Article
Biochemistry & Molecular Biology
Marios Mejdani, April Pawluk, Karen L. Maxwell, Alan R. Davidson
Summary: Anti-CRISPRs are a diverse class of protein inhibitors produced by phages and mobile genetic elements to evade destruction by the CRISPR-Cas system. A study focused on AcrIE2, an anti-CRISPR inhibiting the Pseudomonas aeruginosa type I-E CRISPR-Cas system, revealed its unique ability to bind to the CRISPR-Cas complex without preventing DNA-binding, operating through a distinct mechanism compared to other type I anti-CRISPRs. AcrIE2 likely blocks DNA cleavage by inhibiting the recruitment of the Cas3 nuclease to the Cascade complex.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Lingguang Yang, Yi Zhang, Peipei Yin, Yue Feng
Summary: Phage infection poses a major threat to prokaryotic survival, leading to an eternal arms race. The CRISPR-Cas systems and Acr proteins represent the adaptive immune responses of prokaryotes against phages. Understanding the structural and biochemical mechanisms of Acr proteins can provide insights for future genome editing research.
Review
Biochemistry & Molecular Biology
Peipei Yin, Yi Zhang, Lingguang Yang, Yue Feng
Summary: Bacteria and archaea have developed the CRISPR-Cas system as an adaptive defense mechanism against mobile genetic elements, but these elements have also evolved anti-CRISPR proteins to counteract the immune defenses. This review focuses on the non-canonical inhibition strategies adopted by these proteins and provides insights into the ongoing arms race between prokaryotic hosts and their predators.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Manling Zhang, Ruchao Peng, Qi Peng, Sheng Liu, Zhiteng Li, Yuqin Zhang, Hao Song, Jia Yang, Xiao Xing, Peiyi Wang, Jianxun Qi, George F. Gao
Summary: CRISPR-Cas systems are commonly used in prokaryotes as adaptive antiviral systems. Phages can encode compact or incomplete CRISPR-Cas systems to suppress host defense mechanisms and establish infection. The phage ICP1 encodes a compact type I-F CRISPR-Cas system to inhibit antiphage genetic elements in its host, but the mechanism of target DNA recognition and interference remains unknown.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Yi Zhou, Jack P. K. Bravo, Hannah N. Taylor, Jurre A. Steens, Ryan N. Jackson, Raymond H. J. Staals, David W. Taylor
Summary: The cryo-electron microscopy structure of a type IV-B CRISPR ribonucleoprotein complex was revealed at 3.9-angstrom resolution, showing a resemblance to type III-A CRISPR Csm effector complex but lacking subunits for RNA processing and target DNA cleavage. Surprisingly, the complex does not assemble around a CRISPR-derived RNA, but instead assembles around heterogeneous RNA in a pseudo-A-form configuration. These findings provide insight into the assembly and function of enigmatic type IV CRISPR systems, expanding our understanding of class I CRISPR-Cas system architecture.
Article
Microbiology
Anna Maikova, Pierre Boudry, Anna Shiriaeva, Aleksandra Vasileva, Anais Boutserin, Sofia Medvedeva, Ekaterina Semenova, Konstantin Severinov, Olga Soutourina
Summary: CRISPR-Cas systems provide prokaryotes with adaptive immunity against foreign nucleic acid invaders. This study demonstrates the adaptation process of the type I-B CRISPR-Cas system in Clostridioides difficile and its functional link between adaptation and interference machineries. Understanding the functional PAM motifs and activity levels of CRISPR arrays in this pathogen is crucial for future biotechnological and medical applications.
Article
Microbiology
Gargi Bindal, Lina Amlinger, Magnus Lundgren, Devashish Rath
Summary: Defense against viruses and other MGEs is crucial for many organisms. This study demonstrates the interference ability of a type I-E CRISPR-Cas system from Escherichia coli introduced in Saccharomyces cerevisiae, providing new insights into the potential application of CRISPR technology in eukaryotic cells.
