Phaseolus vulgaris
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ABSTRACT:
PROVIDER: PRJNA325598 | ENA |
REPOSITORIES: ENA
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Project description:A wide range of environmental stresses lead to an elevated production of reactive oxygen species (ROS) in plant cells thus resulting in oxidative stress. The biological nitrogen fixation in the legume - Rhizobium symbiosis is at high risk of damage from oxidative stress. Common bean (Phaseolus vulgaris) active nodules exposed to the herbicide Paraquat (1,1 '-Dimethyl-4, 4'-bipyridinium dichloride hydrate) that generates ROS accumulation, showed a reduced nitrogenase activity and ureide content. We analyzed the global gene response of stressed nodules using the Bean CombiMatrix Custom Array 90K, that includes probes from some 30,000 expressed sequence tags (EST). A total of 4,280 ESTs were differentially expressed in oxidative stressed bean nodules; of these 2,218 were repressed. These genes were grouped in 44 different biological processes as defined by Gene Onthology. Analysis with the PathExpress bioinformatic tool, adapted for bean, identified five significantly repressed metabolic path This work presents the transcriptional profile of bean nodules, induced by strain Rhizobium tropici CIAT 899, under oxidative stress, generated experimentally by adding the herbicide Paraquat (1,1 '-Dimethyl-4, 4'-bipyridinium dichloride hydrate) for 48 hours. We analyzed the transcript profile, via microarray hybridization, using the Bean CombiMatrix Custom Array 90K, that includes probes from some 30,000 expressed sequence tags (EST). A total of 4,280 ESTs were differentially expressed in oxidative stressed bean nodules; of these 2,218 were repressed.
2012-06-30 | E-GEOD-37638 | biostudies-arrayexpress
Project description:A wide range of environmental stresses lead to an elevated production of reactive oxygen species (ROS) in plant cells thus resulting in oxidative stress. The biological nitrogen fixation in the legume - Rhizobium symbiosis is at high risk of damage from oxidative stress. Common bean (Phaseolus vulgaris) active nodules exposed to the herbicide Paraquat (1,1 '-Dimethyl-4, 4'-bipyridinium dichloride hydrate) that generates ROS accumulation, showed a reduced nitrogenase activity and ureide content. We analyzed the global gene response of stressed nodules using the Bean CombiMatrix Custom Array 90K, that includes probes from some 30,000 expressed sequence tags (EST). The experimental design, based on circular hybridizations, included four conditions as, with two independent biological replicates and three technical replicates for each conditions. A total of 2418 differentially expressed genes (DEG) were identified among the different combinations. Our results showed good correspondence among both the GO term and the MapMan enrichment analyses highlighting DEG from PQ-treated nodules assigned to the functional super-categories: trans-membrane transport, hormone signal transduction, stress response, and regulation. In this work we analyzed the effect of VHb-expressing R. etli CE3 in the symbiosis of common bean plants under oxidative stress experimentally generated by the addition of PQ for 48 hours. We analyzed the transcript profile, via microarray hybridization, using the Bean CombiMatrix Custom Array 90K, that includes probes from some 30,000 expressed sequence tags (EST).
2016-06-15 | E-GEOD-83324 | biostudies-arrayexpress
Project description:A wide range of environmental stresses lead to an elevated production of reactive oxygen species (ROS) in plant cells thus resulting in oxidative stress. The biological nitrogen fixation in the legume - Rhizobium symbiosis is at high risk of damage from oxidative stress. Common bean (Phaseolus vulgaris) active nodules exposed to the herbicide Paraquat (1,1 '-Dimethyl-4, 4'-bipyridinium dichloride hydrate) that generates ROS accumulation, showed a reduced nitrogenase activity and ureide content. We analyzed the global gene response of stressed nodules using the Bean CombiMatrix Custom Array 90K, that includes probes from some 30,000 expressed sequence tags (EST). A total of 4,280 ESTs were differentially expressed in oxidative stressed bean nodules; of these 2,218 were repressed. These genes were grouped in 44 different biological processes as defined by Gene Onthology. Analysis with the PathExpress bioinformatic tool, adapted for bean, identified five significantly repressed metabolic path
2012-07-01 | GSE37638 | GEO
Project description:Rhizobium etli is a bacteria that fix nitrogen in symbiotic activity with Phaseolus vulgaris, the common bean plant. In order to accomplish this nitrogen reduction a especial environment is induced in nodules such that gene expression of bacteroid suffer a significant change with respect to its wild type life style. With the purpose to identify genetic alterations between these physiological states, replicates of microarray data were accomplished in similar conditions between bacteria cultivated in free-life (succinate-ammonia) and those carrying on nitrogen fixation inside nodule.
