GEO DataSets

(Submitter supplied) The cell cycle-regulated DNA methyltransferase CcrM is conserved in most Alphaproteobacteria, but its role in bacteria with complex or multicentric genomes remains unexplored. Here, we compare the methylome, the transcriptome and the phenotypes of wild-type and CcrM-depleted Agrobacterium tumefaciens cells with a dicentric genome with two essential replication origins. We find that DNA methylation has a pleiotropic impact on motility, biofilm formation and viability. more...

Organism:

Agrobacterium tumefaciens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34084

9 Samples

Download data: TXT

(Submitter supplied) We investigated the role of the LysR-type transcriptional regulator LsrB (Atu2186) from Agrobacterium tumefaciens C58 (alias A. fabrum C58), which regulates the expression of small-regulatory-RNA (sRNA) and several protein-coding genes, such as ampD (atu2113). In our current study we invesigated the role of LsrB in beta-lactam resistance. For this purpose, we constructed a vtlR/lsrB deletion mutant. more...

Organism:

Agrobacterium fabrum; Agrobacterium fabrum str. C58

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33656

3 Samples

Download data: CSV

(Submitter supplied) Rhizobia are soil bacteria that induce nodule formation on leguminous plants. In the nodules, they reduce dinitrogen to ammonium that can be utilized by plants. Besides nitrogen fixation, rhizobia have other symbiotic functions in plants including phosphorus and iron mobilization and protection of the plants against various abiotic stresses including salinity. Worldwide, about 20% of cultivable and 33% of irrigation land is saline, and it is estimated that around 50% of the arable land will be saline by 2050. more...

Organism:

Rhizobium phaseoli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32769

6 Samples

Download data: CSV, TSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Agrobacterium sp. CGMCC 11546

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26670

12 Samples

Download data: TXT

(Submitter supplied) Purpose： The goal of this study is compare the effect of glnA gene in curdlan synthesis in Agrobacterium sp. CGMCC 11546. methods: The transcriptional and metabolomics analysis the function of glnA in Agrobacterium sp. CGMCC 11546. Results: The transcriptional and metabolomics showed that the decrease of curdlan production in the ΔglnA mutants may be caused by the insufficient supply of energy ATP conclusion: glnA play an important role in curdlan synthesis in Agrobacterium sp. more...

Organism:

Agrobacterium sp. CGMCC 11546

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26670

6 Samples

Download data: TXT

(Submitter supplied) Purpose： The goal of this study is compare the effect of phbC gene in curdlan synthesis in Agrobacterium sp. CGMCC 11546. methods: The transcriptional and metabolomics analysis the function of phbC in Agrobacterium sp. CGMCC 11546. Results:The transcriptional and metabolomics showed that the decrease of curdlan production in the ΔphbC mutants may be caused by the insufficient supply of energy ATP conclusion:phbC play an important role in curdlan synthesis in Agrobacterium sp. more...

Organism:

Agrobacterium sp. CGMCC 11546

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26670

6 Samples

Download data: TXT

(Submitter supplied) Many pathogens and symbionts contain multipartite genomes, but how they are stably maintained is poorly understood. The plant pathogen, Agrobacterium tumefaciens, contains four replicons. Recent work indicates that their replication origins cluster at cell poles in a manner that depends on their ParB-family centromeric proteins. Here, we provide evidence that centromeric clustering is mediated by interactions between these centromeric proteins. more...

Organism:

Agrobacterium tumefaciens; Bacillus subtilis PY79

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL28115 GPL30555

29 Samples

Download data: CSV, TXT, ZIP

(Submitter supplied) Performed en masse sequencing of transposon insertions among A. tumefaciens mutants deficient in unipolar polysaccharide (UPP) production in two different genetic backgrounds, each one specific for one of the two chemical species of UPP (UPPGlcN and UPPGalN)

Organism:

Agrobacterium fabrum str. C58

Type:

Other

Platform:

GPL30075

5 Samples

Download data: TSV

(Submitter supplied) Bacterial species from diverse phyla contain multiple replicons, yet how these multipartite genomes are organized and segregated during the cell cycle remains poorly understood. Agrobacterium tumefaciens has a 2.8 Mb circular chromosome (Ch1), a 2.1 Mb linear chromosome (Ch2), and two large plasmids (pAt and pTi). We used this alpha proteobacterium as a model to investigate the global organization and temporal segregation of a multipartite genome. more...

Organism:

Agrobacterium tumefaciens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL25733 GPL30555

42 Samples

Download data: CSV, TXT

(Submitter supplied) Purpose: High throughput sequencing has revolutionized methods of microbial pathway analysis in response to various envoronmental stimuli. The aim of this study was to determine mechanisms in which Rhizobium phaseoli employ towards tolerance or resistance to aluminium toxicity through RNA sequencing. Methods: Total RNA was extracted from bacteria treated with aluminium after 48 hours with trizol and sequenced with illumina’s Miseq at Novogene Corporation Inc. more...

