A major mechanism in the regulation of gene expression in eukaryotic system is silencing by siRNA/miRNAs. The Yuan lab has determined the structures of many proteins components of the RISC protein machinery by x-ray crystallography and NMR spectroscopy. These structural approaches are now being applied with cyroelectron microscopy to elucidate the structure of the holoenzyme complex and other aspects of the RNAi mechanism.
CRISPR-mediated gene regulation has been considered as an important host-defense mechanism against foreign element invasion in prokaryotic system. The Yuan lab has determined the structures of many proteins components of CRISPR super-complexes by x-ray crystallography and Cryo-EM. Currently, the Yuan’s group is in the progress to overexpress and assemble dozens of CRISPR proteins and crRNAs to mimic the assembly processes of Cascade-CMR-CSM formation.
In addition, The Yuan lab has developed robust structure-based high-throughput platforms to make super enzymes and super rice traits by the combination of structural biology, protein engineering, genome editing and gene manipulations in model genetic systems.
Our group works on two related research topics: 1) Small RNA processing mechanisms and 2) Host-Pathogen interactions by the combinations of X-ray, NMR, Cryo-EM with genetic tools.
Small RNA processing mechanisms
Small RNA plays significant roles for gene regulations both in eukaryotic and prokaryotic systems. Currently we are focusing on several large protein-RNA complexes involved in this pathway. We are focusing on the structural characterization of holo-RISC in Arabidopsis, human systems and CRISPR processing machineries in bacterial systems by the combination of proteomics, biophysics and genetics tools. Such efforts would eventually open a new avenue to understand the small RNA processing mechanisms in vitro and in vivo.
In addition to eukaryotic and prokaryotic systems, virus is another living species. Many viruses are harmful to plants, animals and human. Our current research focuses are on virus structure determination, screening of neutralization antibodies and vaccine development by the combination of structural biology and protein engineering. We also plan to use high-resolution bioimaging tools to directly visualize the virus infection process at single molecular level. Such efforts will open a new avenue to understand the host-pathogen interaction and provide new strategy to fight against virus infection.
Small RNA mechanism
Guo W, Liew JY, Yuan YA. (2014) Structural insights into the arms race between host and virus along RNA silencing pathways in Arabidopsis thaliana. Biol Rev Camb Philos Soc. 89(2):337-55.
Fu Q, Yuan YA. (2013) Structural insights into RISC assembly facilitated by dsRNA-binding domains of human RNA helicase A (DHX9). Nucleic Acids Res. 41(5):3457-70.
Machida S, Yuan YA. (2013) Crystal Structure of Arabidopsis thaliana Dawdle Forkhead-Associated Domain reveals a conserved phospho-threonine recognition cleft for Dicer-like1 binding. Mol Plant. 6(4):1290-300.
Zha X, Xia Q, Yuan YA. (2012) Structural insights into small RNA sorting and mRNA target binding by Arabidopsis Argonaute Mid domains. FEBS Lett. 586(19):3200-7.
Machida S, Chen HY, Yuan YA. (2011) Molecular insights into miRNA processing by Arabidopsis thaliana SERRATE. Nucleic Acids Res. 39(17):7828-36.
Yang X, Tan SH, Teh YJ, Yuan YA. (2011) Structural implications into dsRNA binding and RNAi suppression by Rice Hoja Blanca Tenuivirus NS3. RNA 17(5):903-11.
Wang M, Soyano T, Machida S, Yang JY, Jung C, Chua NH, Yuan YA. (2011) Molecular insights into plant cell proliferation disturbance by Agrobacterium protein 6b. Genes Dev. 25(1):64-76.
Qin H, Chen F, Huan X, Machida S, Song J, Yuan YA. (2010) Structure of Arabidopsis thaliana DCL4 DUF283 domain reveals a non-canonical double-stranded RNA-binding fold for protein-protein interaction. RNA 16, 474-481.
Yang SW, Chen HY, Yang J, Machida S, Chua NH, Yuan YA. (2010) Structure of Arabidopsis HYPONASTIC LEAVES1 and its molecular implications for miRNA processing. Structure 18, 594-605.
Yang J, Yuan YA. (2009) A structural perspective of the protein-RNA interactions involved in virus-induced RNA silencing and its suppression. Biochim. Biophys. Acta. 1789, 642-652.
Chen HY, Yang J, Lin C, Yuan YA. (2008) Structural basis for RNA-silencing suppression by Tomato aspermy virus protein 2b. EMBO Rep. 9(8):754-60.
