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Series GSE156818 Query DataSets for GSE156818
Status Public on Feb 16, 2021
Title Transcriptome analysis and 3‘-end detection of total RNA from Rhodobacter sphaeroides 2.4.1 wildtype, polynucleotide phosphorylase (pnp) mutant and RNase III (rnc) mutant strain
Organism Cereibacter sphaeroides
Experiment type Expression profiling by high throughput sequencing
Summary The polynucleotide phosphorylase (PNPase) is conserved among both Gram-positive and Gram-negative bacteria. As a core part of the degradosome, the PNPase is involved in maintaining proper RNA levels within the bacterial cell. It plays a major role in RNA homeostasis and decay since it acts as a 3’- to 5’-exoribonuclease. Furthermore PNPase can catalyze the reverse reaction by elongating RNA molecules in 5’- to 3’-end direction which finally has a destabilizing effect on the prolonged RNA molecule. RNA degradation can be initiated by an endonucleolytic cleavage and then by further promoted by exoribonucleolytic decay. In this study, we analyzed the importance of the Rhodobacter sphaeroides PNPase regarding the physiology and sRNA homeostasis. Moreover, we developed a pipeline to globally identify differential RNA 3’-ends in RNA NGS sequencing data obtained from PNPase, RNase E and RNase III mutants. The Rhodobacter sphaeroides PNPase mutant exhibits several phenotypical characteristics, including diminished adaption to low temperature, reduced resistance to organic peroxide induced stress and altered growth behavior. Furthermore, the transcriptome composition differs in the pnp mutant strain, resulting in a decreased abundance of most tRNAs and rRNAs. In addition, the PNPase has a major influence on the half-lives of several regulatory sRNAs and can have both a stabilizing or a destabilizing effect. The RNA 3’-end analysis reveals that 82% of all differential 3’-ends are enriched in the pnp mutant and are mostly located in coding sequences or untranslated regions (UTR). A fair percentage of these ends was also identified as differential RNA 3’-end in RNase E and RNase III mutant strains. The PNPase has a major influence in RNA processing and maturation and thus modulates the transcriptome. This includes regulatory sRNAs, stressing the role of PNPase in cellular homeostasis and its importance in regulatory networks. The 3’-end analysis indicates a sequential processing of UTR- and non-UTR derived sRNAs by several ribonucleases. Moreover, we provide a modular pipeline which greatly facilitates the identification of RNA 5’/3’-ends. It is publicly available on GitHub and is distributed under ICS licence.
 
Overall design This data includes the transcriptome data of three different exponentially growing strains each in triplicates: Rhodobacter sphaeroides 2.4.1 (wildtype), R. sphaeroides 2.4.1 pnp mutant (lacking C-terminal KH and S1 domains) and R. sphaeroides 2.4.1 RNase III mutant. Total RNA of all strains was isolated and sequenced.
 
Contributor(s) Spanka D, Reuscher CM, Klug G
Citation(s) 33549057, 34830143
Submission date Aug 25, 2020
Last update date Dec 07, 2021
Contact name Gabriele Klug
E-mail(s) Gabriele.Klug@mikro.bio.uni-giessen.de
Organization name Justus-Liebig University Gießen
Department Molecular- and Microbiology
Street address Heinrich-Buff-Ring 26-32
City Gießen
ZIP/Postal code 35392
Country Germany
 
Platforms (1)
GPL24048 Illumina NextSeq 500 (Rhodobacter sphaeroides)
Samples (9)
GSM4744981 wildtype, rep1
GSM4744982 wildtype, rep2
GSM4744983 wildtype, rep3
Relations
BioProject PRJNA659256
SRA SRP278812

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Supplementary file Size Download File type/resource
GSE156818_3prime_ends_pnp_vs_wt.bed.gz 13.3 Kb (ftp)(http) BED
GSE156818_3prime_ends_rnc_vs_wt.bed.gz 5.0 Kb (ftp)(http) BED
GSE156818_baySeq_pnp_vs_wt.csv.gz 426.5 Kb (ftp)(http) CSV
GSE156818_deseq_comp_pnp_vs_wt_with_annotation_and_countings.csv.gz 1.2 Mb (ftp)(http) CSV
GSE156818_pnp_merged_div_by_29648232.0_multi_by_27421951.0_forward.wig.gz 1.6 Mb (ftp)(http) WIG
GSE156818_pnp_merged_div_by_29648232.0_multi_by_27421951.0_reverse.wig.gz 1.4 Mb (ftp)(http) WIG
GSE156818_wt_merged_div_by_27421951.0_multi_by_27421951.0_forward.wig.gz 548.4 Kb (ftp)(http) WIG
GSE156818_wt_merged_div_by_27421951.0_multi_by_27421951.0_reverse.wig.gz 444.5 Kb (ftp)(http) WIG
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Processed data are available on Series record

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