Different modes of spacer acquisition by the Staphylococcus epidermidis type III-A CRISPR-Cas system

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<ul class="nav navbar-nav navbar-right" style="display: inline-flex; align-items: center; margin-left: 20px;"> <li id="language" class="d-none d-xl-inline-flex"> <a href="javascript:"> <div class="current"> <i class="ivu-icon ivu-icon-md-globe"></i> EN </div> </a> <div class="selection"> <a rel="alternate" hreflang="en" href="https://www.peeref.com/works/23768923" > <span>English</span> </a> <a rel="alternate" hreflang="zh" href="https://www.peeref.com/zh/works/23768923" > <span>中文</span> </a> </div> </li> </ul> </ul> </div> </nav> <main> <div id="top-info-banner" class="container-fluid mb-0"> <div class="container"> <div class="d-flex align-items-center" style="margin-top: 30px;"> <span class="text-white"> <strong class="f18">☆</strong> <span class="f16">4.8</span> </span> <span class="mx-3"></span> <span class="tag">Article</span> </div> <h1 class="title title-for-article"> Different modes of spacer acquisition by the Staphylococcus epidermidis type III-A CRISPR-Cas system </h1> <div class="help-links-left"> <p class="pub-info"> NUCLEIC ACIDS RESEARCH (2022) </p> </div> </div> </div> <div id="article-sticky-navbar"> <div class="container"> <div class="d-flex justify-content-between flex-wrap flex-md-nowrap"> <div class="d-flex align-items-center mb-2"> <ul class="nav nav-underline f16 font-weight-bold"> <li class="active"> <a href="javascript:;"> Overview </a> </li> <li class=""> <a href="https://www.peeref.com/works/23768923/comments"> Write a Review </a> </li> </ul> </div> <div class="d-flex align-items-center justify-content-md-end flex-wrap flex-md-nowrap"> <div class="mr-3 mt-3 mt-md-0 flex-shrink-0"> <a href="https://doi.org/10.1093/nar/gkab1299" target="_blank" class="btn btn-warning btn-circle"> <i class="ivu-icon ivu-icon-md-copy f16"></i> <strong>Get Full Text</strong> </a> </div> <div class="mr-3 mt-3 mt-md-0 flex-shrink-0"> <a href="https://www.peeref.com/works/23768923/add-to-collection" class="btn btn-success btn-circle"> <strong>Add to 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<div id="article-details" class="container"> <div class="col-md-4 px-0 pr-md-3"> <div class="f15 panel-box rounded shadow-none border"> <div class="mb-3 pb-3"> <h4 class="mt-0">Journal</h4> <div class="f16"> <h5 class="title f16"> <a href="https://www.peeref.com/journals/6280/nucleic-acids-research"> NUCLEIC ACIDS RESEARCH </a> </h5> <span> Volume 50, Issue 3, Pages 1661-1672 </span> </div> </div> <div class="mb-3 pb-3"> <h4 class="mt-0">Publisher</h4> <div class="f16"> <h5 class="title f16 text-primary"> OXFORD UNIV PRESS </h5> <div class="my-2"> DOI: 10.1093/nar/gkab1299 </div> </div> </div> <div class="mb-3 pb-3"> <h4 class="mt-0">Keywords</h4> <div class="f16"> - </div> </div> <div class="mb-3 pb-3"> <h4 class="mt-0">Categories</h4> <div class="f16"> <span class="d-block"> <a href="https://www.peeref.com/works/list?category=Biochemistry+%26+Molecular+Biology" target="_blank" class="text-dark btn btn-link p-0 text-left"> Biochemistry & Molecular Biology </a> </span> </div> </div> <div class="mb-3 pb-3"> <h4 class="mt-0">Funding</h4> <div class="f16"> <ol class=""> <li>National Institutes of Health Director's Pioneer Award [1DP1GM128184-01]</li> <li>Burroughs Wellcome Fund PATH Award</li> <li>Investigator of the Howard Hughes Medical Institute</li> <li>Junior Fellow of the Simons Society of Fellows</li> <li>Simons Foundation [578759]</li> <li>Center for New Scientists at theWeizmann Institute of Science</li> <li>NIH</li> </ol> </div> </div> </div> <div class="f15 panel-box rounded shadow-none border"> <h4 class="mt-0 text-center">Ask authors/readers for more resources</h4> <div class="requests"> <div class="requests-item"> <div class="icon"> <img src="https://peeref-open.s3.amazonaws.com/images/file.png" alt=""> </div> <h4>Protocol</h4> <p> <a href="https://www.peeref.com/works/23768923/resource" class="btn btn-outline-primary btn-sm"> Community support </a> </p> </div> <div class="requests-item"> <div class="icon"> <img src="https://peeref-open.s3.amazonaws.com/images/experiment.png" alt=""> </div> <h4>Reagent</h4> <p> <a href="https://www.peeref.com/works/23768923/resource" class="btn btn-outline-primary btn-sm"> Community support </a> </p> </div> </div> </div> </div> <div class="col-md-8 px-0 pl-md-3"> <div id="article-summary-panel" class="mb-4"> <ul class="nav nav-tabs" style="list-style: none; padding-left: 0;"> <li class="active"> <a href="#ai_summary" data-toggle="tab" class="summary-tab mx-0 f16 text-dark"> <strong>Automated Summary</strong> <strong class="text-danger ml-1"><i>New</i></strong> </a> </li> <li class=""> <a href="#raw_abstract" data-toggle="tab" class="abstract-tab mx-0 f16 text-dark"> <strong>Abstract</strong> </a> </li> </ul> <div class="tab-content border border-top-0"> <div id="ai_summary" class="tab-pane active"> <div class="summary-panel panel-box mb-0 rounded shadow-none"> <div class="f16">CRISPR-Cas systems provide prokaryotic organisms with an adaptive defense mechanism that acquires immunological memories of infections. This study investigated the spacer acquisition process in the type III-A CRISPR-Cas system of Staphylococcus epidermidis. It was found that this type of system uses Cas1 and Cas2 to integrate spacers from chromosomal terminus and free dsDNA ends, similar to type I and II systems. Additionally, a different mode of spacer acquisition from rRNA and tRNA loci was identified.</div> </div> </div> <div id="raw_abstract" class="tab-pane "> <div class="abstract-panel panel-box mb-0 rounded shadow-none"> <div class="f16">CRISPR-Cas systems provide prokaryotic organisms with an adaptive defense mechanism that acquires immunological memories of infections. This is accomplished by integration of short fragments from the genome of invaders such as phages and plasmids, called 'spacers', into the CRISPR locus of the host. Depending on their genetic composition, CRISPR-Cas systems can be classified into six types, I-VI, however spacer acquisition has been extensively studied only in type I and II systems. Here, we used an inducible spacer acquisition assay to study this process in the type III-A CRISPR-Cas system of Staphylococcus epidermidis, in the absence of phage selection. Similarly to type I and II spacer acquisition, this type III system uses Cas1 and Cas2 to preferentially integrate spacers from the chromosomal terminus and free dsDNA ends produced after DNA breaks, in a manner that is enhanced by the AddAB DNA repair complex. Surprisingly, a different mode of spacer acquisition from rRNA and tRNA loci, which spans only the transcribed sequences of these genes and is not enhanced by AddAB, was also detected. Therefore, our findings reveal both common mechanistic principles that may be conserved in all CRISPR-Cas systems, as well as unique and intriguing features of type III spacer acquisition.</div> </div> </div> </div> </div> <div class="f15 panel-box rounded shadow-none border"> <h4 class="mt-0 heading-count">Authors</h4> <div class="mb-3"> <article-authors tid="23768923" list="[{"name":"Naama Aviram","sequence":1},{"name":"Ashley N. Thornal","sequence":2},{"name":"David Zeevi","sequence":3},{"name":"Luciano A. Marraffini","sequence":4}]" verified="[]" page="work" ></article-authors> </div> <div class="alert alert-warning mb-0"> <h5 class="mt-0 bg-warning text-dark px-3 rounded d-inline-block"> I am an author on this paper </h5> <div class="font-weight-bold f13"> Click your name to claim this paper and add it to your profile. </div> </div> </div> <div class="f15 panel-box rounded shadow-none border"> <h4 class="mt-0 heading-count">Reviews</h4> <div class="d-flex flex-wrap flex-md-nowrap"> <div class="flex-grow-1"> <h4 class="f16"> Primary Rating <a href="javascript:;" data-toggle="tooltip" data-placement="right" title="The primary rating indicates the level of overall quality for the paper."