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代表性成果

代表性论文

长期聚焦极端厌氧菌—产甲烷古菌的遗传调控和环境适应机制的基础理论研究和分子元件挖掘开发，取得了系列原创性发现，推动了机理认知和厌氧菌元件及底盘开发，主要完成了相互关联的三方面工作：一、发现原核生物新转录调控模式，并揭示了其对重要生理过程的调控功能，为原核生物基因表达调控提供了新策略；二、发现新转录(后)调控因子并揭示其作用机制，开启了新领域；三、突破严格厌氧菌遗传操作技术壁垒，系统开发了极端厌氧菌分子元件和基因编辑工具，得到特色厌氧菌底盘，高效基因编辑工具及遗传/调控元件库，为提升产甲烷古菌在实际生产中的绿色应用奠定了重要基础。已发表论文近40篇，以第一兼(或)通讯作者在Trends Microbiol (2025)、Nat Chem Biol (2024)、Cell Host Microbe (2023)、Nucleic Acids Res (2017, 2020, 2023)、Metab Eng (2023)、eLife (2021)、Curr Res Biotechnol (2023)、Environ Microbiol (2021)、PLoS Genet (2019)、RNA Biol (2023, 2020a, 2020b)、Mol Microbiol(2017)等国际权威期刊上已发表高质量研究论文20余篇；在厌氧菌遗传适应和基因编辑领域的研究已达国际先进水平，具有很好的国际竞争力和影响力。

主要学术成果框架示意图

【#第一 / *通讯作者发表论文】

1.Jie Li*, #, Yueting Liang #, Xiuzhu Dong *. Post-transcriptional regulation in archaea. Trends Microbiol. 2025 Jul;33(7):765-781. doi: 10.1016/j.tim.2025.02.004. (IF₅: 17, Top 2.4%, Q1)

2.Xian Shu^#, Rui Wang^#, Zhihua Li^#, Qiong Xue^#, Jiajun Wang, Jingfang Liu, Feiyue Cheng, Chao Liu, Huiwei Zhao, Chunyi Hu, Jie Li*, Songying Ouyang*, Ming Li*, CRISPR-repressed toxin-antitoxin provides population-level immunity against diverse anti-CRISPR elements. Nat Chem Biol. 2025 Mar;21(3):337-347. doi: 10.1038/s41589-024-01693-3. (IF₅: 14.7, Top 3.4%, Q1)

3.Wenting Zhang, Deron Ren, Zhihua Li, Lei Yue, William B.Whitman, Xiuzhu Dong*, Jie Li*. Internal transcription termination widely regulates differential expression of operon-organized genes including ribosomal protein and RNA polymerase genes in an archaeon. Nucleic Acids Res.2023 Aug 25;51(15):7851-7867. (IF₅=16.1, Top 1.8%, Q1)

4.Chao Liu ^#, Rui Wang ^#, Jie Li ^#, Feiyue Cheng ^#, Xian Shu ^#, Huiwei Zhao, Qiong Xue, Haiying Yu, Aici Wu, Lingyun Wang, Sushu Hu, Yihan Zhang, Jun Yang, Hua Xiang*, Ming Li*. Widespread RNA-based cas regulation monitors crRNA abundance and anti-CRISPR proteins.Cell Host & Microbe. 2023 31(9):1481-1493. (IF₅= 22.1, Top 1.1%, Q1)

5.Lei Yue ^#, Jie Li^#^,*, Bing Zhang, Lei Qi, Zhihua Li, Fangqing Zhao, Lingyan Li, Xiaowei Zheng, Xiuzhu Dong*. The conserved ribonuclease aCPSF1 triggers genome-wide transcription termination of Archaea via a 3′-end cleavage mode. Nucleic Acids Res. 2020, Sep 25;48(17):9589-9605. (IF₅=16.1, Top 1.8%, Q1)

6.Lei Qi, Lei Yue, Deqin Feng, Fengxia Qi, Jie Li *, and Xiuzhu Dong*. Genome-wide mRNA processing in methanogenic archaea reveals post-transcriptional regulation of ribosomal protein synthesis, Nucleic Acids Res.2017, Jul 7;45(12):7285-7298. (IF₅=16.1, Top 1.8%, Q1)

7.Qing Xu, Qing Du, Jian Gao, Lei Chen, Xiuzhu Dong, Jie Li *. A robust genetic toolbox for fine-tuning gene expression in the CO2-Fixing methanogenic archaeon Methanococcus maripaludis. Metab Eng. 2023 Jul 24;79:130-145. (IF₅= 7.6, Top 9.5%, Q1)

8.Jie Li^#,*, Lei Yue ^#, Zhihua Li ^#, Wenting Zhang, Bing Zhang, Fangqing Zhao, Xiuzhu Dong^*. aCPSF1 cooperates with terminator U-tract to dictate archaeal transcription termination efficacy. eLife. 2021 Dec 29;10:e70464. (Top 7.1%, Q1)

9.Jie Li ^#,*, Bo Zhang^#, Liguang Zhou^#, Lei Qi, Lei Yue, Wenting Zhang, Huicai Cheng, William B Whitman*, Xiuzhu Dong*. The archaeal RNA chaperone TRAM0076 shapes the transcriptome and optimizes the growth of Methanococcus maripaludis. PLoS Genet. 2019 Aug 12;15(8):e1008328.

