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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Nucleotide-resolution, genome-wide, 5'-end maps of the transcriptome of Propionibacterium acnes (cultured with and without potassium downshift)

ABSTRACT: The differential RNA-seq data contained within this entry is complemented by global RNA-seq and microarray data, which is also deposited in GEO. Duplicate cultures of Propionibacterium acnes strain KPA171202 were grown exponentially in batch culture under anaerobic growth. Samples were taken following subculture with and without potassium downshift (i.e. removal from medium). This produced 4 samples; 2 replicates x 2 conditions. Aliquots of each of the 4 samples were then incubated with or without incubation TAP (tobacco acid pyrophosphatase) before library construction. Thus, 8 libraries were analysed. TAP treatment allows the cloning and sequencing of 5' ends that were originally triphosphorylated.

ORGANISM(S): Propionibacterium acnes KPA171202

SUBMITTER: David Romero A.

PROVIDER: E-GEOD-46810 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Nucleotide-resolution, genome-wide transcriptome maps of Propionibacterium acnes (cultured with and without potassium downshift)

Project description:This data contained within this entry was produced as part of a study that included differential RNA-sequencing and microarray analysis. The results of the latter two have also been deposited in GEO Duplicate cultures of Propionibacterium acnes strain KPA171202 were grown exponentially in Holland Synthetic Medium (Holland et al.1979. J Appl Bacteriol 47: 383), which supports reproducible anaerobic growth. Samples were taken following subculture with and without potassium downshift (i.e. removal from medium).

2013-05-15 | E-GEOD-46883 | biostudies-arrayexpress

Comparison of nucleotide-resolution, genome-wide transcriptome maps of Escherichia coli K12 strain BW25113 and Streptomyces coelicolor A3(2) strain M145.

Project description:This data contained within this entry was produced as part of a study that included differential RNA-sequencing. S. coelicolor and E. coli reference strains were grown in batch culture with shaking. The E. coli sample was extracted during mid-exponential growth, while the S. coelicolor sample was extracted at the start of pigmented antibiotic production.

2013-04-20 | E-GEOD-46232 | biostudies-arrayexpress

Comparison of the nucleotide-resolution, genome-wide, 5'-end maps of the transcriptomes of Escherichia coli K12 strain BW25113 and Streptomyces coelicolor A3(2) strain M145

Project description:The differential RNA-seq data contained within this entry is complemented by global RNA-seq. S. coelicolor and E. coli reference strains were grown in batch culture with shaking. The E. coli sample was extracted during mid-exponential growth, while the S. coelicolor sample was extracted at the start of pigmented antibiotic production. Each of the two samples was incubated with or without TAP (tobacco acid pyrophosphatase) before library construction. Thus, 4 libraries were analysed. TAP treatment allows the cloning and sequencing of 5' ends that were originally triphosphorylated.

2013-05-01 | E-GEOD-46507 | biostudies-arrayexpress

Candida glabrata transcription profile when grown under Niacin starvation or in human urine

Project description:The transcription profile of Candida glabrata grown under two different Niacin limitation conditions were determined. Condition 1 is comparing log phase C. glabrata cells (O.D. 0.5-0.6) grown in synthetic medium containing 0.016 uM versus 3.25 uM nicotinic acid (NA), a common form of Niacin. The NA concentration of 3.25 uM is the standard concentration in synthetic complete (SC) medium. Condition 2 is comparing log phase C. glabrata cells (O.D. 0.4-0.6) grown in 3 individual human urine samples (supplemented with 2% glucose) versus in SC medium. Keywords: transcriptional profiling by microarray GSM151863, GSM151869 are dye-swap experiment #1 and GSM151880, GSM151881 are dye-swap experiment #2 for Niacin limitation condition 1. GSM151934, GSM152116 are dye-swap experiment #1, GSM152118, GSM152119 are dye-swap experiment #2 and GSM152130, GSM152131 are dye-swap experiment #3 for Niacin limitation condition 2.

