Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Bradyrhizobium diazoefficiens USDA 110

ABSTRACT: Genome-wide transcription start site mapping of Bradyrhizobium japonicum free-living cells and bacteroids - a rich resource to identify new transcripts, proteins and to study gene regulation

PROVIDER: PRJNA284418 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR2033706.fastq.gz	Fastqsanger.gz
	SRR2033707.fastq.gz	Fastqsanger.gz
	SRR2033708.fastq.gz	Fastqsanger.gz
	SRR2033709.fastq.gz	Fastqsanger.gz

Items per page:

1 - 4 of 4

Similar Datasets

Genome-wide transcription start site mapping of Bradyrhizobium japonicum free-living cells and bacteroids - a rich resource to identify new transcripts, proteins and to study gene regulation

Project description:Background: During the symbiosis with legumes, Bradyrhizobium japonicum cells infect roots where they induce the formation of root nodules and differentiate into intracellular nitrogen-fixing bacteroids. We used differential RNA-seq (dRNA-seq) for the genome-wide detection of transcriptional start sites (TSSs) in B. japonicum USDA 110 cells grown free-living or as bacteroids in soybean root nodules. Results: A newly developed TSS recognition procedure based on machine learning allowed us to map 15,923 TSSs: 14,360 in free-living bacteria, 4,329 in bacteroids and 2,766 in both living conditions. Using a proteogenomics approach, we provide evidence for the translation of 107 new transcripts including 14 with TSSs in annotated genes. In addition, we provide evidence for 178 shorter or longer proteins, 109 of them with TSS support. Based on our TSS map and a new de novo promoter prediction algorithm, we identified promoter motifs mainly used in nodules (similar to RpoN-dependent promoters) or under both conditions (similar to RpoD-dependent promoters). The data is made available in a generic feature format (GFF) file along with an updated and extended genome annotation comprising promoters, TSSs and terminators. The value of such a TSS and promoter map beyond the identification of novel transcripts and ORFs is illustrated by the experimental analysis of an antisense RNA, which is a by-product of transcriptional interference in a gene encoding a cytochrome P450 highly expressed in nodules. Conclusions: The genome-wide TSS and promoter map along with the extended genome annotation represents a very useful resource for detailed analyses of gene regulation and further systems biology studies on B. japonicum in symbiosis with soybean.

2016-04-18 | GSE69059 | GEO

Bradyrhizobium diazoefficiens USDA 110

Project description:Characterization of AceA regulons in Bradyrhizobium japonicum under desiccation stress

| PRJNA287441 | ENA

Bradyrhizobium diazoefficiens USDA 110

Project description:Characterization of the Bradyrhizobium japonicum NtrC regulon by DNA Microarray analysis.

| PRJNA275876 | ENA

Bradyrhizobium diazoefficiens USDA 110

Project description:Transcriptional and Physiological Responses of Bradyrhizobium japonicum to Desiccation-Induced Stress

| PRJNA102665 | ENA

Bradyrhizobium japonicum_Bacteroids vs. Bacteria grown in HM-Arabinose

Project description:A transcriptomic analysis of bacteroids isolated from soybean plants inoculated with B. japonicum USDA 110, relative to cells cultured in HM-arabinose medium was performed and the results combined with two other transcriptomic analyses to form a reiterated pool of transcripts that define genes essential for symbiotic nitrogen fixation. Four independent biological replicates for bacteroids and free-living cells. Total of 8 arrays including dye swap.

2014-11-01 | E-GEOD-60279 | biostudies-arrayexpress

Bradyrhizobium diazoefficiens USDA 110

Project description:Identification of a gene responsible for higher N2O reductase activity in Bradyrhizobium japonicum

| PRJDB2097 | ENA

Bradyrhizobium japonicum_Bacteroids Time Course

Project description:A time-course transcriptomic analysis of bacteroids isolated from soybean plants inoculated with B. japonicum USDA 110, relative to cells cultured in HM-arabinose medium was performed to characterize senescence genes. Four independent biological materials for bacteroids and free-living cells at 6 time points. Seven or eight arrays including dye swap are presented at each time point.

2014-11-01 | E-GEOD-60465 | biostudies-arrayexpress

Whole-Genome Transcriptional analysis of Sulfate and Sulfonate assimilation by Bradyrhizobium japonicum USDA 110

Project description:The ability of Bradyrhizobium japonicum and B. elkanii strains to utilize alkane and aromatic sulfonates as sole sources of sulfur for growth was investigated. All of the strains tested were able to utilize alkane sulfonates, but not aromatic sulfonates for growth. Whole-genome transcriptional profiling was used to assess B. japonicum USDA 110 genes involved in growth on alkane sulfonates, as compared to growth on sulfate and cysteine. Two sets of genes, bll7007 to bll7011 and bll6449 to 6456 were highly expressed during growth with sulfate and sulfonates. These genes were predicted to encode alkanesulfonate monooxygenases and ABC transporter components. Reverse transcription-PCR (RT-PCR) analyses showed that these genes were organized in two operon-like structures and expressed as polycistronic messages. The sulfonate monooxygenase encoded by bll7010 (ssuD) complemented an E. coli mutant defective in utilization of sulfonates. The expression of many genes that were induced during growth on cysteine and taurine were under the control of the FixLJ-FixK2-FixK1 symbiotic nitrogen fixation cascade, indicating there is a novel linkage between sulfur metabolism and nitrogen fixation. Taken together, results of this study indicate that Bradyrhizobium sp. strains are metabolically diverse and likely use organosulfur compounds for growth and survival, and for legume nodulation and nitrogen fixation in soil systems.

2009-11-17 | GSE19039 | GEO

Bradyrhizobium diazoefficiens USDA 110

Project description:Bj H2O2 prolonged exposure vs. non-treatment

| PRJNA136971 | ENA

Bradyrhizobium diazoefficiens USDA 110

Project description:Bj Paraquat fulminant shock vs. non-treatment

| PRJNA142337 | ENA