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Versatile plant genome engineering using anti-CRISPR-Cas12a systems. 使用抗CRISPR-Cas12a 系统的多功能植物基因组工程。
IF 8 2区 生物学
Science China Life Sciences Pub Date : 2024-12-01 Epub Date: 2024-08-15 DOI: 10.1007/s11427-024-2704-7
Yao He, Shishi Liu, Long Chen, Dongkai Pu, Zhaohui Zhong, Tang Xu, Qiurong Ren, Chuan Dong, Yawei Wang, Danning Wang, Xuelian Zheng, Fengbiao Guo, Tao Zhang, Yiping Qi, Yong Zhang
{"title":"Versatile plant genome engineering using anti-CRISPR-Cas12a systems.","authors":"Yao He, Shishi Liu, Long Chen, Dongkai Pu, Zhaohui Zhong, Tang Xu, Qiurong Ren, Chuan Dong, Yawei Wang, Danning Wang, Xuelian Zheng, Fengbiao Guo, Tao Zhang, Yiping Qi, Yong Zhang","doi":"10.1007/s11427-024-2704-7","DOIUrl":"10.1007/s11427-024-2704-7","url":null,"abstract":"<p><p>CRISPR-Cas12a genome engineering systems have been widely used in plant research and crop breeding. To date, the performance and use of anti-CRISPR-Cas12a systems have not been fully established in plants. Here, we conduct in silico analysis to identify putative anti-CRISPR systems for Cas12a. These putative anti-CRISPR proteins, along with known anti-CRISPR proteins, are assessed for their ability to inhibit Cas12a cleavage activity in vivo and in planta. Among all anti-CRISPR proteins tested, AcrVA1 shows robust inhibition of Mb2Cas12a and LbCas12a in E. coli. Further tests show that AcrVA1 inhibits LbCas12a mediated genome editing in rice protoplasts and stable transgenic lines. Impressively, co-expression of AcrVA1 mitigates off-target effects by CRISPR-LbCas12a, as revealed by whole genome sequencing. In addition, transgenic plants expressing AcrVA1 exhibit different levels of inhibition to LbCas12a mediated genome editing, representing a novel way of fine-tuning genome editing efficiency. By controlling temporal and spatial expression of AcrVA1, we show that inducible and tissue specific genome editing can be achieved in plants. Furthermore, we demonstrate that AcrVA1 also inhibits LbCas12a-based CRISPR activation (CRISPRa) and based on this principle we build logic gates to turn on and off target genes in plant cells. Together, we have established an efficient anti-CRISPR-Cas12a system in plants and demonstrate its versatile applications in mitigating off-target effects, fine-tuning genome editing efficiency, achieving spatial-temporal control of genome editing, and generating synthetic logic gates for controlling target gene expression in plant cells.</p>","PeriodicalId":21576,"journal":{"name":"Science China Life Sciences","volume":" ","pages":"2730-2745"},"PeriodicalIF":8.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142000630","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Optimizing ABA-based chemically induced proximity for enhanced intracellular transcriptional activation and modification response to ABA. 优化基于 ABA 的化学诱导接近，以增强细胞内转录激活和对 ABA 的修饰响应。
IF 8 2区 生物学
Science China Life Sciences Pub Date : 2024-12-01 Epub Date: 2024-08-19 DOI: 10.1007/s11427-024-2707-9
Zeng Zhou, Yue-Qi Wang, Xu-Nan Zheng, Xiao-Hong Zhang, Lu-Yao Ji, Jun-You Han, Ze-Cheng Zuo, Wei-Liang Mo, Li Zhang