2010-06-05 | E-GEOD-6582 | biostudies-arrayexpress

Response to bile of Lactobacillus casei BL23

Project description:The response to bile of Lactobacillus casei BL23 was investigated. Lactobacillus casei BL23 was grown in MRS medium at 37C without shaking until O.D. 595 nm. reached 0.5. The cultures were then two fold diluted with prewarmed MRS medium (control) or MRS supplemented with 0.2% bovine bile (treatment) and incubation continued for 45 min. Cells were then harvested and total RNA purified.

2011-10-19 | E-GEOD-33047 | biostudies-arrayexpress

Investigation of Role of Eleven TonB Homologs in Carbohydrate Utilization by Bacteroides thetaiotaomicron

Project description:Key conserved features of these transporters include a 22 beta-strand barrel that traverses the outer membrane and houses a plug domain that occludes solute passage until the transporter is activated. Some B. theta TBDTs are also predicted to include two additional domains termed the N-terminal extension (NTE) and the Secretin and TonB N-terminus (STN) domain. The precise rearrangement of the plug domain to allow solute passage through the barrel is poorly understood but is facilitated by pairing to an inner membrane complex that harnesses proton motive force. This complex in E. coli includes the proteins TonB, ExbB, and ExbD. Recent structural analysis of this complex reveals the inner membrane spanning ExbB in a pentameric arrangement enclosed around a dimer of ExbD that extends into the periplasm. The structure of the complex with TonB has not been determined but other characterization of TonB suggests at least one copy of TonB interacts with the ExbBD complex via the TonB N-terminal membrane spanning -helix. This N-terminal -helix is followed by a linker region that spans the periplasm and a well-ordered C-terminal domain. The C-terminal domains of characterized TonB proteins share a common fold of three antiparallel -sheets with two -helices (28, 29). The final -strand at the C-terminus directly contacts the TBDT for -sheet pairing with the N-terminal extension of the TBDT plug domain called the TonBox.

2024-01-26 | PXD041518 | Pride

The transcriptome of erythromycin-resistant Campylobacter jejuni strain selected from NCTC 11168

Project description:Campylobacter, a major foodborne pathogen, is increasingly resistant to macrolide antibibotics. Previous findings suggested that development of macrolide resistance in Campylobacter requires a multi-step process, but the molecular mechanisms involved in the process are not known. In our study, erythromycin-resistant C. jejuni mutant (R) was selected in vitro by stepwise exposure of C. jejuni NCTC11168(S) to increasing concentrations of erythromycin.The resistant were subjected to microarray and the the global transcriptional profile was analyzed. In this series, DNA microarray was used to compare the gene expression profiles of the macrolide-resistant strain with its parent wild-type strain NCTC11168. A large number of gene showed significant changes in R. The up-regulated genes in the resistant strains are involved in miscellaneous periplasmic proteins, efflux protein and putative aminotransferase, while the majority of the down-regulated genes are involved in electron transport, lipoprotein, heat shock protein and unknown function proteins. The over-expression of efflux pump and periplasmic protein was involved in the development of resistance to macrolide in C. jejuni. An eight chip study using total RNA recovered from four separate resistant-type cultures of Erythrocin-resistant Campylobacter jejuni NCTC111168 (R) and four separate cultures of Campylobacter jejuni NCTC111168 (S). Each chip measures the expression level of 1634 genes from Campylobacter jejuni NCTC11168.

