晁彦杰

发布部门：生物与医学工程学院 发布时间：2024-11-28

                        


个人简介

晁彦杰博士，任中国科学院上海免疫与感染研究所研究员、感染与核酸功能研究室主任、微生物RNA系统生物学研究组组长、博士生导师，现主持承担国家重点研发计划国际合作项目、国家重点研发计划十四五项目子课题、国家自然科学基金面上项目、中科院国合局重点项目、上海市自然科学基金等多10余个科研项目。在Nature, Molecular Cell, Nature Comms, EMBO J, EMBO Mol Medicine, Emerging Microbes & Infections, Trends in Microbiology等杂志发表30篇高影响力论文，受到Nature等杂志点评和F1000专家推荐，累计引用超过7000次。兼任EMBO J、NAR、mBio等30多家领域权威期刊的审稿专家和BMC Genomics等多家杂志编委，上海微生物学会基础微生物专业委员会委员，中国生物化学与分子生物学会永久会员。


研究方向

  1. 病原生物学与感染

  2. 非编码RNA与基因调控机制

  3. 新型疫苗研发


主持与承担主要项目情况

1.  国家重点研发计划政府间合作项目：病原细菌无帽小RNA 调控功能的系统研究，2022-2025，主持；

2.  国家重点研发计划十四五项目：重要感染中病原-共生微生物-宿主互作和干预，2022-2025，子课题负责人；

3.  国家自然科学基金面上项目：沙门菌小RNA CpxQ抑制鞭毛基因表达与细菌运动性的机制研究，2023-2026，主持；

4.  中国科学院国际伙伴计划-中日合作项目：病原细菌无帽小RNA的生成机制与功能研究，2023-2026，主持；

5.  上海市自然科学基金面上项目：沙门氏菌启动PhoPQ通路与SPI-2胞内寄生机制的时序调控机理，2021-2024，主持；

6. 中国科学院B类战略性先导科技专项：核糖核酸高效使能的基础与应用研究，2023-2028，参与；

7. 上海市科技重大专项：肠道稳态的生命调控机理及药物靶标结构与功能研究，2019-2022，参与。


发表论著情况

  1. K Wu#, X Lin#, Y Lu#, R Dong, H Jiang, SL Svensson, J Zheng, N Shen, A Camilli, Y Chao*. (2024) RNA interactome of hypervirulent Klebsiella pneumoniae reveals a small RNA inhibitor ofcapsular mucoviscosity and virulence. Nature Communications. In revision.

  2. J Zhang#, S Zhang#, W Zhou#, X Zhang#, G Li, L Li, X Lin, F Liu, Y Gao*, Z Chen*, Y Chao*, C Wang*. (2024) A widely conserved protein Rof inhibits transcription termination factor Rho and promotes Salmonella virulence program. Nature Communications. 15(1):3187.

  3. Y Chen, YX Goh, P Li, J Guan, Y Chao, H Qu*, HY Ou*, X Wang*. (2024). RES-Xre toxin-antitoxin locus knaAT maintains the stability of the virulence plasmid in Klebsiella pneumoniae.Emerging Microbes & Infections.13(1):2316814.

  4. J Li#, Z Chen#, Q Wang, L Du, Y Yang, F Guo, X Li, Y Chao, Y Ma*. (2024). Microbial and metabolic profiles unveil mutualistic microbe-microbe interaction in obesity-related colorectal cancer. Cell Reports Medicine. 5(3):101429

  5. F Liu#, Z Chen#, S Zhang, K Wu, C Bei, C Wang*, Y Chao*. (2023). In vivo RNA interactome profiling reveals 3’UTR-processed sRNA targeting a central regulatory hub. Nature Communications. 14(1):8106.

