Ontology highlight
ABSTRACT:
PROVIDER: PRJNA533816 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8932530_1.fastq.gz | Fastqsanger.gz | |||
| SRR8932530_2.fastq.gz | Fastqsanger.gz | |||
| SRR8932540_1.fastq.gz | Fastqsanger.gz | |||
| SRR8932540_2.fastq.gz | Fastqsanger.gz | |||
| SRR8932531_1.fastq.gz | Fastqsanger.gz |
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Project description:The marine environment holds one of the largest pools of reduced organic carbon on Earth. Within this organic carbon are metabolites produced as a result of microbial activity. This project considers the effects of predation and viral lysis on the metabolites found in the surface ocean. Using seawater from the surface ocean, we experimentally manipulated levels of predation and viral lysis. At the beginning and end of the experiment, we sampled the intracellular and extracellular metabolites. The extracts were analyzed using liquid chromatography-based targeted and untargeted metabolomics methods that we have modified for use with marine samples. The untargeted metabolomics data revealed a complex mixture of organic compounds in all of the experimental treatments. However, changes in the majority of the features could not be linked to viral lysis or predation. Within the targeted metabolomics data, increased intracellular levels of osmolytes (glycine betaine, dimethylsulfoniopropionate, proline, and ectoine) were observed under conditions with limited grazing or viral lysis. The molecular insights derived here will explicitly inform our understanding of microbial processes in the surface ocean and the subsequent impacts on the global carbon cycle.
2017-05-23 | MTBLS461 | MetaboLights
Project description:Bacteriophage P1 along with λ and T4 phages are among the best described bacterial viruses in molecular biology. For years, P1 features as well as its life cycle have been studied and its complete genome was published. Undeciphered phenomenon of improved P1vir lytic development in the absence of DksA protein in cell engaged us to more holistic experimental approach. Bacterial wild type and dksA strains were cultured to OD600 = 0.2. Next, P1vir was added, samples were withdrawn at 0, 10 and 30 minutes after P1vir infection. Total RNA was isolated and checked for quality using the Bioanalyzer 2100. The sequencing run was conducted on the Illumina NovaSeq6000 platform. 30 million pair-end reads per samples were assessed with 101 pb read length. Reference P1 phage genome sequence and annotations were downloaded from GenBank. We have discovered many changes in virus transcriptome. For instance: downregulation of phage genes encoding the main repressor of lysogeny C1 or proteins triggering cell lysis (e.g., lysozyme, holin) and upregulation of genes encoding antiholins in dksA mutant. This results support our gentle lysis hypothesis – less efficient lysis, combined with minor improvements of phage development which may lead to higher phage yield in DksA-devoid cells. We have observed upregulated expression of phage genes responsible for virion-parts production in the dksA mutant. Interestingly, expression of lysogeny-related c8 gene is upregulated in the dksA mutant. We speculate that P1vir developing in the dksA host is at the brink of lysogeny but is unable to established it and eventually enters the lytic pathway. We also found some interesting events in host cells upon infection. P1vir is taking control of the cellular protein, sugar and lipid metabolism in both, the wild type and dksA mutant hosts. However, in dksA mutant several genes involved in sulfur metabolism were uniquely upregulated. It remains unclear if this associates with obtaining new energy sources or with global reprograming via H2S signaling functions. Generally, the hosts are reacting by activating SOS response or upregulating the heat shock proteins. But we also found downregulation of proteolysis which was unique for the dksA strain. We believe that this extensive and comprehensive study not only finds reasonable explanations for the improved P1vir development in dksA strain, but also makes a great contribution to the field of P1 phage biology. Funding: This research was funded by the National Science Center, Poland (grant PRELUDIUM 2013/09/N/NZ2/01899 to G.M.C.)
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Project description:In B. subtilis, the Tat secretion system is essential for effective growth in media lacking iron or NaCl, which is related to the Tat-dependent export of the heme peroxidase EfeB. In Lysogeny Broth (LB) without NaCl, tat mutant bacteria undergo cell lysis in the early exponential growth phase. Part of the population of mutant bacteria then adapts to the salt-deprived condition and resumes growth. The absence of sRNA S313, which has a predicted role in modulating the expression of the efeUOB operon, also leads to a lysis-recovery phenotype. In this study, the transcriptomes of B. subtilis wild type, tat mutant and S313 mutant were analyzed during lysis and recovery phase in order to elucidate the reasons for lysis of mutant bacteria in the absence of NaCl and subsequent adaptation to this condition. It was, e.g., shown that tat mutant cells suffer from severe oxidative stress and starvation.
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2010-06-01 | GSE16837 | GEO
Project description:This data set was downloaded from MetaboLights (http://www.ebi.ac.uk/metabolights/) accession number MTBLS461 Abstract:The marine environment holds one of the largest pools of reduced organic carbon on Earth. Within this organic carbon are metabolites produced as a result of microbial activity. This project considers the effects of predation and viral lysis on the metabolites found in the surface ocean. Using seawater from the surface ocean, we experimentally manipulated levels of predation and viral lysis. At the beginning and end of the experiment, we sampled the intracellular and extracellular metabolites. The extracts were analyzed using liquid chromatography-based targeted and untargeted metabolomics methods that we have modified for use with marine samples. The untargeted metabolomics data revealed a complex mixture of organic compounds in all of the experimental treatments. However, changes in the majority of the features could not be linked to viral lysis or predation. Within the targeted metabolomics data, increased intracellular levels of osmolytes (glycine betaine, dimethylsulfoniopropionate, proline, and ectoine) were observed under conditions with limited grazing or viral lysis. The molecular insights derived here will explicitly inform our understanding of microbial processes in the surface ocean and the subsequent impacts on the global carbon cycle.
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