> <i class="ivu-icon ivu-icon-md-help-circle f18 ml-2"></i> </a> </h4> <div class="d-flex flex-wrap flex-md-nowrap align-items-center alert mb-0"> <div class="d-flex align-items-center justify-content-center"> <Rate disabled allow-half value="4.8" style="font-size: 28px;"></Rate> <strong class="f20 m-3" style="color: #f5a623;">4.8</strong> </div> <div class="text-muted mx-4"> Not enough ratings </div> </div> <h4 class="f16"> Secondary Ratings <a href="javascript:;" data-toggle="tooltip" data-placement="right" title="Secondary ratings independently reflect strengths or weaknesses of the paper."> <i class="ivu-icon ivu-icon-md-help-circle f18 ml-2"></i> </a> </h4> <div class="d-flex flex-wrap flex-md-nowrap alert"> <div class="d-flex flex-shrink-0 align-items-center mr-3"> <h5 class="my-0">Novelty</h5> <strong class="mx-4">-</strong> </div> <div class="d-flex flex-shrink-0 align-items-center mr-3"> <h5 class="my-0">Significance</h5> <strong class="mx-4">-</strong> </div> <div class="d-flex flex-shrink-0 align-items-center mr-3"> <h5 class="my-0">Scientific rigor</h5> <strong class="mx-4">-</strong> </div> </div> </div> <div class="flex-shrink-0"> <div class="border bg-light py-2 px-4"> <h5 class="mb-1">Rate this paper</h5> <Rate class="f24" @on-change="function(value){ location.href='https://www.peeref.com/works/23768923/comments?rating='+value }"></Rate> </div> </div> </div> </div> <div id="collection" class="f15 panel-box rounded shadow-none border"> <h4 class="mt-0 heading-count">Recommended</h4> <div class="my-3"> <ul class="nav nav-pills border-bottom pb-3" style="list-style: none; padding-left: 0;"> <li class="active"> <a href="#articles_from_related" data-toggle="tab" class="mx-0 f15"> <strong>Related</strong> </a> </li> <li class=""> <a href="#articles_from_authors" data-toggle="tab" class="mx-0 f15"> <strong>From Same Authors</strong> </a> </li> <li class=""> <a href="#articles_from_journal" data-toggle="tab" class="mx-0 f15"> <strong>From Same Journal</strong> </a> </li> </ul> <div class="tab-content"> <div id="articles_from_related" class="tab-pane active"> <div class="my-4 border-bottom"> <div> <span class="d-inline-block badge badge-blue"> Article </span> <span class="d-inline-block badge badge-cyan"> Biology </span> </div> <h4> <a href="https://www.peeref.com/works/26813941" class="text-dark hover-underline">Critical roles for 'housekeeping' nucleases in type III CRISPR-Cas immunity</a> </h4> <p class="text-ellipsis-2">Lucy Chou-Zheng, Asma Hatoum-Aslan</p> <div class="d-flex mb-3"> <div class="flex-shrink-0 d-none d-sm-block"> <img src="https://peeref-open.s3.amazonaws.com/storage/images/covers/9431.jpg" alt="" class="border mr-3" width="100"> </div> <div class="p-3 rounded bg-light-blue"> <strong>Summary:</strong> The CRISPR-Cas system is an adaptive immune system that protects prokaryotes from invading plasmids and viruses. This study identifies RNase R as a critical nuclease in completing crRNA maturation and its specific interactions with the type III effector complex member Csm5. The study also demonstrates the importance of RNase R and PNPase in maintaining robust anti-plasmid immunity. </div> </div> <div class="d-flex justify-content-between"> <p class="font-weight-bold"> <span class="text-primary">ELIFE</span> (2022) </p> <div class="flex-shrink-0"> <a class="btn btn-outline-primary btn-sm" href="https://www.peeref.com/works/26813941/add-to-collection" target="_blank"> <strong>Add to Collection</strong> </a> </div> </div> </div> <div class="my-4 border-bottom"> <div> <span class="d-inline-block badge badge-blue"> Review </span> <span class="d-inline-block badge badge-cyan"> Biochemistry & Molecular Biology </span> </div> <h4> <a href="https://www.peeref.com/works/27205124" class="text-dark hover-underline">The biology and type I/III hybrid nature of type I-D CRISPR-Cas systems</a> </h4> <p class="text-ellipsis-2">Tess M. McBride, Shaharn C. Cameron, Peter C. Fineran, Robert D. Fagerlund</p> <div class="d-flex mb-3"> <div class="flex-shrink-0 d-none d-sm-block"> <img src="https://peeref-open.s3.amazonaws.com/storage/images/covers/1081.jpg" alt="" class="border mr-3" width="100"> </div> <div class="p-3 rounded bg-light-blue"> <strong>Summary:</strong> Prokaryotes have adaptive defence mechanisms called CRISPR-Cas systems to protect them from mobile genetic elements and viral infection. Type I and III systems utilize multi-protein complexes, while the type I-D system is a chimera of type I and III systems. This review focuses on the mechanism, evolution, and biotechnological applications of the type I-D CRISPR-Cas system. </div> </div> <div class="d-flex justify-content-between"> <p class="font-weight-bold"> <span class="text-primary">BIOCHEMICAL JOURNAL</span> (2023) </p> <div class="flex-shrink-0"> <a class="btn btn-outline-primary btn-sm" href="https://www.peeref.com/works/27205124/add-to-collection" target="_blank"> <strong>Add to Collection</strong> </a> </div> </div> </div> <div class="my-4 border-bottom"> <div> <span class="d-inline-block badge badge-blue"> Article </span> <span class="d-inline-block badge badge-cyan"> Chemistry, Multidisciplinary </span> </div> <h4> <a href="https://www.peeref.com/works/81599371" class="text-dark hover-underline">Nanopores Reveal the Stoichiometry of Single Oligoadenylates Produced by Type III CRISPR-Cas</a> </h4> <p class="text-ellipsis-2">David Fuentenebro Navas, Jurre A. Steens, Carlos de Lannoy, Ben Noordijk, Michael Pfeffer, Dick de Ridder, Raymond H.j. Staals, Sonja Schmid</p> <div class="d-flex mb-3"> <div class="flex-shrink-0 d-none d-sm-block"> <img src="https://peeref-open.s3.amazonaws.com/storage/images/covers/48.jpg" alt="" class="border mr-3" width="100"> </div> <div class="p-3 rounded bg-light-blue"> <strong>Summary:</strong> This study presents a label-free detection method for single cOA molecules using a protein nanopore assay. The method can sensitively identify the stoichiometry of cOA molecules and can be used to detect mixtures from synthetic and enzymatic sources. By training a convolutional neural network, the method can be used to detect mono- and polydisperse cOA samples. The study also determined the stoichiometric composition of cOAs enzymatically produced by the CRISPR type III-A and III-B variants of Thermus thermophilus and confirmed the results by liquid chromatography-mass spectroscopy. The method has broad application prospects and can be used to detect other signaling molecules and can be integrated into portable handheld devices. </div> </div> <div class="d-flex justify-content-between"> <p class="font-weight-bold"> <span class="text-primary">ACS NANO</span> (2024) </p> <div class="flex-shrink-0"> <a class="btn btn-outline-primary btn-sm" href="https://www.peeref.com/works/81599371/add-to-collection" target="_blank"> <strong>Add to Collection</strong> </a> </div> </div> </div> <div class="my-4 border-bottom"> <div> <span class="d-inline-block badge badge-blue"> Article </span> <span class="d-inline-block badge badge-cyan"> Biochemistry & Molecular Biology </span> </div> <h4> <a href="https://www.peeref.com/works/33797120" class="text-dark hover-underline">CRISPR-Cas immunity is repressed by the LysR-type transcriptional regulator PigU</a> </h4> <p class="text-ellipsis-2">Leah M. Smith, Hannah G. Hampton, Mariya S. Yevstigneyeva, Marina Mahler, Zacharie S. M. Paquet, Peter C. Fineran</p> <div class="d-flex mb-3"> <div class="flex-shrink-0 d-none d-sm-block"> <img src="https://peeref-open.s3.amazonaws.com/storage/images/covers/6280.jpg" alt="" class="border mr-3" width="100"> </div> <div class="p-3 rounded bg-light-blue"> <strong>Summary:</strong> Bacteria protect themselves from infection by bacteriophages using different defence systems, such as CRISPR-Cas. However, these defence systems also come with fitness costs. In this study, PigU is identified as a major regulator of CRISPR-Cas immunity in Serratia, and it shuts off CRISPR-Cas interference against phages and plasmids by repressing its expression. </div> </div> <div class="d-flex justify-content-between"> <p class="font-weight-bold"> <span class="text-primary">NUCLEIC ACIDS RESEARCH</span> (2023) </p> <div class="flex-shrink-0"> <a class="btn btn-outline-primary