Details of the bacteria's "natural immunity" have been revealed

when the virus invades mammalian cells, the protein that initially identifies the pathogen DNA receives this "intelligence" signals that the next protein is transmitted, linking the rings to activate the natural immune response. Mammalian cells use these natural immune path paths to mediate the immune response.
, how do bacteria and other primary nuclear cells "naturally immune identification and response" to external DNA?23 p.m. Beijing time on June 1, 2020, Nature Microbiology published the latest research results from the team of Gao Gao and Zhang New Deal of the Institute of Biophysics of the Chinese Academy of Sciences online. The study looked at an immune defense system for bacteria to identify foreign invading DNA, the Type I Restriction Modification (Type I R-M) system.
researchers systematically analyzed the three-dimensional structure of the Type I R-M system and target DNA and a variety of physiological components of the phage inhibitor protein (Ocr and ArdA), and combined with mutation and bio-chemical analysis to reveal the assembly, catalysis and regulation mechanism of the system.Type I R-M systems are widely found in prokeritons, where the host's own DNA can be methylated and unretouched phage DNA identified and cut to provide strong natural immune protection for host cells.
the system was identified in 1968, many researchers have conducted extensive research on it using microbiology, biochemistry and molecular biology, Gao told China Science Daily.
" for example, we already know that the system includes sub-base (protein) types, different Target DNA sequences specifically identified by the Type I R-M system, how the Type I R-M system is assembled, and how phage-coded proteins inhibit the activity of the system, among others. However
at the molecular or even atomic level, there are still many unanswered questions, including: How do different sub-base interact and assemble into a complex with a specific function? Is the Type I R-M system and how to precisely regulate different enzyme activity through configuration changes? What is the structural basis for type I R-M dynamic composition changes? What are the molecular mechanisms by which phage protein inhibits enzyme activity in the Type I R-M system?
in order to answer these questions, it is important to understand the structural information of the Type I R-M system in different configuration states and assembly methods.
years, Tsao has been working to uncover the assembly, catalysis, and regulation mechanisms of the Type I R-M system. In 2011, while studying for a Ph.D., he analyzed the system's DNA to identify the crystal structure of the sub-base. In 2017, he worked with the
Institute of Biophysics' Liang Dongshing Research Group to analyze the crystal structure of the system's methylase complex in a state that does not bind to the target DNA. The latest result is that their team and Zhang New Deal task force, analysis of the system in a number of physiological states of the frozen electroscope structure.
Based on this latest study, the researchers described the working model of Type I R-M full enzyme as follows:
1, when the target DNA is not binding, the
all-enzyme complex is in a dynamically open Resting State;
3, by hydrolyzing ATP, two R subkeys begin to catalyz DNA translocation and pull DNA from both ends to the Type I R-M complex to form a special loop DNA structure;
4, when DNA translocation is blocked, type I R-M all-enzymes are converted to Intermediate State, where only one R subkey has DNA translocase activity;
5, through the synergy of two R sub-base, the all-enzyme complex enters Therection State, the two R-sub-base Nuclease domains and the two M-sub-base Catalyst domains are close to DNA, performing DNA cutting and methylation modification functions;
6, after cutting and retouching, the whole enzyme complex and DNA are separated from each other and returned to the initial Resting State.To better understand the state transition process, the researchers "solidified" several of these moments with the help of a frozen electroscope.
"The first step in the first experiment was to obtain high-quality composite samples, and we prepared the core complex M2S1 and the all-enzyme complex R2M2S1 using a combination of in-cell co-expression and in-body recombination, using the classic Type I R-M system EcoR124I as the study object. They were then further obtained in composite samples with target DNA and two phage inhibitors (Ocr and ArdA). Mr Gao said.
next, using the frozen electroscope single particle reconstruction method, the researchers explored the samples and data collection conditions of the above-mentioned composite samples, and analyzed the three-dimensional structure of a total of 10 states at different resolutions.In fact, previous studies have shown that the Type I R-M system can trans-position, cut, and modify DNA at different stages, but does not know the root cause of the state change in this large molecular machine.
-frozen electroscope technology provides a "sharp weapon" for understanding the spatial configuration changes of this process. For example, in the first phase, the Type I R-M system has only transdase activity, no cutting and methylation activity, because its enzyme cutting activity center is structurally "crowded" in the middle, forming a "self-inhibition" state, while methylase catalysis domain is also far away from DNA, resulting in it does not have methylation activity.
the results of the "frozen electroscope" are very intuitive and obvious. "Introduction to Gao Wei.imaging center platform of the Institute of Biophysics supports the research of frozen electroscope data collection and sample analysis.the significance of this study, in addition to helping to understand fundamental biology issues, the significance of the Type I R-M system as a biological tool should also be given sufficient attention. In primary nuclear cells, the "R-M system" and "CRISPR-Cas system" are two defense systems for bacteria to remove invading phage DNA, both of which have been developed into powerful biological tools and are widely used in current biomedical research.
stressed that because enzymes in R-M systems can identify specific DNA sequences and modify and cut them, R-M systems are widely used in current experiments such as molecular cloning. However, although the Type I R-M system was first discovered, its tool development has been lagging behind because of a lack of understanding of how it works.
, an understanding of the details of the work of the Type I R-M system will help to develop biological tools for it in the future.
At the same time, in terms of immune identification of bacterial external DNA, this study reveals the molecular mechanisms for the assembly, catalysis, and regulation of the Type I R-M system, most of which have not been previously reported, which helps to better understand the game between the defense system and the phage.
In terms of structural biology technology, the three-dimensional structural analysis of various physiological structures in type I R-M system is a difficult problem that has plagued the field for decades, and this work is the first time that the structural basis of multiple configurations has been systematically revealed.
, the study is also expected to provide a basis and ideas for pathogenic disease-resistant phage therapy. (Source: Gan Xiao, China Science Journal)
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