ACS Infectious Diseases
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2025
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IF 3.8
Xingli Han,Zhiyong Liu,Biao Zhou,Yuanyuan Shi,H.M. Adnan Hameed,Yamin Gao,Cuiting Fang,Xiongfang Zhao,Linzhuan Wu,Xiaoli Xiong,Wei Yu,Bin Hong,Tianyu Zhang
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), represents a global health challenge, necessitating new treatments with distinct mechanisms of action (MOA) to combat drug resistance. Chuangxinmycin (CM), characterized by its indole-dihydrothiopyran heterocyclic skeleton, exhibits potent antibacterial activity both in vitro and in vivo, with a minimum inhibitory concentration (MIC) of 0.25 μg/mL against Mtb. However, the MOA of CM against Mtb has remained obscure. Through comprehensive genetic, chemical rescue, and protein-drug interaction studies, coupled with biochemical analyses, we reveal that CM selectively binds and inhibits tryptophanyl-tRNA synthetase (TrpRS) encoded by trpS, rather than anthranilate synthase (TrpE). Overexpression of trpS in Mtb results in a 128-fold increase in the MIC of CM, indicating a fundamental cause of resistance, whereas overexpression of trpE leads to modest resistance, suggesting a secondary effect. Conversely, knockdown of trpS or trpE enhances the susceptibility of Mtb to CM. Meanwhile, promoters of trpS in CM-resistant Mtb mutants exhibit increased activity compared to the wild type. Furthermore, drug–protein interaction and biochemical assays have confirmed that while CM effectively inhibits TrpRS, mutants of TrpE show decreased affinity for tryptophan. These results establish that CM exerts its anti-Mtb effects by interfering with the tryptophan-tRNA linkage essential for protein synthesis.
研究领域:
微生物学
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药理学
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DOI
PubMed
高影响因子
Nature Communications
·
2025
·Vol. 16
·期 1
·1-16
·
IF 15.7
Zhang Qiang,Chen Wanyi,Qin Ming,Wang Yuhao,Pu Zhongji,Ding Keyan,Liu Yuyue,Zhang Qunfeng,Li Dongfang,Li Xinjia,Zhao Yu,Yao Jianhua,Huang Lei,Wu Jianping,Yang Lirong,Chen Huajun,Yu Haoran
Traditional protein engineering methods, such as directed evolution, while effective, are often slow and labor-intensive. Advances in machine learning and automated biofoundry present new opportunities for optimizing these processes. This study devises a protein language model-enabled automatic evolution platform, a closed-loop system for automated protein engineering within the Design-Build-Test-Learn cycle. The protein language model ESM-2 makes zero-shot prediction of 96 variants to initiate the cycle. The biofoundry constructs and evaluates these variants, and feeds the results back to a multi-layer perceptron to train a fitness predictor, which then makes prediction of second round of 96 variants with improved fitness. With the tRNA synthetase as a model enzyme, four-rounds of evolution carried out within 10 days lead to mutants with enzyme activity improved by up to 2.4-fold. Our system significantly enhances the speed and accuracy of protein evolution, driving faster advancements in protein engineering for industrial applications.
研究领域:
生物信息学
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合成生物学
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产品关联
DOI
PubMed
高影响因子
CELL
·
2023
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IF 64.5
Qinqin Cui,Hongyun Bi,Zhanyun Lv,Qigui Wu,Jianfeng Hua,Bokai Gu,Chanjuan Huo,Mingmin Tang,Yanqin Chen,Chongjiu Chen,Sihan Chen,Xinrui Zhang,Zhangrui Wu,Zhengkai Lao,Nengyin Sheng,Chengyong Shen,Yongdeng Zhang,Zhi-Ying Wu,Zhigang Jin,Peiguo Yang,Huaqing Liu,Jinsong Li,Ge Bai
Summary Complex diseases often involve the interplay between genetic and environmental factors. Charcot-Marie-Tooth type 2 neuropathies (CMT2) are a group of genetically heterogeneous disorders, in which similar peripheral neuropathology is inexplicably caused by various mutated genes. Their possible molecular links remain elusive. Here, we found that upon environmental stress, many CMT2-causing mutant proteins adopt similar properties by entering stress granules (SGs), where they aberrantly interact with G3BP and integrate into SG pathways. For example, glycyl-tRNA synthetase (GlyRS) is translocated from the cytoplasm into SGs upon stress, where the mutant GlyRS perturbs the G3BP-centric SG network by aberrantly binding to G3BP. This disrupts SG-mediated stress responses, leading to increased stress vulnerability in motoneurons. Disrupting this aberrant interaction rescues SG abnormalities and alleviates motor deficits in CMT2D mice. These findings reveal a stress-dependent molecular link across diverse CMT2 mutants and provide a conceptual framework for understanding genetic heterogeneity in light of environmental stress.