Article
Microbiology
Richard Bauer, Dorina Haider, Aline Grempels, Rebecca Roscher, Stefanie Mauerer, Barbara Spellerberg
Summary: This study analyzed the CRISPR-Cas systems in Streptococcus anginosus and found two types of CRISPR-Cas II systems. One type contained a long csn2 gene, similar to Streptococcus thermophilus, while the other type contained a short csn2 gene, similar to S. pyogenes.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Infectious Diseases
Shigang Yao, Xinyi Wu, Yi Li, Yuqin Song, Chao Wang, Gang Zhang, Jie Feng
Summary: In this study, a native Type I-F CRISPR-Cas system for gene editing and regulation was developed and demonstrated to be effective through research on Acinetobacter baumannii. This system provides a tool for further exploration of the genetic characteristics and pathogenesis of A. baumannii.
INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS
(2023)
Article
Microbiology
Qibing Liu, Siwei Wang, Juying Long, Zhuoyue Chen, Bing Yang, Fei Lin
Summary: The study revealed that Xanthomonas oryzae pv. oryzae possesses a functional CRISPR system and analyzed the effects of CRISPR array, PAM sequence, and gRNA on self-target killing, as well as the role of Cas proteins in CRISPR RNA processing and DNA interference. The findings contribute to a better understanding of the functional aspects of the Xoo CRISPR/Cas system and present a new perspective on utilizing bacterial endogenous systems for gene editing purposes.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemical Research Methods
Zhijie Qin, Yutong Yang, Shiqin Yu, Li Liu, Yue Chen, Jian Chen, Jingwen Zhou
Summary: A CRISPRi system based on the endogenous CRISPR/Cas system in Gluconobacter oxydans was developed, showing effective multiplex gene repression. The study further investigated the role of central carbon metabolism pathways and demonstrated potential metabolic engineering applications, enriching gene regulation tools and promoting performance improvements in G. oxydans.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Food Science & Technology
Ling Wang, Li Wang, Youzhao Liu, Zhiyun Wang, Qing Chen, Zhihua Liu, Jing Hu
Summary: The study identified two CRISPR systems in Laribacter hongkongensis, with the CRISPR1-Cas system being present in the majority of isolates. It also highlighted the potential for molecular typing of L. hongkongensis based on the conservation of CRISPR loci and variable repeat-spacer arrays.
INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Chuan-min Zhou, Qun Wu, Biao Wang, Ping Lin, Min Wu, Xue-jie Yu
Summary: Calcium positively regulates the transcription of CRISPR-Cas system via LadS, while RsmA functions as a post-transcriptional regulator; the modulation of CRISPR-Cas system by calcium depends on LadS and RsmA, highlighting their previously unrecognized role in sensing calcium.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Plant Sciences
Dandan Jiang, Dandan Zhang, Shengnan Li, Yueting Liang, Qianwei Zhang, Xu Qin, Jinlan Gao, Jin-Long Qiu
Summary: Efficient genome editing using an identified type I-C CRISPR-Cas system in Xoo allows for precise modifications of the genome, providing a valuable tool for functional genomics studies of rice bacterial blight and potentially other CRISPR-harboring bacterial plant pathogens.
MOLECULAR PLANT PATHOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Yingnan Li, Boyu Huang, Jian Chen, Liangliang Huang, Jianghai Xu, Yingying Wang, Guanghui Cui, Haiming Zhao, Beibei Xin, Weibin Song, Jian-Kang Zhu, Jinsheng Lai
Summary: We developed a new Dvu I-C system for plant genome editing, which can efficiently achieve controllable large fragment deletions with an editing efficiency of up to 86.67%. This system is sensitive to spacer length and mismatch, benefiting target specificity.