btn-sm" href="https://www.peeref.com/works/33797120/add-to-collection" target="_blank"> <strong>Add to Collection</strong> </a> </div> </div> </div> <div class="my-4 border-bottom"> <div> <span class="d-inline-block badge badge-blue"> Article </span> <span class="d-inline-block badge badge-cyan"> Biochemistry & Molecular Biology </span> </div> <h4> <a href="https://www.peeref.com/works/33758494" class="text-dark hover-underline">EspB and HtpG interact with the type III-A CRISPR/Cas system of Mycobacterium tuberculosis</a> </h4> <p class="text-ellipsis-2">Mingmin Shi, Hongtai Zhang, Joy Fleming, Wenjing Wei, Hong Chen, Xiaowei Dai, Yi Liu, Chuanyou Li, Fanlei Ran, Zhilong Wu, Yaguo Wang, Xilin Zhang, Huizhi Zhang, Lijun Bi</p> <div class="d-flex mb-3"> <div class="flex-shrink-0 d-none d-sm-block"> <img src="https://peeref-open.s3.amazonaws.com/storage/images/covers/10650.jpg" alt="" class="border mr-3" width="100"> </div> <div class="p-3 rounded bg-light-blue"> <strong>Summary:</strong> This study identified two proteins, EspB and HtpG, in the mycobacterial CRISPR/Cas system, which were previously not associated with this system. EspB was found to be a novel crRNA-binding protein that interacts directly with the MTB crRNP complex, while HtpG influences the accumulation of MTB Csm proteins and interferes with the defense mechanism of the crRNP complex against foreign DNA in vivo. </div> </div> <div class="d-flex justify-content-between"> <p class="font-weight-bold"> <span class="text-primary">FRONTIERS IN MOLECULAR BIOSCIENCES</span> (2023) </p> <div class="flex-shrink-0"> <a class="btn btn-outline-primary btn-sm" href="https://www.peeref.com/works/33758494/add-to-collection" target="_blank"> <strong>Add to Collection</strong> </a> </div> </div> </div> <div class="my-4 border-bottom"> <div> <span class="d-inline-block badge badge-blue"> Article </span> <span class="d-inline-block badge badge-cyan"> Biochemistry & Molecular Biology </span> </div> <h4> <a href="https://www.peeref.com/works/26723767" class="text-dark hover-underline">The effect of crRNA-target mismatches on cOA-mediated interference by a type III-A CRISPR-Cas system</a> </h4> <p class="text-ellipsis-2">Mohamed Nasef, Sarah A. A. Khweis, Jack A. A. Dunkle</p> <div class="d-flex mb-3"> <div class="flex-shrink-0 d-none d-sm-block"> <img src="https://peeref-open.s3.amazonaws.com/storage/images/covers/7308.jpg" alt="" class="border mr-3" width="100"> </div> <div class="p-3 rounded bg-light-blue"> <strong>Summary:</strong> This study investigates the factors influencing target recognition by type III CRISPR systems. The results show that the sequence context and the position of mismatches within the target-crRNA duplex affect the recognition by crRNA. Additionally, the study confirms the importance of a Cas10-activating region and the Cas10-proximal region in regulating cOA synthesis. </div> </div> <div class="d-flex justify-content-between"> <p class="font-weight-bold"> <span class="text-primary">RNA BIOLOGY</span> (2022) </p> <div class="flex-shrink-0"> <a class="btn btn-outline-primary btn-sm" href="https://www.peeref.com/works/26723767/add-to-collection" target="_blank"> <strong>Add to Collection</strong> </a> </div> </div> </div> <div class="my-4 border-bottom"> <div> <span class="d-inline-block badge badge-blue"> Article </span> <span class="d-inline-block badge badge-cyan"> Biochemistry & Molecular Biology </span> </div> <h4> <a href="https://www.peeref.com/works/82960442" class="text-dark hover-underline">Cas1 mediates the interference stage in a phage-encoded CRISPR-Cas system</a> </h4> <p class="text-ellipsis-2">Laixing Zhang, Hao Wang, Jianwei Zeng, Xueli Cao, Zhengyu Gao, Zihe Liu, Feixue Li, Jiawei Wang, Yi Zhang, Maojun Yang, Yue Feng</p> <div class="d-flex mb-3"> <div class="flex-shrink-0 d-none d-sm-block"> <img src="https://peeref-open.s3.amazonaws.com/storage/images/covers/6057.jpg" alt="" class="border mr-3" width="100"> </div> <div class="p-3 rounded bg-light-blue"> <strong>Summary:</strong> This study reveals a novel mechanism of Cas1 mediating the interference stage in a phage-encoded CRISPR-Cas system. The Cas8f of the ICP1 CRISPR-Cas system lacks the helical bundle domain, but antiviral defense is achieved by Cas1 connecting Cas2/3 to the DNA-bound Csy complex. The study also sheds light on a unique model of primed adaptation. </div> </div> <div class="d-flex justify-content-between"> <p class="font-weight-bold"> <span class="text-primary">NATURE CHEMICAL BIOLOGY</span> (2024) </p> <div class="flex-shrink-0"> <a class="btn btn-outline-primary btn-sm" href="https://www.peeref.com/works/82960442/add-to-collection" target="_blank"> <strong>Add to Collection</strong> </a> </div> </div> </div> <div class="my-4 border-bottom"> <div> <span class="d-inline-block badge badge-blue"> Article </span> <span class="d-inline-block badge badge-cyan"> Biochemistry & Molecular Biology </span> </div> <h4> <a href="https://www.peeref.com/works/23768996" class="text-dark hover-underline">Unique properties of spacer acquisition by the type III-A CRISPR-Cas system</a> </h4> <p class="text-ellipsis-2">Xinfu Zhang, Sandra Garrett, Brenton R. Graveley, Michael P. Terns</p> <div class="d-flex mb-3"> <div class="flex-shrink-0 d-none d-sm-block"> <img src="https://peeref-open.s3.amazonaws.com/storage/images/covers/6280.jpg" alt="" class="border mr-3" width="100"> </div> <div class="p-3 rounded bg-light-blue"> <strong>Summary:</strong> This study characterized the uptake of CRISPR spacers by type III CRISPR-Cas systems within their native host, Streptococcus thermophilus. The results showed that Cas1 and Cas2 proteins are critical for type III adaptation, while genes responsible for crRNA biogenesis or interference do not significantly affect spacer uptake patterns. Type III spacers are acquired in a PAM- and orientation-independent manner, and certain regions of plasmids and the host genome are preferentially sampled during type III adaptation. Additionally, the type III system can adapt to and protect host cells from lytic phage infection. </div> </div> <div class="d-flex justify-content-between"> <p class="font-weight-bold"> <span class="text-primary">NUCLEIC ACIDS RESEARCH</span> (2022) </p> <div class="flex-shrink-0"> <a class="btn btn-outline-primary btn-sm" href="https://www.peeref.com/works/23768996/add-to-collection" target="_blank"> <strong>Add to Collection</strong> </a> </div> </div> </div> <div class="my-4 border-bottom"> <div> <span class="d-inline-block badge badge-blue"> Article </span> <span class="d-inline-block badge badge-cyan"> Multidisciplinary Sciences </span> </div> <h4> <a href="https://www.peeref.com/works/82983793" class="text-dark hover-underline">The application of CRISPR-Cas system in Staphylococcus aureus infection</a> </h4> <p class="text-ellipsis-2">Jiamin Wang, Fang Liu, Jinzhao Long, Yuefei Jin, Shuaiyin Chen, Guangcai Duan, Haiyan Yang</p> <div class="d-flex mb-3"> <div class="flex-shrink-0 d-none d-sm-block"> <img src="https://peeref-open.s3.amazonaws.com/storage/images/covers/11459.jpg" alt="" class="border mr-3" width="100"> </div> <div class="p-3 rounded bg-light-blue"> <strong>Summary:</strong> The CRISPR-Cas system plays an important role in bacterial immunity and can also be used in genetic engineering. This article reviews the application of this system in Staphylococcus aureus infections and discusses its prospects and drawbacks. </div> </div> <div class="d-flex justify-content-between"> <p class="font-weight-bold"> <span class="text-primary">HELIYON</span> (2024) </p> <div class="flex-shrink-0"> <a class="btn btn-outline-primary btn-sm" href="https://www.peeref.com/works/82983793/add-to-collection" target="_blank"> <strong>Add to Collection</strong> </a> </div> </div> </div> <div class="my-4 border-bottom"> <div> <span class="d-inline-block badge badge-blue"> Article </span> <span class="d-inline-block badge badge-cyan"> Multidisciplinary Sciences </span> </div> <h4> <a href="https://www.peeref.com/works/26871159" class="text-dark hover-underline">Host nucleases generate prespacers for primed adaptation in the E. coli type I-E CRISPR-Cas