NTUIMCB_Eng

Recent Research Topics

Study of RNA folding and structural dynamics at the single-molecule level.

Study of translation by ribosomes at the single-molecule level.

Laboratory: Single-Molecule Biology

We are interested in understanding the molecular mechanisms of translation, a process of protein synthesis catalyzed by ribosomes. In bacteria, the ribosome recognizes the Shine-Dalgarno (SD) sequence and AUG start codon of an mRNA to initiate translation. The ribosomal binding site (RBS) and the flanking sequences may fold into structures to modulate the interaction with the ribosome, and thus translation of the mRNA can be turned on or off through RNA folding. By using optical tweezers, a single-molecule technique that allows us to mechanically pull a single RNA molecule from both ends, we can unfold the RNA structure and measure its stability. From the study we may infer the energy barrier the ribosome encounters during the attempt of translation initiation. In addition, we have also established another single-molecule assay platform, called smFRET (single-molecule Forster Resonance Energy Transfer), in our laboratory. We can label a pair of dyes on different moieties of the RNA or ribosome to report their distance changes during a reaction. With that, we are able to follow the molecular dynamic process in real time. Such measurements and observations are challenging to most conventional methods. 

In addition to the translation initiation, we have also focused on the regulation during elongation, a process the ribosome reads codons along the mRNA frame and moves three nucleotides a time. Regulation may occur through folding part of the RNA into a structure, usually a hairpin or pseudoknot, to hinder translocation of the ribosome, while it is reading a specific sequence, called slippery sequence. Under the circumstances, the ribosome will have a chance to lose the tempo and slip backwards by one nucleotide to another reading frame. This is called -1 frameshifting and occurs in many viruses and bacteria. By studying at the single-molecule level, we are attempting to reveal how the RNA structures stimulates frameshifting, as this mechanism is still poorly understood.

Reference papers: 

1.    Chen, Y.-L. & Wen, J.-D. Translation initiation site of mRNA is selected through dynamic interaction with the ribosome. Proc. Natl. Acad. Sci. U.S.A. 119, e2118099119 (2022). https://doi.org/10.1073/pnas.2118099119

2.    Chang, K.-C. & Wen, J.-D. Programmed -1 ribosomal frameshifting from the perspective of the conformational dynamics of mRNA and ribosomes. Comput. Struct. Biotechnol. J. 19, 3580-3588 (2021).Invited review article. https://doi.org/10.1016/j.csbj.2021.06.015

3.    Hsu, C.-F., Chang, K.-C., Chen, Y.-L., Hsieh, P.-S., Lee, A.-I., Tu, J.-Y., Chen, Y.-T. & Wen, J.-D. Formation of frameshift-stimulating RNA pseudoknots is facilitated by remodeling of their folding intermediates. Nucleic Acids Res. 49, 6941-6957 (2021). https://doi.org/10.1093/nar/gkab512

4.    Wen, J.-D., Kuo, S.-T. & Chou, H.-D. The diversity of Shine-Dalgarno sequences sheds light on the evolution of translation initiation. RNA Biol. 18, 1489-1500 (2021). Invited review article. https://doi.org/10.1080/15476286.2020.1861406

5.    Kuo, S.-T., Jahn, R.-L., Cheng, Y.-J., Chen, Y.-L., Lee, Y.-J., Hollfelder, F., Wen, J.-D. & Chou, H.-D. Global fitness landscapes of the Shine-Dalgarno sequence. Genome Res. 30, 711-723 (2020). https://genome.cshlp.org/content/30/5/711

6.    Chang, K.C., Salawu, E.O., Chang, Y.Y., Wen, J.D. & Yang, L.W. Resolution-exchanged structural modeling and simulations jointly unravel that subunit rolling underlies the mechanism of programmed ribosomal frameshifting. Bioinformatics 35, 945-952 (2019). https://doi.org/10.1093/bioinformatics/bty762

7.    Wen, J.-D., Kuo, S.T. & Chou, H.-H.D. The diversity of Shine-Dalgarno sequences sheds light on the evolution of translation initiation. RNA Biol., Published online: 21 Dec 2020 (DOI: 10.1080/15476286.2020.1861406).

