Cloning, molecular characterization, and expression analysis of several red clover cDNAs

2006 ◽  
Vol 86 (2) ◽  
pp. 465-468
Author(s):  
Michael L. Sullivan ◽  
Sharon L. Thoma
Keyword(s):  
Medicago Truncatula ◽  
Expression Analysis ◽  
Binding Protein ◽  
Sequence Similarity ◽  
Expression Patterns ◽  
Molecular Genetic ◽  
Red Clover ◽  
Model Legume ◽  
Gene Set ◽  
Wide Range

To begin gathering information regarding nucleotide sequence similarity between red clover genes and other plant species, especially the model legume Medicago truncatula, several random red clover cDNAs were sequenced. The analyzed cDNAs included genes encoding actin; several proteins involved in photosynthesis including PsaH, PsbR, PsbX, early light-induced protein (ELIP), ferredoxin, chlorophyll a/b binding protein; fructose-bisphosphate aldolase;chloroplastic superoxide dismutase; and GTP-binding protein typA. The gene set had a median sequence identity of 92% with their counterparts from M. truncatula, suggesting its available genomics tools can be applied to red clover. An expression analysis of the gene set in various red clover tissues indicates the genes show a wide range of expression patterns. Consequently, this set of cDNAs and associated data are proving useful as controls in molecular genetic experiments involving red clover. Key words: Red clover, Trifolium pratense, Medicago truncatula, forage legume, genomics, inquiry-based learning

scholarly journals LeGOO: An Expertized Knowledge Database for the Model Legume Medicago truncatula

2019 ◽  
Vol 61 (1) ◽  
pp. 203-211 ◽  
Author(s):  
S�bastien Carr�re ◽  
Marion Verdenaud ◽  
Clare Gough ◽  
J�r�me Gouzy ◽  
Pascal Gamas
Keyword(s):  
Medicago Truncatula ◽  
Reverse Genetics ◽  
Arbuscular Mycorrhizal ◽  
Biological Information ◽  
Model Species ◽  
Model Legume ◽  
Wide Range ◽  
Legume Symbiosis ◽  
Symbiotic Nodule ◽  
Set Up

Abstract Medicago truncatula was proposed, about three decades ago, as a model legume to study the Rhizobium-legume symbiosis. It has now been adopted to study a wide range of biological questions, including various developmental processes (in particular root, symbiotic nodule and seed development), symbiotic (nitrogen-fixing and arbuscular mycorrhizal endosymbioses) and pathogenic interactions, as well as responses to abiotic stress. With a number of tools and resources set up in M. truncatula for omics, genetics and reverse genetics approaches, massive amounts of data have been produced, as well as four genome sequence releases. Many of these data were generated with heterogeneous tools, notably for transcriptomics studies, and are consequently difficult to integrate. This issue is addressed by the LeGOO (for Legume Graph-Oriented Organizer) knowledge base (https://www.legoo.org), which finds the correspondence between the multiple identifiers of the same gene. Furthermore, an important goal of LeGOO is to collect and represent biological information from peer-reviewed publications, whatever the technical approaches used to obtain this information. The information is modeled in a graph-oriented database, which enables flexible representation, with currently over 200,000 relations retrieved from 298 publications. LeGOO also provides the user with mining tools, including links to the Mt5.0 genome browser and associated information (on gene functional annotation, expression, methylome, natural diversity and available insertion mutants), as well as tools to navigate through different model species. LeGOO is, therefore, an innovative database that will be useful to the Medicago and legume community to better exploit the wealth of data produced on this model species.

