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An Italian functional genomic resource for Medicago truncatula
Andrea Porceddu, Francesco Panara, Ornella Calderini, Lorna Molinari, Paola Taviani, Luisa Lanfaloni, Carla Scotti, Maria Carelli, Laura Scaramelli, Gianluca Bruschi, Viviane Cosson, Pascal Ratet, Henri de Larembergue, Gerard Duc, Efisio Piano, Sergio Arcioni
BMC Research Notes , 2008, DOI: 10.1186/1756-0500-1-129
Abstract: Our report is on the production of three complementary mutant collections of the model species Medicago truncatula produced in Italy in the frame of a national genomic initiative. Well established strategies were used: Tnt1 mutagenesis, TILLING and activation tagging. Both forward and reverse genetics screenings proved the efficiency of the mutagenesis approaches adopted, enabling the isolation of interesting mutants which are in course of characterization. We anticipate that the reported collections will be complementary to the recently established functional genomics tools developed for Medicago truncatula both in Europe and in the United States.Medicago truncatula has emerged as one of the two model systems for legume species.The Medicago truncatula consortium (supported by US National Science Foundation and Samuel Roberts Noble Foundation in the USA, and in Europe, mainly by the European Union) has made significant achievements in genome and EST sequencing with a goal of completion of the gene space in 2008 [1]. The amount of information gained from the sequencing will assist studies related to gene function discovery. At the moment three complementary strategies have been chosen to create large mutant collections in M. truncatula: transposon tagging, fast neutron mutagenesis and TILLING. T-DNA tagging, one of the most popular strategies in Arabidopsis, did not represent the best option for M. truncatula because of the lack of a high throughput transformation system [2,3]. A population of more than 7600 Tnt1 lines was recently published [4] and is being developed as a public resource at the Samuel Roberts Noble Foundation http://www.noble.org webcite. Functional genomics platforms are also available in Europe at the John Innes Genome Laboratory http://jicgenomelab.co.uk/ webcite which, at the moment, provides access to a large population of deletion tilled lines and tilled lines for reverse genetic screening. Both resources were established during the course of
Identification of drought-responsive microRNAs in Medicago truncatula by genome-wide high-throughput sequencing
Tianzuo Wang, Lei Chen, Mingui Zhao, Qiuying Tian, Wen-Hao Zhang
BMC Genomics , 2011, DOI: 10.1186/1471-2164-12-367
Abstract: Two hundreds eighty three and 293 known miRNAs were identified from the control and drought stress libraries, respectively. In addition, 238 potential candidate miRNAs were identified, and among them 14 new miRNAs and 15 new members of known miRNA families whose complementary miRNA*s were also detected. Both high-throughput sequencing and RT-qPCR confirmed that 22 members of 4 miRNA families were up-regulated and 10 members of 6 miRNA families were down-regulated in response to drought stress. Among the 29 new miRNAs/new members of known miRNA families, 8 miRNAs were responsive to drought stress with both 4 miRNAs being up- and down-regulated, respectively. The known and predicted targets of the drought-responsive miRNAs were found to be involved in diverse cellular processes in plants, including development, transcription, protein degradation, detoxification, nutrient status and cross adaptation.We identified 32 known members of 10 miRNA families and 8 new miRNAs/new members of known miRNA families that were responsive to drought stress by high-throughput sequencing of small RNAs from M. truncatula. These findings are of importance for our understanding of the roles played by miRNAs in response of plants to abiotic stress in general and drought stress in particular.Endogenous small interfering RNAs (siRNAs) and microRNAs (miRNAs) are the two most abundant classes of plant small RNAs (sRNAs). The small RNAs are processed in the nucleus from longer precursor transcripts that form distinct secondary structures. The miRNAs down-regulate gene expression by targeting specific messenger RNAs (mRNAs) in both plants and animals [1,2].miRNAs were initially discovered in Caenorhabditis elegans as developmental timing regulators in 1994 [3]. The existence of miRNAs in organisms including plants, mammals and virus has widely been recognized. The biogenesis of miRNAs in plants is a multi-step enzymatic process involving incorporation of miRNAs into the RNA-induced silencing comp