8.    Kuo, S.-T., Jahn, R.-L., Cheng, Y.-J., Chen, Y.-L., Lee, Y.-J., Hollfelder, F., Wen, J.-D., and Chou, H.-H.D. Global fitness landscapes of the Shine-Dalgarno sequence. Genome Res. 30, 711-723 (2020).

9.    Chang, K.-C., Salawu, E.O., Chang, Y.-Y., Wen, J.-D., & Yang, L.-W. Resolution-exchanged structural modeling and simulations jointly unravel that subunit rolling underlies the mechanism of programmed ribosomal frameshifting. Bioinformatics 35, 945-952 (2019). 

10. Chen, Y.-T., Chang, K.-C., Hu, H.-T., Chen, Y.-L., Lin, Y.-H., Hsu, C.-F., Chang, C.-F., Chang, K.-Y., and Wen, J.-D. (2017). Coordination among tertiary base pairs results in an efficient frameshift-stimulating RNA pseudoknot. Nucleic Acids Res. 45, 6011-6022 (2017). 
https://doi.org/10.1093/nar/gkx134

11. Chang, K.-C., Wen, J.-D., Yang, L.-W. Functional Importance of Mobile Ribosomal Proteins. BioMed Research International volume 2015, ID: 539238 (2015) 

12. Yan, S., Wen, J.-D., Bustamante, C. & Tinoco, I., Jr. Ribosome excursions during mRNA translocation mediate broad branching of frameshift pathways. Cell 160, 870-881 (2015) 

13. Liu, T., Kaplan, A., Alexander, L., Yan, S., Wen, J.-D., Lancaster, L., Wickersham, C. E., Fredrik, K., Noller, H., Tinoco, I., Jr. & Bustamante, C. Direct measurement of the mechanical work during translocation by the ribosome. eLife 3, e03406 (2014)

14. Wu, Y.-J., Wu, C.-H., Yeh, A. Y.-C. & Wen, J.-D. Folding a stable RNA pseudoknot through rearrangement of two hairpin structures. Nucleic Acids Res. 42, 4505-4515 (2014)

15. Qu, X., Wen, J.-D., Lancaster, L., Noller, H. F., Bustamante, C., Tinoco, I., Jr. The ribosome uses two active mechanisms to unwind messenger RNA during translation. Nature 475, 118-121 (2011)

16. 溫進德，解開遺傳密碼的解碼者 – 核醣體，於「化學」第六十八卷，第四期，第 293 – 301 頁， 中國化學會 (2010)

17. Tinoco, I., Jr. & Wen, J.-D. Simulation and analysis of single-ribosome translation. Phys. Biol. 6, 025006 (2009)

18. Wen, J.-D., Lancaster , L., Hodges, C., Zeri, A., Yoshimura, S., Noller, H. F., Bustamante, C. & Tinoco, I. , Jr. Following translation by single ribosomes one codon at a time. Nature 452, 598-603 (2008) (cover-featured article)

19. Chen, G., Wen, J.-D. & Tinoco, I., Jr. Single-molecule mechanical unfolding and folding of a pseudoknot in human telomerase RNA. RNA 13, 2175-2188 (2007) 

20. Wen, J.-D., Manosas, M., Li, P. T., Smith, S. B., Bustamante, C., Ritort, F. & Tinoco, I., Jr. Force unfolding kinetics of RNA using optical tweezers. I. Effects of experimental variables on measured results. Biophys. J. 92, 2996-3009 (2007) 