Structure based super enzyme design
Yin B, Cui D, Zhang L, Jiang S, Machida S, Yuan YA*, Wei D*. (2014) Structural insights into substrate and coenzyme preference by SDR family protein Gox2253 from Gluconobater oxydans. Proteins. 2014 May 13. doi: 10.1002/prot.24603. (*-co-corresponding authors)
Liu X, Wang C, Zhang L, Yao Z, Cui D, Wu L, Lin J, Yuan YA*, Wei D*. (2014) Structural and mutational studies on an aldo-keto reductase AKR5C3 from Gluconobacter oxydans. Protein Sci. 2014 Aug 11. doi: 10.1002/pro.2531. (*-co-corresponding authors)
Zhang L, Gao B, Yuan Z, He X, Yuan YA, Zhang JZ, Wei D. (2014) Structure, mechanism, and enantioselectivity shifting of lipase LipK107 with a simple way. Biochim Biophys Acta. 1844(7):1183-92.
Zhang L, Tang X, Cui D, Yao Z, Gao B, Jiang S, Yin B, Yuan YA*, Wei D*. (2014) A method to rationally increase protein stability based on the charge-charge interaction, with application to lipase LipK107. Protein Sci. 23(1):110-6. (*-co-corresponding authors)
Cui D, Zhang L, Yao Z, Liu X, Lin J, Yuan YA*, Wei D*. (2013) Computational design of short-chain dehydrogenase Gox2181 for altered coenzyme specificity. J Biotechnol. 167(4):386-92. (*-co-corresponding authors)
Yuan Z, Yin B, Wei D*, Yuan YA*. (2013) Structural basis for cofactor and substrate selection by cyanobacterium succinic semialdehyde dehydrogenase. J Struct Biol. 182(2):125-35. (*-co-corresponding authors)
Liu X, Yuan Z, Yuan YA, Lin J, Wei D. (2011) Biochemical and structural analysis of Gox2181, a new member of the SDR superfamily from Gluconobacter oxydans. Biochem Biophys Res Commun. 415(2):410-5.
Hou Y, Li J, Li Y, Dong Z, Xia Q, Yuan YA. (2014) Crystal structure of Bombyx mori arylphorins reveals a 3:3 heterohexamer with multiple papain cleavage sites. Protein Sci. 23(6):735-46.
Gu Y, Cao F, Wang L, Hou W, Zhang J, Hew CL, Li S*, Yuan YA*, Xia N*. (2013) Structure of a Novel Shoulder-to-Shoulder p24 Dimer in Complex with the Broad-Spectrum Antibody A10F9 and Its Implication in Capsid Assembly. PLoS One. 8(4):e61314. (*-co-corresponding authors)
Hou Y, Xia Q, Yuan YA. (2012) Crystal structure of BmNPV ORF75 reveals a pseudo-dimer of sulfhydryl oxidase domains with a putative substrate binding pocket. J Gen Virol. 93(10):2142-51.
Zhang T, Cheng T, Wei L, Cai Y, Yeo AE, Han J, Yuan YA, Zhang J, Xia N. (2012) Efficient inhibition of HIV-1 replication by an artificial polycistronic miRNA construct. Virol J. 9:118.
Cheng A, Wong SM, Yuan YA. (2009) Structural basis for dsRNA recognition by NS1 protein of influenza A virus. Cell Res. 19(2):187-95.
Wu L, Xu D, Zhou L, Xie B, Yu L, Yang H, Huang L, Ye J, Deng H, Yuan YA, Chen S, Li P. (2014) Rab8a-AS160-MSS4 Regulatory Circuit Controls Lipid Droplet Fusion and Growth. Dev Cell. 30(4):378-93.
Sun Y, Wang C, Yuan YA, He CY. (2012) An intra-cellular membrane junction mediated by flagellum adhesion glycoproteins links flagellum biogenesis to cell morphogenesis in Trypanosoma brucei. J Cell Sci. 2012 Nov 23.
Li FJ, Shen Q, Wang C, Sun Y, Yuan YA, He CY. (2012) A role of autophagy in Trypanosoma brucei cell death. Cell Microbiol. 14(8):1242-56.
Chatterjee K, Blaby IK, Thiaville PC, Majumder M, Grosjean H, Yuan YA, Gupta R, de Crécy-Lagard V. (2012) The archaeal COG1901/DUF358 SPOUT-methyltransferase members, together with pseudouridine synthase Pus10, catalyze the formation of 1-methylpseudouridine at position 54 of tRNA. RNA. 18(3):421-33.
Chen HY, Yuan YA. (2010) Crystal structure of Mj1640/DUF358 protein reveals a putative SPOUT-class RNA methyltransferase. J Mol Cell Biol. 2(6):366-74.
Cheng A, Speir JA, Yuan YA, Johnson JE, Wong SM. (2009) Preliminary X-ray data analysis of crystalline hibiscus chlorotic ringspot virus. Acta Crystallogr Sect F Struct Biol Cryst Commun. 65(Pt 6):589-93.
Lin C, Yuan YA. (2008) Structural insights into histone H3 lysine 56 acetylation by Rtt109. Structure. 16(10):1503-10.