ACS Infectious Diseases
·
2025
·
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
·
药理学
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DOI
PubMed
高影响因子
MOLECULAR CELL
·
2021
·
IF 17.97
Zihao Dai,Haining Liu,Junbin Liao,Cheng Huang,Xiaoxue Ren,Wanjie Zhu,Shenghua Zhu,Baogang Peng,Shaoqiang Li,Jiaming Lai,Lijian Liang,Lixia Xu,Sui Peng,Shuibin Lin,Ming Kuang
Summary Cancer cells selectively promote translation of specific oncogenic transcripts to facilitate cancer survival and progression, but the underlying mechanisms are poorly understood. Here, we find that N 7 -methylguanosine (m 7 G) tRNA modification and its methyltransferase complex components, METTL1 and WDR4, are significantly upregulated in intrahepatic cholangiocarcinoma (ICC) and associated with poor prognosis. We further reveal the critical role of METTL1/WDR4 in promoting ICC cell survival and progression using loss- and gain-of-function assays in vitro and in vivo . Mechanistically, m 7 G tRNA modification selectively regulates the translation of oncogenic transcripts, including cell-cycle and epidermal growth factor receptor (EGFR) pathway genes, in m 7 G-tRNA-decoded codon-frequency-dependent mechanisms. Moreover, using overexpression and knockout mouse models, we demonstrate the crucial oncogenic function of Mettl1-mediated m 7 G tRNA modification in promoting ICC tumorigenesis and progression in vivo . Our study uncovers the important physiological function and mechanism of METTL1-mediated m 7 G tRNA modification in the regulation of oncogenic mRNA translation and cancer progression.
研究领域:
癌症生物学
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分子生物学
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转化医学
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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
·
酶学
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DOI
PubMed
高影响因子
DEVELOPMENTAL CELL
·
2024
·
IF 10.7
Rongrong He,Ziwei Lv,Yinan Li,Shuchao Ren,Jiaqi Cao,Jun Zhu,Xinrong Zhang,Huimin Wu,Lihao Wan,Ji Tang,Shutong Xu,Xiao-Lin Chen,Zhipeng Zhou
Ergosterols are essential components of fungal plasma membranes. Inhibitors targeting ergosterol biosynthesis (ERG) genes are critical for controlling fungal pathogens, including Magnaporthe oryzae , the fungus that causes rice blast. However, the translational mechanisms governing ERG gene expression remain largely unexplored. Here, we show that the Trm6/Trm61 complex catalyzes dynamic N 1 -methyladenosine at position 58 (m 1 A58) in 51 transfer RNAs (tRNAs) of M. oryzae , significantly influencing translation at both the initiation and elongation stages. Notably, tRNA m 1 A58 promotes elongation speed at most cognate codons mainly by enhancing eEF1-tRNA binding rather than affecting tRNA abundance or charging. The absence of m 1 A58 leads to substantial decreases in the translation of ERG genes, ergosterol production, and, consequently, fungal virulence. Simultaneously targeting the Trm6/Trm61 complex and the ergosterol biosynthesis pathway markedly improves rice blast control. Our findings demonstrate an important role of m 1 A58-mediated translational regulation in ergosterol production and fungal infection, offering a potential strategy for fungicide development.
