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Herbaspirillum seropedicae strain:Z67

ABSTRACT: Herbaspirillum seropedicae global studies

PROVIDER: PRJNA422797 | ENA |

REPOSITORIES: ENA

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Herbaspirillum seropedicae transcript profile on maize rhizosphere

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

D-xylose catabolic pathways expressed in Herbaspirillum seropedicae

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

Herbaspirillum seropedicae strain:AG215

Project description:Herbaspirillum seropedicae AG215 genome sequencing

| PRJNA463041 | ENA

Herbaspirillum seropedicae strain:DS1323

Project description:Herbaspirillum seropedicae DS1323 genome sequencing

| PRJNA710619 | ENA

Herbaspirillum seropedicae SmR1

Project description:Herbaspirillum seropedicae SmR1 Genome sequencing

| PRJNA47945 | ENA

Genome wide transcriptional profiling of Herbaspirillum seropedicae SmR1 grown in the presence of naringenin

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

Herbaspirillum seropedicae strain:Z69

Project description:Herbaspirillum seropedicae strain:Z69 Genome sequencing

| PRJNA607503 | ENA

Herbaspirillum seropedicae strain:HS1_2

Project description:Herbaspirillum seropedicae strain:HS1_2 Genome sequencing

| PRJNA1130394 | ENA

Herbaspirillum seropedicae strain:AU13965

Project description:Herbaspirillum seropedicae strain:AU13965 Genome sequencing

| PRJNA508889 | ENA

Transcriptome profile of Herbaspirillum seropedicae SmR1 grown in the presence of aromatic compounds

Project description:Herbaspirillum seropedicae SmR1 was grown in NFbHPN medium until OD600nm of 0.6, when 5mM phenol or 2,5mM benzoic acid was added to the medium. After 30 minutes of growth, the cells were collected by centrifugation and total RNA was extracted with RiboPureBacteria. Also, a derivative strain from Herbaspirillum seropedicae SmR1 resistant to 1mM phenol (named strain RP) was grown in NFbHPN medium containing 1mM phenol until OD600nm of 0.6, then 5mM phenol was added to the medium. After 30 minutes of growth, the cells were collected by centrifugation and total RNA was extracted with RiboPureBacteria. All samples were depleted for ribossomal RNA e sequenced with Solid plataform.

2016-04-01 | E-MTAB-3467 | biostudies-arrayexpress

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