Azoarcus olearius strain:BH72
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ABSTRACT:
PROVIDER: PRJNA13217 | ENA |
REPOSITORIES: ENA
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Project description:Azoarcus olearius strain BH72 is a plant endophyte that can fix atmospheric nitrogen for plant assimilation. Our recent directional RNA-Seq analysis detected widespread presence of reads mapping in the antisense orientation to the annotated genes. Although this has been discovered for several bacteria, the stable expression and functional relevance of such antisense RNAs (asRNAs) are still being debated. In this study we ventured to confirm the single-cell expression and unravel the functionality of antisense transcription in strain BH72. First, from the directional RNA-Seq data we predicted 798 asRNAs that were encoded against 709 genes (18 % of the annotated genome). Using a cassette encoding for two fluorescent reporters (GFP and TdTomato), in convergent orientation with transcriptional terminators in between, we were able to confirm the single-cell co-expression of both the sense and the antisense transcripts within azo1349 in at least 90 % of the bacterial population. By modifying the above experimental setup, we observed the interference exhibited by these overlapping transcripts. Further, decreasing the ribosomal occupancy on one of the overlapping transcripts increased its repression of the complimentary transcript. However, RNA-Seq analysis of a RNase III deficient mutant indicated a minimal effect of the endoribonuclease on the regulation of sense-antisense pairs in strain BH72. Lastly, we elucidated the control mediated by RNase III and asRNA on the expression of genes in the type six secretion system-1 cluster.
2026-06-30 | GSE203041 | GEO
Project description:Model endophyte Azoarcus sp. BH72 is known to contribute fixed nitrogen to its host Kallar grass by nitrogen fixation and also expresses nitrogenase genes endophytically in rice seedlings in gnotobiotic culture. Availability of fixed nitrogen is one of the important signals regulating the transcription of nitrogenase genes and hence nitrogen fixing activity. Therefore, we analysed global transcription in response to differences in the nitrogen source. Transcription profiles of cells grown microaerobically (0.6% oxygen) on minimal medium with nitrogen (N2-fixing) versus ammonium (combined nitrogen) were compared using a genome-wide microarray approach and differences in the gene expression profile were monitored.
2013-08-01 | GSE49394 | GEO
Project description:Transcriptional profiling of Oryza sativa japonica Nipponbare roots after 14 days post inoculation with Azoarcus olearius BH72, the goal is to understand the transcriptomic response of rice roots to colonization by bacterial endophyte
2019-09-01 | GSE136707 | GEO
Project description:Model endophyte Azoarcus sp. BH72 is known to contribute fixed nitrogen to its host Kallar grass by nitrogen fixation and also expresses nitrogenase genes endophytically in rice seedlings in gnotobiotic culture. Availability of fixed nitrogen is one of the important signals regulating the transcription of nitrogenase genes and hence nitrogen fixing activity. Therefore, we analysed global transcription in response to differences in the nitrogen source. Transcription profiles of cells grown microaerobically (0.6% oxygen) on minimal medium with nitrogen (N2-fixing) versus ammonium (combined nitrogen) were compared using a genome-wide microarray approach and differences in the gene expression profile were monitored. RNA from cells grown on nitrogen-free synthetic medium under nitrogen fixation (experiment) and combined nitrogen source as ammonium chloride (control) was used for two-color whole-genome microarray approach.
2013-08-01 | E-GEOD-49394 | biostudies-arrayexpress
Project description:Azoarcus sp. BH72 is known to express nitrogenase genes endophytically in rice seedlings in gnotobiotic culture. Availability of fixed nitrogen is one of the important signals regulating the transcription of nitrogenase genes and hence nitrogen fixing activity. NifA is the essential transcription activator of nif genes. RNA isolated from the nifA knockout mutant of strain BH72 was compared with the transcriptome of wild type under nitrogen fixing condition using a global genome wide microarray approach and the differences in the gene expression profile were monitered.