Transcriptional profiling of Medicago truncatula under salt stress identified a novel CBF transcription factor MtCBF4 that plays an important role in abiotic stress responses
Daofeng Li, Yunqin Zhang, Xiaona Hu, Xiaoye Shen, Lei Ma, Zhen Su, Tao Wang, Jiangli Dong
BMC Plant Biology , 2011, DOI: 10.1186/1471-2229-11-109
Abstract: A microarray experiment was conducted using root samples collected 6, 24, and 48 h after application of 180 mM NaCl. Analysis of 11 statistically significant expression profiles revealed different behaviors between primary and secondary metabolism pathways in response to external stress. Secondary metabolism that helps to maintain osmotic balance was induced. One of the highly induced transcription factor genes was successfully cloned, and was named MtCBF4. Phylogenetic analysis revealed that MtCBF4, which belongs to the AP2-EREBP transcription factor family, is a novel member of the CBF transcription factor in M. truncatula. MtCBF4 is shown to be a nuclear-localized protein. Expression of MtCBF4 in M. truncatula was induced by most of the abiotic stresses, including salt, drought, cold, and abscisic acid, suggesting crosstalk between these abiotic stresses. Transgenic Arabidopsis over-expressing MtCBF4 enhanced tolerance to drought and salt stress, and activated expression of downstream genes that contain DRE elements. Over-expression of MtCBF4 in M. truncatula also enhanced salt tolerance and induced expression level of corresponding downstream genes.Comprehensive transcriptomic analysis revealed complex mechanisms exist in plants in response to salt stress. The novel transcription factor gene MtCBF4 identified here played an important role in response to abiotic stresses, indicating that it might be a good candidate gene for genetic improvement to produce stress-tolerant plants.Salt stress has a major effect on food production and quality worldwide by limiting the growth, development, and yield of crops [1]. More than one-fifth of the world's arable land is now under the threat of salt stress. As the global population increases, water resource management is deteriorating and environmental pollution is worsening; salinization of land is becoming more extreme and has begun to hinder development of agricultural economics.Salt stress can damage plants by several mech
Overall picture of expressed Heat Shock Factors in Glycine max, Lotus japonicus and Medicago truncatula
Soares-Cavalcanti, Nina M.;Belarmino, Luís C;Kido, Ederson A.;Pandolfi, Valesca;Marcelino-Guimar?es, Francismar C.;Rodrigues, Fabiana A.;Pereira, Gon?alo A.G.;Benko-Iseppon, Ana M.;
Genetics and Molecular Biology , 2012, DOI: 10.1590/S1415-47572012000200006
Abstract: heat shock (hs) leads to the activation of molecular mechanisms, known as hs-response, that prevent damage and enhance survival under stress. plants have a flexible and specialized network of heat shock factors (hsfs), which are transcription factors that induce the expression of heat shock proteins. the present work aimed to identify and characterize the glycine max hsf repertory in the soybean genome project (genosoja platform), comparing them with other legumes (medicago truncatula and lotus japonicus) in view of current knowledge of arabidopsis thaliana. the hsf characterization in leguminous plants led to the identification of 25, 19 and 21 candidate ests in soybean, lotus and medicago, respectively. a search in the supersage libraries revealed 68 tags distributed in seven hsf gene types. from the total number of obtained tags, more than 70% were related to root tissues (water deficit stress libraries vs. controls), indicating their role in abiotic stress responses, since the root is the first tissue to sense and respond to abiotic stress. moreover, as heat stress is related to the pressure of dryness, a higher hsf expression was expected at the water deficit libraries. on the other hand, expressive hsf candidates were obtained from the library inoculated with asian soybean rust, inferring crosstalk among genes associated with abiotic and biotic stresses. evolutionary relationships among sequences were consistent with different hsf classes and subclasses. expression profiling indicated that regulation of specific genes is associated with the stage of plant development and also with stimuli from other abiotic stresses pointing to the maintenance of hsf expression at a basal level in soybean, favoring its activation under heat-stress conditions.
