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PROVIDER: PRJEB24130 | ENA |
REPOSITORIES: ENA
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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: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:It was investigated the changes in protein expression in maize roots in response to treatment with Herbaspirillum seropedicae. To identify maize proteins whose expression levels were altered in the presence of bacteria, a label-free quantitative proteomic approach was used.
2024-07-02 | PXD019200 | Pride
Project description:iron response-Transcriptomic response to iron signaling
| PRJNA100753 | ENA
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:Leishmania iron response
| PRJNA244311 | ENA
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
Project description:Herbaspirillum seropedicae are β-proteobacteria that establish as endophytes in various plants. They are able to consume diverse carbon sources, including hexoses and pentoses like D-xylose. D-xylose catabolism pathways have been described in some microorganisms, but databases of genes involved in these routes are limited. This is of special interest in biotechnology, considering that D-xylose is the second most abundant sugar in nature. Furthermore, it is found in some potential raw materials such as lignocellulosic biomass. In this work we present a study of D-xylose catabolism pathways in H. seropedicae strain Z69, using RNA-seq analysis and the subsequent study of phenotypes determined in targeted mutants in corresponding identified genes. G5B88_22805 gene, designated xylB, encodes a NAD+- dependent D-xylose dehydrogenase. Mutant Z69∆xylB was still able to grow on D-xylose, although at a reduced rate. This is due to expression of an L-arabinose dehydrogenase encoded by G5B88_05250 gene, and was thus able to use D-xylose as substrate. According to our results, H. seropedicae Z69 uses non-phosphorylative pathways to catabolize D-xylose. The lower portion of metabolism involves co-expression of two routes: Weimberg pathway that produces α-ketoglutarate and a novel pathway recently described that produces pyruvate and glycolate. This novel pathway seems to be essential since a mutant in the last step of this pathway, Z69∆G5B88_06410, was unable to grow on D‑xylose.
2021-03-01 | GSE162430 | GEO