Ailong Ke

Ailong Ke is a Professor in the Department of Molecular Biology and Genetics. Dr. Ke is a member of the Graduate Field of Biochemistry, Molecular and Cell Biology, the Graduate Field of Biophysics, and the Graduate Field of Chemistry and Chemical Biology. The Ke lab studies the structure and function of RNA molecules.

Research Focus

CRISPR interference in Prokaryotes

The use of small RNAs to regulate gene expression is ubiquitous in all living organisms including bacteria. In one remarkable instance, bacteria and archaea acquire resistance to invading foreign nucleic acids - such as conjugative plasmids, transposable elements and phages - by employing an RNA-mediated defense mechanism. In this process, short fragments (~24 to 48 nucleotides) of the invading DNA are integrated in the genome as spacers between similarly sized clusters of regularly interspaced short palindromic repeats (CRISPRs). CRISPRs are a novel class of repetitive DNA that have been identified in 88% of the archaeal genomes and 39% of the bacterial genomes thus far sequenced, including important human pathogens such as Campylobacter jejuni, Clostridium botulinum, Listeria monocytogenes, Mycobacterium tuberculosis, Yersinia pestis, and enteropathogenic and enterohaemorrhagic Escherichia coli. Adjacent to the CRISPR repeats and spacers is a set of conserved CRISPR-associated (cas) genes that encode the Cas proteins. Owing to its widespread occurrence, the CRISPR defense system has attracted a great deal of attention.

Riboswitch

Riboswitches are structured RNAs that recognize specific small molecules, usually key metabolites inside the cell, and “switch” on or off gene expression at either transcription or translation level. The discovery of these short cis-acting RNA elements has drastically changed our understanding of gene regulation. Majority of riboswitches were found in prokaryotic genomes, while only a few examples of eukaryotic riboswitches have been reported. Riboswitches are especially prevalent in Gram-positive bacteria, exemplified by Bacillus subtilis as a model organism, but also in a number of important pathogens such as Bacillus anthracis, Staphylococcus, Enterococcus, Streptococcus, Listeria, Clostridium, and Mycobacterium. This and other characteristics attract increasing attention to target riboswitches for antibiotic development.

Of the twelve different riboswitch classes that recognize nine different key metabolites, S-adenosyl methionine (SAM) riboswitches are the most commonly found. For example, nearly half of all known riboswitches identified in B. anthracis bear consensus primary sequence and secondary structures of the S box motif. Three classes of SAM riboswitches have been found. They contain completely different secondary structures, representing nature’s three independent RNA solutions to achieve specific SAM recognition. We recently determined the crystal structures of two (out of three) SAM riboswitch classes: the E. faecalis SMK and the B. subtilis S-box.

Bacteriophage Phi29 Packaging RNA

How bacteriophage f29 packages its genome into protein capsids is a mystery and a marvel. The DNA genome is packed to near crystalline density inside the capsid, against internal pressure of up to 2000 psi, through a molecular motor composed of a dodecameric head-tail protein connector, and a pentameric prohead RNA (pRNA) and ATPase gp16. We are working on the structures of the packaging motor components to explain how this natural nano-machine works and why RNA is needed as a component.

Outreach and Extension Focus

Cornell University’s summer undergraduate research programs and their graduate programs.

Teaching Focus

I developed a new course called "The RNA world". The course, BIOBM438 is being taught in the spring of past 8 years for undergraduate and graduate students. The course has become an elective for the Biochemistry Major, and receive an enrollment between 20-35 students each year.

RNA biology is a very active area of research, I as a faculty hire with expertise in biochemistry and structural biology applied to RNA, has the expertise to mount a comprehensive course in RNA biology that will be of interest to advanced undergraduate students and graduate students. Some of the material taught in this course will necessarily be taught in entry-level biochemistry courses at both the undergraduate level but because of the breadth of subject matter in these courses, in-depth coverage of RNA-related topics is not possible. This course will provide a panoramic view of the fast-evolving RNA research field and cover the field in a systematic way.

Selected Publications

Journal Publications

• Hayes, R., Xiao, Y., Ding, F., & Ke, A. (2016). Structural basis for promiscuous PAM recognition in type I-E Cascade from E. coli. Nature.
• Johnson, C. M., Chen, Y., Lee, H., Ke, A., Weaver, K. E., & Dunny, G. M. (2014). Identification of a conserved branched RNA structure that functions as a factor-independent terminator. PNAS: Proceedings of the National Academy of Sciences of the United States of America. 111:3573-3578.
• Huo, Y., Nam, K., Ding, F. F., Lee, H., Wu, L., Xiao, Y., Farchione , M. D., Zhou, S., Rajashankar , K., Kourinov, I., Zhang, R., Ailong, K., & , (2014). Structures of CRISPR Cas3 offer mechanistic insights into Cascade-activated DNA unwinding and degradation. Nature Structural & Molecular Biology. 10.1038:2875.
• Liu, J. J., Bratkowski, M. A., Liu, X., Niu, C. Y., Ke, A., & Wang, H. W. (2014). Visualization of distinct substrate-recruitment pathways in the yeast exosome by EM. Nature Structural & Molecular Biology. 21:95-102. .
• Grigg, J. C., Chen, Y., Grundy, F. J., Henkin, T. M., Pollack, L., & Ke, A. (2013). T box RNA decodes both the information content and geometry of tRNA to affect gene expression. PNAS: Proceedings of the National Academy of Sciences of the United States of America. 110:7240-5.
• Nam, K., Kurinov, I., & Ke, A. (2012). Crystal structure of clustered regularly interspaced short palindromic repeats (CRISPR)-associated Csn2 protein revealed Ca2+-dependent double-stranded DNA binding activity. JBC: Journal of Biological Chemistry. 286:30759-68.
• Wang, H. -., Wang, J., Ding, F., Kevin, C., Butler, J. S., Nogales, E., & Ke, A. (2007). Architecture of the Yeast Rrp44-Exosome Complex Suggests Routes of RNA Recruitment for 3’-end Processing. PNAS: Proceedings of the National Academy of Sciences of the United States of America. 104:16844-16849.

Book Chapters

• Ke, A., & Doudna, J. A. (2005). Catalytic strategies of self-cleaving ribozymes: Relics of an RNA world? The RNA World.