifies a collection of novel genes induced during Medicago truncatula root endosymbioses. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2004; 17:1063-77. [PMID: 15497399 DOI: 10.1094/mpmi.2004.17.10.1063] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Transcriptome profiling based on cDNA array hybridizations and in silico screening was used to identify Medicago truncatula genes induced in both root nodules and arbuscular mycorrhiza (AM). By array hybridizations, we detected several hundred genes that were upregulated in the root nodule and the AM symbiosis, respectively, with a total of 75 genes being induced during both interactions. The second approach based on in silico data mining yielded several hundred additional candidate genes with a predicted symbiosis-enhanced expression. A subset of the genes identified by either expression profiling tool was subjected to quantitative real-time reverse-transcription polymerase chain reaction for a verification of their symbiosis-induced expression. That way, induction in root nodules and AM was confirmed for 26 genes, most of them being reported as symbiosis-induced for the first time. In addition to delivering a number of novel symbiosis-induced genes, our approach identified several genes that were induced in only one of the two root endosymbioses. The spatial expression patterns of two symbiosis-induced genes encoding an annexin and a beta-tubulin were characterized in transgenic roots using promoter-reporter gene fusions.
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Affiliation(s)
- Katja Manthey
- Lehrstuhl für Genetik, Fakultät für Biologie, Universität Bielefeld, Postfach 100131, D-33501 Bielefeld, Germany
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Andersen SU, Cvitanich C, Hougaard BK, Roussis A, Grønlund M, Jensen DB, Frøkjaer LA, Jensen EO. The glucocorticoid-inducible GVG system causes severe growth defects in both root and shoot of the model legume Lotus japonicus. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2003; 16:1069-1076. [PMID: 14651340 DOI: 10.1094/mpmi.2003.16.12.1069] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
During the past decade, the legume Lotus japonicus has emerged as an important model system for study of symbiotic nitrogen fixation. Controlled expression of genes involved in symbiosis from an inducible promoter at specific time points would be a valuable tool for investigating gene function in L. japonicus. We have attempted to study the function of the putative transcription factors LjNDX and LjCPP1 by expression from the GVG inducible system. This study showed that the GVG system itself causes growth disturbances in L. japonicus. Shoot internode elongation and root pericycle cell division are affected when the chimeric GVG transcription factor is activated. We suggest that deficient auxin signaling could cause the phenotype observed and conclude that the GVG inducible system is not well suited for use in the model legume L. japonicus.
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Affiliation(s)
- Stig Uggerhøj Andersen
- Laboratory of Gene Expression, Department of Molecular Biology, University of Aarhus, Gustav Wieds Vej 10, DK-8000 Aarhus C., Denmark
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