[Press coverage]

  1. Z Liu, J Guan, Z Chen, C Tai, Z Deng, Y Chao*, HY Ou*. (2023) CpxR promotes antibiotic resistance by activating plasmid-borne blaKPC expression and plasmid transfer in carbapenem-resistant Klebsiella pneumoniae. Emerging Microbes & Infections. 12(2):2256427

  2. Z Chen, W Jin, Y Chao*, Y Ma*. (2023) Decoding the microbiome: advances in genetic manipulation for gut bacteria. Trends in Microbiology. 31(11):1143-1161

  3. PK Grucela, F Tobias, S Uwe, Y Chao*, YE Zhang*. Ribose 5-phosphate: the key metabolite bridging the metabolisms of nucleotides and amino acids during stringent response in Escherichia coli. Microbial Cell. 10 (7), 141-144

  4. Jin WY, Guo JX, Zhang M, Teng LZ, Chao Y, Sansonetti PJ*, Gao YZ*. (2023)Absolute quantification of the microbiota spatial distribution in the murine large intestine.Innovation Life. 1(2):100030

  5. S Zhao, Q Xu, Y Cui, S Yao, S Jin, Q Zhang, Z Wen, H Ruan, X Liang, Y Chao, S Gong, P Sansonetti, K Wei*, H Tang*, Y Jiu*. (2023) Salmonella effector SopB reorganizes cytoskeletal vimentin to maintain replication vacuoles for efficient infection. Nature Communications. 14 (1), 478

  6. SL Svenson, Y Chao*. (2022) RNase III-CLASH brings bacterial RNA networks into focus. Trends in Microbiology. 30 (12):1125-1127

  7. Zhao Y, Yuan Z, Wang S, Wang H, Chao Y, Sederoff RR, Sederoff H, Yan H, Pan J, Peng M, Wu D, Borriss R, Niu B*. (2022) Gene sdaB Is Involved in the Nematocidal Activity of Enterobacter ludwigii AA4 Against the Pine Wood Nematode Bursaphelenchus xylophilus. Front Microbiol. 13:870519.

  8. Dong X#, Chao Y#, Zhou Y, Zhou R, Zhang W, Fischetti VA, Wang X, Feng Y*, Li J*. (2021) The global emergence of a novel Streptococcus suis clade associated with human infections. EMBO Mol Medicine. 13(7):e13810.

[Highlighted by Nature]

  1. Islam MS, Bandyra KJ, Chao Y, Vogel J, Luisi BF*. (2021) RNase E endonuclease activity and its inhibition by pseudouridine. RNA. 27(11):1339-1352.

  2. Li L, Chao Y*. (2020) sPepFinder expedites genome-wide identification of small proteins in bacteria. BioRxiv. doi: 10.1101/2020.05.05.079178.

  3. Wang C*, Chao Y, Matera G, Gao Q, Vogel J*. (2020) The conserved 3′ UTR-derived small RNA NarS mediates mRNA crossregulation during nitrate respiration. Nucleic Acids Research. 48 (4), 2126-2143.

  4. Li L, Förstner KU, Chao Y*. (2018) Computational analysis of RNA-protein interactions via deep sequencing. Methods in Molecular Biology. 1751:171-182.

  5. Chao Y, Li L, Girodat D, Förstner KU, Said N, Corcoran C, Smiga M, Papenfort K, Reinhardt R, Wieden HJ, Luisi BF, Vogel J*. (2017) In vivo cleavage map illuminates the central role of RNase E in coding and non-coding RNA pathways. Molecular Cell. 65(1):39-51.

[Previewed in Mol Cell] [Recommendation by F1000prime]

  1. Chao Y, Vogel J*. (2016) A 3’ UTR-derived small RNA provides the regulatory noncoding arm of the inner membrane stress response. Molecular Cell. 61(3):352-63.

  2. Westermann AJ, Förstner KU, Amman F, Barquist L, Chao Y, Schulte LN, Müller L, Reinhardt R, Stadler PF, Vogel J*. (2016) Dual RNA-seq unveils noncoding RNA functions in host–pathogen interactions. Nature. 529(7587):496-501.

[Commentary in Nature] [Highlighted in Nat. Rev. Genet.][Recommendation by F1000] [Press coverage]

  1. Saadeh B, Caswell CC, Chao Y, Berta P, Wattam AR, Roop II M, O'Callaghan D*. (2016) Transcriptome-wide identification of Hfq-associated RNAs in Brucella suis by deep sequencing. J Bacteriol. 198(3):427-435.

  2. Fan B*, Li L#, Chao Y#, Förstner K, Vogel J, Borriss R, Wu XQ*. (2015) dRNA-seq reveals genomewide TSSs and noncoding RNAs of plant beneficial rhizobacterium Bacillus amyloliquefaciens FZB42. PLoS ONE. 10(11): e0142002.