Genome-Wide Characterization of PDI Gene Family in Medicago truncatula and their Roles in Response to ER stress

Genome ◽  
2020 ◽  
Author(s):  
Zhe Meng ◽  
Yuwei Zhao ◽  
Lijie Liu ◽  
Xihua Du
Keyword(s):  
Protein Folding ◽  
Er Stress ◽  
Gene Family ◽  
Medicago Truncatula ◽  
Environmental Changes ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Protein Structures ◽  
Pcr Analysis ◽  
Model Legume

Protein disulfide isomerases (PDIs) are pivotal protein folding catalysts in the endoplasmic reticulum (ER) through formation of disulfide bond, isomerization, and inhibition of misfolded protein aggregation. When protein folding capacity is overwhelmed by the demands during transitions between growth phases or under environmental changes, the accumulation of unfolded or misfolded proteins in the ER triggers ER stress. However, little is known about PDI gene family in the model legume, Medicago truncatula, especially the responses to ER stress. Therefore, we identified 17 putative PDIs from the genome of M. truncatula and presented their gene and protein structures, phylogenetic relationships, chromosomal distributions, and synteny analysis with the orthologs in other four eudicot species inculding A. thaliana, G. max, B. rapa, and V. vinifera. Moreover, expression profiles derived from transcriptome data showed distinct expression patterns of MtPDI genes among plant organs, while real-time quantitative PCR analysis and data from the proteome revealed the potential roles of MtPDIs in response to ER stress. Our study provides a foundation for further investigations of the biological roles of PDIs in Medicago, especially their roles in response to ER stress.

scholarly journals Systematic Analysis of Gibberellin Pathway Components in Medicago truncatula Reveals the Potential Application of Gibberellin in Biomass Improvement

2020 ◽  
Vol 21 (19) ◽  
pp. 7180
Author(s):  
Hongfeng Wang ◽  
Hongjiao Jiang ◽  
Yiteng Xu ◽  
Yan Wang ◽  
Lin Zhu ◽  
...  
Keyword(s):  
Medicago Truncatula ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Ectopic Expression ◽  
Feedback Regulation ◽  
Specific Expression ◽  
Systematic Analysis ◽  
Model Legume ◽  
Genome Wide ◽  
A Genome

Gibberellins (GAs), a class of phytohormones, act as an essential natural regulator of plant growth and development. Many studies have shown that GA is related to rhizobial infection and nodule organogenesis in legume species. However, thus far, GA metabolism and signaling components are largely unknown in the model legume Medicago truncatula. In this study, a genome-wide analysis of GA metabolism and signaling genes was carried out. In total 29 components, including 8 MtGA20ox genes, 2 MtGA3ox genes, 13 MtGA2ox genes, 3 MtGID1 genes, and 3 MtDELLA genes were identified in M. truncatula genome. Expression profiles revealed that most members of MtGAox, MtGID1, and MtDELLA showed tissue-specific expression patterns. In addition, the GA biosynthesis and deactivation genes displayed a feedback regulation on GA treatment, respectively. Yeast two-hybrid assays showed that all the three MtGID1s interacted with MtDELLA1 and MtDELLA2, suggesting that the MtGID1s are functional GA receptors. More importantly, M. truncatula exhibited increased plant height and biomass by ectopic expression of the MtGA20ox1, suggesting that enhanced GA response has the potential for forage improvement.

scholarly journals The Endosymbiosis-Induced Genes ENOD40 and CCS52a Are Involved in Endoparasitic-Nematode Interactions in Medicago truncatula

2002 ◽  
Vol 15 (10) ◽  
pp. 1008-1013 ◽  
Author(s):  
Bruno Favery ◽  
Arnaud Complainville ◽  
Jose Maria Vinardell ◽  
Philippe Lecomte ◽  
Daniàle Vaubert ◽  
...  
Keyword(s):  
Host Plant ◽  
Medicago Truncatula ◽  
Root Nodules ◽  
Expression Patterns ◽  
Cyclin D3 ◽  
Nodule Development ◽  
Cell Cycle Gene ◽  
Root Knot Nematode ◽  
Regulatory Pathways ◽  
Wide Range