{"title":"Optimizing ABA-based chemically induced proximity for enhanced intracellular transcriptional activation and modification response to ABA.","authors":"Zeng Zhou, Yue-Qi Wang, Xu-Nan Zheng, Xiao-Hong Zhang, Lu-Yao Ji, Jun-You Han, Ze-Cheng Zuo, Wei-Liang Mo, Li Zhang","doi":"10.1007/s11427-024-2707-9","DOIUrl":"10.1007/s11427-024-2707-9","url":null,"abstract":"<p><p>Abscisic acid (ABA)-based chemically induced proximity (CIP) is primarily mediated by the interaction of the ABA receptor pyrabactin resistance 1-like 1 (PYL1) and the 2C-type protein phosphatase ABI1, which confers ABA-induced proximity to their fusion proteins, and offers precise temporal control of a wide array of biological processes. However, broad application of ABA-based CIP has been limited by ABA response intensity. In this study, we demonstrated that ABA-induced interaction between another ABA receptor pyrabactin resistance 1 (PYR1) and ABI1 exhibited higher ABA response intensity than that between PYL1 and ABI1 in HEK293T cells. We engineered PYR1-ABI1 and PYL1-ABI1 into ABA-induced transcriptional activation tools in mammalian cells by integration with CRISPR/dCas9 and found that the tool based on PYR1-ABI1 demonstrated better ABA response intensity than that based on PYL1-ABI1 for both exogenous and endogenous genes in mammalian cells. We further achieved ABA-induced RNA m<sup>6</sup>A modification installation and erasure by combining ABA-induced PYR1-ABI1 interaction with CRISPR/dCas13, successfully inhibiting tumor cell proliferation. We subsequently improved the interaction of PYR1-ABI1 through phage-assisted continuous evolution (PACE), successfully generating a PYR1 mutant (PYR1m) whose interaction with ABI1 exhibited a higher ABA response intensity than that of the wild-type. In addition, we tested the transcriptional activation tool based on PYRm-ABI1 and found that it also showed a higher ABA response intensity than that of the wild type. These results demonstrate that we have developed a novel ABA-based CIP and further improved upon it using PACE, providing a new approach for the modification of other CIP systems.</p>","PeriodicalId":21576,"journal":{"name":"Science China Life Sciences","volume":" ","pages":"2650-2663"},"PeriodicalIF":8.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142018420","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Identification of malignant plasma cells in the primary mediastinal large B-cell lymphoma. 原发性纵隔大 B 细胞淋巴瘤中恶性浆细胞的鉴定。
IF 8 2区 生物学
Science China Life Sciences Pub Date : 2024-12-01 Epub Date: 2024-09-24 DOI: 10.1007/s11427-024-2715-4
Changchun Wang, Lianhui Duan, Guanyin Huang, Chang Yu, Xuping Yang, Dangchi Li, Yueyu Huang, Wenhui Shen, Xuefei Liu, Qiaoli Lv, Haiyan Yang, Weimin Mao, An Zhao
{"title":"Identification of malignant plasma cells in the primary mediastinal large B-cell lymphoma.","authors":"Changchun Wang, Lianhui Duan, Guanyin Huang, Chang Yu, Xuping Yang, Dangchi Li, Yueyu Huang, Wenhui Shen, Xuefei Liu, Qiaoli Lv, Haiyan Yang, Weimin Mao, An Zhao","doi":"10.1007/s11427-024-2715-4","DOIUrl":"10.1007/s11427-024-2715-4","url":null,"abstract":"","PeriodicalId":21576,"journal":{"name":"Science China Life Sciences","volume":" ","pages":"2777-2779"},"PeriodicalIF":8.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142353122","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
rAAV-CRISPR/Cas9-mediated in vivo delivery of porcine embryos to construct knockout pigs. rAAV-CRISPR/Cas9 介导的猪胚胎体内传递，构建基因敲除猪。
IF 8 2区 生物学
Science China Life Sciences Pub Date : 2024-12-01 Epub Date: 2024-11-11 DOI: 10.1007/s11427-024-2749-8
Mengyu Gao, YuTing He, XingLong Zhu, WanLiu Peng, Xinmei Liu, Yanyan Zhou, Yang Deng, Qin Liu, Guangneng Liao, Yi Li, Wei Ni, Guang Yang, Jiayin Yang, Yang Yang, Lang Bai, Hong Bu, Ji Bao
{"title":"rAAV-CRISPR/Cas9-mediated in vivo delivery of porcine embryos to construct knockout pigs.","authors":"Mengyu Gao, YuTing He, XingLong Zhu, WanLiu Peng, Xinmei Liu, Yanyan Zhou, Yang Deng, Qin Liu, Guangneng Liao, Yi Li, Wei Ni, Guang Yang, Jiayin Yang, Yang Yang, Lang Bai, Hong Bu, Ji Bao","doi":"10.1007/s11427-024-2749-8","DOIUrl":"10.1007/s11427-024-2749-8","url":null,"abstract":"","PeriodicalId":21576,"journal":{"name":"Science China Life Sciences","volume":" ","pages":"2587-2589"},"PeriodicalIF":8.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142626738","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A biobank of patient derived glioma organoids. 患者胶质瘤组织细胞生物库。