10.Du Qing^#, Yufei Wei^#, Liuyang Zhang^#, Derong Ren, Jian Gao, Xiuzhu Dong, Liping Bai*, Jie Li*. An improved CRISPR and CRISPR interference (CRISPRi) toolkit for engineering the model methanogenic archaeon Methanococcus maripaludis. Microb Cell Fact. 2024 Sep 4;23(1):239. doi: 10.1186/s12934-024-02492-0. (IF₅: 5.5, Q1)

11.Lei Qi, Huan Liu, Jian Gao, Kai Deng, Xiaoyan Wang, Xiuzhu Dong, Jie Li *. Endonucleolytic processing plays a critical role in the maturation of ribosomal RNA in Methanococcus maripaludis. RNA Biol. 2023 Jan;20(1):760-773.

12.Jie Li^#,*, Yanjie Hou^#, Xien Gu^#, Lei Yue, Lu Guo, Defeng Li*, Xiuzhu Dong*. A newly identified duplex RNA unwinding activity of archaeal RNase J depends on processive exoribonucleolysis coupled steric occlusion by its structural archaeal loops. RNA Biol. 2020b, Oct;17(10):1480-1491.

13.Jie Li, Taiwo S. Akinyemi, Nana Shao, Can Chen, Xiuzhu Dong, Yuchen Liu, William B. Whitman*. Genetic and metabolic engineering of Methanococcus spp, CURR RES BIOTECHNOL, 5 (2023) 100115

14.Jie Li ^#,*, Liuyang Zhang ^#, Qing Xu ^#, Wenting Zhang, Zhihua Li, Lei Chen, Xiuzhu Dong^*. CRISPR-Cas9 toolkit for genome editing in an autotrophic CO₂ fixing methanogenic archaeon. Microbiol Spectr. 2022. Aug 31;10(4):e0116522.

15.Jia Jia^#, Jie Li ^#,*, Lei Qi, Lingyan Li, Lei Yue, Xiuzhu Dong*. Post-transcriptional regulation is involved in the cold active methanol-based methanogenic pathway of a psychrophilic methanogen, Environ Microbiol. 2021 Jul;23(7):3773-3788. doi: 10.1111/1462-2920.15420.

16.Jie Li ^#, Xiaowei Zheng^#, Lingyan Li, Shengjie Zhang, Mifang Ren, Li Huang^*, Xiuzhu Dong^*. The Archaeal Transcription Termination Factor aCPSF1 Is a Robust Phylogenetic Marker for Archaeal Taxonomy. Microbiol Spectr. 2021 Dec 22;9(3):e0153921.

17.Xiaoyan Wang^#, Xien Gu^#, Jie Li^#,*, Lei Yue, Defeng Li, Xiuzhu Dong*. Characterization of the Methanomicrobial Archaeal RNase Zs for Processing the CCA-Containing tRNA Precursors. Front Microbiol. 2020, Aug 25;11:1851.

18.Lei Qi^#,, Jie Li^#,*, Jia Jia, Lei Yue, Xiuzhu Dong*. Comprehensive analysis of the pre-ribosomal RNA maturation pathway in a methanoarchaeon exposes the conserved circularization and linearization mode in archaea. RNA Biol. 2020a, Oct;17(10):1427-1441.

19.Bo Zhang, Lei Yue, Liguang Zhou, Lei Qi, Jie Li *, Xiuzhu Dong*. The conserved TRAM domain functions as the archaeal cold shock protein via RNA chaperone activity, Front Microbiol. 2017, Aug 22;8:1597.

20.Xin Zheng^#, Na Feng^#, Defeng Li*, Xiuzhu Dong* and Jie Li ^#,*. New molecular insights into an archaeal RNase J reveal a conserved processive exoribonucleolysis mechanism of the RNase J family, Mol Microbiol. 2017, Nov;106(3):351-366.

21.Jie Li ^#, Lei Qi^#, Yang Guo, Lei Yue, Yanping Li, Weizhen Ge, Jun Wu, Wenyuan Shi, Xiuzhu Dong*. Global mapping transcriptional start sites revealed both transcriptional and post-transcriptional regulation of cold adaptation in the methanogenic archaeon Methanolobus psychrophilus, Sci Rep. 2015 Mar 18;5:9209.

22.Jie Li ^#, Xin Zheng^#, Xiaopeng Guo, Lei Qi, Xiuzhu Dong*. Characterization of an archaeal two-component system that regulates methanogenesis in Methanosaeta harundinacea, PLoS One. 2014 Apr 18;9(4):e95502.

23.Jie Li, Jingfang Liu, Jian Zhou, Hua Xiang*. Functional evaluation of four putative DNA-binding regions in Thermoanaerobacter tengcongensis reverse gyrase, Extremophiles. 2011 Mar;15(2):281-91.

24.Jie Li, Jingfang Liu, Ligang Zhou, Huadong Pei, Jian Zhou, Hua Xiang*. Two distantly homologous DnaG primases from Thermoanaerobacter tengcongensis exhibit distinct initiation specificities and priming activities, J Bacteriol. 2010 Jun;192(11):2670-81.

研究中代表性图片