2013-08-13 | E-GEOD-49257 | biostudies-arrayexpress

Expression analysis of N. europaea (ATCC 19718) wildtype and pFur::Kan mutant grown in Fe-replete and Fe-limited media

Project description:Investigation of whole genome gene expression level changes in a Nitrosomonas europaea (ATCC 19718) wildtype and pFur::Kan mutant [kanamycin resistance cassette insertion in the promoter region of the fur gene (NE0616)] strains grown in Fe-replete and Fe-limited media. The Nitrosomonas europaea (ATCC 19718) wiltype cells grown in Fe-limited media were compared to cells grown in Fe-replete media to gain a better understanding of the metabolic changes occurring in response to iron stress. The Nitrosomonas europaea (ATCC 19718) pFur::Kan mutant strain grown in Fe-replete & Fe-limited media were compared to wildtype cells grown in Fe=replete & Fe-limited media to gain a better understanding of the role Fur (NE0616) plays in iron homeostasis control. A 4-plex 3 chip study using total RNA recovered from three separate wild-type cultures each of N. europaea grown in Fe-replete media and Fe-limited media and three seperate cultures each of N. europaea pFur::Kan mutant strain grown in Fe-replete and Fe-limited media. Each chip measures the expression level of 2368 genes from Nitrosomonas europaea (ATCC19718) with 4 X 72,000 60-mer 14 probe pairs per gene, with two-fold technical redundancy.

2010-06-20 | E-GEOD-18709 | biostudies-arrayexpress

Proteomic comparison of Chlamydomonas wildtype and calredoxin knock-down mutants via 14N/15N metabolic labeling

Project description:Calcium (Ca2+) and redox signaling play important roles in acclimation processes from archaea to eukaryotic organisms. Herein we characterized a unique protein from Chlamydomonas reinhardtii that has the competence to integrate Ca2+- and redox-related signaling. This protein, designated as calredoxin (CRX), combines four Ca2+-binding EF-hands and a thioredoxin (TRX) domain. A crystal structure of CRX, at 1.6 Å resolution, revealed an unusual calmodulin-fold of the Ca2+-binding EF-hands, which is functionally linked via an inter-domain communication path with the enzymatically active TRX domain. CRX is chloroplast-localized and interacted with a chloroplast 2-Cys-peroxiredoxin (PRX1). Ca2+-binding to CRX is critical for its TRX activity and for efficient binding and reduction of PRX1. Thereby, CRX represents a new class of Ca2+-dependent "sensor-responder" proteins. Genetically engineered Chlamydomonas strains with strongly diminished amounts of CRX revealed altered photosynthetic electron transfer and were affected in oxidative stress response underpinning a function of CRX in stress acclimation.

2016-10-12 | PXD003759 | Pride

Identification of RNA-RNA interactions in Bacillus Subtilis by in vivo UV crosslinking

Project description:Small RNAs (sRNAs) are a taxonomically-restricted but transcriptomically-abundant class of post-transcriptional regulators. While potentially of importance, we know the function of few. This is in no small part because we lack global-scale methodology enabling target identification, this being especially acute in species without known RNA meeting point proteins (e.g. Hfq). We apply a combination of psoralen RNA cross-linking and Illumina-sequencing to identify RNA-RNA interacting pairs in vivo in Bacillus subtilis, resolving previously well-described interactants. Although sRNA-sRNA pairings are rare (compared with sRNA/mRNA), we identify a robust example involving the unusually conserved sRNA (RoxS/RsaE) and an unstudied sRNA that we term Regulator of small RNA A (RosA). This interaction is found in independent samples across multiple conditions. Given the possibility of a novel associated regulatory mechanism, and the rarity of well-characterised bacterial sRNA-sRNA interactions, we mechanistically dissect RosA and its interactants. RosA we show to be a sponge RNA, the first to be described in a Gram-positive bacterium. RosA interacts with at least two sRNAs, RoxS and FsrA. Unexpectedly, it acts differently on each. As expected of a sponge RNA, FsrA is sequestered by RosA. The RosA/RoxS interaction is more complex affecting not only the level of RoxS but also its processing and efficacy. Importantly, RosA provides the condition-dependent intermediary between CcpA, the key regulator of carbon metabolism, and RoxS. This not only provides evidence for a novel, and functionally important, regulatory mechanism, but in addition, provides the missing link between transcriptional and post-transcriptional regulation of central metabolism.

2021-08-25 | E-MTAB-8490 | biostudies-arrayexpress

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