Ontology highlight
ABSTRACT:
PROVIDER: PRJNA543770 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9093161_1.fastq.gz | Fastqsanger.gz | |||
| SRR9093161_2.fastq.gz | Fastqsanger.gz | |||
| SRR9093162_1.fastq.gz | Fastqsanger.gz | |||
| SRR9093162_2.fastq.gz | Fastqsanger.gz | |||
| SRR9093163_1.fastq.gz | Fastqsanger.gz |
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Project description:Dictyostelium amoebae feed on bacteria, which are taken up by phagocytosis. Using DNA microarrays we have investigated gene expression during phagocytosis of Dictyostelium cells incubated with Escherichia coli. The gene expression profiles of cells incubated for a short time with bacteria were compared with cells either exposed to axenic culture medium or exponentially growing on bacteria. Transcriptional changes during exponential growth either in axenic medium or on bacteria were also compared, in order to identify genes differentially expressed during growth on bacteria. We recognized 443 and 59 genes, which are differentially regulated by phagocytosis or growth on bacteria, respectively, and 102 genes, which are common to both processes. Roughly one third of the genes is up- and two third down-regulated compared to growth in axenic medium. Functional annotation of differentially regulated genes revealed that phagocytosis induces profound changes in carbohydrate, aminoacid and lipid metabolism, in the translation machinery and in cytoskeletal components. Among the up-regulated genes are genes encoding proteins involved in transcription and translation, sterol metabolism and mitochondrial biogenesis. Very few changes were detected in genes required for endocytosis and intracellular traffic, suggesting that the intracellular traffic machinery is mostly in common between phagocytosis and pinocytosis. A few putative receptor or adhesion proteins and components of signal transduction have been identified, which could be involved in regulating phagocytosis.
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Project description:Previous studies have demonstrated that the iron content in marine heterotrophic bacteria is comparatively higher than that of phytoplankton. Therefore, they have been indicated to play a major role in the biogeochemical cycling of iron. In this study, we aimed to investigate the potential of viral lysis as a source of iron for marine heterotrophic bacteria. Viral lysates were derived from the marine heterotrophic bacterium, Vibrio natriegens PWH3a (A.K.A Vibrio alginolyticus). The bioavailability of Fe in the lysates was determined using a model heterotrophic bacterium, namely, Dokdonia sp. strain Dokd-P16, isolated from Fe-limited waters along Line P transect in the Northeastern Pacific Ocean. The bacteria were grown under Fe-deplete or Fe-replete conditions before being exposed to the viral lysate. Differential gene expression following exposure to the viral lysate was analyzed via RNA sequencing to identify differentially expressed genes under iron-replete and iron-deplete conditions. This study would provide novel insights into the role of viral lysis in heterotrophic bacteria in supplying bioavailable iron to other marine microorganisms under iron-limiting and non-limiting conditions. First, the marine heterotrophic bacterium genome, Dokdonia sp. strain Dokd-P16, was sequenced to provide a genomic context for the expression studies. Subsequently, the relative gene expression in Dokdonia sp. strain Dokd-P16 grown under Fe limiting and non-limiting conditions were analyzed. This transcriptomic approach would be utilized to elucidate genes regulated by Fe availability in Dokdonia sp. strain Dokd-P16, which indicate its Fe-related response viral lysate exposure. Taken together, in this study, the transcriptomic responses of Fe-limited and non-limited marine heterotrophic bacteria were analyzed, which provided novel insights into the biological availability of Fe from the viral lysates.
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