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 |
Items per page: 5 1 - 5 of 24 |
Similar Datasets
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.
2020-11-12 | GSE141742 | GEO
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.
2022-04-08 | PXD013642 | Pride
Project description:Rhizobium favelukesii Genome sequencing
| PRJNA1214187 | ENA
Project description:Rhizobium favelukesii strain:OR191 Genome sequencing and assembly
| PRJNA165297 | ENA
Project description:Rhizobium favelukesii strain ORY1, an alfalfa inefficient symbiont
| PRJNA760535 | ENA
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.
2018-05-17 | GSE108074 | GEO
Project description:The acidity of soils significantly reduces the productivity of legumes mainly because of the detrimental effects of hydrogen ions on the legume plants, leading to the establishment of an inefficient symbiosis and poor biological nitrogen fixation. We recently reported the analysis of the fully sequenced genome of Rhizobium favelukesii LPU83, an alfalfa-nodulating rhizobium with a remarkable ability to grow, nodulate and compete in acidic conditions. To gain more insight into the genetic mechanisms leading to acid tolerance in R. favelukesii LPU83, we constructed a transposon mutant library and screened for mutants displaying a more acid-sensitive phenotype than the parental strain. We identified mutant Tn833 carrying a single-transposon insertion within LPU83_2531, an uncharacterized short ORF located immediately upstream from ubiF homolog. This gene encodes a protein with an enzymatic activity involved in the biosynthesis of ubiquinone. As the transposon was inserted near the 3' end of LPU83_2531 and these genes are cotranscribed as a part of the same operon, we hypothesized that the phenotype in Tn833 is most likely due to a polar effect on ubiF transcription.We found that a mutant in ubiF was impaired to grow at low pH and other abiotic stresses including 5 mM ascorbate and 0.500 mM Zn2+. Although the ubiF mutant retained the ability to nodulate alfalfa and Phaseolus vulgaris, it was unable to compete with the R. favelukesii LPU83 wild-type strain for nodulation in Medicago sativa and P. vulgaris, suggesting that ubiF is important for competitiveness. Here, we report for the first time an ubiF homolog being essential for nodulation competitiveness and tolerance to specific stresses in rhizobia.
| S-EPMC9433554 | biostudies-literature
Project description:Dissecting acid stress response in Rhizobium tropici CIAT 899
| PRJNA422403 | ENA
Project description:Coevolutionary change requires reciprocal selection between interacting species, i.e., that the partner genotypes that are favored in one species depend on the genetic composition of the interacting species. Coevolutionary genetic variation is manifested as genotype ´ genotype (G ´ G) interactions for fitness from interspecific interactions. Although quantitative genetic approaches have revealed abundant evidence for G ´ G interactions in symbioses, the molecular basis of this variation remains unclear. Here we study the molecular basis of G ´ G interactions in a model legume-rhizobium mutualism using gene expression microarrays. We find that, like quantitative traits such as fitness, variation in the symbiotic transcriptome may be partitioned into additive and interactive genetic components. Our results suggest that plant genetic variation is the largest influence on nodule gene expression, and that plant genotype and the plant genotype ´ rhizobium genotype interaction determine global shifts in rhizobium gene expression that in turn feedback to influence plant fitness benefits. Moreover, the transcriptomic variation we uncover implicates regulatory changes in both species as drivers of symbiotic gene expression variation. Our study is the first to partition genetic variation in a symbiotic transcriptome, and illuminates potential molecular routes of coevolutionary change. We assayed gene expression using three biological replicates for each plant genotype × rhizobium genotype combination (4 combinations) for a total of 12 chips.
2012-05-01 | GSE29027 | GEO