system</a> </h4> <p class="text-ellipsis-2">Anna A. Shiriaeva, Konstantin Kuznedelov, Ivan Fedorov, Olga Musharova, Timofey Khvostikov, Yuliya Tsoy, Elena Kurilovich, Gerald R. Smith, Ekaterina Semenova, Konstantin Severinov</p> <div class="d-flex mb-3"> <div class="flex-shrink-0 d-none d-sm-block"> <img src="https://peeref-open.s3.amazonaws.com/storage/images/covers/10342.jpg" alt="" class="border mr-3" width="100"> </div> <div class="p-3 rounded bg-light-blue"> <strong>Summary:</strong> CRISPR-Cas systems provide prokaryotes with adaptive immunity against foreign nucleic acids. In E. coli, the integration of 33-bp spacers into CRISPR arrays leads to the acquisition of immunity. During the process called primed adaptation, DNA targets complementary to spacers are degraded and serve as a source of new spacers. This study identifies RecJ as the main exonuclease involved in trimming the 5' ends of prespacer precursors, and reveals the functional interactions between genome maintenance proteins and CRISPR interference and adaptation machineries. </div> </div> <div class="d-flex justify-content-between"> <p class="font-weight-bold"> <span class="text-primary">SCIENCE ADVANCES</span> (2022) </p> <div class="flex-shrink-0"> <a class="btn btn-outline-primary btn-sm" href="https://www.peeref.com/works/26871159/add-to-collection" target="_blank"> <strong>Add to Collection</strong> </a> </div> </div> </div> <div class="my-4 border-bottom"> <div> <span class="d-inline-block badge badge-blue"> Article </span> <span class="d-inline-block badge badge-cyan"> Multidisciplinary Sciences </span> </div> <h4> <a href="https://www.peeref.com/works/81589419" class="text-dark hover-underline">Mechanisms used for cDNA synthesis and site-specific integration of RNA into DNA genomes by a reverse transcriptase-Cas1 fusion protein</a> </h4> <p class="text-ellipsis-2">Georg Mohr, Jun Yao, Seung Kuk Park, Laura Markham, Alan M. Lambowitz</p> <div class="d-flex mb-3"> <div class="flex-shrink-0 d-none d-sm-block"> <img src="https://peeref-open.s3.amazonaws.com/storage/images/covers/10342.jpg" alt="" class="border mr-3" width="100"> </div> <div class="p-3 rounded bg-light-blue"> <strong>Summary:</strong> This study found that Marinomonas mediterranea RT-Cas1/Cas2 can add short 3' -DNA tails to RNA protospacers, enabling their direct integration into CRISPR arrays. The reverse transcription of RNA protospacers can be initiated at the 3' proximal site through multiple mechanisms, capable of synthesizing near full-length cDNAs of various RNAs. At higher protospacer concentrations, the integration of 3' -dN-RNAs or single-stranded DNAs is preferred over duplexes. This study reveals the mechanism of site-specific integration of RNA into DNA genomes, with potential biotechnological applications. </div> </div> <div class="d-flex justify-content-between"> <p class="font-weight-bold"> <span class="text-primary">SCIENCE ADVANCES</span> (2024) </p> <div class="flex-shrink-0"> <a class="btn btn-outline-primary btn-sm" href="https://www.peeref.com/works/81589419/add-to-collection" target="_blank"> <strong>Add to Collection</strong> </a> </div> </div> </div> <div class="my-4 border-bottom"> <div> <span class="d-inline-block badge badge-blue"> Review </span> <span class="d-inline-block badge badge-cyan"> Biochemistry & Molecular Biology </span> </div> <h4> <a href="https://www.peeref.com/works/82109185" class="text-dark hover-underline">The structural biology of type III CRISPR-Cas systems</a> </h4> <p class="text-ellipsis-2">Xuzichao Li, Jie Han, Jie Yang, Heng Zhang</p> <div class="d-flex mb-3"> <div class="flex-shrink-0 d-none d-sm-block"> <img src="https://peeref-open.s3.amazonaws.com/storage/images/covers/5188.jpg" alt="" class="border mr-3" width="100"> </div> <div class="p-3 rounded bg-light-blue"> <strong>Summary:</strong> The CRISPR-Cas system is an adaptive immune system in bacteria and archaea. Type III CRISPR-Cas is the oldest with multiple enzymatic activities, providing immune defense through different mechanisms. This article studies the structures of type III-A, III-B, and III-E systems, explaining their roles in target RNA cleavage, self/non-self discrimination, and the regulation of enzymatic subunits. </div> </div> <div class="d-flex justify-content-between"> <p class="font-weight-bold"> <span class="text-primary">JOURNAL OF STRUCTURAL BIOLOGY</span> (2024) </p> <div class="flex-shrink-0"> <a class="btn btn-outline-primary btn-sm" href="https://www.peeref.com/works/82109185/add-to-collection" target="_blank"> <strong>Add to Collection</strong> </a> </div> </div> </div> <div class="my-4 border-bottom"> <div> <span class="d-inline-block badge badge-blue"> Review </span> <span class="d-inline-block badge badge-cyan"> Biotechnology & Applied Microbiology </span> </div> <h4> <a href="https://www.peeref.com/works/23017685" class="text-dark hover-underline">CRISPR-Cas System: The Powerful Modulator of Accessory Genomes in Prokaryotes</a> </h4> <p class="text-ellipsis-2">Anca Butiuc-Keul, Anca Farkas, Rahela Carpa, Dumitrana Iordache</p> <div class="d-flex mb-3"> <div class="flex-shrink-0 d-none d-sm-block"> <img src="https://peeref-open.s3.amazonaws.com/storage/images/covers/11301.jpg" alt="" class="border mr-3" width="100"> </div> <div class="p-3 rounded bg-light-blue"> <strong>Summary:</strong> The CRISPR-Cas system is an adaptive defense mechanism developed by bacteria and archaea to combat foreign nucleic acids, recognizing and inactivating targets using guide RNAs. Different types and families of CRISPR-Cas systems have independent parts with distinct evolutionary trajectories. This system plays a crucial role in modulating accessory genomes in prokaryotes, affecting physiology and ecology, and suppressing horizontal gene transfer events. </div> </div> <div class="d-flex justify-content-between"> <p class="font-weight-bold"> <span class="text-primary">MICROBIAL PHYSIOLOGY</span> (2022) </p> <div class="flex-shrink-0"> <a class="btn btn-outline-primary btn-sm" href="https://www.peeref.com/works/23017685/add-to-collection" target="_blank"> <strong>Add to Collection</strong> </a> </div> </div> </div> <div class="my-4 border-bottom"> <div> <span class="d-inline-block badge badge-blue"> Review </span> <span class="d-inline-block badge badge-cyan"> Microbiology </span> </div> <h4> <a href="https://www.peeref.com/works/24936234" class="text-dark hover-underline">Adaptation by Type III CRISPR-Cas Systems: Breakthrough Findings and Open Questions</a> </h4> <p class="text-ellipsis-2">Xinfu Zhang, Xinmin An</p> <div class="d-flex mb-3"> <div class="flex-shrink-0 d-none d-sm-block"> <img src="https://peeref-open.s3.amazonaws.com/storage/images/covers/9447.jpg" alt="" class="border mr-3" width="100"> </div> <div class="p-3 rounded bg-light-blue"> <strong>Summary:</strong> This review summarizes our knowledge regarding CRISPR-Cas adaptation, with a focus on type III systems, and discusses open questions in type III adaptation studies. </div> </div> <div class="d-flex justify-content-between"> <p class="font-weight-bold"> <span class="text-primary">FRONTIERS IN MICROBIOLOGY</span> (2022) </p> <div class="flex-shrink-0"> <a class="btn btn-outline-primary btn-sm" href="https://www.peeref.com/works/24936234/add-to-collection" target="_blank"> <strong>Add to Collection</strong> </a> </div> </div> </div> <div class="my-4 "> <div> <span class="d-inline-block badge badge-blue"> Article </span> <span class="d-inline-block badge badge-cyan"> Genetics & Heredity </span> </div> <h4> <a href="https://www.peeref.com/works/25617038" class="text-dark hover-underline">Adaptation by Type V-A and V-B CRISPR-Cas Systems Demonstrates Conserved Protospacer Selection Mechanisms Between Diverse CRISPR-Cas Types</a> </h4> <p class="text-ellipsis-2">Wen Y. Wu, Simon A. Jackson, Cristobal Almendros, Anna C. Haagsma, Suzan Yilmaz, Gerrit Gort, John van der Oost, Stan J. J. Brouns, Raymond H. J. Staals</p> <div class="d-flex mb-3"> <div class="flex-shrink-0 d-none d-sm-block"> <img src="https://peeref-open.s3.amazonaws.com/storage/images/covers/10886.jpg" alt="" class="border