IF 8 2区 生物学
Science China Life Sciences Pub Date : 2024-12-01 Epub Date: 2024-09-13 DOI: 10.1007/s11427-024-2632-0
Yulin Wen, Hongmin Bai, Qing Li, Sainan Huang, Xiaokun Jia, Guangjin Pan, Hongjie Yao
{"title":"A biobank of patient derived glioma organoids.","authors":"Yulin Wen, Hongmin Bai, Qing Li, Sainan Huang, Xiaokun Jia, Guangjin Pan, Hongjie Yao","doi":"10.1007/s11427-024-2632-0","DOIUrl":"10.1007/s11427-024-2632-0","url":null,"abstract":"","PeriodicalId":21576,"journal":{"name":"Science China Life Sciences","volume":" ","pages":"2780-2782"},"PeriodicalIF":8.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142294427","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
NeoI represents a group of transcriptional repressors regulating the biosynthesis of multiple aminoglycosides. NeoI 代表一组转录抑制因子，调节多种氨基糖苷类化合物的生物合成。
IF 8 2区 生物学
Science China Life Sciences Pub Date : 2024-12-01 Epub Date: 2024-10-21 DOI: 10.1007/s11427-024-2665-9
Yue Li, Xiangxi Meng, Dong Li, Xiulei Xia, Jihui Zhang, Yihua Chen, Huarong Tan
{"title":"NeoI represents a group of transcriptional repressors regulating the biosynthesis of multiple aminoglycosides.","authors":"Yue Li, Xiangxi Meng, Dong Li, Xiulei Xia, Jihui Zhang, Yihua Chen, Huarong Tan","doi":"10.1007/s11427-024-2665-9","DOIUrl":"10.1007/s11427-024-2665-9","url":null,"abstract":"<p><p>In general, the initiation or closure of antibiotic biosynthesis is determined by regulatory proteins, but most of their mechanisms of action remain unknown. The 2-deoxystreptamine-containing aminoglycosides (2-DOS AGs) form a unique category among antibiotics. Genomic analysis revealed that a group of hypothetical regulatory genes represented by neoI are widely distributed in the biosynthetic gene clusters (BGCs) of natural products from Streptomyces species, including several 2-DOS AGs. Only limited knowledge is available for the roles of NeoI-type regulators although neomycin and some of the related AGs have been developed as therapeutic drugs for decades. This study focuses on the functional determination of neoI and its homologues situated in the BGCs of six AGs. We found that the yield of neomycin in neoI disruption mutant (ΔneoI) increased by 50% compared to the wild-type (WT) strain ((420.6±44.1) mg L<sup>-1</sup>), while it was partially restored by the complementation of neoI, demonstrating that NeoI acted as a repressor in neomycin biosynthesis. Further electrophoretic mobility shift assays (EMSAs) and DNase I footprinting assays indicated that NeoI could specifically bind to the promoter region between neoE and neoI with conserved nucleotides (5'-CVHYMRCHDKAGYGGACR-3'), as determined by site-directed mutagenesis. Interestingly, cross-bindings of the NeoI homologues from the six different BGCs to their corresponding DNA targets were manifested, and the five exogenous NeoI homologues could complement NeoI function of repressing neomycin biosynthesis. Our results suggested that NeoI-type regulators represent widespread and conservative regulatory characteristics in the biosynthesis of 2-DOS AGs, which would be significant for optimizing the biosynthetic pathways of valuable commercialized aminoglycoside antibiotics.</p>","PeriodicalId":21576,"journal":{"name":"Science China Life Sciences","volume":" ","pages":"2761-2770"},"PeriodicalIF":8.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142507075","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