研究领域:
分子生物学
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微生物学
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植物病理学
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产品关联
DOI
PubMed
高影响因子
Journal of Translational Medicine
·
2024
·Vol. 22
·期 1
·1-17
·
IF 6.1
Mo Dongping,Tang Xun,Ma Yuyan,Chen Dayu,Xu Weiguo,Jiang Ning,Zheng Junyu,Yan Feng
Background Drug resistance, including Adriamycin-based therapeutic resistance, remains a challenge in breast cancer (BC) treatment. Studies have revealed that macrophages could play a pivotal role in mediating the chemoresistance of cancer cells. Accumulating evidence suggests that tRNA-Derived small RNAs (tDRs) are associated the physiological and pathological processes in multiple cancers. However, the underlying mechanisms of tDRs on chemoresistance of BC in tumor-associated macrophages remain largely unknown.Methods The high-throughput sequencing technique was used to screen tDRs expression profile in BC cells. Gain- and loss-of-function experiments and xenograft models were performed to verify the biological function of 3′tRF-Ala-AGC in BC cells. The CIBERSORT algorithm was used to investigate immune cell infiltration in BC tissues. To explore the role of 3′tRF-Ala-AGC in macrophages, M2 macrophages transfected with 3′tRF-Ala-AGC mimic or inhibitor were co-cultured with BC cells. Effects on Nuclear factor-κb (NF-κb) pathway were investigated by NF-κb nuclear translocation assay and western blot analysis. RNA pull-down assay was performed to identify 3′tRF-Ala-AGC interacting proteins.Results A 3′tRF fragment of 3′tRF-AlaAGC was screened, which is significantly overexpressed in BC specimens and Adriamycin-resistant cells. 3′tRF-AlaAGC could promote cell malignant activity and facilitate M2 polarization of macrophages in vitro and in vivo. Higher expression of M2 macrophages were more likely to have lymph node metastasis and deeper invasion in BC patients. Mechanistically, 3′tRF-AlaAGC binds Type 1-associated death domain protein (TRADD) in BC cells, and suppression of TRADD partially abolished the enhanced effect of 3′tRF-AlaAGC mimic on phenotype of M2. The NF-κb signaling pathway was activated in BC cells co-cultured with M2 macrophages transfected with 3′tRF-AlaAGC mimic.Conclusion s3′tRF-AlaAGC might modulate macrophage polarization via binding to TRADD and increase the effect of M2 on promoting the chemoresistance in BC cells through NF-κb signaling pathway.
研究领域:
肿瘤学
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免疫学
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分子生物学
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癌症生物学
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DOI
PubMed
高影响因子
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
·
2024
·Vol. 121
·期 43
·e2407579121
·
IF 9.4
Xiaoge Liang,Dian Chen,Aimin Su,Yu Liu
Ribonuclease P (RNase P) plays a vital role in the maturation of tRNA across bacteria, archaea, and eukaryotes. However, how RNase P assembles various components to achieve specific cleavage of precursor tRNA (pre-tRNA) in different organisms remains elusive. In this study, we employed single-molecule fluorescence resonance energy transfer to probe the dynamics of RNase P from E. coli (Escherichia coli) and Mja (Methanocaldococcus jannaschii) during pre-tRNA cleavage by incorporating five Cy3-Cy5 pairs into pre-tRNA and RNase P. Our results revealed significant differences in the assembly and catalytic mechanisms of RNase P between E. coli and Mja at both the RNA and protein levels. Specifically, the RNA of E. coli RNase P (EcoRPR) can adopt an active conformation that is capable of binding and cleaving pre-tRNA with high specificity independently. The addition of the protein component of E. coli RNase P (RnpA) enhances and accelerates pre-tRNA cleavage efficiency by increasing and stabilizing the active conformation. In contrast, Mja RPR is unable to form the catalytically active conformation on its own, and at least four proteins are required to induce the correct folding of Mja RPR. Mutation experiments suggest that the functional deficiency of Mja RPR arises from the absence of the second structural layer, and proper intermolecular assembly is essential for Mja RNase P to be functional over a broad temperature range. We propose models to illustrate the distinct catalytic patterns and RNA–protein interactions of RNase P in these two organisms.