mr-3" width="100"> </div> <div class="p-3 rounded bg-light-blue"> <strong>Summary:</strong> This study characterized CRISPR adaptation of the type V-A system from Francisella novicida and the type V-B system from Alicyclobacillus acidoterrestris using a high-throughput sequencing approach. It was found that Cas12 nucleases are dispensable for spacer acquisition in both systems, with only Cas1 and Cas2 (type V-A) or Cas4/1 and Cas2 (type V-B) being necessary. Cas4 activity was shown to be required for protospacer adjacent motif selection and prespacer trimming. The study also revealed a preference for spacers derived from foreign DNA rather than the host chromosome. </div> </div> <div class="d-flex justify-content-between"> <p class="font-weight-bold"> <span class="text-primary">CRISPR JOURNAL</span> (2022) </p> <div class="flex-shrink-0"> <a class="btn btn-outline-primary btn-sm" href="https://www.peeref.com/works/25617038/add-to-collection" target="_blank"> <strong>Add to Collection</strong> </a> </div> </div> </div> </div> <div id="articles_from_authors" class="tab-pane "> <div class="my-4 border-bottom"> <div> <span class="d-inline-block badge badge-blue"> Article </span> <span class="d-inline-block badge badge-cyan"> Biochemistry & Molecular Biology </span> </div> <h4> <a href="https://www.peeref.com/works/27286875" class="text-dark hover-underline">A systematic proximity ligation approach to studying protein-substrate specificity identifies the substrate spectrum of the Ssh1 translocon</a> </h4> <p class="text-ellipsis-2">Nir Cohen, Naama Aviram, Maya Schuldiner</p> <div class="d-flex mb-3"> <div class="p-3 rounded bg-light-blue"> <strong>Summary:</strong> This study presents a novel approach called Cel-lctiv for systematically comparing stable or transient protein-protein interactions (PPIs) between two yeast proteins. The approach utilizes high-throughput pairwise proximity biotin ligation to compare PPIs systematically and in vivo. Using homologous translocation pores Sec61 and Ssh1 as a proof of concept, the study demonstrates how Cel-lctiv can uncover substrate specificity and determine specificity determinants for protein interactions, even in highly homologous proteins. </div> </div> <div class="d-flex justify-content-between"> <p class="font-weight-bold"> <span class="text-primary">EMBO JOURNAL</span> (2023) </p> <div class="flex-shrink-0"> <a class="btn btn-outline-primary btn-sm" href="https://www.peeref.com/works/27286875/add-to-collection" target="_blank"> <strong>Add to Collection</strong> </a> </div> </div> </div> <div class="my-4 border-bottom"> <div> <span class="d-inline-block badge badge-blue"> Article </span> <span class="d-inline-block badge badge-cyan"> Multidisciplinary Sciences </span> </div> <h4> <a href="https://www.peeref.com/works/24066829" class="text-dark hover-underline">Peroxisome function relies on organelle-associated mRNA translation</a> </h4> <p class="text-ellipsis-2">Noa Dahan, Yury S. Bykov, Elizabeth A. Boydston, Amir Fadel, Zohar Gazi, Hodaya Hochberg-Laufer, James Martenson, Vlad Denic, Yaron Shav-Tal, Jonathan S. Weissman, Naama Aviram, Einat Zalckvar, Maya Schuldiner</p> <div class="d-flex mb-3"> <div class="p-3 rounded bg-light-blue"> <strong>Summary:</strong> This study discovered that translation of specific peroxisomal membrane proteins (PMPs) occurs on the surface of peroxisomes in yeast, similar to chloroplasts, mitochondria, and the endoplasmic reticulum. This localized translation process ensures the correct insertion of hydrophobic proteins into the peroxisomal membrane. Proper targeting of PMP transcripts to peroxisomes is crucial for cellular and peroxisomal function, highlighting the importance of localized translation in cellular physiology. </div> </div> <div class="d-flex justify-content-between"> <p class="font-weight-bold"> <span class="text-primary">SCIENCE ADVANCES</span> (2022) </p> <div class="flex-shrink-0"> <a class="btn btn-outline-primary btn-sm" href="https://www.peeref.com/works/24066829/add-to-collection" target="_blank"> <strong>Add to Collection</strong> </a> </div> </div> </div> <div class="my-4 border-bottom"> <div> <span class="d-inline-block badge badge-blue"> Article </span> <span class="d-inline-block badge badge-cyan"> Multidisciplinary Sciences </span> </div> <h4> <a href="https://www.peeref.com/works/15552156" class="text-dark hover-underline">An ER surface retrieval pathway safeguards the import of mitochondrial membrane proteins in yeast</a> </h4> <p class="text-ellipsis-2">Katja G. Hansen, Naama Aviram, Janina Laborenz, Chen Bibi, Maren Meyer, Anne Spang, Maya Schuldiner, Johannes M. Herrmann</p> <div class="d-flex justify-content-between"> <p class="font-weight-bold"> <span class="text-primary">SCIENCE</span> (2018) </p> <div class="flex-shrink-0"> <a class="btn btn-outline-primary btn-sm" href="https://www.peeref.com/works/15552156/add-to-collection" target="_blank"> <strong>Add to Collection</strong> </a> </div> </div> </div> <div class="my-4 border-bottom"> <div> <span class="d-inline-block badge badge-blue"> Article </span> <span class="d-inline-block badge badge-cyan"> Biochemistry & Molecular Biology </span> </div> <h4> <a href="https://www.peeref.com/works/3619553" class="text-dark hover-underline">hSnd2 protein represents an alternative targeting factor to the endoplasmic reticulum in human cells</a> </h4> <p class="text-ellipsis-2">Sarah Hassdenteufel, Mark Sicking, Stefan Schorr, Naama Aviram, Claudia Fecher-Trost, Maya Schuldiner, Martin Jung, Richard Zimmermann, Sven Lang</p> <div class="d-flex justify-content-between"> <p class="font-weight-bold"> <span class="text-primary">FEBS LETTERS</span> (2017) </p> <div class="flex-shrink-0"> <a class="btn btn-outline-primary btn-sm" href="https://www.peeref.com/works/3619553/add-to-collection" target="_blank"> <strong>Add to Collection</strong> </a> </div> </div> </div> <div class="my-4 border-bottom"> <div> <span class="d-inline-block badge badge-blue"> Article </span> <span class="d-inline-block badge badge-cyan"> Cell Biology </span> </div> <h4> <a href="https://www.peeref.com/works/3878693" class="text-dark hover-underline">Multiple pathways facilitate the biogenesis of mammalian tail-anchored proteins</a> </h4> <p class="text-ellipsis-2">Joseph Casson, Michael McKenna, Sarah Hassdenteufel, Naama Aviram, Richard Zimmerman, Stephen High</p> <div class="d-flex justify-content-between"> <p class="font-weight-bold"> <span class="text-primary">JOURNAL OF CELL SCIENCE</span> (2017) </p> <div class="flex-shrink-0"> <a class="btn btn-outline-primary btn-sm" href="https://www.peeref.com/works/3878693/add-to-collection" target="_blank"> <strong>Add to Collection</strong> </a> </div> </div> </div> <div class="my-4 border-bottom"> <div> <span class="d-inline-block badge badge-blue"> Article </span> <span class="d-inline-block badge badge-cyan"> Cell Biology </span> </div> <h4> <a href="https://www.peeref.com/works/3878792" class="text-dark hover-underline">Targeting and translocation of proteins to the endoplasmic reticulum at a glance</a> </h4> <p class="text-ellipsis-2">Naama Aviram, Maya Schuldiner</p> <div class="d-flex justify-content-between"> <p class="font-weight-bold"> <span class="text-primary">JOURNAL OF CELL SCIENCE</span> (2017) </p> <div class="flex-shrink-0"> <a class="btn btn-outline-primary btn-sm" href="https://www.peeref.com/works/3878792/add-to-collection" target="_blank"> <strong>Add to Collection</strong> </a> </div> </div> </div> <div class="my-4 border-bottom"> <div> <span class="d-inline-block badge badge-blue"> Article </span> <span class="d-inline-block badge badge-cyan"> Multidisciplinary Sciences </span> </div> <h4> <a href="https://www.peeref.com/works/2886897" class="text-dark hover-underline">The SND proteins constitute an alternative targeting route to the endoplasmic reticulum</a> </h4> <p class="text-ellipsis-2">Naama Aviram, Tslil Ast, Elizabeth A. Costa, Eric C. Arakel, Silvia G. Chuartzman, Calvin H. Jan, Sarah Hassenteufel, Johanna Dudek, Martin Jung, Stefan Schorr, Richard Zimmermann, Blanche Schwappach, Jonathan S. Weissman, Maya Schuldiner</p> <div