Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1271991 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR33824100_1.fastq.gz | Fastqsanger.gz | |||
| SRR33824100_2.fastq.gz | Fastqsanger.gz | |||
| SRR33824101_1.fastq.gz | Fastqsanger.gz | |||
| SRR33824101_2.fastq.gz | Fastqsanger.gz | |||
| SRR33824102_1.fastq.gz | Fastqsanger.gz |
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Project description:A longitudinal multi-omics analysis was carried out over a 26-hour small-scale fermentation of B. pertussis. Fermentations were performed in batch mode and under culture conditions intended to mimic industrial processes.
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2016-04-29 | GSE40526 | GEO
Project description:This work was designed to identify yeast cellular functions specifically affected by the stress factors predominating during the first stages of wine fermentation and genes required for optimal growth under these conditions. The main experimental method used was quantitative fitness analysis by means of competition experiments of whole genome barcoded yeast knock-out collections in continuous culture. This methodology allowed the identification of haploinsufficient genes and homozygous deletions resulting in growth impairment in synthetic must. However, genes identified as haploproficient or homozygous deletions resulting in fitness advantage were of little predictive power concerning optimal growth in this medium. The relevance of these functions for enological performance of yeast was assessed in batch cultures with single strains. Previous studies addressing yeast adaptation to winemaking conditions by quantitative fitness analysis, were not specifically focused on the proliferative stages, and their results were greatly dependent on the effects of gene deletions on yeast survival during stationary phase. Since biomass production has a great influence on the whole fermentation kinetics, focusing on the proliferative stages of the fermentation process has practical implications. In some instances our results highlight the importance of genes not previously linked to winemaking. In other cases our results are complementary to those reported in previous studies concerning, for example, the relevance of some genes involved in vacuolar, peroxisomal, or ribosomal functions. Transport processes and glucose signaling seem to be negatively affected by the stress factors encountered by yeast in synthetic must. Vacuolar activity is important for continued growth during the transition to stationary phase. Finally, reduced biogenesis of peroxisomes also seems to be advantageous. However, in contrast to what was described for later stages, reduced protein synthesis is not advantageous for the first stages of the fermentation, when most cell proliferation takes place. Competition experiments of the genome-wide collections of mutants were performed in triplicate using conditions that mimicked Phases I or II of a batch fermentation (equivalent to around 14 and 22 hours after inoculation of a batch fermentation, respectively), as well as on YPD (complete medium) for reference purposes. To this end, different feed formulations were used. One mL of either the homozygote or heterozygote pool stored at -80 ºC was added to 50 mL of YPD broth supplemented with 200 µg/mL G418 and incubated overnight at 28 °C and 150 rpm to serve as inoculum for the competition experiments. Samples were taken before the onset of the continuous culture as t=0 (preculture) references. Variations in pool composition were always estimated against the cognate preculture (most often a single preculture served as inoculum for several competitions). After 10 or 20 generations in continuous culture, samples of cells were used for the genomic DNA extraction. lification of the barcodes (uptags and downtags), hybridization, and scanning were performed according to the protocol described elsewhere [Pierce SE, Davis RW, Nislow C, Giaever G (2007) Genome-wide analysis of barcoded Saccharomyces cerevisiae gene-deletion mutants in pooled cultures. Nat Protocols 2: 2958-2974]. Slight modifications concerning the hybridization of Tag4 microarrays by using reagents and protocols from the GeneChip Hybridization, Wash and Stain Kit (Affymetrix) were made.
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Project description:Ribosome pausing slows down translation and can affect protein synthesis. Improving translation efficiency can therefore be of commercial value. Here, we investigated the occurrence of ribosome pausing during amylase secretion by the industrial production organism Bacillus subtilis under semi fed-batch fermentation conditions. We first assessed our ribosome profiling setup by inducing ribosome stalling at isoleucine codons using the antibiotic mupirocin, and found a pause preference for isoleucine codons preceded by E and P site codons with guanosine residues in their first nucleotide position. Interestingly, when we applied standard ribosomal profiling conditions we found again an enrichment of guanosine residues in the E and P site of ribosome pause sites, but this time also upstream of the ribosome pause site. This sequence motif deviates from previously described ribosome pausing motifs. For the highly expressed amylase gene amyM several strong ribosome pausing sites were detected, which remained present during the 64-hour long fermentation, and were neither related to rare codons nor to secondary protein structures. When surveying the genome, an interesting finding was the presence of strong ribosome pausing sites in several toxins genes. These potential ribosome stall sites may function in preventing inadvertent activity in the cytosol.
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