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Jeong Hwan Hur, Chan Young Kang, Sungjin Lee, Nazia Parveen, Jihyeon Yu, Amen Shamim, Wanki Yoo, Ambarnil Ghosh, Sangsu Bae, Chin-Ju Park, Kyeong Kyu Kim
Summary: The study identifies a stable secondary structure, termed 'adenine:cytosine-motif (AC-motif)', formed by adenine and cytosine repeats in DNA sequences, which is similar to the i-motif structure. This AC-motif plays a key regulatory role in gene expression in response to magnesium, expanding the repertoire of non-canonical DNA structures with potential regulatory functions in cells.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
So Young Bak, Youngri Jung, Jinho Park, Keewon Sung, Hyeon-Ki Jang, Sangsu Bae, Seong Keun Kim
Summary: This study utilized single-molecule FRET assay to investigate the dynamics of DNA:RNA heteroduplexation for various engineered Cas9 variants, revealing a strong correlation between their conformational structure and nuclease activity. Quantitative analysis showed that these engineered Cas9 variants exhibit a more rapid decrease in cleavage-competent state with increasing base-pair mismatch, leading to enhanced target specificity. The critical specificity enhancement step was found to be activated during DNA:RNA heteroduplexation for some variants, highlighting the importance of conformational dynamics in Cas9 target specificity.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Hyeon-Ki Jang, Dong Hyun Jo, Seu-Na Lee, Chang Sik Cho, You Kyeong Jeong, Youngri Jung, Jihyeon Yu, Jeong Hun Kim, Jae-Sung Woo, Sangsu Bae
Summary: Ribonucleoprotein (RNP) complex-mediated base editing is promising for therapeutic applications due to its reduced off-target effects. However, obtaining highly purified CBE/ABE proteins from bacterial systems is challenging. ABE RNPs showed significantly reduced off-target effects in both DNA and RNA compared to plasmid-encoded ABE.
Article
Biotechnology & Applied Microbiology
Sung-Ah Hong, Jung Hwa Seo, Soohyun Wi, Eul Sik Jung, Jihyeon Yu, Gue-Ho Hwang, Ji Hea Yu, Ahreum Baek, Soeon Park, Sangsu Bae, Sung-Rae Cho
Summary: This study successfully increased the expression levels of the ABCD1 gene and reduced the levels of metabolites associated with ADLD using gene editing strategies in cells and mouse models derived from ADLD patients. These findings suggest that gene editing could be a promising therapeutic strategy for treating ADLD.
Article
Biochemistry & Molecular Biology
Omer Habib, Gizem Habib, Gue-Ho Hwang, Sangsu Bae
Summary: Prime editing is a precise and versatile genome editing technique that can directly copy desired genetic modifications into target DNA sites. It has great potential for gene function analysis, disease modeling, and correction of pathogenic mutations. In this study, prime editing was successfully tested in human pluripotent stem cells (hPSCs) and compared with base editing. Whole-genome sequencing showed that prime editing does not lead to guide RNA-independent off-target mutations in the genome.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Medicine, Research & Experimental
Ju-Chan Park, Hyeon-Ki Jang, Jumee Kim, Jun Hee Han, Youngri Jung, Keuntae Kim, Sangsu Bae, Hyuk-Jin Cha
Summary: Precise genome editing of human pluripotent stem cells (hPSCs) is essential for both basic science and biomedical applications. This study demonstrated that high expression of DNA glycosylases, such as uracil DNA glycosylase (UNG), in human embryonic stem cells (hESCs) significantly reduced the editing efficiency of cytosine base editor (CBE) and affected the purity of C to T base substitutions. Transient knockdown of UNG improved the editing efficiency and product purity in hESCs.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2022)
Article
Biotechnology & Applied Microbiology
Sung-Ah Hong, Song-Ee Kim, A-Young Lee, Gue-Ho Hwang, Jong Hoon Kim, Hiroaki Iwata, Soo-Chan Kim, Sangsu Bae, Sang Eun Lee
Summary: In this study, researchers identified and corrected pathogenic mutations in the COL7A1 gene using adenine base editors and prime editors in patients with recessive dystrophic epidermolysis bullosa (RDEB). The edited patient-derived skin equivalents showed positive outcomes in terms of C7 deposition and anchoring fibril formation, suggesting the feasibility of ex vivo gene editing as a potential treatment for RDEB.
