Details of bacteria's "natural immunity" revealed

When the virus invades mammalian cells, the protein that initially identifies the pathogen's DNA receives this "intelligence" sends a signal that transmits the next protein, looping together, activating the natural immune responseMammal cells use such natural immune pathways to mediate immune responsesHow do primary nuclear cells such asbacteria"natural immune recognition and response" to external DNA?at 23 p.mBeijing time on June 1, 2020, Nature Microbiology published the latest research results of the team of Gao Hao and Zhang New Deal of the Institute of Biophysics of the Chinese Academy of SciencesThe study looked at an immune defense system thatbacteriaidentify foreign invading DNA, the Type I R-M systemthe researchers systematically analyzed the three-dimensional structure of the Type I R-M system and target DNA and two phage inhibition proteins (Ocr and ArdA) using the frozen mirror technology, and combined with mutation and biochemical analysis, revealed the assembly, catalysis and regulatory mechanism of the system6 steps to expand the details
Type I R-M system is widely present in protonuclear organisms, the host's own DNA can be methylated, and unmodified phage DNA can be identified and cut, thus providing strong natural immune protection for the host cellGao told the China Science Daily that since the system was identified in 1968, many researchers have conducted extensive research on the system using microbiology, biochemistry and molecular biology" For example, we already know that the system includes sub-types (proteins), target DNA sequences specifically identified by different Type I R-M systems, how the Type I R-M system is assembled, and phage coding proteins that inhibit the activity of the system"
but, at the molecular or even atomic level, there are still many questions that remain unanswered, including: how do different subtypes interact and assemble them into complexes with specific functions?" Does type I R-M system precisely regulate different enzyme activity through conformational changes? What is the structural basis for Type I R-M dynamic conformation changes? What is the molecular mechanism of phage protein strains the enzyme activity of Type I R-M system?To answer these questions, you must understand the structure of the Type I R-M system in different conformation altogether states and assembly methodsForyears, Takahashi has been working to uncover the assembly, catalysis and regulatory mechanisms of Type I R-M systemsIn 2011, while studying for a Ph.D., he parsed the crystal structure of the system's DNA-identifying sub-basesIn 2017, he worked with the group of academicians of Liang Dongzhu of the Institute of Biophysics of the Chinese Academy of Sciences to analyze the crystal structure of the system methylase complex in a state of non-binding target DNAThe latest achievement is that their team and Zhang New Deal task force, analyzed the system in a number of physiological state of the frozen mirror structurebased on this latest study, the researchers described the Type I R-M whole enzyme working model as six steps:1, when the target DNA is not bound, the whole enzyme complex is in a dynamically open Resting State; Between the -1 and Motor-2 domains;3, through hydrolyzed ATP, two R subtypes began to catalyze THE DNA translocation and pull the DNA from both ends to the Type I R-M complex to form a special DNA loop structure;, Type I R-M whole enzyme transformed into Intermediate when DNA translocation was blocked, At this time, only one R subtype has DNA translocase activity;5, through the synergy of two R sub-bases, the whole enzyme complex enters The Cle State, the nuclease domain of the two R sub-bases and the two M sub-bases of the Catalytic domain are close to the DNA, performing DNA cutting and methylmodification functions, and6, after cutting and finishing, the whole enzyme complex is separated from DNA and returned to the initial Resting Statethe frozen electric mirror sits to help "solidify" the moment
in order to better understand the above state transition process, the researchers with the help of the frozen electric mirror "solidified" several of these moments " the first step in the experiment is to obtain high-quality composite samples, we take the combination of intracellular co-expression and in vitro recombination, with the classic Type I R-M system EcoR124I as the object of research, the preparation of the core compound M2S1 and the whole enzyme compound R2M2S1 Samples of their compounds with target DNA and two phage inhibitor proteins (Ocr and ArdA) were then obtained Gao said the next, the researchers used the single-particle reconstruction method of the frozen electric mirror to explore the samples and data collection conditions of the various composite samples mentioned above, and analyzed the three-dimensional structure of a total of 10 states at different resolutions In fact, previous studies have seen how the Type I R-M system can transposition, cut, and modify DNA, and previous studies have seen different enzyme activity at different stages, but not the underlying cause of state changes in this large molecular machine the technology of the frozen mirror provides a "sharp weapon" for understanding the spatial structure changes in this process For example, in the first stage, the Type I R-M system had only translocation enzyme activity, no cutting and methylation activity, because its enzyme-cutting activity center was "squeezed" in the middle of the structure, forming a "self-inhibition" state, while the methylase catalytic domain was also far away from DNA, resulting in its lack of methylation activity " frozen mirror results, it's very intuitive and obvious "Gao Gao introduced the imaging center platform of the Institute of Biophysics of the Chinese Academy of Sciences provides support for the study of cryoscope data collection and sample analysis The significance of the development of type I R-M systems as biological tools should be given sufficient attention the significance of this study, in addition to helping to understand basic biological issues In protonuclear cells, the R-M system and the CRISPR-Cas system are two defense systems that bacteria 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, The R-M system should be 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, precisely because people do not understand its working mechanism seuph therefore, an understanding of the details of the work of the Type I R-M system will help develop its biological tools in the future at the same time, in terms of the immune identification of bacteria external DNA, this study reveals the molecular mechanisms of the assembly, catalysis, and regulation of type I R-M systems, most of which are previously unreported, which helps to gain an in-depth understanding of the mutual game between the system and the phage in structural biology technology, the three-dimensional structural analysis of various physiological structures of Type I R-M system is a difficult problem that has plagued the field for decades, and this work is the first systematic revelation of the structural basis of multiple structures in addition, , the study is expected to provide a basis and ideas for bacteriophage therapy against pathogen infection (
Bioon.com of Biological Valley)