CELL
·
2024
·
IF 45.5
Tongtong Zhang,Shengjun Tan,Na Tang,Yuanqing Li,Chenze Zhang,Jing Sun,Yanyan Guo,Hui Gao,Yujia Cai,Wen Sun,Chenxin Wang,Liangzheng Fu,Huijing Ma,Yachao Wu,Xiaoxuan Hu,Xuechun Zhang,Peter Gee,Weihua Yan,Yahui Zhao,Qiang Chen,Baocheng Guo,Haoyi Wang,Yong E. Zhang
Experimental studies on DNA transposable elements (TEs) have been limited in scale, leading to a lack of understanding of the factors influencing transposition activity, evolutionary dynamics, and application potential as genome engineering tools. We predicted 130 active DNA TEs from 102 metazoan genomes and evaluated their activity in human cells. We identified 40 active (integration-competent) TEs, surpassing the cumulative number (20) of TEs found previously. With this unified comparative data, we found that the Tc1/ mariner superfamily exhibits elevated activity, potentially explaining their pervasive horizontal transfers. Further functional characterization of TEs revealed additional divergence in features such as insertion bias. Remarkably, in CAR-T therapy for hematological and solid tumors, Mariner2_AG (MAG), the most active DNA TE identified, largely outperformed two widely used vectors, the lentiviral vector and the TE-based vector SB100X. Overall, this study highlights the varied transposition features and evolutionary dynamics of DNA TEs and increases the TE toolbox diversity.
研究领域:
分子生物学
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遗传学
·
基因组学
·
医学
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DOI
PubMed
高影响因子
TOXICOLOGY IN VITRO
·
2015
·
IF 2.903
Lizhen Huang,Shuxiang Zou,Jifeng Deng,Tianming Dai,Jingwei Jiang,Ying Jia,Renke Dai,Shuilin Xie
Drug-induced hepatotoxicity is often caused by cytochrome P450 (CYP)-dependent metabolism of drugs into reactive metabolites. Assessment of hepatotoxicity induced by bioactive compounds is hampered by low CYP expression within in vitro cell lines. To overcome this limitation, piggyBac transposition and monoclonal expansion were used to generate a HepG2 cell line with stable and homogenously high expression of CYP3A4, a prominent CYP isoform. Our studies demonstrate the generated line's constant CYP3A4 expression and activity for over 40 cell passages; to date, it has been in subculture for more than a year without addition of Puromycin. This cell line was utilized to evaluate cytotoxicity of two bioactive (troglitazone and acetaminophen) and two non-bioactive (citrate and galactosamine) compounds by MTT assay. Cell viability significantly decreased upon treatment with bioactive drugs. Moreover, cell lines used in the present study were more sensitive to toxic effects of troglitazone than previously reported. Therefore, this HepG2 cell-based assay system may provide a suitable hepatic model for predicting CYP3A4-mediated hepatotoxicity during preclinical drug development.
研究领域:
药理学
·
分子生物学
·
毒理学
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DOI
PubMed
高影响因子
Nature Plants
·
2021
·Vol. 7
·期 8
·1026-1036
·
IF 15.793
Xiong Xingyao,Gou Junbo,Liao Qinggang,Li Yanlin,Zhou Qian,Bi Guiqi,Li Chong,Du Ran,Wang Xiaotong,Sun Tianshu,Guo Lvjun,Liang Haifei,Lu Pengjun,Wu Yaoyao,Zhang Zhonghua,Ro Dae-Kyun,Shang Yi,Huang Sanwen,Yan Jianbin
The ancient gymnosperm genus Taxus is the exclusive source of the anticancer drug paclitaxel, yet no reference genome sequences are available for comprehensively elucidating the paclitaxel biosynthesis pathway. We have completed a chromosome-level genome of Taxus chinensis var. mairei with a total length of 10.23 gigabases. Taxus shared an ancestral whole-genome duplication with the coniferophyte lineage and underwent distinct transposon evolution. We discovered a unique physical and functional grouping of CYP725A s (cytochrome P450) in the Taxus genome for paclitaxel biosynthesis. We also identified a gene cluster for taxadiene biosynthesis, which was formed mainly by gene duplications. This study will facilitate the elucidation of paclitaxel biosynthesis and unleash the biotechnological potential of Taxus .