CRISPR beyond: harnessing compact RNA-guided endonucleases for enhanced genome editing. 超越 CRISPR：利用小型 RNA 引导的内切酶加强基因组编辑。
IF 8 2区 生物学
Science China Life Sciences Pub Date : 2024-12-01 Epub Date: 2024-07-12 DOI: 10.1007/s11427-023-2566-8
Feizuo Wang, Shengsheng Ma, Senfeng Zhang, Quanquan Ji, Chunyi Hu
{"title":"CRISPR beyond: harnessing compact RNA-guided endonucleases for enhanced genome editing.","authors":"Feizuo Wang, Shengsheng Ma, Senfeng Zhang, Quanquan Ji, Chunyi Hu","doi":"10.1007/s11427-023-2566-8","DOIUrl":"10.1007/s11427-023-2566-8","url":null,"abstract":"<p><p>The CRISPR-Cas system, an adaptive immunity system in prokaryotes designed to combat phages and foreign nucleic acids, has evolved into a groundbreaking technology enabling gene knockout, large-scale gene insertion, base editing, and nucleic acid detection. Despite its transformative impact, the conventional CRISPR-Cas effectors face a significant hurdle-their size poses challenges in effective delivery into organisms and cells. Recognizing this limitation, the imperative arises for the development of compact and miniature gene editors to propel advancements in gene-editing-related therapies. Two strategies were accepted to develop compact genome editors: harnessing OMEGA (Obligate Mobile Element-guided Activity) systems, or engineering the existing CRISPR-Cas system. In this review, we focus on the advances in miniature genome editors based on both of these strategies. The objective is to unveil unprecedented opportunities in genome editing by embracing smaller, yet highly efficient genome editors, promising a future characterized by enhanced precision and adaptability in the genetic interventions.</p>","PeriodicalId":21576,"journal":{"name":"Science China Life Sciences","volume":" ","pages":"2563-2574"},"PeriodicalIF":8.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141620830","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Gut microbiota and healthy longevity. 肠道微生物群与健康长寿
IF 8 2区 生物学
Science China Life Sciences Pub Date : 2024-12-01 Epub Date: 2024-08-02 DOI: 10.1007/s11427-023-2595-5
Jia Luo, Shan Liang, Feng Jin
{"title":"Gut microbiota and healthy longevity.","authors":"Jia Luo, Shan Liang, Feng Jin","doi":"10.1007/s11427-023-2595-5","DOIUrl":"10.1007/s11427-023-2595-5","url":null,"abstract":"<p><p>Recent progress on the underlying biological mechanisms of healthy longevity has propelled the field from elucidating genetic modification of healthy longevity hallmarks to defining mechanisms of gut microbiota influencing it. Importantly, the role of gut microbiota in the healthy longevity of the host may provide unprecedented opportunities to decipher the plasticity of lifespan on a natural evolutionary scale and shed light on using microbiota-targeted strategies to promote healthy aging and combat age-related diseases. This review investigates how gut microbiota affects healthy longevity, focusing on the mechanisms through which gut microbiota modulates it. Specifically, we focused on the ability of gut microbiota to enhance the intestinal barrier integrity, provide protection from inflammaging, ameliorate nutrientsensing pathways, optimize mitochondrial function, and improve defense against age-related diseases, thus participating in enhancing longevity and healthspan.</p>","PeriodicalId":21576,"journal":{"name":"Science China Life Sciences","volume":" ","pages":"2590-2602"},"PeriodicalIF":8.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141898133","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
