Ontology highlight
ABSTRACT:
PROVIDER: PRJEB24005 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| ERR2226921.fastq.gz | Fastqsanger.gz | |||
| ERR2226922.fastq.gz | Fastqsanger.gz | |||
| ERR2226923.fastq.gz | Fastqsanger.gz | |||
| ERR2226924.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Herbaspirillum seropedicae global studies
| PRJNA422797 | ENA
Project description:Purpose: The global changes of H. seropedicae SmR1 were evaluated in response to environmental Pi conditions, based on differential intracellular polyP levels Methods: Three independent samples (biological replicates) of H. seropedicae SmR1 cells grown in NFb5 or NFb50 media after 9 h of growth were used to construct 6 sequencing libraries.The libraries were amplified and enriched using the Ion PI Hi-QTM OT2 200 Kit, and sequenced with the Ion PI Hi-QTM Sequencing 200 kit on an Ion PITM Chip Kit v3. Obtained sequences were trimmed, mapped and analyzed using CLC Genomics Workbench 7.5.1 (Qiagen) against the H. seropedicae SmR1 genome (NC_014323). Differential gene expression was accessed using the DESeq2 package. qRT–PCR validation was performed using High Capacity cDNA Reverse Transcription Kit (Applied Biosystems), and quantified in triplicate using the Power SYBR-Green PCR MasterMix on a Step-One Plus Real Time-PCR System (Applied Biosystems). Results: After sequencing, 26 and 35 total million reads were obtained for NFb50 and NFb5 conditions, respectively, and from those, 12 million and 16 million reads were uniquely mapped to the H. seropedicae SmR1 genome. Biological replicates showed a very high level of correlation (r2 > 0.98). Among the 4805 genes of the H. seropedicae SmR1 genome, 3976 genes were expressed considering a read coverage equal or higher than three-fold. 1330 genes show expression levels statistically different (p-value ≤ 0.05) from which 670 had fold changes of 2 or higher and were considered differentially expressed genes (DEG) in NFb50 vs NFb5 transcriptome, being 385 down-regulated and 285 up-regulated. To confirm the differential expression observed by the RNA-seq data, the regulation of some genes was confirmed by RT-qPCR. Molecular and physiological analyses revealed that features related to Pi metabolism, bacterial flagella biosynthesis and chemotaxis, energy production, and polyhydroxybutyrate metabolism were induced in the mentioned condition, while aspects involved in adhesion, and stress response were repressed. Since environmental conditions can influence the effectiveness of the PGPB, enhancement of bacterial robustness to withstand different conditions is an interesting challenge Conclusions: The present study demonstrated that variations in environmental Pi concentration affect H. seropedicae bacterial traits related to survival and other important physiological characteristics. The obtained data could serve not only to understand the bacterial behavior in respect to changes in rhizospheric Pi gradients, but also as a base to design strategies to improve different bacterial features focusing in biotechnological and/or agricultural purposes.
2021-03-06 | GSE168341 | GEO
Project description:The molecular role of iron in gene expression remains poorly characterized. Moreover, the alterations in global gene expression after iron chelation remains unclear and are important to assess for understanding the molecular pathology of iron-depletion and the biological effects of iron chelators. We assessed the effect on whole genome gene expression of two iron chelators (desferrioxamine and Dp44mT). These studies are important for understanding the molecular and cellular effects of iron-depletion.
2011-12-31 | GSE26920 | GEO
Project description:To determine the direct promoter targets of Fnr proteins, we correlated transcriptional changes observed in single fnr1 and fnr3 mutants (E-MTAB-5741) with ChIP-Seq analysis, taking advantage of C-terminally 3xFlag fnr alleles engineered into the H. seropedicae genome. ChIP-seq data were obtained from cultures grown under limited oxygen availability. Using this approach, DNA-binding targets for the H. seropedicae Fnr1 and Fnr3 proteins were unambiguously revealed and correlated with transcript profiles to determine the specific regulons of each protein.