研究领域:
植物生物学
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基因组学
·
生物化学
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药理学
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产品关联
DOI
PubMed
高影响因子
Microbiology Spectrum
·
2022
·Vol. 11
·期 1
·
IF 9.043
Xiayu Liu,Xinxin Pang,Yansha Wu,Yajing Wu,Linan Xu,Qihe Chen,Jianrui Niu,Xinglin Zhang
Listeria monocytogenes is a foodborne pathogen that can tolerate a variety of extreme environments. In particular, its acid resistance (AR) capability is considered one of the key factors threating food safety. Here, we employed a microbial functional genomic technology termed transposon sequencing (Tn-seq), leading to the identification of two genes involved in cell wall peptidoglycan biosynthesis (murF) and phosphate transport (lmo2248) that play key roles in lactic acid resistance (LAR) of L. monocytogenes. Deletion of lmo2248 significantly impaired the ability of LAR in L. monocytogenes, demonstrating the accuracy of the Tn-seq results. Transcriptome analysis revealed that 31.7% of the L. monocytogenes genes on the genome were differentially expressed under lactic acid (LA) treatment, in which genes involved in phosphate transport were influenced most significantly. These findings shed light on the LAR mechanisms of L. monocytogenes, which may contribute to the development of novel strategies against foodborne pathogens.IMPORTANCE Listeria monocytogenes is a Gram-positive foodborne pathogen with high lethality and strong stress resistance, and its strong acid tolerance leads to many foodborne illnesses occurring in low-pH foods. Lactic acid is a generally recognized as safe (GRAS) food additive approved for use by the FDA. However, the genetic determinants of lactic acid resistance in L. monocytogenes have not been fully identified. In this study, the lactic acid resistance determinants of L. monocytogenes were comprehensively identified by Tn-seq on a genome-wide scale. Two genes, murF (cell wall peptidoglycan biosynthesis) and lmo2248 (phosphate transport), were identified to play an important role in the lactic acid resistance. Moreover, genome-wide transcriptomic analysis showed that phosphotransferase system (PTS)-related genes play a key role at the transcriptional level. These findings contribute to a better understanding of the lactic acid resistance mechanism of L. monocytogenes and may provide unique targets for the development of other novel antimicrobial agents.
研究领域:
微生物学
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功能基因组学
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食品安全
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产品关联
DOI
PubMed
高影响因子
Microbiome
·
2025
·Vol. 13
·期 1
·1-17
·
IF 12.7
Liu Youhua,Liu Jiaqi,Ren Ruiti,Xin Zimeng,Luo Yaojun,Chen Yushi,Huang Chaoqun,Liu Yuxi,Yang Tongyudan,Wang Xinxia
Background Although short-term high-fat diet (S-HFD) and long-term high-fat diet (L-HFD) induce metabolic disorder, the underlying epigenetic mechanism is still unclear. Results Here, we found that both 4 days of S-HFD and 10 weeks of L-HFD increased mRNA m 6 A level in epididymal white adipose tissue (eWAT) and impaired metabolic health. Interestingly, S-HFD activated transposable elements (TEs), especially endogenous retroviruses (ERVs) in eWAT, while L-HFD activated long interspersed elements (LINEs). Subsequently, we demonstrated that both S-HFD and L-HFD increased m 6 A level of Ehmt2 and decreased EHMT2 protein expression and H3K9me2 level, accounting for activation of ERVs and LINEs. Overexpression of EHMT2 in eWAT or inhibition of ERVs and LINEs by antiviral therapy improved metabolic health under HFD feeding. Notably, we found that both short-term and long-term HFD feeding increased Fimicutes/Bacteroidota ratio and decreased the gut microbiome health index. Fecal microbiota transplantation (FMT) experiments demonstrated that gut microbiota from S-HFD and L-HFD was responsible for increased m 6 A level in eWAT, resulting in glucose intolerance and insulin insensitivity. Furthermore, we identified that both S-HFD and L-HFD increased the abundance of the gut microbial metabolite homogentisic acid (HGA), and HGA level was positively correlated with unclassified_f__Lachnospiraceae which was both increased in S-HFD and L-HFD feeding mice. Administration of HGA increased the m 6 A level of Ehmt2 and decreased the EHMT2 protein expression and H3K9me2 level in eWAT, leading to metabolic disorder in mice. Conclusions Together, this study reveals a novel mechanism that S-HFD and L-HFD induce metabolism disorder through gut microbiota-HGA-m 6 A- Ehmt2 -ERV/LINE signaling. These findings may provide a novel insight for prevention and treatment of metabolism disorder upon short-term or long-term dietary fat intake.
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研究领域:
分子生物学
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营养学
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微生物学
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产品关联
DOI
PubMed
高影响因子
STAR Protocols
·
2022
·
IF 0
Jiwen Yang,Minjie Hu,Yongyu Wang
Summary In human pluripotent stem cells (hPSCs), traditional approaches for gene overexpression have low efficiency and are often laborious. Here, we provide a relatively simple protocol for gene overexpression with the Dox-inducible PiggyBac transposon system. We detail the steps for overexpression of FLI1 and/or YAP in H1 embryonic stem cells (H1 ESCs) as an example. Our protocol can be applied to any gene of interest in a variety of hPSCs. For complete details on the use and execution of this protocol, please refer to Quan et al. (2021) .