Organism:

Rhizobium phaseoli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31224

6 Samples

Download data: CSV

(Submitter supplied) Performed RNASeq analysis comparing A. tumefaciens C58 (fabrum) harboring a plasmid driving ectopic expression of mirA regulator gene (ATU_RS08050) from Plac promoter with the isogenic strain haboring the same plasmid with no mirA (Vector control)

Organism:

Agrobacterium fabrum str. C58

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30075

6 Samples

Download data: TXT

(Submitter supplied) Unlike other bacteria, cell growth in rhizobiales is unipolar and asymmetric. The regulation of cell division, and its coordination with metabolic processes is an active field of research. In Rhizobium etli, gene RHE_PE00024, located in a secondary chromosome, is essential for growth. This gene encodes a hybrid histidine kinase sensor protein, participating in a, as yet undescribed, two-component signaling system. more...

Organism:

Rhizobium etli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30652

6 Samples

Download data: XLSX

(Submitter supplied) We report the analysis of differentially gene expression after 7 hours and 24 hours fermentation of curdlan in Agrobacterium sp. CGMCC 11546.

Organism:

Agrobacterium sp. CGMCC 11546

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26670

6 Samples

Download data: TXT

(Submitter supplied) Purpose: The goal of this study is compare the effect of MetH and MetZ gene in curdlan synthesis in Agrobacterium sp. CGMCC 11546. methods: The transcriptional and metabolomics analysis the function of metH and metZ in Agrobacterium sp. CGMCC 11546. Results: The transcriptional and metabolomics showed that the decrease of curdlan production in the ΔmetH and ΔmetZ mutants may be caused by the insufficient supply of energy ATP conclusion: MetH and MetZ play an important role in curdlan synthesis in Agrobacterium sp. more...

Organism:

Agrobacterium sp. CGMCC 11546

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26670

9 Samples

Download data: TXT

(Submitter supplied) We report that depletion of PBP1a in Agrobacterium tumefaciens induces transcriptional changes remarkably similar to the RSI invasion switch. Using RNA-seq with NextSeq 500 sequencing, we identified genes that are differentially expressed during depletion of PBP1a after 6 hours and after 16 hours. Depletion of PBP1a after 6 hours results in upregulation in genes associated with Type VI Secretion and succinoglycan production and downregulation of genes associated with flagellar motility and chemotaxis. more...

Organism:

Agrobacterium fabrum str. C58

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30075

20 Samples

Download data: XLSX

(Submitter supplied) Interactions between plants and each neighboring microbial species are fundamental building blocks that collectively determine the structure and function of the plant microbiota, but the molecular basis of such interactions is poorly characterized. Here, we monocolonized Arabidopsis leaves with nine plant-associated bacteria from all major phyla of the plant microbiota and profiled co-transcriptomes of plants and bacteria. more...

Organism:

Plantibacter sp. Leaf1; Rhizobium sp. Leaf155; Acinetobacter sp. Leaf130; Arthrobacter sp. Soil763; Flavobacterium sp. Root935; Exiguobacterium sp. Leaf187; Arabidopsis thaliana; Pedobacter sp. Leaf176; Burkholderia sp. Leaf177; Chryseobacterium sp. Leaf404

Type:

Expression profiling by high throughput sequencing

10 related Platforms

125 Samples

Download data: FNA, TXT

(Submitter supplied) 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. more...

Organism:

Rhizobium favelukesii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27888

6 Samples

Download data: XLS

(Submitter supplied) We investigated the role of the LysR-type transcriptional regulator VtlR/LsrB (Atu2186) from Agrobacterium tumefaciens C58 (alias A. fabrum C58), which regulates the expression of small-regulatory-RNA (sRNA) genes such as AbcR1 and the expression of genes encoding small proteins with a domain of unknown function DUF1127. For this purpose, we constructed a vtlR/lsrB deletion mutant. Total RNA was isolated from this mutant as well as from an AbcR1 deletion mutant (Wilms et al., 2011) at optical densities (OD) of 0.5 or 0.5 and 1.5, respectively. more...

Organism:

Agrobacterium fabrum str. C58

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28562

9 Samples

Download data: CSV

(Submitter supplied) The genome of Agrobacterium tumefaciens C58 harbors three genes encoding small proteins (<50 aa) with a domain of unknown function DUF1127 (ATU_RS08170, ATU_RS08175, ATU_RS21905). To investigate their function we created a triple-deletion mutant lacking those genes. Total RNA was isolated from A. tumefaciens wild type and from the triple mutant (∆∆∆) at optical densities (OD) of 0.5 and 1.5, and after 24 h of growth (30 °C in YEB medium at 180 rpm) and sequenced on an Illumina platform. more...

Organism:

Agrobacterium fabrum str. C58

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28562

18 Samples

Download data: TXT

(Submitter supplied) Purpose: The goals of this study is to compare the reponse of Agrobacterium tumefaciens C58 in the presence of GHB and GABA to delineated the key-genes associated to the response of these metabolites in A. tumefaciens C58.

Organism:

Agrobacterium tumefaciens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25733

12 Samples

Download data: TXT