2013-08-15 | GSE49912 | GEO
Project description:Azoarcus sp. BH72 is known to express nitrogenase genes endophytically in rice seedlings in gnotobiotic culture. Availability of fixed nitrogen is one of the important signals regulating the transcription of nitrogenase genes and hence nitrogen fixing activity. NifA is the essential transcription activator of nif genes. RNA isolated from the nifA knockout mutant of strain BH72 was compared with the transcriptome of wild type under nitrogen fixing condition using a global genome wide microarray approach and the differences in the gene expression profile were monitered. RNA isolated from wild type strain BH72 and nifLA mutant strain BHLAO grown respectively under microaerobic nitrogen fixing condition with glutamate as poor nitrogen source was used for two color whole genome microarray approach
2013-08-15 | E-GEOD-49912 | biostudies-arrayexpress
Project description:Azoarcus sp. BH72 is able to communicate via cell density-dependent gene regulation. Here, the impact of cell-free conditioned culture supernatants, obtained from stationary phase Azoarcus wild type cultures, on gene expression was investigated determining changes in transcript profiles when early exponential aerobic cultures were incubated with cell-free culture supernatants for one and four hours. Bacterial communication via quorum sensing (QS) is involved in the regulation of several cellular mechanisms such as metabolic processes, microbe-host interactions or biofilm formation. The nitrogen-fixing model endophyte of grasses Azoarcus sp. strain BH72 shows density-dependent gene regulation in the absence of common hydrophobic autoinducers for pilA encoding the structural protein of type IV pili that are essential for plant colonization. Here, we used a transcriptomic approach to identify target genes differentially regulated under QS conditions in conditioned supernatants in comparison to standard growth conditions.
2011-12-01 | GSE25939 | GEO
Project description:Azoarcus olearius BH72 is a diazotrophic endophyte carrying out biological nitrogen fixation (BNF) and supplying nitrogen to its host plant. Our previous microarray approach provided insights in the transcriptome of strain BH72 under N2-fixation in comparison to ammonium-grown conditions, which already indicated induction of genes not related to the BNF process. Due to the known limitations of the technique, we might have missed additional differentially regulated genes (DEGs). Thus we used directional RNA-Seq to better comprehend the transcriptional landscape under these growth conditions. RNA-Seq detected almost 24 % of the annotated genes to be regulated, twice the amount identified by microarray. In addition to confirming entire regulated operons containing known DEGs, the new approach detected induction of genes involved in carbon metabolism and flagellar and twitching motility. On the other hand, genes encoding for proteins involved in translation and vitamin biosynthesis were detected to be suppressed. Nonetheless, strain BH72 appears not to be content with N2-fixation but is primed for alternative economic N-sources, such as nitrate, urea or amino acids: we detected strong induction of machineries for uptake and assimilation.
2021-09-06 | GSE176473 | GEO
Project description: Not available
| S-EPMC6423157 | biostudies-literature
Project description:Azoarcus sp. BH72 is able to communicate via cell density-dependent gene regulation. Here, the impact of cell-free conditioned culture supernatants, obtained from stationary phase Azoarcus wild type cultures, on gene expression was investigated determining changes in transcript profiles when early exponential aerobic cultures were incubated with cell-free culture supernatants for one and four hours. Bacterial communication via quorum sensing (QS) is involved in the regulation of several cellular mechanisms such as metabolic processes, microbe-host interactions or biofilm formation. The nitrogen-fixing model endophyte of grasses Azoarcus sp. strain BH72 shows density-dependent gene regulation in the absence of common hydrophobic autoinducers for pilA encoding the structural protein of type IV pili that are essential for plant colonization. Here, we used a transcriptomic approach to identify target genes differentially regulated under QS conditions in conditioned supernatants in comparison to standard growth conditions. Analysis used RNA from the early exponential growth phase as control samples for comparison to the quorum-sensing condition samples taken at one hour and four hours after incubation with cell-free culture supernatants.
2011-12-01 | E-GEOD-25939 | biostudies-arrayexpress