研究领域:
神经病学
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分子生物学
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遗传学
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产品关联
DOI
PubMed
高影响因子
Advanced Science
·
2024
·
IF 14.3
Dingyuan Guo,Nan Li,Xiaoyan Zhang,Runxin Zhou,Jie He,Xiao-Ping Ding,Weixing Yu,Fuqiang Tong,Sibi Yin,Yu Wang,Xin Xu,Long Wang,Mingzhu Fan,Shan Feng,Ke Liu,Ke Tang,Zhuqing Ouyang,Yusong R Guo,Yugang Wang
N 6 -acetyl- L - lysine residue is abundant in dietary protein but little is known about its potential influences on the diet-consumers. Herein, it is reported that Lysyl-tRNA synthetase (KARS) mediates co-translational deposition of diet-derived N 6 -acetyl- L -lysine (AcK) in nascent proteins to contribute to the acetylome in cells. Acetylated dietary protein is a direct source of AcK that can widely and substantially regulate the acetylome in multiple organs of mice. By analyzing the mechanisms underlying AcK contributing to the acetylome in mammalian cells, it is found that KARS can utilize AcK as an alternative substrate to produce N 6 -acetyl- l -lysyl-tRNA. The crystal structure of KARS in complex with AcK at 2.26 Å resolution shows that AcK shares the same substrate-binding pocket as L -lysine, allowed by a sidechain flip of Tyr499. The generated N 6 -acetyl- L -lysyl-tRNA introduces AcK into growing nascent polypeptide and results in protein acetylation, including the regions buried inside folded proteins that are post-translational modification (PTM)-inaccessible and functionally important. This undocumented protein modification mechanism is inherently different from PTM and termed as co-translational modification (coTM). It is expected to extend the repertoire of acetylome and improve the understanding of protein modification mechanisms in cells.
研究领域:
分子生物学
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蛋白质组学
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细胞生物学
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营养科学
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产品关联
DOI
PubMed
高影响因子
BIOORGANIC CHEMISTRY
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2025
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IF 4.7
Bingjie Wang,Rui Shi,Wanqing Du,Jiaojiao Guo,Nihan He,Yinghong Zhu,Han Yu,Hongyu Lu,Liyuan Zhong,Xingli Li,Wen Zhou,Fei Yang,Xiangling Feng
The recurrence of drug-resistant and expensive treatment drugs are major causes of the low survival rate of multiple myeloma (MM) patients. Exploring a safe, effective, low-cost and novel drug treatment for MM is a promising strategy to relieve the burden of MM patients. In this study, we found that prodigiosin could inhibit MM cell proliferation and induce MM cell apoptosis, however, it had a lesser cytotoxic effect on normal B cells within the IC 50 range of MM cells. In addition, prodigiosin could inhibit the growth of xenograft MM cells in mice. Transcriptomics and targeted amino acid metabolomics confirmed that prodigiosin could regulate amino acid metabolism, and decrease in amino acid utilization by down-regulated aminoacyl tRNA synthetases expression, resulting in slower growth of MM. In conclusion, prodigiosin exerts anticancer effects on MM cells by interfering with the use of amino acids, indicating its potential novel therapeutic application in MM.
研究领域:
肿瘤学
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药理学
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生物化学
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分子生物学
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血液学
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癌症研究
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代谢
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细胞生物学
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产品关联
DOI
PubMed
高影响因子
Nature Communications
·
2025
·Vol. 16
·期 1
·1-17
·
IF 15.7
Zhang Qunfeng,Jiang Ling,Niu Yadan,Li Yujie,Chen Wanyi,Cheng Jingxi,Ding Haote,Chen Binbin,Liu Ke,Cao Jiawen,Wang Junli,Ye Shilin,Yang Lirong,Wu Jianping,Xu Gang,Lin Jianping,Yu Haoran
The pyrrolysyl-tRNA synthetase (PylRS) is widely used to incorporate noncanonical amino acids (ncAAs) into proteins. However, the yields of most ncAA-containing protein remain low due to the limited activity of PylRS variants. Here, we apply machine learning to engineer the tRNA-binding domain of PylRS. The FFT-PLSR model is first applied to explore pairwise combinations of 12 single mutations, generating a variant Com1-IFRS with an 11-fold increase in stop codon suppression (SCS) efficiency. Deep learning models ESM-1v, Mutcompute, and ProRefiner are then used to identify additional mutation sites. Applying FFT-PLSR on these sites yields a variant Com2-IFRS showing a 30.8-fold increase in SCS efficiency, and up to 7.8-fold improvement in the catalytic efficiency ( k cat / K m tRNA ). Transplanting these mutations into 7 PylRS-derived synthetases significantly improves the yields of proteins containing 6 types of ncAAs. This paper presents improved PylRS variants and a machine learning framework for optimizing the enzyme activity.
研究领域:
合成生物学
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分子生物学
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计算生物学
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蛋白质工程
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酶学
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DOI
PubMed
高影响因子
JOURNAL OF CONTROLLED RELEASE
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2024
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IF 10.5
Yu Sun,Xiuhua Zhang,Wanrong Hong,Yingfeng Qin,Yunan Man,Maolin He,Jin-Wen Liu,Jia Chen
Growth factor holds great promise for bone regeneration, and spatiotemporal control of their expressing through site-specific reactions is crucial but challenging for on-demand therapy. In this study, we present the development of a novel unnatural amino acids (UAAs)-triggered therapeutic switch (UATS) system, composed of an orthogonal aminoacyl-tRNA-synthase (aaRS)-tRNA pair and a bone morphogenetic protein 2 (BMP2) gene harboring premature stop codon, which enable in situ and on-demand initiation of the expression of BMP2. The resulting UATS system allowed specifically control of base expressing on the BMP2 mRNA that switched to the BMP2 protein with complete structure and function to facilitate bone regeneration. Our investigations showed that the UATS system exhibits remarkable attributes of rapid, sensitive, reversible, and sustained BMP2 expression both in vitro and in vivo settings. Moreover, the implantation of microencapsulated cells with UATS system is applied to a mouse femur defect model, demonstrating high effciency in controlled expressing of BMP2 protein and substantial repair of bone defect following oral administration of UAAs. Therefore, our findings underscore the great potential of UATS system for on-demand awakening of functional growth factor, thus offering promising prospects in the realm of regenerative medicine.
研究领域:
再生医学
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分子生物学
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生物医学工程
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组织工程
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产品关联
DOI
PubMed
高影响因子
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