Plants associate with a wide range of mutualistic and parasitic biotrophic organisms. Here, we investigated whether beneficial plant symbionts and biotrophic pathogens induce distinct or overlapping regulatory pathways in Medicago truncatula. The symbiosis between Sinorhizobium meliloti and this plant results in the formation of nitrogen-fixing root nodules requiring the activation of specific genes in the host plant. We studied expression patterns of nodule-expressed genes after infection with the root-knot nematode Meloidogyne incognita. Two regulators induced during nodule organogenesis, the early nodulin gene ENOD40 involved in primordium formation and the cell cycle gene CCS52a required for cell differentiation and en-doreduplication, are expressed in galls of the host plant. Expression analysis of promoter-uidA fusions indicates an accumulation of CCS52a transcripts in giant cells undergoing endoreduplication, while ENOD40 expression is localized in surrounding cell layers. Transgenic plants overexpressing ENOD40 show a significantly higher number of galls. In addition, out of the 192 nodule-expressed genes tested, 38 genes were upregulated in nodules at least threefold compared with control roots, but only two genes, nodulin 26 and cyclin D3, were found to be induced in galls. Taken together, these results suggest that certain events, such as endoreduplication, cell-to-cell communication with vascular tissues, or water transport, might be common between giant cell formation and nodule development.

scholarly journals MtExpress, a Comprehensive and Curated RNAseq-based Gene Expression Atlas for the Model Legume Medicago truncatula

2021 ◽  
Author(s):  
Sebastien Carrere ◽  
Jerome Verdier ◽  
Pascal Gamas
Keyword(s):  
Gene Expression ◽  
Medicago Truncatula ◽  
Orthologous Gene ◽  
Model Legume ◽  
Fully Integrated ◽  
Gene Expression Atlas ◽  
Rnaseq Data ◽  
Wide Range ◽  
Complementary Resource ◽  
Expression Atlas

Abstract Although RNA sequencing has been becoming the main transcriptomic approach in the model legume Medicago truncatula, there is currently no genome-wide gene expression atlas covering the whole set of RNAseq data published for this species. Nowadays, such tool is highly valuable to provide a global view of gene expression in a wide range of conditions and tissues/organs. Here, we present MtExpress, a gene expression atlas that compiles an exhaustive set of published M. truncatula RNAseq data (https://medicago.toulouse.inrae.fr/MtExpress). MtExpress makes use of recent releases of M. truncatula genome sequence and annotation, as well as up-to-date tools to perform mapping, quality control, statistical analysis and normalization of RNAseq data. MtExpress combines semi-automated pipelines with manual re-labelling and organization of samples, to produce an attractive and user-friendly interface, fully integrated with other available Medicago genomic resources. Importantly, MtExpress is highly flexible, in terms of both queries, e.g. allowing searches with gene names and orthologous gene IDs from Arabidopsis and other legume species, and outputs, to customize visualization and redirect gene study to relevant Medicago webservers. Thanks to its semi-automated pipeline, MtExpress will be frequently updated to follow the rapid pace of M. truncatula RNAseq data publications, as well as the constant improvement of genome annotation. MtExpress also hosts legacy GeneChip expression data originally stored in the Medicago Gene Expression Atlas (MtGEA), as a very valuable and complementary resource.

scholarly journals Easy and efficient ensemble gene set testing with EGSEA

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 2010 ◽  
Author(s):  
Monther Alhamdoosh ◽  
Charity W. Law ◽  
Luyi Tian ◽  
Julie M. Sheridan ◽  
Milica Ng ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Expression ◽  
Expression Analysis ◽  
Differential Expression Analysis ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Gene Set ◽  
P Gene ◽  
Wide Range ◽  
Gene Set Testing