2014-02-03 | GSE21638 | GEO
Project description:A wide range of environmental stresses lead to an elevated production of reactive oxygen species (ROS) in plant cells thus resulting in oxidative stress. The biological nitrogen fixation in the legume - Rhizobium symbiosis is at high risk of damage from oxidative stress. Common bean (Phaseolus vulgaris) active nodules exposed to the herbicide Paraquat (1,1 '-Dimethyl-4, 4'-bipyridinium dichloride hydrate) that generates ROS accumulation, showed a reduced nitrogenase activity and ureide content. We analyzed the global gene response of stressed nodules using the Bean CombiMatrix Custom Array 90K, that includes probes from some 30,000 expressed sequence tags (EST). The experimental design, based on circular hybridizations, included four conditions as, with two independent biological replicates and three technical replicates for each conditions. A total of 2418 differentially expressed genes (DEG) were identified among the different combinations. Our results showed good correspondence among both the GO term and the MapMan enrichment analyses highlighting DEG from PQ-treated nodules assigned to the functional super-categories: trans-membrane transport, hormone signal transduction, stress response, and regulation.
2016-06-15 | GSE83324 | GEO
Project description:Rhizobium etli is a bacteria that fix nitrogen in symbiotic activity with Phaseolus vulgaris, the common bean plant. In order to accomplish this nitrogen reduction a especial environment is induced in nodules such that gene expression of bacteroid suffer a significant change with respect to its wild type life style. With the purpose to identify genetic alterations between these physiological states, replicates of microarray data were accomplished in similar conditions between bacteria cultivated in free-life (succinate-ammonia) and those carrying on nitrogen fixation inside nodule. Three independent biological materials with one dyeswap were performed.
2014-02-03 | E-GEOD-21638 | biostudies-arrayexpress
Project description:89 small non-coding RNAs (ncRNAs) were identified in the soil-dwelling alpha-proteobacterium Rhizobium etli by comparing an extensive compilation of ncRNA predictions to intergenic expression data of a whole-genome tiling array. The differential expression levels of some of these ncRNAs during free-living growth and during interaction with the eukaryotic host plant may indicate a role in adaptation to changing environmental conditions. In order to study expression in the free-living state, wild-type R. etli CFN42 was grown at 30ËC in acid minimal salts medium supplied with 10 mM NH4Cl and 10 mM succinate while monitoring the optical density (OD) of the culture. Samples were taken at OD600 = 0.3, 0.7 and 6 hours after reaching the maximum OD, representing early/late exponential and stationary phase, respectively. In order to study gene expression during host-associated growth, common bean plants (Phaseolus vulgaris cv. Limburgse vroege) were cultivated and inoculated as described previously. Nodules were harvested 2 and 3 weeks after inoculation and the bacteroids were purified by differential centrifugation.
2010-06-19 | E-GEOD-18580 | biostudies-arrayexpress
Project description:Gene expression during stationary phase and symbiosis of R. etli CFN42 was compared to that of exponentially growing cells. This allowed us to better understand how R. etli adapts to a non-growing lifestyle, both the free-living and symbiotic state, as well as to determine to what extent this adaptation is similar in both states. R. etli CFN42 was grown at 30˚C in AMS medium supplied with 10 mM NH4Cl and 10 mM succinate while monitoring the optical density (OD) of the culture. Free-living samples were taken at OD600 = 0.3 and 6 hours after reaching the maximum OD, representing early exponential and stationary phase respectively. Bacteroid samples were obtained from nodules 3 weeks after inoculation of Common bean plants (Phaseolus vulgaris cv Limburgse vroege).
2010-11-04 | E-GEOD-25094 | biostudies-arrayexpress
Project description:A Phaseolus vulgaris genome-wide analysis led to identify the small RNAs (sRNA) of this agronomical important legume. It revealed newly identified P. vulgaris-specific microRNAs (miRNAs) that could be involved in the regulation of the rhizobia-symbiotic process. Generally, novel miRNAs are difficult to identify and study because they are very lowly expressed in a tissue- or cell-specific manner. We aimed to analyze sRNAs from common bean root hairs (RH), a single-cell model, induced with pure Rhizobium etli-Nod factors (NF), a unique type of signal molecule. The sequence analysis of samples from NF-induced and control libraries led to identify 132 mature miRNAs, including 63 novel miRNAs and 1984 phasiRNAs. From these, six miRNAs were significantly differentially expressed during NF-induction, including one novel miRNA: miR-RH82. A parallel degradome analysis of the same samples revealed 29 targets potentially cleaved by novel miRNAs specifically in NF-induced RH samples, however these novel miRNAs were not differentially accumulated in this tissue. This study reveals Phaseolus vulgaris-specific novel miRNA candidates and their corresponding targets that meet all criteria to be involved in the regulation of the early nodulation events.
2017-05-01 | GSE81176 | GEO
Project description:We report an small RNA sequencing (sRNA-seq) approach to identify host sRNAs involved in the nitrogen fixing symbiosis between Mesoamerican Phaseolus vulgaris and Rhizobium etli strains with different degrees in nodulation efficiency. This approach identified conserved and known microRNAs (miRNAs) differentially accumulated in Mesoamerican P. vulgaris roots in response to a highly efficient strain, to a less efficient one or to both strains.
2020-11-01 | GSE155414 | GEO