Selene F H Shore, Michael Ptacek, Andrew D Steen, Elizabeth M Fozo
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Using our custom database, we found that these gene pairs are widespread across <i>E. coli</i> and have expression potential via BLASTn. We identified an alternative, dominant sequence variant of TisB and confirmed that it is toxic upon overproduction. Additionally, analyses revealed a highly conserved sequence in the <i>zorO</i> mRNA untranslated region that is required for full toxicity. We further noted that over 30% of <i>E. coli</i> genomes contain an <i>orz</i> antitoxin gene only and confirmed its expression in a representative strain: the first confirmed report of a type I antitoxin without its cognate toxin. Our results add to our understanding of these systems, and our methodology is applicable for other type I loci to identify critical regulatory and functional features.IMPORTANCEChromosomal type I toxin-antitoxins are a class of genes that have gained increasing attention over the last decade for their roles in antibiotic persistence which may contribute to therapeutic failures. However, the control of many of these genes and when they function have remained elusive. We demonstrate that a simple genetic conservation-based approach utilizing free, publicly available data yields known and novel insights into the regulation and function of three chromosomal type I toxin-antitoxins in <i>Escherichia coli</i>. 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引用次数: 0
摘要
细菌染色体 I 型毒素-抗毒素系统由一个通常小于 60 个氨基酸的小蛋白质和一个抑制毒素翻译的小 RNA(sRNA)组成。在过去十年中,这些基因对因其对细菌的抗生素持久性和噬菌体耐受性的贡献而备受关注。然而,由于基因缺失往往无法产生可观察到的表型,许多基因的生物功能仍然难以确定。对于许多基因对来说,毒素和/或抗毒素基因何时在细菌内原生表达仍是未知数。我们研究了 2,000 多株大肠杆菌(包括致病菌和共生菌)中三种 I 型毒素-抗毒素系统(tisB/istR-1、shoB/ohsC 和 zor/orz)的序列保存情况。利用我们的定制数据库,我们通过 BLASTn 发现这些基因对广泛存在于大肠杆菌中,并具有表达潜力。我们确定了 TisB 的另一种显性序列变体,并证实它在过度生产时具有毒性。此外,分析还揭示了 zorO mRNA 非翻译区的一个高度保守序列,该序列是完全毒性所必需的。我们进一步注意到,超过 30% 的大肠杆菌基因组仅含有 orz 抗毒素基因,并在一个代表性菌株中证实了该基因的表达:这是首次证实 I 型抗毒素不含同源毒素的报告。我们的研究结果加深了我们对这些系统的了解,我们的方法也适用于其他 I 型基因座,以确定关键的调控和功能特征。重要意义染色体 I 型毒素-抗毒素是一类基因,在过去十年中因其在抗生素持久性中的作用而受到越来越多的关注,这可能会导致治疗失败。然而,这些基因中的许多基因的控制以及它们何时起作用仍然难以捉摸。我们的研究表明,利用免费、公开的数据,一种简单的基于基因保护的方法对大肠杆菌中三种染色体 I 型毒素-抗毒素的调控和功能产生了已知的和新的见解。这项研究还为如何将这种方法应用于其他相关基因提供了一个框架。
A simple BLASTn-based approach generates novel insights into the regulation and biological function of type I toxin-antitoxins.
Bacterial chromosomal type I toxin-antitoxin systems consist of a small protein, typically under 60 amino acids, and a small RNA (sRNA) that represses toxin translation. These gene pairs have gained attention over the last decade for their contribution to antibiotic persistence and phage tolerance in bacteria. However, biological functions for many remain elusive as gene deletions often fail to produce an observable phenotype. For many pairs, it is still unknown when the toxin and/or antitoxin gene are natively expressed within the bacterium. We examined sequence conservation of three type I toxin-antitoxin systems, tisB/istR-1, shoB/ohsC, and zor/orz, in over 2,000 Escherichia coli strains, including pathogenic and commensal isolates. Using our custom database, we found that these gene pairs are widespread across E. coli and have expression potential via BLASTn. We identified an alternative, dominant sequence variant of TisB and confirmed that it is toxic upon overproduction. Additionally, analyses revealed a highly conserved sequence in the zorO mRNA untranslated region that is required for full toxicity. We further noted that over 30% of E. coli genomes contain an orz antitoxin gene only and confirmed its expression in a representative strain: the first confirmed report of a type I antitoxin without its cognate toxin. Our results add to our understanding of these systems, and our methodology is applicable for other type I loci to identify critical regulatory and functional features.IMPORTANCEChromosomal type I toxin-antitoxins are a class of genes that have gained increasing attention over the last decade for their roles in antibiotic persistence which may contribute to therapeutic failures. However, the control of many of these genes and when they function have remained elusive. We demonstrate that a simple genetic conservation-based approach utilizing free, publicly available data yields known and novel insights into the regulation and function of three chromosomal type I toxin-antitoxins in Escherichia coli. This study also provides a framework for how this approach could be applied to other genes of interest.
mSystemsBiochemistry, Genetics and Molecular Biology-Biochemistry
CiteScore
10.50
自引率
3.10%
发文量
308
审稿时长
13 weeks
期刊介绍:
mSystems™ will publish preeminent work that stems from applying technologies for high-throughput analyses to achieve insights into the metabolic and regulatory systems at the scale of both the single cell and microbial communities. The scope of mSystems™ encompasses all important biological and biochemical findings drawn from analyses of large data sets, as well as new computational approaches for deriving these insights. mSystems™ will welcome submissions from researchers who focus on the microbiome, genomics, metagenomics, transcriptomics, metabolomics, proteomics, glycomics, bioinformatics, and computational microbiology. mSystems™ will provide streamlined decisions, while carrying on ASM''s tradition of rigorous peer review.