  3. Miyakoshi M, Chao Y, Vogel J*. (2015) Cross talk between ABC transporter mRNAs via a target mRNA-derived sponge of the GcvB small RNA. EMBO J. 34:1478-1492.

[Previewed in EMBO J]

  1. Miyakoshi M, Chao Y, Vogel J*. (2015) Regulatory small RNAs from the 3' regions of bacterial mRNAs. Curr Opin Microbiol. 24:132-139.

  2. Caldelari I, Chao Y, Romby P*, Vogel J*. (2013) RNA-mediated regulation in pathogenic bacteria. Cold Spring Harb Perspect Med. 3:a010298.

  3. Papenfort K, Corcoran CP, Gupta SK, Miyakoshi M, Heidrich N, Chao Y, Fröhlich KS, Sharma CM, Ziebuhr W, Böhm A, and Vogel J*. (2013) Regulatory Mechanisms of Special Significance: Role of Small RNAs in Virulence Regulation. Regulation of Bacterial Virulence (eds. Vasil ML, Darwin AJ), ASM Press. pp: 493-527.

  4. Chao Y, Papenfort K, Reinhardt R, Sharma CM, Vogel J*. (2012) An atlas of Hfq-bound transcripts reveals 3' UTRs as a genomic reservoir of regulatory small RNAs. EMBO J. 31(20):4005-19.

[Previewed in EMBO J] [Multiple recommendations by F1000]

  1. Kröger C, Dillon SC, Cameron AD, Papenfort K, Sivasankaran SK, Hokamp K, Chao Y, Sittka A, Hébrard M, Händler K, Colgan A, Leekitcharoenphon P, Langridge GC,Lohan AJ, Loftus B, Lucchini S, Ussery DW, Dorman CJ, Thomson NR, Vogel J, Hinton JCD *. (2012) The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium. Proc Natl Acad Sci U S A. 109(20):E1277-86.

[Press coverage]

  1. Deltcheva E, Chylinski K#, Sharma CM#, Gonzales K, Chao Y, Pirzada ZA, Eckert MR, Vogel J, Charpentier E*. (2011) CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature. 471(7340):602-7.

[Previewed in Nature] [Multiple recommendations by F1000] [Press coverage][Kavli Prize Collection][2020 Nobel Prize in Chemistry]

  1. Chao Y, Vogel J*. (2010) The role of Hfq in bacterial pathogens. Curr Opin Microbiol. 13(1):24-33.

[Top 5 most cited articles in COM, 2011-2015]

  1. Sun Z#,*, Chao Y#, Zhang X, Zhang J, Li Y, Qiu Y, Liu Y, Nie L, Guo A, Li C*. (2008) Characterization of extensively drug-resistant Mycobacterium tuberculosis clinical isolates in China. J Clin Microbiol. 46:4075-7.

  2. Chen Y#, Chao Y#, Deng Q#, Liu T, Xiang J, Chen J, Zhou J, Zhan Z, Kuang Y, Cai H, Chen H, Guo A*. (2009) Potential challenges to the Stop TB Plan for humans in China; cattle maintain M. bovis and M. tuberculosis. Tuberculosis (Edinb). 89:95-100.

  3. Yan BF#, Chao YJ#, Chen Z, Tian KG, Wang CB, Lin XM, Chen HC, Guo AZ*. (2008) Serological survey of bovine herpesvirus type 1 infection in China. Vet Microbiol.  127:136-41.

  4. Xu Z#,*, Chao Y#, Si Y, Wang J, Jin M, Guo A, Qian P, Zhou R, Chen H*. (2008) The GTP binding sites interacted with RNA-dependent RNA polymerase of classical swine fever virus in de novo initiation. In Silico Biol. 8(1):21-32.   

  5. Han H, Wang F, Xiao Y, Ren Y, Chao Y, Guo A, Ye L*. (2007) Utility of mycobacterial interspersed repetitive unit typing for differentiating Mycobacterium tuberculosis isolates in Wuhan, China. J Med Microbiol. 56:1219-23.  



联系方式

Email：yjchao@siii.cas.cn 

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