Gene set enrichment analysis is a popular approach for prioritising the biological processes perturbed in genomic datasets. The Bioconductor project hosts over 80 software packages capable of gene set analysis. Most of these packages search for enriched signatures amongst differentially regulated genes to reveal higher level biological themes that may be missed when focusing only on evidence from individual genes. With so many different methods on offer, choosing the best algorithm and visualization approach can be challenging. The EGSEA package solves this problem by combining results from up to 12 prominent gene set testing algorithms to obtain a consensus ranking of biologically relevant results.This workflow demonstrates how EGSEA can extend limma-based differential expression analyses for RNA-seq and microarray data using experiments that profile 3 distinct cell populations important for studying the origins of breast cancer. Following data normalization and set-up of an appropriate linear model for differential expression analysis, EGSEA builds gene signature specific indexes that link a wide range of mouse or human gene set collections obtained from MSigDB, GeneSetDB and KEGG to the gene expression data being investigated. EGSEA is then configured and the ensemble enrichment analysis run, returning an object that can be queried using several S4 methods for ranking gene sets and visualizing results via heatmaps, KEGG pathway views, GO graphs, scatter plots and bar plots. Finally, an HTML report that combines these displays can fast-track the sharing of results with collaborators, and thus expedite downstream biological validation. EGSEA is simple to use and can be easily integrated with existing gene expression analysis pipelines for both human and mouse data.

scholarly journals MtExpress, a Comprehensive and Curated RNAseq-based Gene Expression Atlas for the Model Legume Medicago truncatula

2021 ◽  
Author(s):  
Sebastien Carrere ◽  
Jerome Verdier ◽  
Pascal Gamas
Keyword(s):  
Gene Expression ◽  
Medicago Truncatula ◽  
Orthologous Gene ◽  
Model Legume ◽  
Fully Integrated ◽  
Gene Expression Atlas ◽  
Rnaseq Data ◽  
Wide Range ◽  
Expression Atlas ◽  
Gene Study

Although RNA sequencing has been becoming the main transcriptomic approach in the model legume Medicago truncatula, there is currently no genome-wide gene expression atlas covering the whole set of RNAseq data published for this species. Nowadays, such tool is highly valuable to provide a global view of gene expression in a wide range of conditions and tissues/organs. Here, we present MtExpress, a gene expression atlas that compiles an exhaustive set of published M. truncatula RNAseq data (https://medicago.toulouse.inrae.fr/MtExpress). MtExpress makes use of recent releases of M. truncatula genome sequence and annotation, as well as up-to-date tools to perform mapping, quality control, statistical analysis and normalization of RNAseq data. MtExpress combines semi-automated pipelines with manual re-labelling and organization of samples, to produce an attractive and user-friendly interface, fully integrated with other available Medicago genomic resources. Importantly, MtExpress is highly flexible, in terms of both queries, e.g. allowing searches with gene names and orthologous gene IDs from Arabidopsis and other legume species, and outputs, to customize visualization and redirect gene study to relevant Medicago webservers. Thanks to its semi-automated pipeline, MtExpress will be frequently updated to follow the rapid pace of M. truncatula RNAseq data publications, as well as the constant improvement of genome annotation.

scholarly journals Calmodulin-Like (CML) Gene Family in Medicago truncatula: Genome-Wide Identification, Characterization and Expression Analysis

2020 ◽  
Vol 21 (19) ◽  
pp. 7142
Author(s):  
Qiguo Sun ◽  
Shuhan Yu ◽  
Zhenfei Guo
Keyword(s):  
Gene Family ◽  
Medicago Truncatula ◽  
Expression Analysis ◽  
Model Legume ◽  
Cis Acting ◽  
Biotic Stresses ◽  
Genome Wide ◽  
Legume Plant ◽  
Ef Hand ◽  
Blast Database

Calcium is an important second messenger in mediating adaptation responses of plants to abiotic and biotic stresses. Calmodulin-like (CML) protein is an important calcium-signaling protein that can sense and decode Ca2+ signal in plants. Medicago truncatula is a model legume plant; however, investigations of MtCML proteins are limited. Using genome analysis and BLAST database searches, fifty MtCML proteins that possess EF-hand motifs were identified. Phylogenetic analysis showed that CML homologs between M. truncatula, Arabidopsis thaliana and Oryza sativa shared close relationships. Gene structure analysis revealed that these MtCML genes contained one to four conserved EF-hand motifs. All MtCMLs are localized to eight chromosomes and underwent gene duplication. In addition, MtCML genes were differentially expressed in different tissues of M. truncatula. Cis-acting elements in promoter region and expression analysis revealed the potential response of MtCML protein to abiotic stress and hormones. The results provide a basis of further functional research on the MtCML gene family and facilitate their potential use for applications in the genetic improvement on M. truncatula in drought, cold and salt stress environments.

