Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk, 80-308, Poland.
Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, Gdansk, 80-308, Poland.
Sci Rep. 2019 Apr 9;9(1):5808. doi: 10.1038/s41598-019-42311-w.
Restriction-modification (R-M) systems are highly widespread among bacteria and archaea, and they appear to play a pivotal role in modulating horizontal gene transfer, as well as in protecting the host organism against viruses and other invasive DNA particles. Type II R-M systems specify two independent enzymes: a restriction endonuclease (REase) and protective DNA methyltransferase (MTase). If the cell is to survive, the counteracting activities as toxin and antitoxin, must be finely balanced in vivo. The molecular basis of this regulatory process remains unclear and current searches for regulatory elements in R-M modules are focused mainly at the transcription step. In this report, we show new aspects of REase control that are linked to translation. We used the EcoVIII R-M system as a model. Both, the REase and MTase genes for this R-M system contain an unusually high number of rare arginine codons (AGA and AGG) when compared to the rest of the E. coli K-12 genome. Clusters of these codons near the N-terminus of the REase greatly affect the translational efficiency. Changing these to higher frequency codons for E. coli (CGC) improves the REase synthesis, making the R-M system more potent to defend its host against bacteriophages. However, this improved efficiency in synthesis reduces host fitness due to increased autorestriction. We hypothesize that expression of the endonuclease gene can be modulated depending on the host genetic context and we propose a novel post-transcriptional mode of R-M system regulation that alleviates the potential lethal action of the restriction enzyme.
限制-修饰（R-M）系统在细菌和古菌中广泛存在，它们似乎在调节水平基因转移以及保护宿主免受病毒和其他入侵 DNA 颗粒方面发挥着关键作用。II 型 R-M 系统指定两种独立的酶：限制内切酶（REase）和保护性 DNA 甲基转移酶（MTase）。如果细胞要存活，细胞内必须精细平衡拮抗活性作为毒素和抗毒素。这种调节过程的分子基础仍不清楚，目前对 R-M 模块中的调节元件的搜索主要集中在转录步骤。在本报告中，我们展示了与翻译相关的 REase 控制的新方面。我们使用 EcoVIII R-M 系统作为模型。与大肠杆菌 K-12 基因组的其余部分相比，该 R-M 系统的 REase 和 MTase 基因都包含异常高数量的稀有精氨酸密码子（AGA 和 AGG）。这些密码子簇靠近 REase 的 N 端，极大地影响翻译效率。将这些密码子更改为大肠杆菌的高频密码子（CGC）可以提高 REase 的合成效率，使 R-M 系统更有效地防御噬菌体。然而，这种合成效率的提高会因自身限制增加而降低宿主适应性。我们假设内切酶基因的表达可以根据宿主的遗传背景进行调节，并且我们提出了一种新的 R-M 系统调节的转录后模式，该模式减轻了限制酶的潜在致命作用。