2018-02-26 | E-MTAB-6395 | biostudies-arrayexpress
Project description:Herbaspirillum seropedicae is a diazotrophic bacterium which associates endophytically with economically important gramineae. Flavonoids such as naringenin, have been shown to have an effect on the interaction between H. seropedicae and its host plants. We used a high-throughput sequencing based method (RNA-Seq) to access the influence of naringenin on the whole transcriptome profile of H. seropedicae.
2015-04-30 | E-MTAB-3435 | biostudies-arrayexpress
Project description:Herbaspirillum seropedicae is a Betaproteobacterium capable of colonizing epiphytically and endophytically commercial grasses, promoting plant growth. In this study, we utilized RNA-seq to compare the transcriptional profiles of planktonic and maize root-attached H. seropedicae SmR1.
2015-02-28 | E-MTAB-3026 | biostudies-arrayexpress
Project description:Project Description: The interaction between microorganisms and plants plays a key role in plant development and environmental adaptation. Among these microorganisms, plant growth-promoting bacteria (PGPB) enhance agricultural productivity sustainably. Beyond direct effects on plant physiology, epigenetic modifications such as DNA methylation regulate gene expression and adaptive responses. This study investigates how DNA hypomethylation influences early interactions between maize (Zea mays) and the PGPB Herbaspirillum seropedicae, focusing on plant growth, metabolism, and root microbiome. Treatment with the hypomethylating agent 5-azacytidine (5-azaC) did not affect bacterial growth but induced notable phenotypic changes in maize, particularly in root morphology. Inoculation with H. seropedicae enhanced plant growth across biometric parameters. Microscopy revealed bacterial colonization primarily in root mucilage, with higher bacterial accumulation in 5-azaC-treated roots. Global methylation analysis indicated that H. seropedicae modulates cytosine methylation similarly to 5-azaC, suggesting a role in epigenetic regulation. Gene expression analysis of DNA methylation machinery supports hypomethylation as a driver of plant-microbe interactions. Root microbiome profiling showed that 5-azaC significantly altered microbial composition, whereas bacterial inoculation partially restored it toward control profiles. Proteomic analysis identified 1,818 proteins, highlighting significant shifts in metabolic pathways, especially carbon metabolism and the citric acid cycle. These findings demonstrate that DNA hypomethylation, combined with bacterial interaction, profoundly impacts cellular and metabolic processes, offering new insights into early plant-microbe interactions. This knowledge may contribute to developing sustainable agricultural practices through epigenetic and microbial modulation.
2026-05-05 | PXD077098 | Pride
Project description:Herbaspirillum seropedicae is an endophytic bacterium that can fix nitrogen and promote a hormonal imbalance that leads to a plant growth-promoting effect when used as a microbial inoculant. Studies focused on mechanisms of action are crucial for a better understanding of the bacteria-plant interaction and optimization of plant growth-promoting response. The work aims to understand the underlined mechanisms responsible for the early stimulatory growth effects of the H. seropedicae inoculation in maize. To perform it, we combined transcriptomic and proteomic approaches with physiological analysis. The results obtained with the inoculation showed increased root biomass (233 and 253%) and shoot biomass (249 and 264%), respectively, for the fresh and dry mass of maize seedlings and increased green content and development. Omics data analysis for the positive biostimulation phenotype revealed that inoculation increases N-uptake and N-assimilation machinery through differential expressed nitrate transporters and amino acids pathway, as well carbon/nitrogen metabolism integration by the tricarboxylic acid cycle and the polyamines pathway. Additionally, phytohormone levels of root and shoot tissues increased in bacterium-inoculated-maize plants leading to feedback regulation by the ubiquitin-proteasome system. The early biostimulatory effect of H. seropedicae partially results from hormonal imbalance coupled with efficient nutrient uptake-assimilation and a boost in primary anabolic metabolism of carbon-nitrogen integrative pathways.
2023-03-11 | PXD038609 | Pride