Genomic inversions in Escherichia coli alter gene expression and are associated with nucleoid protein binding sites.

IF 2.3 3区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Genome Pub Date : 2022-05-01 Epub Date: 2022-01-24 DOI:10.1139/gen-2021-0102
Daniella F Lato, Qing Zeng, G Brian Golding
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引用次数: 1

Abstract

Genomic reorganization, such as rearrangements and inversions, influences how genetic information is organized within the bacterial genomes. Inversions, in particular, facilitate genome evolution through gene gain and loss, and can alter gene expression. Previous studies have investigated the impact inversions have on gene expression induced inversions targeting specific genes or examine inversions between distantly related species. This fails to encompass a genome-wide perspective of naturally occurring inversions and their post-adaptation impact on gene expression. Here, we used bioinformatic techniques and multiple RNA-seq datasets to investigate the short- and long-range impact inversions have on genomic gene expression within Escherichia coli. We observed differences in gene expression between homologous inverted and non-inverted genes even after long-term exposure to adaptive selection. In 4% of inversions representing 33 genes, differential gene expression between inverted and non-inverted homologs was detected, with greater than two-thirds (71%) of differentially expressed inverted genes having 9.4-85.6-fold higher gene expression. The identified inversions had more overlap than expected with nucleoid-associated protein binding sites, which assist in the regulation of genomic gene expression. Some inversions can drastically impact gene expression, even between different strains of E. coli, and could provide a mechanism for the diversification of genetic content through controlled expression changes.

大肠杆菌的基因组倒置改变了基因表达,并与类核蛋白结合位点相关。
基因组重组,如重排和倒位,影响细菌基因组内遗传信息的组织方式。逆转录,特别是通过基因的获得和损失促进基因组的进化,并可以改变基因的表达。以前的研究已经研究了逆转录对基因表达的影响,诱导了针对特定基因的逆转录,或者研究了远亲物种之间的逆转录。这未能涵盖自然发生的反转及其对基因表达的适应后影响的全基因组视角。在这里,我们使用生物信息学技术和多个RNA-seq数据集来研究反转对大肠杆菌基因组基因表达的短期和长期影响。我们观察到同源倒置基因和非倒置基因在长期暴露于适应选择后的基因表达差异。在代表33个基因的4%的倒置中,检测到倒置和非倒置同源物之间的差异基因表达,超过三分之二(71%)的差异表达倒置基因的基因表达量高出9.4-85.6倍。所鉴定的倒位与核相关蛋白结合位点有比预期更多的重叠,这有助于调节基因组基因的表达。一些倒位可以极大地影响基因表达,甚至在不同的大肠杆菌菌株之间,并且可以通过控制表达变化提供遗传内容多样化的机制。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
Genome
Genome 生物-生物工程与应用微生物
CiteScore
5.30
自引率
3.20%
发文量
42
审稿时长
6-12 weeks
期刊介绍: Genome is a monthly journal, established in 1959, that publishes original research articles, reviews, mini-reviews, current opinions, and commentaries. Areas of interest include general genetics and genomics, cytogenetics, molecular and evolutionary genetics, developmental genetics, population genetics, phylogenomics, molecular identification, as well as emerging areas such as ecological, comparative, and functional genomics.
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