研究领域:
干细胞生物学
·
分子生物学
·
基因工程
✓ 已验证
DOI
PubMed
ENVIRONMENTAL MICROBIOLOGY
·
2021
·Vol. 23
·期 6
·3265-3273
·
IF 5.491
Mingliang Zhang,Yijun Ren,Shilong Du,Yidong Zhou,Wankui Jiang,Zhijian Ke,Mingli Jiang,Jiguo Qiu,Jian He,Qing Hong
Summary Pymetrozine is a synthetic pesticide that can be utilized as the sole carbon source by Pseudomonas sp. strain BYT-1. However, the genes involved in the degradation of pymetrozine remain unknown. We used transposon mutagenesis to create a mutant that unable to hydrolyze pymetrozine. The transposon interrupted the gene pyzH , which was cloned by self-formed adaptor PCR. PyzH hydrolyzed the C=N double bond of pymetrozine to produce 4-amino-6-methyl-4,5-dihydro-2 H -[1,2,4]triazin-3-one (AMDT) and nicotinaldehyde; the latter inhibits PyzH activity. PyzH can completely hydrolyze pymetrozine in the presence of dehydrogenase ORF6, which can convert nicotinaldehyde into nicotinic acid and relieve the inhibition. H 2 18 O-labeling experiments showed that the oxygen atom of nicotinaldehyde came from water instead of oxygen. PyzH homologous genes were also found in other soil isolates able to degrade pymetrozine.
研究领域:
微生物学
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环境科学
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生物化学
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分子生物学
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产品关联
DOI
PubMed
高影响因子
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
·
2016
·Vol. 82
·期 2
·
IF 3.823
Hong-Jun Chao,Yan-Fei Chen,Ti Fang,Ying Xu,Wei E. Huang,Ning-Yi Zhou
In addition to growing on p-cresol, Pseudomonas putida NCIMB 9866 is the only reported strain capable of aerobically growing on 2,4-xylenol, which is listed as a priority pollutant by the U.S. Environmental Protection Agency. Several enzymes involved in the oxidation of the para-methyl group, as well as the corresponding genes, have previously been reported. The enzyme catalyzing oxidation of the catabolic intermediate 4-hydroxyisophthalate to the ring cleavage substrate protocatechuate was also purified from strain NCIMB 9866, but its genetic determinant is still unavailable. In this study, the gene hipH, encoding 4-hydroxyisophthalate hydroxylase, from strain NCIMB 9866 was cloned by transposon mutagenesis. Purified recombinant HipH-His6 was found to be a dimer protein with a molecular mass of approximately 110 kDa. HipH-His6 catalyzed the hydroxylation of 4-hydroxyisophthalate to protocatechuate with a specific activity of 1.54 U mg−1 and showed apparent Km values of 11.40 ± 3.05 μM for 4-hydroxyisophthalate with NADPH and 11.23 ± 2.43 μM with NADH and similar Km values for NADPH and NADH (64.31 ± 13.16 and 72.76 ± 12.06 μM, respectively). The identity of protocatechuate generated from 4-hydroxyisophthalate hydroxylation by HipH-His6 has also been confirmed by high-performance liquid chromatography and mass spectrometry. Gene transcriptional analysis, gene knockout, and complementation indicated that hipH is essential for 2,4-xylenol catabolism but not for p-cresol catabolism in this strain. This fills a gap in our understanding of the gene that encodes a critical step in 2,4-xylenol catabolism and also provides another example of biochemical and genetic diversity of microbial catabolism of structurally similar compounds.
研究领域:
微生物学
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环境科学
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生物化学
·
遗传学
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DOI
PubMed
高影响因子
CELL
·
2025
·
IF 42.5
Ziqiang Zhou,Shicong Zhu,Yaqiang Hong,Guangpu Jin,Rui Ma,Fan Lin,Yiyang Zhang,Hsiang-Ying Lee,Nian Liu
Discrete genomic units can recombine into composite transposons that transcribe and transpose as single units, but their regulation and function are not fully understood. We report that composite transposons harbor bivalent histone marks, with activating and repressive marks in distinct regions. Genome-wide CRISPR-Cas9 screening, using a reporter driven by the hominid-specific composite transposon SVA (SINE [short interspersed nuclear element]-VNTR [variable number of tandem repeats]-Alu) in human cells, identified diverse genes that modify bivalent histone marks to regulate SVA transcription. SVA transcripts are critical for SVA’s cis -regulatory function in selectively contacting and activating long-range gene expression. Remarkably, a subset of bivalent SVAs is activated during erythropoiesis to boost multiple erythroid gene expression, and knocking down these SVAs leads to deficient erythropoiesis. The RNA-dependent cis -regulatory function of SVA activates genes for myelopoiesis and can contribute to aging-associated myeloid-biased hematopoiesis. These results reveal that the cis -regulatory functions of composite transposons are bivalently regulated to control cell fate transitions in development and aging.
