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Pseudolysogeny RNAseq

ABSTRACT: S-PM2 infecting Synechococcus WH7803 under P-stress conditions

PROVIDER: PRJEB64420 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	ERR11738551_1.fastq.gz	Fastqsanger.gz
	ERR11738551_2.fastq.gz	Fastqsanger.gz
	ERR11738552_1.fastq.gz	Fastqsanger.gz
	ERR11738552_2.fastq.gz	Fastqsanger.gz
	ERR11738553_1.fastq.gz	Fastqsanger.gz

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Expression of intergenic regions of Synechococcus WH 7803 under environmentally relevant stresses

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Transcription profiling of cyanophage S-PM2 as it infects Synechococcus WH7803 over a 9 hr time series

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Project description:We constructed a tiling microarray, covering nearly all of the intergenic regions larger than 50 bp on both strands of the genome of the marine picocyanobacterium Synechococcus WH7803. We analyzed transcript levels from cultures grown under ecologically relevant stress conditions. The investigated stress conditions were cold stress, high light stress, phosphate depletion and iron depletion. We identified several previously unknown small RNAs, partially differentially expressed. The detected RNAs provide a starting point for further investigations on the acclimatisation to different stresses for Synechococcus WH7803. For every applied growth condition the cultures were grown in triplicates as were the respective controls. Respective controls were treated the same as the stressed bacterial cultures in terms of centrifugation and / or dilution. Bacteria were harvested by rapid filtering and directly freezed by liquid nitrogen.

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Project description:Whole-genome expression dynamics of cyanopodovirus P-SSP7 and its host Prochlorococcus strain MED4 have been reported. To investigate whether cyanopodoviruses infecting Prochlorococcus and Synechococcus have similar transcription strategy and host response to phage infection, genomic and transcriptomic analyses were conducted on cyanopodovirus S-SBP1 that infects Synechococcus strain WH7803. S-SBP1 has a latent period of 8 h and a burst size of 30 progeny phages per cell. S-SBP1 was most similar to cyanopodovirus S-RIP2 that also infects Synechococcus WH7803, in terms of whole genome phylogenetic relationship and average nucleotide identity (ANI). Three hypervariable genomic islands were found when comparing the genomes of S-SBP1 and S-RIP2, and single nucleotide variants (SNV) were observed on three genes of S-SBP1, which are located within the island regions. Based on RNA-seq analysis, genes of S-SBP1 were clustered into three temporal express classes, with gene content within each class similar to that of P-SSP7. Thirty-two host genes were upregulated during phage infection, including those involved in carbon metabolism, ribosome component and stress response. These upregulated genes were also similar to those of Prochlorococcus MED4 in response to infection by P-SSP7. Our study demonstrates a programmed temporal expression pattern of cyanopodoviruses and hosts during infection.

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