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RNA Sequencing analysis of transcriptomics to investigate the bile stress response in L. paracasei L9

ABSTRACT: RNA Sequencing analysis of transcriptomics to investigate the bile stress response in L. paracasei L9

PROVIDER: PRJNA428354 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6436963_1.fastq.gz	Fastqsanger.gz
	SRR6436963_2.fastq.gz	Fastqsanger.gz
	SRR6436964_1.fastq.gz	Fastqsanger.gz
	SRR6436964_2.fastq.gz	Fastqsanger.gz
	SRR6436965_1.fastq.gz	Fastqsanger.gz

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RNA Sequencing analysis of transcriptomics to investigate the bile stress response in L. paracasei L9

Project description:Purpose: To understand the bile salts resistance mechanisms in L. paracasei L9 Methods: Samples from L9 cultured with or without bile salts were sequenced on an Illumina Hiseq platform. Three independent biological replicates were produced including 6 samples in total. Results: Raw data were firstly processed through in-house perl scripts to generate clean data, and then clean date were mapped to the reference genome, getting about 8-10 million total mapped reads per sample.

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Lacticaseibacillus paracasei strain:L9

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Global Transcriptomic Analysis and Function Identification of Malolactic Enzyme Pathway of Lactobacillus paracasei L9 in Response to Bile Stress.

Project description:Tolerance to bile stress is crucial for Lactobacillus paracasei to survive in the intestinal tract and exert beneficial actions. In this work, global transcriptomic analysis revealed that 104 genes were significantly changed (log2FoldChange > 1.5, P < 0.05) in detected transcripts of L. paracasei L9 when exposed to 0.13% Ox-bile. The different expressed genes involved in various biological processes, including carbon source utilization, amino acids and peptide metabolism processes, transmembrane transport, transcription factors, and membrane proteins. It is noteworthy that gene mleS encoding malolactic enzyme (MLE) was 2.60-fold up-regulated. Meanwhile, L-malic acid was proved to enhance bile tolerance, which could be attributed to the intracellular alkalinization caused by MLE pathway. In addition, membrane vesicles were observed under bile stress, suggesting a disturbance in membrane charge without L-malic acid. Then, genetic and physiological experiments revealed that MLE pathway enhanced the bile tolerance by maintaining a membrane balance in L. paracasei L9, which will provide new insight into the molecular basis of MLE pathway involved in bile stress response in Lactic acid bacteria.

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Project description:A shotgun microarray-based approach was used to identify candidate genes encoding the FOS utilization pathway in L. paracasei 1195. Differential expression profiles between cells grown on FOS and glucose provided a basis for identifying genes specifically induced by FOS. In addition, transcriptional analysis of cells grown on FOS or FOS + glucose allowed us to investigate the effect of catabolite repression on the expression of the FOS-induced genes. For sugar induction experiment (FOS vs. glucose; FOS vs. fructose), L. paracasei were grown in modified MRS (mMRS) basal medium to a final OD625 nm of ca. 0.3, at which point all of the residual sugars in the medium were consumed (based on HPLC analysis of the supernatants). The culture was then divided into equal portions, where FOS or glucose was added to a 1% final concentration. Cells were collected for total RNA isolation after 30 min (OD625 nm ca. 0.3 â 0.4). For glucose repression experiment (FOS vs. FOS + glucose), cells were grown in mMRS supplemented with 2% FOS to an OD625 nm 0.6. The culture was split into equal portions, and glucose was added to one of the portions at a 2% final concentration. Both cultures were grown for another 60 min (OD625 nm ca. 1.0) before harvested for total RNA isolation. Both experiments were performed in independent replicates (two biological replicates per experiment) with incubation at 37 degree celsius in ambient atmosphere.

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2014-06-29 | E-GEOD-46446 | biostudies-arrayexpress

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Sphingomonas carotinifaciens L9-754

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Next generation sequencing based transcriptomic analysis of bile stress response in Bifidobacterium longum BBMN68

Project description:Bifidobacterium longum is one of the natural inhabitants in human gastrointestinal tract. In order to colonize and exert particular functions in the gut, it has to be tolerant to the physiological concentrations of bile salts. In this work, we used RNA-Seq transcriptomics based on the Next-Generation Sequencing to investigate the global response to bile in B. longum BBMN68, a potential probiotic strain isolated from a healthy centenarian. In the presence of 0.75 g liter-1 ox-bile, the transcription of 236 genes were regulated (≥ 3-fold, p < 0.001). Function analysis and Gene Ontology suggested that the bile stress response of B. longum BBMN68 covers almost all biological processes, including bile stress resistance, general stress response, central metabolic process, transmembrane transport, gene expression, cell proliferation and interaction with the host. Remarkably, 3 two-component systems and 11 transcription factors were up- or down-regulated by bile, and target genes of the regulators were identified by bacterial one-hybrid system and bioinformatics methods, resulting in a putative regulatory network that controls bile stress response in B. longum for the first time. This study significantly develops our understanding on bile stress response and brings new insight to the regulatory mechanism in bifidobateria.

2014-06-29 | GSE46446 | GEO

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