21. Manosas, M., Wen, J.-D., Li, P. T., Smith, S. B., Bustamante, C., Tinoco, I., Jr. & Ritort, F. Force unfolding kinetics of RNA using optical tweezers. II. Modeling experiments. Biophys. J. 92, 3010-3021 (2007) 

22. Gray, D. M., Wen, J.-D., Gray, C. W., Repges, R., Repges, C., Raabe, G. & Fleischhauer, J. Measured and calculated CD Spectra of G-quartets stacked with the same or opposite polarities. Chirality 20, 431-440 (2008)

23. Wen, J.-D. & Gray, D. M. Selection of genomic sequences that bind tightly to Ff gene 5 protein: primer-free genomic SELEX. Nucleic Acids Res. 32, e182 (2004)

24. Wen, J.-D. & Gray, D. M. Ff gene 5 single-stranded DNA-binding protein assembles on nucleotides constrained by a DNA hairpin. Biochemistry 43, 2622-2634 (2004)

25. Gray, D. M., Gray, C. W., Mou, T.-C. & Wen, J.-D. CD of single-stranded, double-stranded, and G-quartet nucleic acids in complexes with a single-stranded DNA-binding protein. Enantiomer 7, 49-58 (2002)

26. Wen, J.-D. & Gray, D. M. The Ff gene 5 single-stranded DNA-binding protein binds to the transiently folded form of an intramolecular G-quadruplex. Biochemistry 41, 11438-11448 (2002)

27. Wen, J.-D., Gray, C. W. & Gray, D. M. SELEX selection of high-affinity oligonucleotides for bacteriophage Ff gene 5 protein. Biochemistry 40, 9300-9310 (2001)

28. Hashem, G. M., Wen, J.-D., Do, Q. & Gray, D. M. Evidence from CD spectra and melting temperatures for stable Hoogsteen-paired oligomer duplexes derived from DNA and hybrid triplexes. Nucleic Acids Res. 27, 3371-3379 (1999)

29. Shin, S.-J., Lai, F.-J., Wen, J.-D., Hsiao, P.-J., Hsieh, M.-C., Tzeng, T.-F., Chen, H.-C., Guh, J.-Y. & Tsai, J.-H. Neuronal and endothelial nitric oxide synthase expression in outer medulla of streptozotocin-induced diabetic rat kidney. Diabetologia 43, 649-659 (2000)

30. Shin, S.-J., Lai, F.-J., Wen, J.-D., Lin, S.-R., Hsieh, M.-C., Hsiao, P.-J. & Tsai, J.-H. Increased nitric oxide synthase mRNA expression in the renal medulla of water-deprived rats. Kidney Int. 56, 2191-2202 (1999)

31. Shin, S.-J., Wen, J.-D., Chen, I.-H., Lai, F.-J., Hsieh, M.-C., Hsieh, T.-J., Tan, M.-S. & Tsai, J.-H. Increased renal ANP synthesis, but decreased or unchanged cardiac ANP synthesis in water-deprived and salt-restricted rats. Kidney Int. 54, 1617-1625 (1998)

32. Shin, S.-J., Wen, J.-D., Lee, Y.-J., Chen, I.-H. & Tsai, J.-H. Increased C-type natriuretic peptide mRNA expression in the kidney of diabetic rats. J. Endocrinol. 158, 35-42 (1998)

33. Lee, S.-C., Kuan, C.-Y., Wen, Z.-D. & Yang, S.-D. The naturally occurring PKC inhibitor sphingosine and tumor promoter phorbol ester potentially induce tyrosine phosphorylation/activation of oncogenic proline-directed protein kinase FA/GSK-3alpha in a common signalling pathway. J. Protein Chem. 17, 15-27 (1998)

34. Yang, S.-D., Yu, J.-S. & Wen, Z.-D. Tumor promoter phorbol ester reversibly modulates tyrosine dephosphorylation/inactivation of protein kinase FA/GSK-3 alpha in A431 cells. J. Cell Biochem. 56, 550-558 (1994)

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