scholarly journals UGT84F9 is the major flavonoid UDP-glucuronosyltransferase in Medicago truncatula

2021 ◽  
Author(s):  
Olubu A Adiji ◽  
Maite L Docampo-Palacios ◽  
Anislay Alvarez-Hernandez ◽  
Giulio M Pasinetti ◽  
Xiaoqiang Wang ◽  
...  
Keyword(s):  
Medicago Truncatula ◽  
Phase Ii ◽  
Loss Of Function ◽  
In Planta ◽  
Model Legume ◽  
Flavonoid Compounds ◽  
Wide Range ◽  
Udp Glucuronosyltransferase ◽  
Phase Ii Metabolites

Abstract Mammalian phase II metabolism of dietary plant flavonoid compounds generally involves substitution with glucuronic acid. In contrast, flavonoids mainly exist as glucose conjugates in plants, and few plant UDP-glucuronosyltransferase enzymes have been identified to date. In the model legume Medicago truncatula, the major flavonoid compounds in the aerial parts of the plant are glucuronides of the flavones apigenin and luteolin. Here we show that the M. truncatula glycosyltransferase UGT84F9 is a bi-functional glucosyl/glucuronosyl transferase in vitro, with activity against a wide range of flavonoid acceptor molecules including flavones. However, analysis of metabolite profiles in leaves and roots of M. truncatula ugt84f9 loss of function mutants revealed that the enzyme is essential for formation of flavonoid glucuronides, but not most flavonoid glucosides, in planta. We discuss the use of plant UGATs for the semi-synthesis of flavonoid phase II metabolites for clinical studies.

scholarly journals Planarian CREB-binding protein (CBP) gene family regulates stem cell maintenance and differentiation

2020 ◽  
Author(s):  
Susanna Fraguas ◽  
Sheila Cárcel ◽  
Coral Vivancos ◽  
Ma Dolores Molina ◽  
Jordi Ginés ◽  
...  
Keyword(s):  
Stem Cell ◽  
Gene Family ◽  
Binding Protein ◽  
Expression Patterns ◽  
Stem Cell Differentiation ◽  
Transferase Activity ◽  
Creb Binding Protein ◽  
Stem Cell Maintenance ◽  
Wide Range ◽  
Cell Maintenance

ABSTRACTThe regulation of stem cells plasticity and differentiation is still an open question in developmental biology. CBP (CREB-binding protein)/p300 is a conserved gene family which functions as a transcriptional co-activator and shows an important role in a wide range of cellular processes, such as cell death, DNA damage response and tumorigenesis. Moreover, CBPs have an acetyl transferase activity that is relevant as histone and non-histone acetylation results in changes in chromatin architecture and protein activity that affects gene expression. Many studies have shown the conserved functions of CBP/p300 on stem cell proliferation and differentiation. The planarian Schmidtea mediterranea is an excellent model to study in vivo the molecular mechanism underlying stem cell differentiation during regeneration. We have identified five different Smed-cbp genes in S. mediterranea that show different expression patterns. Functional analyses indicate that Smed-cbp-2 seems to be essential for stem cell maintenance and cell survival. On the other hand, the silencing of Smed-cbp-3 results in the growth of apparently normal blastemas; however, these remain largely depigmented and undifferentiated. Smed-cbp-3 silencing affects the differentiation of several cell lineages including neural, epidermal, digestive and excretory cell types. Finally, we have analyzed the predicted interactomes of CBP-2 and CBP-3 as an initial step to better understand their function on planarian stem cell biology.

Sign in / Sign up

Export Citation Format

Share Document