研究领域:
分子生物学
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遗传学
·
表观遗传学
·
发育生物学
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细胞生物学
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血液学
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衰老研究
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产品关联
DOI
PubMed
高影响因子
Crop Journal
·
2024
·
IF 6
Yue Lu,Ahmed Gharib,Rujia Chen,Hanyao Wang,Tianyun Tao,Zhihao Zuo,Qing Bu,Yanze Su,Yaoqing Li,Yanmo Luo,Hamdi F. El-Mowafi,Zhichao Wang,Qianfeng Huang,Shuting Wang,Yang Xu,Pengcheng Li,Chenwu Xu,Zefeng Yang
In a study of DNA methylation changes in melatonin-deficient rice mutants, mutant plants showed premature leaf senescence during grain-filling and reduced grain yield. Melatonin deficiency led to transcriptional reprogramming, especially of genes involved in chlorophyll and carbon metabolism, redox regulation, and transcriptional regulation, during dark-induced leaf senescence. Hypomethylation of mCG and mCHG in the melatonin-deficient rice mutants was associated with the expression change of both protein-coding genes and transposable element-related genes. Changes in gene expression and DNA methylation in the melatonin-deficient mutants were compensated by exogenous application of melatonin. A decreased S-adenosyl-L-methionine level may have contributed to the DNA methylation variations in rice mutants of melatonin deficiency under dark conditions.
研究领域:
植物学
·
遗传学
·
植物生理学
·
分子生物学
✓ 已验证
产品关联
DOI
高影响因子
Cell Reports
·
2023
·
IF 8.8
Ting Zeng,Jie Yin,Ziwen Liu,Zhaoxing Li,Yu Zhang,Yang Lv,Mei-Ling Lu,Min Luo,Meirong Chen,Yibei Xiao
Summary The type V-K CRISPR-associated transposons (CASTs) allow RNA-guided DNA integration and have great potential as a programmable site-specific gene insertion tool. Although all core components have been independently characterized structurally, the mechanism of how the transposase TnsB associates with AAA+ ATPase TnsC and catalyzes donor DNA cleavage and integration remains ambiguous. In this study, we demonstrate that TniQ-dCas9 fusion can direct site-specific transposition by TnsB/TnsC in ShCAST. TnsB is a 3′-5′ exonuclease that specifically cleaves donor DNA at the end of the terminal repeats and integrates the left end prior to the right end. The nucleotide preference and the cleavage site of TnsB are markedly different from those of the well-documented MuA. We also find that TnsB/TnsC association is enhanced in a half-integration state. Overall, our results provide valuable insights into the mechanism and application expansion of CRISPR-mediated site-specific transposition by TnsB/TnsC.
研究领域:
分子生物学
·
基因工程
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CRISPR技术
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产品关联
DOI
PubMed
高影响因子
SCIENCE OF THE TOTAL ENVIRONMENT
·
2023
·
IF 9.8
Ligui Wu,Qiaofeng Wu,Jingcheng Xu,Lingling Rong,Xiaoli Yu,Chen Cai,Xiangfeng Huang,Xiaoming Zou
The effects of antibiotics on the proliferation of antibiotic resistant genes (ARGs) in WWTPs have drawn great attention in recent years. The effects of antibiotics on ARGs in the enhanced biological phosphorus removal (EBPR) system and its mechanisms, however, are still not well understood. In this study, EBPR systems were constructed using activated sludge to investigate the effects of ten commonly detected antibiotics in the environment on the proliferation of ARGs and the mechanisms involved. The results showed that the total abundance of ARGs increased to varying degrees with the addition of different antibiotics (0.05 mmol/L), and the top 30 ARGs increased by 271.1 % to 370.0 %. Mobile genetic elements (MGEs), functional modules, and the bacteria community were consistently related to the changes in ARGs. Refractory antibiotics, in particular, have a stronger promoting effect on transduction in the EBPR system. The insertion sequence common region (ISCR) and transposon (Tnp) were identified as crucial factors in the proliferation of ARGs. Moreover, the risk of polyphosphate accumulating organisms (PAOs) carrying ARGs in the presence of antibiotics should not be ignored. Our findings emphasize the potential efficacy of employing strategies that target the reduction of MGEs, regulation of cellular communication, and management of microbial communities to effectively mitigate the risks associated with ARGs.
研究领域:
环境工程
·
微生物学
·
污水处理
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遗传学
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产品关联
DOI
PubMed
高影响因子
危险品化学品经营许可证（带存储）