News Item
Biochemistry & Molecular Biology
Beomjong Song, Sangsu Bae
Summary: A TnpB-based adenine base editor has been developed and can be loaded into a single AAV vector without compromising editing activity, showing potential for efficient gene editing.
NATURE CHEMICAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Jong Hee Kim, Jihyeon Yu, Hee Kyoung Kim, Jin Young Kim, Me-Sun Kim, Yong-Gu Cho, Sangsu Bae, Kwon Kyoo Kang, Yu Jin Jung
Summary: Researchers have successfully conducted targeted mutagenesis and golden SNP replacement of the LcyE gene in rice using CRISPR/Cas9 and geminiviral replicon. This breakthrough has the potential to replace all genes within one generation and greatly improve agriculturally important traits.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Jin Young Kim, Jong Hee Kim, Young Hee Jang, Jihyeon Yu, Sangsu Bae, Me-Sun Kim, Yong-Gu Cho, Yu Jin Jung, Kwon Kyoo Kang
Summary: In this study, a tomato SGR1-knockout null line was generated using gene editing technology, and it was found that the SGR1 knockout mutants exhibited a turbid brown color in the fruit, with significantly higher levels of chlorophyll and carotenoids compared to the wild-type. Differential gene expression analysis identified 728 differentially expressed genes, most of which were related to photosynthesis, chloroplasts, and carotenoid biosynthesis. These results provide new evidence for understanding the function of SGR1 and the molecular pathways involved in photosynthesis, chloroplasts, and carotenoid biosynthesis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Hee Kyoung Kim, Jin Young Kim, Jong Hee Kim, Ji Yun Go, Yoo-Seob Jung, Hyo Ju Lee, Mi-Jeong Ahn, Jihyeon Yu, Sangsu Bae, Ho Soo Kim, Sang-Soo Kwak, Me-Sun Kim, Yong-Gu Cho, Yu Jin Jung, Kwon Kyoo Kang
Summary: We generated an orange-colored rice callus line by targeted mutagenesis of the orange gene (OsOr) using the CRISPR-Cas9 system. The OC line accumulated higher levels of lutein, beta-carotene, and two beta-carotene isomers compared to the WT line. The expression levels of carotenoid biosynthesis genes were also altered in the OC line.
Correction
Biochemistry & Molecular Biology
Beomjong Song, Sangsu Bae
NATURE CHEMICAL BIOLOGY
(2023)
Article
Chemistry, Analytical
Siheon Seong, Sewon Lee, Sunghyun Bae, Minjae Lee
Summary: This paper presents a fully-differential touch screen panel (TSP) self-capacitance sensing (SCS) system with a self-capacitance mismatch calibration technique. Due to the self-capacitance mismatch of TSP, the SNR loss for the TSP SCS system is caused by the degradation of the AFE dynamic range and gain limitations. The proposed calibration method effectively relieves the mismatch effect in terms of area and power consumption, restoring the SNR by 19.54 dB even under the worst self-capacitance mismatch case.
Review
Chemistry, Analytical
Sunghyun Bae, Hyeon-June Kim
Summary: This paper proposes the use of a two-channel optical time-division multiplexed system with multilevel pulse-amplitude modulation to achieve >100 Gb/s data-center interconnects. Unlike the conventional four-channel system, the two-channel system can be implemented cost-effectively using a wide pulse and integrated transmitter. The paper reviews the current research on the two-channel system and discusses future directions, highlighting the ability to transmit 200 Gb/s signals over standard single-mode fiber using phase-alternating pulses.
Review
Geosciences, Multidisciplinary
Sang-Hun Lee, Sunghyun Bae
Summary: This study focuses on the emission and dispersion of ammonia from livestock manure facilities, as well as on the treatment and recovery of ammonia. It recommends the use of low-cost monitoring sensors integrated with information technology to improve data quality. Emission factors should be classified based on various scenarios and conditions.
GEOSYSTEM ENGINEERING
(2022)