class="d-flex justify-content-between"> <p class="font-weight-bold"> <span class="text-primary">NATURE</span> (2016) </p> <div class="flex-shrink-0"> <a class="btn btn-outline-primary btn-sm" href="https://www.peeref.com/works/2886897/add-to-collection" target="_blank"> <strong>Add to Collection</strong> </a> </div> </div> </div> <div class="my-4 border-bottom"> <div> <span class="d-inline-block badge badge-blue"> Article </span> <span class="d-inline-block badge badge-cyan"> Cell Biology </span> </div> <h4> <a href="https://www.peeref.com/works/11326375" class="text-dark hover-underline">A cytosolic degradation pathway, prERAD, monitors pre-inserted secretory pathway proteins</a> </h4> <p class="text-ellipsis-2">Tslil Ast, Naama Aviram, Silvia Gabriela Chuartzman, Maya Schuldiner</p> <div class="d-flex justify-content-between"> <p class="font-weight-bold"> <span class="text-primary">JOURNAL OF CELL SCIENCE</span> (2014) </p> <div class="flex-shrink-0"> <a class="btn btn-outline-primary btn-sm" href="https://www.peeref.com/works/11326375/add-to-collection" target="_blank"> <strong>Add to Collection</strong> </a> </div> </div> </div> <div class="my-4 "> <div> <span class="d-inline-block badge badge-blue"> Article </span> <span class="d-inline-block badge badge-cyan"> Cell Biology </span> </div> <h4> <a href="https://www.peeref.com/works/8781847" class="text-dark hover-underline">Embracing the void-how much do we really know about targeting and translocation to the endoplasmic reticulum?</a> </h4> <p class="text-ellipsis-2">Naama Aviram, Maya Schuldiner</p> <div class="d-flex justify-content-between"> <p class="font-weight-bold"> <span class="text-primary">CURRENT OPINION IN CELL BIOLOGY</span> (2014) </p> <div class="flex-shrink-0"> <a class="btn btn-outline-primary btn-sm" href="https://www.peeref.com/works/8781847/add-to-collection" target="_blank"> <strong>Add to Collection</strong> </a> </div> </div> </div> </div> <div id="articles_from_journal" class="tab-pane "> <div class="my-4 border-bottom"> <div> <span class="d-inline-block badge badge-blue"> Article </span> <span class="d-inline-block badge badge-cyan"> Biochemistry & Molecular Biology </span> </div> <h4> <a href="https://www.peeref.com/works/83048562" class="text-dark hover-underline">Dual genetic level modification engineering accelerate genome evolution of Corynebacterium glutamicum</a> </h4> <p class="text-ellipsis-2">Qing Wang, Jie Zhang, Zhe Zhao, Yichen Li, Jiajia You, Yi Wang, Xiangfei Li, Meijuan Xu, Zhiming Rao</p> <div class="d-flex mb-3"> <div class="p-3 rounded bg-light-blue"> <strong>Summary:</strong> This study presents an evolutionary tool oMut-Cgts based on dual genetic level modification engineering in Corynebacterium glutamicum, which can significantly increase the mutation rate and achieve rapid genome evolution. The tool has powerful functions in multi-dimensional biological engineering, and its strategies for rapid genome evolution are expected to be applicable to all prokaryotic cells. </div> </div> <div class="d-flex justify-content-between"> <p class="font-weight-bold"> <span class="text-primary">NUCLEIC ACIDS RESEARCH</span> (2024) </p> <div class="flex-shrink-0"> <a class="btn btn-outline-primary btn-sm" href="https://www.peeref.com/works/83048562/add-to-collection" target="_blank"> <strong>Add to Collection</strong> </a> </div> </div> </div> <div class="my-4 border-bottom"> <div> <span class="d-inline-block badge badge-blue"> Article </span> <span class="d-inline-block badge badge-cyan"> Biochemistry & Molecular Biology </span> </div> <h4> <a href="https://www.peeref.com/works/83604218" class="text-dark hover-underline">Multiplexed in-situ mutagenesis driven by a dCas12a-based dual-function base editor</a> </h4> <p class="text-ellipsis-2">Yaokang Wu, Yang Li, Yanfeng Liu, Xiang Xiu, Jiaheng Liu, Linpei Zhang, Jianghua Li, Guocheng Du, Xueqin Lv, Jian Chen, Rodrigo Ledesma-Amaro, Long Liu</p> <div class="d-flex mb-3"> <div class="p-3 rounded bg-light-blue"> <strong>Summary:</strong> MultiduBE is a dCas12a-based multiplexed dual-function base editor that can perform combinatorial in-situ mutagenesis in an all-in-one plasmid. It creates two synthetic effectors by merging multiple functionalities and introduces a synthetic separator to reduce interference. MultiduBE is successfully used for cell physiology reprogramming and metabolic regulation, and a new mutation is identified in Bacillus subtilis, which also improves the titres of surfactin and riboflavin. It provides a convenient and efficient way to perform multiplexed in-situ mutagenesis. </div> </div> <div class="d-flex justify-content-between"> <p class="font-weight-bold"> <span class="text-primary">NUCLEIC ACIDS RESEARCH</span> (2024) </p> <div class="flex-shrink-0"> <a class="btn btn-outline-primary btn-sm" href="https://www.peeref.com/works/83604218/add-to-collection" target="_blank"> <strong>Add to Collection</strong> </a> </div> </div> </div> <div class="my-4 border-bottom"> <div> <span class="d-inline-block badge badge-blue"> Article </span> <span class="d-inline-block badge badge-cyan"> Biochemistry & Molecular Biology </span> </div> <h4> <a href="https://www.peeref.com/works/83495974" class="text-dark hover-underline">FRAME: flap endonuclease 1-engineered PAM module for precise and sensitive modulation of CRISPR/Cas12a trans-cleavage activity</a> </h4> <p class="text-ellipsis-2">Tongshan Zuo, Chen Shen, Zhen Xie, Guanhong Xu, Fangdi Wei, Jing Yang, Xiaolei Zhu, Qin Hu, Zheng Zhao, Ben Zhong Tang, Yao Cen</p> <div class="d-flex mb-3"> <div class="p-3 rounded bg-light-blue"> <strong>Summary:</strong> The CRISPR/Cas12a system shows excellent performance in molecular diagnostics and biosensing, but the reported Cas12a activity regulation methods have limitations. The researchers demonstrated an enzyme activity engineering strategy using FEN1 to regulate the accessibility of the PAM module, which not only precisely programmed Cas12a's activity but also triggered isothermal cyclic amplification. The FRAME strategy was applied to construct a sensing platform for detecting myeloperoxidase and miR-155, with high sensitivity and specificity, and it can detect multiple targets without redesign. The FRAME strategy opens up a new way to modulate Cas12a's activity and has great potential in the field of medical diagnostics. </div> </div> <div class="d-flex justify-content-between"> <p class="font-weight-bold"> <span class="text-primary">NUCLEIC ACIDS RESEARCH</span> (2024) </p> <div class="flex-shrink-0"> <a class="btn btn-outline-primary btn-sm" href="https://www.peeref.com/works/83495974/add-to-collection" target="_blank"> <strong>Add to Collection</strong> </a> </div> </div> </div> <div class="my-4 border-bottom"> <div> <span class="d-inline-block badge badge-blue"> Article </span> <span class="d-inline-block badge badge-cyan"> Biochemistry & Molecular Biology </span> </div> <h4> <a href="https://www.peeref.com/works/85251900" class="text-dark hover-underline">Proximity-activated guide RNA of CRISPR-Cas12a for programmable diagnostic detection and gene regulation</a> </h4> <p class="text-ellipsis-2">Zhian Hu, Shen Ling, Jialin Duan, Zixiao Yu, Yanfei Che, Song Wang, Sichun Zhang, Xinrong Zhang, Zhengping Li</p> <div class="d-flex mb-3"> <div class="p-3 rounded bg-light-blue"> <strong>Summary:</strong> This paper introduces the discovery and application of the CRISPR-Cas12 system. The flexibility and programmability of this system make it have broad application prospects in biomarker diagnostics and gene regulation. Through the modification of guide RNA, precise regulation of genes has been achieved, and a series of detection platforms and biosensors based on this system have been developed. </div> </div> <div class="d-flex justify-content-between"> <p class="font-weight-bold"> <span class="text-primary">NUCLEIC ACIDS RESEARCH</span> (2025) </p> <div class="flex-shrink-0"> <a class="btn btn-outline-primary btn-sm" href="https://www.peeref.com/works/85251900/add-to-collection" target="_blank"> <strong>Add to Collection</strong> </a> </div> </div> </div> <div class="my-4 