研究领域:
分子生物学
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生物化学
·
微生物学
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DOI
PubMed
高影响因子
PLANT PHYSIOLOGY
·
2023
·
IF 7.4
Li Yuanyuan,Gao Junping,Wang Ying,Cai Jun,Wu Dousheng,Wang Long,Pu Wenxuan,Yu Feng,Zhu Sirui
Transfer RNA (tRNA) can produce smaller RNA fragments called tRNA-derived fragments (tRFs). tRFs play critical roles in multiple cellular programs, although the functional mechanisms of tRFs remain largely unknown in plants. In this study, we examined the phenotype associated with 5′ tRF-Ala (tRF-Ala, produced from tRNA-Ala) overexpression and knockdown lines (tDR-Ala-OE and tDR-Ala-kd, respectively) and the mechanisms by which tRF-Ala affects mRNA levels in Arabidopsis (Arabidopsis thaliana). We investigated the candidate proteins associated with tRF-Ala by quantitative proteomics and confirmed the direct interaction between tRF-Ala and the splicing factor SERINE-ARGININE RICH PROTEIN 34 (SR34). A transcriptome sequencing analysis showed that 318 genes among all the genes (786) with substantial alternative splicing (AS) variance in tDR-Ala-OE lines are targets of SR34. tRF-Ala diminished the binding affinity between SR34 and its targets by direct competition for interaction with SR34. These findings reveal the critical roles of tRF-Ala in regulating mRNA levels and splicing.
研究领域:
植物生物学
·
分子遗传学
·
RNA生物学
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DOI
PubMed
高影响因子
BMC PLANT BIOLOGY
·
2025
·Vol. 25
·期 1
·1-17
·
IF 4.8
Deng Dehai,Qin Yichao,Lin Xiuying,Chu Meng,Lv Daizhu,Lin Huan
Background The oil palm ( Elaeis guineensis ) is a crucial agricultural commodity, yielding the highest oil output among oil-bearing crops. Despite its significance, productivity challenges persist due to genetic and environmental factors. This study breaks new ground by mapping tRNA modifications in oil palm, exploring their roles during fruit ripening, an area not extensively studied in non-model crops. Results Utilizing advanced RNA mass spectrometry techniques, we identified 48 distinct tRNA modifications across 88 sites, alongside 164 genes associated with tRNA modifying enzymes. This comprehensive mapping reveals the decreasing nature of most tRNA modifications during fruit development, except for adenosine 2’-O methylation (Am). It hints at a gradual weakening of protein translation quality control and highlights a unique role for Am during fruit ripening. Additionally, lipidomic analysis tracked 674 lipids in oil palm fruits, indicating a correlation between tRNA modifications and the accumulation of specific lipids. Conclusions This study mapped tRNA modifications in oil palm for the first time and showed the diversity of dynamic changes in tRNA modifications as the fruits develop.
研究领域:
植物学
·
分子生物学
·
农业科学
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DOI
PubMed
高影响因子
NUCLEIC ACIDS RESEARCH
·
2022
·Vol. 50
·期 17
·9858-9872
·
IF 19.16
You Xue-Jiao,Zhang Shan,Chen Juan-Juan,Tang Feng,He Jingang,Wang Jie,Qi Chu-Bo,Feng Yu-Qi,Yuan Bi-Feng
RNA molecules harbor diverse modifications that play important regulatory roles in a variety of biological processes. Over 150 modifications have been identified in RNA molecules. N6-methyladenosine (m6A) and 1-methyladenosine (m1A) are prevalent modifications occurring in various RNA species of mammals. Apart from the single methylation of adenosine (m6A and m1A), dual methylation modification occurring in the nucleobase of adenosine, such as N6,N6-dimethyladenosine (m6,6A), also has been reported to be present in RNA of mammals. Whether there are other forms of dual methylation modification occurring in the nucleobase of adenosine other than m6,6A remains elusive. Here, we reported the existence of a novel adenosine dual methylation modification, i.e. 1,N6-dimethyladenosine (m1,6A), in tRNAs of living organisms. We confirmed that m1,6A is located at position 58 of tRNAs and is prevalent in mammalian cells and tissues. The measured level of m1,6A ranged from 0.0049% to 0.047% in tRNAs. Furthermore, we demonstrated that TRMT6/61A could catalyze the formation of m1,6A in tRNAs and m1,6A could be demethylated by ALKBH3. Collectively, the discovery of m1,6A expands the diversity of RNA modifications and may elicit a new tRNA modification-mediated gene regulation pathway.