A Medicago truncatula EF-Hand Family Gene, MtCaMP1, Is Involved in Drought and Salt Stress Tolerance  [PDF]
Tian-Zuo Wang, Jin-Li Zhang, Qiu-Ying Tian, Min-Gui Zhao, Wen-Hao Zhang
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0058952
Abstract: Background Calcium-binding proteins that contain EF-hand motifs have been reported to play important roles in transduction of signals associated with biotic and abiotic stresses. To functionally characterize gens of EF-hand family in response to abiotic stress, an MtCaMP1 gene belonging to EF-hand family from legume model plant Medicago truncatula was isolated and its function in response to drought and salt stress was investigated by expressing MtCaMP1 in Arabidopsis. Methodology/Principal Findings Transgenic Arabidopsis seedlings expressing MtCaMP1exhibited higher survival rate than wild-type seedlings under drought and salt stress, suggesting that expression of MtCaMP1 confers tolerance of Arabidopsis to drought and salt stress. The transgenic plants accumulated greater amounts of Pro due to up-regulation of P5CS1 and down-regulation of ProDH than wild-type plants under drought stress. There was a less accumulation of Na+ in the transgenic plants than in WT plants due to reduced up-regulation of AtHKT1 and enhanced regulation of AtNHX1 in the transgenic plants compared to WT plants under salt stress. There was a reduced accumulation of H2O2 and malondialdehyde in the transgenic plants than in WT plants under both drought and salt stress. Conclusions/Significance The expression of MtCaMP1 in Arabidopsis enhanced tolerance of the transgenic plants to drought and salt stress by effective osmo-regulation due to greater accumulation of Pro and by minimizing toxic Na+ accumulation, respectively. The enhanced accumulation of Pro and reduced accumulation of Na+ under drought and salt stress would protect plants from water default and Na+ toxicity, and alleviate the associated oxidative stress. These findings demonstrate that MtCaMP1 encodes a stress-responsive EF-hand protein that plays a regulatory role in response of plants to drought and salt stress.
Recent Advances in Medicago truncatula Genomics  [PDF]
Jean-Michel Ané,Hongyan Zhu,Julia Frugoli
International Journal of Plant Genomics , 2008, DOI: 10.1155/2008/256597
Abstract: Legume rotation has allowed a consistent increase in crop yield and consequently in human population since the antiquity. Legumes will also be instrumental in our ability to maintain the sustainability of our agriculture while facing the challenges of increasing food and biofuel demand. Medicago truncatula and Lotus japonicus have emerged during the last decade as two major model systems for legume biology. Initially developed to dissect plant-microbe symbiotic interactions and especially legume nodulation, these two models are now widely used in a variety of biological fields from plant physiology and development to population genetics and structural genomics. This review highlights the genetic and genomic tools available to the M. truncatula community. Comparative genomic approaches to transfer biological information between model systems and legume crops are also discussed.
Comparative Analysis of the Symbiotic Efficiency of Medicago truncatula and Medicago sativa under Phosphorus Deficiency  [PDF]
Saad Sulieman,Joachim Schulze,Lam-Son Phan Tran
International Journal of Molecular Sciences , 2013, DOI: 10.3390/ijms14035198
Abstract: Phosphorus (P)-deficiency is a major abiotic stress that limits legume growth in many types of soils. The relationship between Medicago and Sinorhizobium, is known to be affected by different environmental conditions. Recent reports have shown that, in combination with S. meliloti 2011, Medicago truncatula had a lower symbiotic efficiency than Medicago sativa. However, little is known about how Medicago–Sinorhizobium is affected by P-deficiency at the whole-plant level. The objective of the present study was to compare and characterize the symbiotic efficiency of N2 fixation of M. truncatula and M. sativa grown in sand under P-limitation. Under this condition, M. truncatula exhibited a significantly higher rate of N2 fixation. The specific activity of the nodules was much higher in M. truncatula in comparison to M. sativa, partially as a result of an increase in electron allocation to N2 versus H+. Although the main organic acid, succinate, exhibited a strong tendency to decrease under P-deficiency, the more efficient symbiotic ability observed in M. truncatula coincided with an apparent increase in the content of malate in its nodules. Our results indicate that the higher efficiency of the M. truncatula symbiotic system is related to the ability to increase malate content under limited P-conditions.
