Unknown,Transcriptomics,Genomics,Proteomics

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Profiling of miRNA expression of HeLa cells infected with Salmonella Typhimurium

ABSTRACT: We identified miRNAs differentially regulated upon Salmonella infection by comparative deep-sequencing analysis of cDNA libraries prepared from the small RNA population (10M-bM-^@M-^S29 nt) of HeLa cells infected with Salmonella (20 hpi) and mock-treated cells. Considering that at a MOI of 25 Salmonella is internalized in only 10-15% of the HeLa cells, we separated the fraction of cells which had internalized Salmonella (Salmonella+) from the bystander fraction (Salmonella-) by fluorescence-activated cell sorting (FACS), and extended the analysis of miRNA changes to these samples. Interestingly, we observed that Salmonella infection induces a significant decrease in the expression of all the detected members of the miR-15 family miRNA profiles of HeLa cells infected with Salmonella Typhimurium were generated by deep sequencing, using Illumina HiSeq2000.

ORGANISM(S): Homo sapiens

SUBMITTER: Konrad FM-CM-6rstner

PROVIDER: E-GEOD-53278 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:The M-NM-1-proteobacterium Sinorhizobium fredii NGR234 has an exceptionally wide host range as it forms nitrogen-fixing nodules with more legumes than any other known microsymbiont. Within its 6.9 Mbp genome it encodes two N-acyl-homoserine-lactone synthase genes (i.e. traI and ngrI) involved in the biosynthesis of two distinct autoinducer I-type molecules. Here we report on the construction of a NGR234-M-NM-^TtraI and a NGR234-M-NM-^TngrI mutant and the genome wide RNA-seq-based transcriptome analysis in the parent strain and in the two constructed mutants. A high-resolution RNA-seq analysis of early stationary phase cultures in the background of NGR234-M-NM-^TtraI suggested that up to 316 genes (4.9% of all predicted genes) were differentially expressed in the mutant vs. the parent strain. Similarly, in the background of NGR234-M-NM-^TngrI 466 differentially regulated genes (7.3% of all predicted genes) were identified. A considerable overlap in the gene expression pattern was uncovered between both mutants resulting in a common set of 186 genes which were almost identically regulated. Co-regulated genes that were linked to the ngrI- and the traI-dependent autoinducer regulatory circuits included 53 flagella biosynthesis genes and genes linked to EPS succinoglycan biosynthesis. Among the genes and ORFs that were differentially regulated in NGR234-M-NM-^TtraI were those linked to replication of the pNGR234a symbiotic plasmid and cytochrome c-related genes. In the NGR234-M-NM-^TngrI mutant biotin and pyrroloquinoline quinone (PQQ) biosynthesis genes were differentially expressed as well as the entire cluster of 21 genes linked to assembly of the NGR234 type three secretion system II (T3SS-II). We also discovered that genes responsible for octopine catabolism in NGR234 are strongly repressed in the presence of high levels of N-acyl-homoserine-lactones (AHLs). Surprisingly, only few truly symbiosis-related genes were identified that appeared to be quorum sensing regulated. Together with nodulation assays, the RNAseq-based findings suggested that QS-dependent gene regulation appears to be of higher relevance during non-symbiotic growth rather than for life within root nodules. In total 12 samples were analyzed (six different treatments with two independent samples), treatment A: NGR234 wild type strain in stationary phase, treatment B: NGR234 traI-mutant strain in stationary phase, treatment C: NGR234 ngrI-mutant strain in stationary phase, treatment D: NGR234 wild type strain in exponential phase, treatment E: NGR234 wild type supplemented with 0.05 M-BM-5M AHLs in exponential phase, treatment F: NGR234 wild type supplemented with 50 M-BM-5M AHLs in exponential phase

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Profiling of miRNA expression of HeLa cells infected with Salmonella Typhimurium

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