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Streptococcus suis strain:05ZYH33

ABSTRACT: RNA-seq analysis of genes regulated by stk in Streptococcus suis serotype 2 Transcriptome

PROVIDER: PRJNA344836 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR4341213_1.fastq.gz	Fastqsanger.gz
	SRR4341213_2.fastq.gz	Fastqsanger.gz
	SRR4341214_1.fastq.gz	Fastqsanger.gz
	SRR4341214_2.fastq.gz	Fastqsanger.gz

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Streptococcus suis 05ZY: control vs. treated by licochalcone A

Project description:Streptococcus suis is an important emerging worldwide pig pathogen and zoonotic agent with rapid evolution of virulence and drug resistance. Licochalcone A, used in traditional Chinese medicine, exhibits antimicrobial, antioxidant and anti-inflammatory activities. Herein, a whole-genome DNA microarray was used to investigate the global transcriptional regulation of Streptococcus suis 05ZYH33 treated by subinhibitory concentration of licochalcone A. 132 genes were differentially regulated upon liochalcone A treatment, including 78 genes up-regulated and 54 genes down-regulated which included many central biological functions such as metabolism, transcription and translation. We tried to investigate the antimicrobial mechanism of licochalcone A in the aspect of bacterial cell cycle control. Our analysis indicated that licochalcone A might inhibit the growth of S. suis by controlling the replication initiation and cell division through amino acid metabolism. A cDNA microarray imprinted with 2156 genes representing about 98% of Streptococcus suis serotype 2 genome was used for transcriptome analysis. For two-sample (reference vs. test) microarray hybridization, four independent bacterial cultures from each condition were prepared as biological replicates for RNA isolation. Four dual-fluorescence-labeled cDNA probes were prepared to hybridize with four slides, respectively. Pairwise comparisons were made using dye swaps to avoid labeling bias. A ratio of mRNA levels (test/reference) was calculated for each gene. Significant changes of gene expression were identified with the SAM software. After the SAM analysis, only genes with at least 2-fold changes in expression were collected for further analysis.

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Quantitative proteomics revealed modulation of macrophages by MetQ gene of Streptococcus suis serotype 2.

Project description:MetQ gene of Streptococcus suis serotype 2 deletion strain has attenuated antiphagocytosis. However,the mechanism of antiphagocytosis and pathogenesis of MetQ in SS2 has remained unclear. In this study, stable isotope labeling by amino acids in cell culture (SILAC) based liquid chromatography-mass spectrometry (LC-MS) and subsequent bioinformatics analysis was used to determine differentially expressed proteins of RAW264.7 cells infected with △MetQ and ZY05719, aimed at elucidating the mechanism of antiphagocytosis and innate immunity of macrophages infected by Streptococcus suis.

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Project description:To investigate the effect of CodY mutation on the gene expression in Streptococcus suis serotype 2 SC19 strain, we have employed whole genome microarray expression profiling as a discovery platform to identify genes regulated by CodY mutation. DNA microarray analysis was performed using an Agilent custom-designed oligonucleotide microarray. Based upon the whole genome sequence of SC19 , specific 60-mer oligonucleotide probes were designed using eArray (https://earray.chem.agilent.com/earray/), to cover all annotated genes. Probes were printed seven times on microarray slides. Three biological replicates of total RNA from two wild type strains and from two codY mutant strains were amplified and labeled with Cy3-CTP using Low Input Quick Amp Labeling Kit, one-color(Agilent technologies, US), following the manufacturer’s instructions. Labeled cRNA was purified using the RNeasy mini kit (Qiagen). After fragmentation, microarray slides were hybridized with 600 ng Cy3-labeled cRNA. Hybridization was performed at 65 °C for 17 h with rotation at 10 rpm. Microarray slides were washed and scanned by an Agilent Microarray Scanner (G2565BA). Those genes with greater than two-fold change ratios were regarded as differentially expressed genes. codY mutation induced gene expression in Streptococcus suis serotype 2 SC19 was detected in two wild type and two codY mutated strain of Streptococcus suis serotype 2.

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