Project description:The bacterial type VI secretion system is a widespread secretion mechanism important for competition in many Gram-negative bacteria. Killing and lysing of competing bacteria can provide advantages such as nutrients or acquisition of new genes by DNA uptake. Here, we show that T6SS-dependent lysis of prey cells by the naturally competent Acinetobacter baylyi results in extensive filamentation of a significant subpopulation of A. baylyi cells. This is dependent on the release of genomic DNA from the lysed prey cells and its uptake by the competence system of A. baylyi. Single-cell level analysis using live-cell imaging shows that filamentous A. baylyi cells appear at the interface between the species. The analysis of A. baylyi transcriptome and the response of transcriptional reporters suggest that the uptake of genomic DNA results in a highly upregulated SOS response, which often leads to the cell division arrest. Using competition experiments, we show that the parental strain is outcompeted by a strain lacking the DNA uptake machinery because such mutant shows no SOS response-dependent cell division arrest. Our data suggest that the cost of SOS-response may drive selection of decreased DNA uptake in T6SS positive bacteria.

2019-12-20 | GSE136239 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of E. coli K-12 LE392, P. putida KT2440, and Acinetobacter baylyi ADP1 Transcriptomes under various antidepressant exposure

Project description:The goals of this study are to use Next-generation sequencing (NGS)to detect bacterial mRNA profiles of E. coli K-12 LE392, P. putida KT2440 and Acinetobacter baylyi ADP1 in response to various antidepressant concentrations for 2 h, in triplicate, using Illumina HiSeq 2500.The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp. The clean reads of each sample were aligned to the E. coli reference genome (NC_000913), Pseudomonas putida KT2440 genome (NCBI:txid160488) and Acinetobacter baylyi ADP1 genome (NCBI:txid62977) using SeqAlto (version 0.5). Cufflinks (version 2.2.1) was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/). Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM, a normalized value generated from the frequency of detection and the length of a given gene.

2022-08-03 | GSE181900 | GEO

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