Global transcriptome analysis of Rhizobium favelukesii LPU83 in response to acid stress.
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA594606 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10620184_1.fastq.gz | Fastqsanger.gz | |||
| SRR10620184_2.fastq.gz | Fastqsanger.gz | |||
| SRR10620185_1.fastq.gz | Fastqsanger.gz | |||
| SRR10620185_2.fastq.gz | Fastqsanger.gz | |||
| SRR10620186_1.fastq.gz | Fastqsanger.gz |
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Project description:Acid environments are worldwide distributed due to their natural conditions or by the inappropriate use of the intensive agriculture. The moderately low pHs from the soils are an important barrier in the plant-rhizobia interaction. These low pHs affect the establishment of the efficient rhizobia usually used as biofertilizer. This negative effect in the rhizobia-legume is mainly due the low acid-tolerance of the bacteria. Here, we described and identified relevant factors in the acid tolerance of Rhizobium. favelukesii, using RNA-Seq. A total of 1924 genes were differentially expressed under acidic condition, with ca. 60% underexpressed. Remarkably, 60% of the CDS of the symbiotic plasmid were also underexpressed. The in silico functional analysis showed that R. favelukesii acid response involves both general and specific response. Regarding the general response, it includes mainly changes in energetic metabolism and protein turnover, while the specific response is a combination of mechanisms that would contribute to the general phenotype of acid-tolerant in R. favelukesii. GABA and Histidine metabolism, cell envelope changes and reverse proton efflux were significant. Moreover, we confirmed a phenotype acid sensible of a mutant in braD, this gene showed a higher expression under acid stress. Remarkably, we evidenced that a strain without pSym presented an improved performance in acidic condition. Hence, this work supply relevant information in the characterization of genes associated with tolerance or adaptation to abiotic stresses of R. favelukesii LPU83 using transcriptomic tools.
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Project description:Rhizobium tropici CIAT899 is a nodule-forming α-proteobacterium displaying intrinsic resistance to several abiotic stress conditions such as low soil pH and high temperatures, which are common in tropical environments. It is a good competitor for Phaseolus vulgaris (common bean) nodule occupancy at low pH values, however little is known about the genetic or physiological basis of acid tolerance about gene expression under acidic conditions. To identify genes responding to pH stress we studied the transcriptomes of cells grown under different pH conditions. RNA was extracted from cells grown for several generations in minimal medium at 6.8 or 4.5 (adapted cells). In addition, we acid-shocked cells pre-grown at pH 6.8 for 45 minutes at pH 4.5. Transcriptomes were determined by RNA-Seq. From a total of 6289 protein-coding genes, 383 were found to be differentially expressed under acidic conditions versus control, among which 351 were induced and 32 repressed; only 11 genes were induced upon acid shock. The acid stress response of R. tropici CIAT899 is versatile: we found genes encoding response regulators and membrane transporters, but also enzymes involved in amino acid and carbohydrate metabolism and proton extrusion. Our findings enhance our understanding of the core genes that are important during the acid stress response in R. tropici.
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Project description:Acid soils constitute a severe problem for leguminous crops mainly through a disturbance in rhizobia-legume interactions. Rhizobium favelukesii—an acid-tolerant rhizobium able to nodulate alfalfa—is highly competitive for nodule occupation under acid conditions, but inefficient in biologic nitrogen fixation. In this work, we obtained a general description of the acid-stress response of R. favelukesii LPU83 by means of proteomics by comparing the total proteome profiles in the presence or absence of acid stress by nanoflow ultrahigh-performance liquid chromatography coupled to mass spectrometry. Thus, a total of 336 proteins were identified with a significant differential expression, 136 of which species were significantly overexpressed and 200 underexpressed in acidity. An in-silico functional characterization with those respective proteins revealed a complex and pleiotropic response by these rhizobia involving components of oxidative phosphorylation, glutamate metabolism, and peptidoglycan biosynthesis, among other pathways. Furthermore, a lower permeability was evidenced in the acid-stressed cells along with several overexpressed proteins related to γ-aminobutyric-acid metabolism, such as the gene product of livK, which was mutated. This mutant exhibited an acid-sensitive phenotype in agreement with the proteomics results. We conclude that both γ-aminobutyric-acid metabolism and a modified cellular envelope could be relevant to acid tolerance in R. favelukesii.
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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.
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