border-bottom"> <div> <span class="d-inline-block badge badge-blue"> Review </span> <span class="d-inline-block badge badge-cyan"> Biochemistry & Molecular Biology </span> </div> <h4> <a href="https://www.peeref.com/works/83048571" class="text-dark hover-underline">Multiplexed in situ protein imaging using DNA-barcoded antibodies with extended hybridization chain reactions</a> </h4> <p class="text-ellipsis-2">Yu Wang, Xiaoyu Liu, Yitian Zeng, Sinem K. Saka, Wenxin Xie, Isabel Goldaracena, Richie E. Kohman, Peng Yin, George M. Church</p> <div class="d-flex mb-3"> <div class="p-3 rounded bg-light-blue"> <strong>Summary:</strong> This paper presents a novel DNA-conjugated antibody staining protocol that addresses the issue of nonspecific binding of DNA-conjugated antibodies and demonstrates superior performance in suppressing nonspecific signals. The protocol also extends the application of DNA-conjugated antibodies in signal-amplified in situ protein imaging through the hybridization chain reaction and designs a novel HCR DNA pair, increasing multiplexing. Finally, the technique is successfully applied in cultured cells and tissue sections. </div> </div> <div class="d-flex justify-content-between"> <p class="font-weight-bold"> <span class="text-primary">NUCLEIC ACIDS RESEARCH</span> (2024) </p> <div class="flex-shrink-0"> <a class="btn btn-outline-primary btn-sm" href="https://www.peeref.com/works/83048571/add-to-collection" target="_blank"> <strong>Add to Collection</strong> </a> </div> </div> </div> <div class="my-4 border-bottom"> <div> <span class="d-inline-block badge badge-blue"> Article </span> <span class="d-inline-block badge badge-cyan"> Biochemistry & Molecular Biology </span> </div> <h4> <a href="https://www.peeref.com/works/83121908" class="text-dark hover-underline">Multiplexed sequential imaging in living cells with orthogonal fluorogenic RNA aptamer/dye pairs</a> </h4> <p class="text-ellipsis-2">Ru Zheng, Rigumula Wu, Yuanchang Liu, Zhining Sun, Zhaolin Xue, Yousef Bagheri, Sima Khajouei, Lan Mi, Qian Tian, Raymond Pho, Qinge Liu, Sidrat Siddiqui, Kewei Ren, Mingxu You</p> <div class="d-flex mb-3"> <div class="p-3 rounded bg-light-blue"> <strong>Summary:</strong> This study introduces a multiplexed imaging strategy called "sequential Fluorogenic RNA Imaging-Enabled Sensor" (seqFRIES), which enables live-cell target detection via sequential rounds of imaging-and-stripping. The study also identified four pairs of fluorogenic RNA aptamer/dye that can be used for multiplexed imaging in living cells and optimized their fluorescence activation and deactivation kinetics. Simultaneous detection of critical signalling molecules and mRNA targets within individual living cells was also achieved. This strategy is expected to facilitate the development of multiplexed and dynamic live-cell imaging and cell biology studies. </div> </div> <div class="d-flex justify-content-between"> <p class="font-weight-bold"> <span class="text-primary">NUCLEIC ACIDS RESEARCH</span> (2024) </p> <div class="flex-shrink-0"> <a class="btn btn-outline-primary btn-sm" href="https://www.peeref.com/works/83121908/add-to-collection" target="_blank"> <strong>Add to Collection</strong> </a> </div> </div> </div> <div class="my-4 border-bottom"> <div> <span class="d-inline-block badge badge-blue"> Article </span> <span class="d-inline-block badge badge-cyan"> Biochemistry & Molecular Biology </span> </div> <h4> <a href="https://www.peeref.com/works/83570248" class="text-dark hover-underline">CRISETR: an efficient technology for multiplexed refactoring of biosynthetic gene clusters</a> </h4> <p class="text-ellipsis-2">Fuqiang He, Xinpeng Liu, Min Tang, Haiyi Wang, Yun Wu, Shufang Liang</p> <div class="d-flex mb-3"> <div class="p-3 rounded bg-light-blue"> <strong>Summary:</strong> CRISETR is a technique for multiplexed refactoring of natural product BGCs, which combines efficient homologous recombination mediated by RecET and the CRISPR/Cas9 system. It shows enhanced tolerance to repetitive sequences within gene clusters, enabling efficient refactoring of complex BGCs and facilitating the discovery of novel bioactive metabolites. </div> </div> <div class="d-flex justify-content-between"> <p class="font-weight-bold"> <span class="text-primary">NUCLEIC ACIDS RESEARCH</span> (2024) </p> <div class="flex-shrink-0"> <a class="btn btn-outline-primary btn-sm" href="https://www.peeref.com/works/83570248/add-to-collection" target="_blank"> <strong>Add to Collection</strong> </a> </div> </div> </div> <div class="my-4 border-bottom"> <div> <span class="d-inline-block badge badge-blue"> Article </span> <span class="d-inline-block badge badge-cyan"> Biochemistry & Molecular Biology </span> </div> <h4> <a href="https://www.peeref.com/works/83466446" class="text-dark hover-underline">Site-specific N-alkylation of DNA oligonucleotide nucleobases by DNAzyme-catalyzed reductive amination</a> </h4> <p class="text-ellipsis-2">Robert D. Boyd, Morgan M. Kennebeck, Aurora A. Miranda, Zehui Liu, Scott K. Silverman</p> <div class="d-flex mb-3"> <div class="p-3 rounded bg-light-blue"> <strong>Summary:</strong> This study identified DNAzymes that can specifically N-alkylate specific nucleotides in DNA substrates through in vitro selection. These DNAzymes require specific metal ion cofactors and have catalytic activity, which can be used for covalent modification and labeling of DNA and RNA substrates. </div> </div> <div class="d-flex justify-content-between"> <p class="font-weight-bold"> <span class="text-primary">NUCLEIC ACIDS RESEARCH</span> (2024) </p> <div class="flex-shrink-0"> <a class="btn btn-outline-primary btn-sm" href="https://www.peeref.com/works/83466446/add-to-collection" target="_blank"> <strong>Add to Collection</strong> </a> </div> </div> </div> <div class="my-4 border-bottom"> <div> <span class="d-inline-block badge badge-blue"> Article </span> <span class="d-inline-block badge badge-cyan"> Biochemistry & Molecular Biology </span> </div> <h4> <a href="https://www.peeref.com/works/83284474" class="text-dark hover-underline">Template-independent synthesis and 3′-end labelling of 2′-modified oligonucleotides with terminal deoxynucleotidyl transferases</a> </h4> <p class="text-ellipsis-2">Leping Sun, Yuming Xiang, Yuhui Du, Yangming Wang, Jiezhao Ma, Yaxin Wang, Xueting Wang, Guangyuan Wang, Tingjian Chen</p> <div class="d-flex mb-3"> <div class="p-3 rounded bg-light-blue"> <strong>Summary:</strong> This study explored the activities of three terminal deoxynucleotidyl transferases (TdTs) in the synthesis and labeling of 2'-modified xenobiotic nucleic acids (XNAs), and utilized these activities to establish a strategy for protecting single-stranded DNA from exonuclease I degradation, as well as methods for 3'-end labeling of 2'-modified XNAs. In addition, a DNA-2'-fluoroarabino nucleic acid (FANA) chimeric hydrogel was successfully constructed. </div> </div> <div class="d-flex justify-content-between"> <p class="font-weight-bold"> <span class="text-primary">NUCLEIC ACIDS RESEARCH</span> (2024) </p> <div class="flex-shrink-0"> <a class="btn btn-outline-primary btn-sm" href="https://www.peeref.com/works/83284474/add-to-collection" target="_blank"> <strong>Add to Collection</strong> </a> </div> </div> </div> <div class="my-4 border-bottom"> <div> <span class="d-inline-block badge badge-blue"> Article </span> <span class="d-inline-block badge badge-cyan"> Biochemistry & Molecular Biology </span> </div> <h4> <a href="https://www.peeref.com/works/83726204" class="text-dark hover-underline">PROTAC-DB 3.0: an updated database of PROTACs with extended pharmacokinetic parameters</a> </h4> <p class="text-ellipsis-2">Jingxuan Ge, Shimeng Li, Gaoqi Weng, Huating Wang, Meijing Fang, Huiyong Sun, Yafeng Deng, Chang- Yu Hsieh, Dan Li, Tingjun Hou</p> <div class="d-flex mb-3"> <div class="p-3 rounded bg-light-blue"> <strong>Summary:</strong> PROTAC is an emerging therapeutic technology that uses the ubiquitin-proteasome system to target protein degradation. It can regulate traditionally non-druggable targets. AI-aided drug design has accelerated its development, but rational