CRISPR-based genetic screens advance cancer immunology. 基于 CRISPR 的基因筛选推动了癌症免疫学的发展。
IF 8 2区 生物学
Science China Life Sciences Pub Date : 2024-12-01 Epub Date: 2024-07-23 DOI: 10.1007/s11427-023-2571-0
Yuanfang Cao, Xueting Li, Yumu Pan, Huahe Wang, Siyu Yang, Lingjuan Hong, Lupeng Ye
{"title":"CRISPR-based genetic screens advance cancer immunology.","authors":"Yuanfang Cao, Xueting Li, Yumu Pan, Huahe Wang, Siyu Yang, Lingjuan Hong, Lupeng Ye","doi":"10.1007/s11427-023-2571-0","DOIUrl":"10.1007/s11427-023-2571-0","url":null,"abstract":"<p><p>CRISPR technologies have revolutionized research areas ranging from fundamental science to translational medicine. CRISPR-based genetic screens offer a powerful platform for unbiased screening in various fields, such as cancer immunology. Immune checkpoint blockade (ICB) therapy has been shown to strongly affect cancer treatment. However, the currently available ICBs are limited and do not work in all cancer patients. Pooled CRISPR screens enable the identification of previously unknown immune regulators that can regulate T-cell activation, cytotoxicity, persistence, infiltration into tumors, cytokine secretion, memory formation, T-cell metabolism, and CD4<sup>+</sup> T-cell differentiation. These novel targets can be developed as new immunotherapies or used with the current ICBs as new combination therapies that may yield synergistic efficacy. Here, we review the progress made in the development of CRISPR technologies, particularly technological advances in CRISPR screens and their application in novel target identification for immunotherapy.</p>","PeriodicalId":21576,"journal":{"name":"Science China Life Sciences","volume":" ","pages":"2554-2562"},"PeriodicalIF":8.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141760789","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
AAV-mediated gene therapies by miniature gene editing tools. 利用微型基因编辑工具进行 AAV 介导的基因治疗。
IF 8 2区 生物学
Science China Life Sciences Pub Date : 2024-12-01 Epub Date: 2024-09-27 DOI: 10.1007/s11427-023-2608-5
Xiangfeng Kong, Tong Li, Hui Yang
{"title":"AAV-mediated gene therapies by miniature gene editing tools.","authors":"Xiangfeng Kong, Tong Li, Hui Yang","doi":"10.1007/s11427-023-2608-5","DOIUrl":"10.1007/s11427-023-2608-5","url":null,"abstract":"<p><p>The advent of CRISPR-Cas has revolutionized precise gene editing. While pioneering CRISPR nucleases like Cas9 and Cas12 generate targeted DNA double-strand breaks (DSB) for knockout or homology-directed repair, next generation CRISPR technologies enable gene editing without DNA DSB. Base editors directly convert bases, prime editors make diverse alterations, and dead Cas-regulator fusions allow nuanced control of gene expression, avoiding potentially risks like translocations. Meanwhile, the discovery of diminutive Cas12 orthologs and Obligate Mobile Element-Guided Activity (OMEGA) nucleases has overcome cargo limitations of adeno-associated viral vectors, expanding prospects for in vivo therapeutic delivery. Here, we review the ever-evolving landscape of cutting-edge gene editing tools, focusing on miniature Cas12 orthologs and OMEGA effectors amenable to single AAV packaging. We also summarize CRISPR therapies delivered using AAV vectors, discuss challenges such as efficiency and specificity, and look to the future of this transformative field of in vivo gene editing enabled by AAV vectors delivery.</p>","PeriodicalId":21576,"journal":{"name":"Science China Life Sciences","volume":" ","pages":"2540-2553"},"PeriodicalIF":8.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142473713","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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