研究领域:
分子生物学
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表观遗传学
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生物化学
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产品关联
DOI
PubMed
高影响因子
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
·
2023
·Vol. 24
·期 6
·5999
·
IF 5.6
Xiaoxiao Sun,Suyuan Liu,Jiangxue Cai,Miaoxin Yang,Chenxuan Li,Meiling Tan,Bin He
Various studies have revealed the association of metabolic diseases with inflammation. Mitochondria are key organelles involved in metabolic regulation and important drivers of inflammation. However, it is uncertain whether the inhibition of mitochondrial protein translation results in the development of metabolic diseases, such that the metabolic benefits related to the inhibition of mitochondrial activity remain unclear. Mitochondrial methionyl-tRNA formyltransferase (Mtfmt) functions in the early stages of mitochondrial translation. In this study, we reveal that feeding with a high-fat diet led to the upregulation of Mtfmt in the livers of mice and that a negative correlation existed between hepaticMtfmtgene expression and fasting blood glucose levels. A knockout mouse model ofMtfmtwas generated to explore its possible role in metabolic diseases and its underlying molecular mechanisms. Homozygous knockout mice experienced embryonic lethality, but heterozygous knockout mice showed a global reduction in Mtfmt expression and activity. Moreover, heterozygous mice showed increased glucose tolerance and reduced inflammation, which effects were induced by the high-fat diet. The cellular assays showed thatMtfmtdeficiency reduced mitochondrial activity and the production of mitochondrial reactive oxygen species and blunted nuclear factor-κB activation, which, in turn, downregulated inflammation in macrophages. The results of this study indicate that targetingMtfmt-mediated mitochondrial protein translation to regulate inflammation might provide a potential therapeutic strategy for metabolic diseases.Keywords:Mitochondrial methionyl-tRNA formyltranse (Mtfmt);mitochondria;mitochondrial reactive oxygen species (mROS);metaflammation;metabolic disorder
研究领域:
代谢
·
炎症
·
分子生物学
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遗传学
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DOI
PubMed
高影响因子
RESPIRATORY RESEARCH
·
2026
·
IF 5.7
Zhou Weitao,Dai Dan,Chen Yao,Han Xiao,Dong Xinran,Liao Yunfei,Chen Tong,Wang Huixian,He Chen,Lu Yilei,Zheng Chenxin,Zhou Yufeng,Qian Liling
Biallelic isoleucyl-tRNA synthetase 1 ( IARS1 ) variants are associated with an IARS1 -related phenotype characterized by growth retardation, intellectual disability, muscular hypotonia, infantile hepatopathy, and interstitial lung disease. This rare, early-onset disorder is often lethal. Although several variants have been identified in recent years, their pathogenicity and underlying molecular mechanisms remain poorly understood. In this study, we generated Iars1 Y148C/R444* compound heterozygous mice, which exhibited pulmonary alveolar proteinosis - like lesions, growth retardation, and muscular hypotonia. Lipid metabolomic profiling of these mice revealed dysregulation of cholesterol metabolism pathways. Furthermore, the Iars1 mutation increased surfactant deposition in alveolar macrophages by impairing lysosomal degradation and disrupting lysosome-autophagosome fusion. We also found that partial loss of IARS1 activity interfered with the post-translational processing of cathepsin Z by inhibiting its ubiquitin-mediated degradation. Importantly, exogenous expression of cathepsin Z improved surfactant clearance in macrophages with partial loss of Iars1 activity. Collectively, our findings demonstrate that partial loss of IARS1 activity induces lysosomal dysfunction in alveolar macrophages and promotes pulmonary surfactant accumulation in the alveoli, thereby contributing to the development of pulmonary alveolar proteinosis.
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DOI
高影响因子
JOURNAL OF CONTROLLED RELEASE
·
2024
·
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
·
分子生物学
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生物医学工程
·
组织工程
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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）