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Article

Deletion of the cheZ gene results in the loss of swimming ability and the decrease of adhesion ability to Caco-2 cells in Escherichia coli Nissle 1917

Ou, Bingming
Author Ou, Bingming School of Life Sciences, Zhaoqing University, Zhaoqing, 526061, China Laboratory of Microbial Resources Exploitation and Application, Zhaoqing University, Zhaoqing, 526061, China
Lv, Haihui
Author Lv, Haihui School of Life Sciences, Zhaoqing University, Zhaoqing, 526061, China
Ge, Hua
Author Ge, Hua School of Life Sciences, Zhaoqing University, Zhaoqing, 526061, China
Fu, Dexiang
Author Fu, Dexiang School of Life Sciences, Zhaoqing University, Zhaoqing, 526061, China
Lin, Xin
Author Lin, Xin School of Life Sciences, Zhaoqing University, Zhaoqing, 526061, China
Huang, Saiqiao
Author Huang, Saiqiao School of Life Sciences, Zhaoqing University, Zhaoqing, 526061, China
Chen, Xiaojie
Author Chen, Xiaojie School of Life Sciences, Zhaoqing University, Zhaoqing, 526061, China
Liu, Yufu
Author Liu, Yufu School of Life Sciences, Zhaoqing University, Zhaoqing, 526061, China
Li, Sainan
Author Li, Sainan School of Life Sciences, Zhaoqing University, Zhaoqing, 526061, China Laboratory of Microbial Resources Exploitation and Application, Zhaoqing University, Zhaoqing, 526061, China
Liu, Wenhua
Author Liu, Wenhua School of Life Sciences, Zhaoqing University, Zhaoqing, 526061, China

Folia microbiologica. 2023 ; 68 (3) : 395-402. [pub] 20221125

Folia microbiol. (Prague)
ISSN 1874-9356
Medvik
Source

The aim of this study was to elucidate the biological functions of the motility regulatory protein CheZ in the probiotic strain Escherichia coli Nissle 1917. A cheZ gene deletion strain Nissle 1917ΔcheZ was constructed using the CRISPR/Cas9 two-plasmid system, and the corresponding complemented strain Nissle 1917ΔcheZ/pBR322-cheZ was established. Combined studies of growth kinetics testing, motility assays, swarming motility assays, and bacterial adherence assays were performed to study the motility regulatory protein CheZ-mediated functions in the prototype Nissle 1917 strain, its isogenic cheZ mutant, and the corresponding complemented strain. The growth rate of the cheZ mutant strain was lower than that of the wild-type strain in the exponential growth phase. The motility of the cheZ mutant strain was significantly lower than that of the wild-type strain. And the adhesion ability of ΔcheZ mutant to the Caco-2 cells was significantly lower than that of the wild-type strain and complemented strain. In conclusion, the results presented in our study suggested that the deletion of the cheZ gene in E. coli Nissle 1917 led to a significant reduction of its swimming ability and a subsequent marked decrease of adhesion to the Caco-2 cells.

Online article

Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing

Nature biotechnology. 2021 ; 39 (9) : 1151-1160. [pub] 20210909

Nat Biotechnol
ISSN 1546-1696
Medvik
Source

The lack of samples for generating standardized DNA datasets for setting up a sequencing pipeline or benchmarking the performance of different algorithms limits the implementation and uptake of cancer genomics. Here, we describe reference call sets obtained from paired tumor-normal genomic DNA (gDNA) samples derived from a breast cancer cell line-which is highly heterogeneous, with an aneuploid genome, and enriched in somatic alterations-and a matched lymphoblastoid cell line. We partially validated both somatic mutations and germline variants in these call sets via whole-exome sequencing (WES) with different sequencing platforms and targeted sequencing with >2,000-fold coverage, spanning 82% of genomic regions with high confidence. Although the gDNA reference samples are not representative of primary cancer cells from a clinical sample, when setting up a sequencing pipeline, they not only minimize potential biases from technologies, assays and informatics but also provide a unique resource for benchmarking 'tumor-only' or 'matched tumor-normal' analyses.