研究以产甲烷古菌为代表的厌氧微生物，系统解析其驱动地球碳循环的新途径与机制，在机理认知的基础上推动对产甲烷排放管控及生物能源开发提供理论依据和新技术方案；揭示古菌域中的新遗传及转录调控机制，建立原核生物中的遗传调控新理论，推动三域生命遗传机制进化及真核生物起源认知；开发厌氧微生物新基因编辑工具及功能元件，推动研究包括产甲烷古菌在内的厌氧微生物在环境修复、宿主健康及绿色生物制造中的开发应用。

[1] Yueting Liang #, Wen Qi #, Xiuzhu Dong, Jie Li *. Archaeal RNA Processing and Regulation: Expanding the Functional Landscape. Microbiol Mol Biol Rev. 2025  
[2] Jie Li*, #, Yueting Liang #, Xiuzhu Dong *. Post-transcriptional regulation in archaea. Trends Microbiol 2025. 2025 Mar 5:S0966-842X(25)00035-6.
[3] 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.
[4] 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. Microbial Cell Factories, 2024 Sep 4;23(1):239.
[5] 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.
[6] 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. (
[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.
[8] 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.
[9] Jie Li, Taiwo S. Akinyemi, Nana Shao, Can Chen, Xiuzhu Dong, Yuchen Liu, William B. Whitman*. Genetic and metabolic engineering of Methanococcus spp, Current Research in Biotechnology 5 (2023) 100115
[10] 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. (Research article)
[11] 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. (Research article)
[12] 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.
[13] 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.
[14] 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.
[15] 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.
[16] 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.
[17] 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.
[18] 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.
[19] 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.
[20] 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.
[21] 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.

[1] 国家自然科学基金重大项目子课题，32393974，古菌—真核生物细胞膜结构与能量生成的演化，2024.01-2028.12，125万，主持
[2] 国家自然科学基金面上项目，32270054，aCPSF1介导古菌转录终止的分子机制和新调控功能，2023.01-2026.12，54万，主持
[3] 国家重点研发计划项目子课题，2020YFA090681，“极端微生物合成生物学元件的挖掘与鉴定” ，2020.04-2025.03，125万，主持
[4] 国家重点研发计划项目子课题，2019YFA0905501，“活性污泥人工多细胞体系构建与应用” ，2020.01-2024.12，80万，主持
[5] 国家自然科学基金面上项目，31670049，古菌RNA加工流转关键酶生理生化功能及分子机制，2017.01-2020.12，62万，主持
[6] 中科院先导项目B子任务，新型基因编辑系统机制研究，2024.05-2028.04，150万，主持
[7] 国家重点实验室重任基金，厌氧菌基因编辑及合成生物学元件挖掘，2023.01-2027.12，25万，主持
[8] 技术开发合作项目，“协助植物抗冻耐寒生物肥料研发项目”，2022.01-2026.12，300万，主持
[9] 国家自然科学基金青年科学基金项目，31100035，竹节状甲烷鬃菌群感效应调控机制，2012.01-2014.12，23 万，主持