In Medicago truncatula, water deficit modulates the transcript accumulation of components of small RNA pathways
Cláudio Capit?o, Jorge AP Paiva, Dulce M Santos, Pedro Fevereiro
BMC Plant Biology , 2011, DOI: 10.1186/1471-2229-11-79
Abstract: A bioinformatic search in Medicago truncatula genome databases, using Arabidopsis thaliana AGO and DCL cDNA and protein sequences, identified three sequences encoding for putative Dicer-like genes and twelve sequences encoding for putative Argonaute genes. Under water deficit conditions and mainly in roots, MtDCL1 and MtAGO1, two enzymes probably involved in the processing and activation of microRNAs (miRNAs), increased their transcript levels. mir162 which target DCL1 mRNA and mir168 which target AGO1 mRNA reduced their expression in the roots of plants subjected to water deficit. Three putative genes, MtDCL3, MtAGO4b and MtAGO4c probably involved in DNA methylation mechanisms, increased their mRNA levels. However, the mRNA levels of MtAGO6 reduced, which probably encodes a protein with functions similar to MtAGO4. MtAGO7 mRNA levels increased and possibly encodes a protein involved in the production of trans-acting small interfering RNAs. The transcript abundance of MtAGO12a, MtAGO12b and MtAGO12c reduced under water deprivation. Plants recovered from water deprivation reacquire the mRNA levels of the controls.Our work demonstrates that in M. truncatula the transcript accumulation of the components of small RNA pathways is being modulated under water deficit. This shows that the transcriptional and post-transcriptional control of gene expression mediated by sRNAs is probably involved in plant adaptation to abiotic environmental changes. In the future this will allow the manipulation of these pathways providing a more efficient response of legumes towards water shortage.In plants, the transcriptional and post-transcriptional regulation of gene expression mediated by sRNAs [1] is involved in several biological processes, ranging from organ differentiation to biotic and abiotic stress responses [2-4]. Small RNAs are divided into two main classes based on their biogenesis: the small interfering RNAs (siRNAs) are processed from perfect and long double-stranded RNAs whi
Sub-cellular proteomics of Medicago truncatula  [PDF]
Jeonghoon Lee,Bonnie S. Watson,Lloyd W. Sumner*
Frontiers in Plant Science , 2013, DOI: 10.3389/fpls.2013.00112
Abstract: Medicago truncatula is a leading model species and substantial molecular, genetic, genomics, proteomics, and metabolomics resources have been developed for this species to facilitate the study of legume biology. Currently, over 60 proteomics studies of M. truncatula have been published. Many of these have focused upon the unique symbiosis formed between legumes and nitrogen fixing rhizobia bacteria, while others have focused on seed development and the specialized proteomes of distinct tissues/organs. These include the characterization of sub-cellular organelle proteomes such as nuclei and mitochondria, as well as proteins distributed in plasma or microsomal membranes from various tissues. The isolation of sub-cellular proteins typically requires a series of steps that are labor-intensive. Thus, efficient protocols for sub-cellular fractionation, purification, and enrichment are necessary for each cellular compartment. In addition, protein extraction, solubilization, separation, and digestion prior to mass spectral identification are important to enhance the detection of low abundance proteins and to increase the overall detectable proportion of the sub-cellular proteome. This review summarizes the sub-cellular proteomics studies in M. truncatula.
Medicago truncatula transporter database: a comprehensive database resource for M. truncatula transporters
Zhenyan Miao, Daofeng Li, Zhenhai Zhang, Jiangli Dong, Zhen Su, Tao Wang
BMC Genomics , 2012, DOI: 10.1186/1471-2164-13-60
Abstract: The M. truncatula transporter database (MTDB) contains comprehensive information on the transporters in M. truncatula. Based on the TransportTP method, we have presented a novel prediction pipeline. A total of 3,665 putative transporters have been annotated based on International Medicago Genome Annotated Group (IMGAG) V3.5 V3 and the M. truncatula Gene Index (MTGI) V10.0 releases and assigned to 162 families according to the transporter classification system. These families were further classified into seven types according to their transport mode and energy coupling mechanism. Extensive annotations referring to each protein were generated, including basic protein function, expressed sequence tag (EST) mapping, genome locus, three-dimensional template prediction, transmembrane segment, and domain annotation. A chromosome distribution map and text-based Basic Local Alignment Search Tools were also created. In addition, we have provided a way to explore the expression of putative M. truncatula transporter genes under stress treatments.In summary, the MTDB enables the exploration and comparative analysis of putative transporters in M. truncatula. A user-friendly web interface and regular updates make MTDB valuable to researchers in related fields. The MTDB is freely available now to all users at http://bioinformatics.cau.edu.cn/MtTransporter/ webcite.Medicago truncatula is closely related to an important forage legume, alfalfa. Because of its advantageous characteristics such as small size, short generation time, self-fertility, and diploid genome, M. truncatula has been used as a model species in genomic studies [1,2]. Arabidopsis thaliana is a model plant whose genome was sequenced by an international consortium and is well annotated. Very high sequence identity exists between genes from M. truncatula and their counterparts from alfalfa (98.7% at the amino acid level for isoflavone reductase and 99.1% at the amino acid level for vestitone reductase), so it serves as
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