design remains a challenge. The PROTAC-DB 3.0 database has been updated, including more PROTACs, warheads, linkers, E3 ligands, and complex structures, as well as pharmacokinetic data and sorting features. It can be accessed at http://cadd.zju.edu.cn/protacdb/. </div> </div> <div class="d-flex justify-content-between"> <p class="font-weight-bold"> <span class="text-primary">NUCLEIC ACIDS RESEARCH</span> (2024) </p> <div class="flex-shrink-0"> <a class="btn btn-outline-primary btn-sm" href="https://www.peeref.com/works/83726204/add-to-collection" target="_blank"> <strong>Add to Collection</strong> </a> </div> </div> </div> <div class="my-4 border-bottom"> <div> <span class="d-inline-block badge badge-blue"> Article </span> <span class="d-inline-block badge badge-cyan"> Biochemistry & Molecular Biology </span> </div> <h4> <a href="https://www.peeref.com/works/83974212" class="text-dark hover-underline">MicroEpitope: an atlas of immune epitopes derived from cancer microbiomes</a> </h4> <p class="text-ellipsis-2">Donghao Li, Yangyang Cai, Kefan Liu, Dezhong Lv, Mengqian Zeng, Luan Wen, Chongwen Lv, Jiyu Guo, Kang Xu, Na Ding, Yongsheng Li, Juan Xu</p> <div class="d-flex mb-3"> <div class="p-3 rounded bg-light-blue"> <strong>Summary:</strong> MicroEpitope is an online resource for analyzing microbiota-derived epitopes in cancer. It integrates HLA immunopeptidome data from 1190 samples across 24 cancer types and aligns them with a theoretical library containing 1298 bacterial and 124 viral species. This resource provides detailed information on epitopes, including their immunogenic features, biochemical properties, and clinical relevance, and offers a variety of analytical tools and visualization methods to assist researchers in better understanding the role of microbiota-derived epitopes in cancer immunity. </div> </div> <div class="d-flex justify-content-between"> <p class="font-weight-bold"> <span class="text-primary">NUCLEIC ACIDS RESEARCH</span> (2024) </p> <div class="flex-shrink-0"> <a class="btn btn-outline-primary btn-sm" href="https://www.peeref.com/works/83974212/add-to-collection" target="_blank"> <strong>Add to Collection</strong> </a> </div> </div> </div> <div class="my-4 border-bottom"> <div> <span class="d-inline-block badge badge-blue"> Article </span> <span class="d-inline-block badge badge-cyan"> Biochemistry & Molecular Biology </span> </div> <h4> <a href="https://www.peeref.com/works/83570511" class="text-dark hover-underline">DrugMAP 2.0: molecular atlas and pharma-information of all drugs</a> </h4> <p class="text-ellipsis-2">Fengcheng Li, Minjie Mou, Xiaoyi Li, Weize Xu, Jiayi Yin, Yang Zhang, Feng Zhu</p> <div class="d-flex mb-3"> <div class="p-3 rounded bg-light-blue"> <strong>Summary:</strong> The escalating costs and high failure rates of drug development have led to increased research interest in combinatorial/repurposed drugs and off-target ADR. Existing databases lack relevant data, so DrugMAP was updated to include combinatorial drugs, repurposed drugs, off-target drugs, and related information. This database can facilitate drug discovery. </div> </div> <div class="d-flex justify-content-between"> <p class="font-weight-bold"> <span class="text-primary">NUCLEIC ACIDS RESEARCH</span> (2024) </p> <div class="flex-shrink-0"> <a class="btn btn-outline-primary btn-sm" href="https://www.peeref.com/works/83570511/add-to-collection" target="_blank"> <strong>Add to Collection</strong> </a> </div> </div> </div> <div class="my-4 border-bottom"> <div> <span class="d-inline-block badge badge-blue"> Article </span> <span class="d-inline-block badge badge-cyan"> Biochemistry & Molecular Biology </span> </div> <h4> <a href="https://www.peeref.com/works/85208145" class="text-dark hover-underline">Direct repeat region 3′ end modifications regulate Cas12a activity and expand its applications</a> </h4> <p class="text-ellipsis-2">Wei Zhang, Yinyin Zhong, Jiaqi Wang, Guangrong Zou, Qiaozhen Chen, Chaoxing Liu</p> <div class="d-flex mb-3"> <div class="p-3 rounded bg-light-blue"> <strong>Summary:</strong> This study reveals a regulatory mechanism for LbCas12a through direct repeat region 3' end modifications and de-modifications, which can regulate its cis- and trans-cleavage activities. Clinical applications show promising results in ALP, AFP, and trace Epstein-Barr virus detection, paving the way for future universal CRISPR diagnostic strategies. </div> </div> <div class="d-flex justify-content-between"> <p class="font-weight-bold"> <span class="text-primary">NUCLEIC ACIDS RESEARCH</span> (2025) </p> <div class="flex-shrink-0"> <a class="btn btn-outline-primary btn-sm" href="https://www.peeref.com/works/85208145/add-to-collection" target="_blank"> <strong>Add to Collection</strong> </a> </div> </div> </div> <div class="my-4 border-bottom"> <div> <span class="d-inline-block badge badge-blue"> Article </span> <span class="d-inline-block badge badge-cyan"> Biochemistry & Molecular Biology </span> </div> <h4> <a href="https://www.peeref.com/works/82952797" class="text-dark hover-underline">CRISPR-Cas12a exhibits metal-dependent specificity switching</a> </h4> <p class="text-ellipsis-2">Giang T. Nguyen, Michael A. Schelling, Akshara Raju, Kathryn A. Buscher, Aneisha Sritharan, Dipali G. Sashital</p> <div class="d-flex mb-3"> <div class="p-3 rounded bg-light-blue"> <strong>Summary:</strong> This study found that the specificity of Cas12a can change depending on the concentration of metal ions. At the actual metal ion concentration in cells, its specificity is reversed compared to the traditional test-tube assay results. This finding reveals the importance of physiological metal ion conditions on the specificity of Cas effectors and emphasizes the need to consider these conditions in biotechnology applications. </div> </div> <div class="d-flex justify-content-between"> <p class="font-weight-bold"> <span class="text-primary">NUCLEIC ACIDS RESEARCH</span> (2024) </p> <div class="flex-shrink-0"> <a class="btn btn-outline-primary btn-sm" href="https://www.peeref.com/works/82952797/add-to-collection" target="_blank"> <strong>Add to Collection</strong> </a> </div> </div> </div> <div class="my-4 "> <div> <span class="d-inline-block badge badge-blue"> Article </span> <span class="d-inline-block badge badge-cyan"> Biochemistry & Molecular Biology </span> </div> <h4> <a href="https://www.peeref.com/works/85238556" class="text-dark hover-underline">An evolved, orthogonal ssDNA generator for targeted hypermutation of multiple genomic loci</a> </h4> <p class="text-ellipsis-2">Weiran Chu, Rongzhen Tian, Yaxin Guo, Yaokang Wu, Fabian B. H. Rehm, Long Liu, Jianghua Li, Guocheng Du, Jian Chen, Yanfeng Liu</p> <div class="d-flex mb-3"> <div class="p-3 rounded bg-light-blue"> <strong>Summary:</strong> This paper introduces a method of T7 RNA polymerase mutant-assisted continuous evolution (T7ACE), which can achieve targeted hypermutation of specific genomic sequences without affecting other regions. This method is effective in both prokaryotic and eukaryotic microorganisms, and can improve the drug resistance and xylose utilization efficiency of microorganisms. </div> </div> <div class="d-flex justify-content-between"> <p class="font-weight-bold"> <span class="text-primary">NUCLEIC ACIDS RESEARCH</span> (2025) </p> <div class="flex-shrink-0"> <a class="btn btn-outline-primary btn-sm" href="https://www.peeref.com/works/85238556/add-to-collection" target="_blank"> <strong>Add to Collection</strong> </a> </div> </div> </div> </div> </div> </div> </div> </div> </div> <div class="modal fade" id="export-citation" tabindex="-1"> <div class="modal-dialog"> <div class="modal-content"> <div class="modal-header"> <button type="button" class="close" data-dismiss="modal"><span>×</span></button> <h4 class="modal-title">Export Citation <b class="text-primary"></b></h4> </div> <div class="modal-body"> <div class="my-3 px-4 f16"> <form action="https://www.peeref.com/works/citation/download" 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Different modes of spacer acquisition by the Staphylococcus epidermidis type III-A CRISPR-Cas system - Peeref