Kiong Ho

Assistant Professor

Eukaryotic Gene Expression: RNA Processing and Repair.

Ph.D. 1997 Cornell University, Graduate School of Medical Sciences
Post-Doctoral Research Fellow (1997-1999) Sloan Kettering Institute for Cancer Research
Senior Research Scientist (2000-2003) Sloan Kettering Institute for Cancer Research

curriculum vitae

Fall 2006

BIO 302 (Intro to Molecular Biology) : Lecture Notes.

BIO 401/501 (Advanced Biochemistry) : Lecture Notes.

Spring 2006

BIO 404/504 (Moelcular Genetics): Lecture Notes.

RESEARCH SUMMARY

Parasitic protozoa are causative agents of widespread human diseases, including malaria (caused by Plasmodium falciparum), African sleeping sickness (Trypanosome brucei), and Chagas' disease (Trypanosome cruzi). Because these parasites diverged early from the main branch of the eukaryotic lineage, their unusual mechanisms of gene expression reflect ancient eukaryotic functions that have been preserved to present. By studying the process of gene expression, not only may we learn about the evolution of higher eukaryotes, but we can also identify parasite specific processes that can be exploited as targets for novel therapeutic intervention.

mRNA Cap Formation in Parasitic Protozoa

mRNA processing plays a critical role in the expression of eukaryotic genes. Processing occurs cotranscriptionally on nascent chains synthesized by RNA polymerase II. The earliest modification event is the addition of m7GpppN cap. This structural hallmark is present on all eukaryotic cellular mRNAs and is essential for viability. The cap enhances several downstream events in gene expression including mRNA stability, splicing of pre-mRNAs, and initiation of protein synthesis.

Structure of Mammalian RNA Triphosphatase
Structure of Fungal RNA Triphosphatase

Cap formation is mediated by three enzymatic reactions in which the 5' triphosphate end of pre-mRNA is hydrolyzed to a 5' diphosphate by RNA triphosphatase, then capped with GMP by RNA guanylyltransferase, and methylated by RNA (guanine-N7) methyltransferase. The sequential steps in the capping reaction are universal to all eukaryotes, yet there is a significant divergence in the catalytic mechanism of the triphosphatase component. Metazoan triphosphatases belong to a superfamily of phosphatases that act via the formation and hydrolysis of a cysteinyl-phosphate intermediate. Fungal and viral triphosphatases comprise a novel family of metal-dependent phosphohydrolases with a unique tertiary structure.

Initial analysis of the mRNA capping apparatus of T. brucei and the malarial parasite P. falciparum has illuminated an evolutionary connection to fungi rather than metazoans. T. brucei and P. falciparum encode a triphosphatase that is structurally and mechanistically similar to the fungal enzymes. RNA triphosphatase is an attractive drug target because the mechanism of cap formation is completely different from the metazoan host and metazoan species encode no recognizable homologue of the fungal/protozoan enzymes. Thus, a mechanism-based inhibitor against triphophatase should be highly selective for the parasite and have minimal effect on the human host or arthropod vector.

To further exploit the mechanistic differences in mRNA capping between the parasites and humans, we are carrying out series of molecular and biochemical studies to explore the capping apparatus of T. brucei, an organism that possesses unique features for controlling gene expression, including polycistronic transcription, trans-splicing of pre-mRNAs, and a hypermethylated cap 4 structure. The cap 4 structure is formed from standard m7GpppN cap by cotranscriptional methylataion within the first four nucleosides of the splice leader RNA (SL RNA). This modification is essential for the trans-splicing process, which entails the addition of capped SL RNA to the 5’ ends of individual mRNAs derived from polycistronic pre-mRNAs. Our long-term goal is to identify the molecular components that participate in cap4 formation to understand the mechanism and evolution of capping apparatus in parasitic protozoan.

RNA Ligase and Repair

A second project aim is to understand the RNA repair pathway. RNA ligase participates in the repair, splicing and editing pathway of RNAs or in altering their primary structure. For example, T4 RNA ligase (gp63, Rnl1) reparis nicks in the anticodon domain of tRNAs. In yeast, a RNA ligase is involved in removal of introns from tRNA precursors. A specific RNA ligase has also been found in the mitochondria of kinetoplastid protozoa and participate in RNA editing.

Structure of Rnl2 complex with AMP

Recently we identified a second, novel RNA ligase (Rnl2) encoded by bacteriophage T4. Rnl2 defines a new family of RNA ligase, which include the trypanosome editing ligases and a group of putative RNA ligases encoded by eukaryotic DNA viruses and archaeabacteria. To address whether the Rnl2-like protein participates in RNA recombination or in a yet unknown repair process, genetic systems using the yeast is under development and would provide an in vivo functional assay for Rnl2-like proteins. Insights from the analysis of RNA ligase will illuminate the structural basis for protein-catalyzed RNA recombination/repair events and evolutionary transitions from RNA-world to DNA-world.




 

SELECTED PUBLICATIONS

  • Ho CK, Sriskanda V, McCracken S, Bentley D, Schwer B, and Shuman S. (1998)
    The Guanylyltransferase Domain of Mammalian mRNA Capping Enzyme Binds to the Phosphrylated Carboxyl-Terminal Domain of RNA Polymerase II.
    J. Biol. Chem. 273: 9577-9585. [Abstract|PDF ]
  • Ho CK, Schwer B, and Shuman S. (1998)
    Genetic, Physical and Functional Interactions between the Triphosphatase and Guanylyltransferase Components of the Yeast mRNA Capping Apparatus.
    Mol. Cell. Biol. 18: 5189-5198. [Abstract|PDF ]

  • Ho CK, Pei Y, and Shuman S. (1998)
    Yeast and Viral RNA 5’ Triphosphatase Compromise a New Nucleoside Triphosphatase Family.
    J. Biol. Chem. 273: 34151-34156. [Abstract|PDF ]

  • Ho CK and Shuman S. (1999)
    Distinct Roles for CTD Ser2 and Ser5 Phosphorylation in the Recruitment and Allosteric Activation of Mammalian mRNA Capping Enzyme.
    Molecular Cell 3: 405-411.[Abstract|PDF ]

  • Ho CK, Martins A, and Shuman S. (2000)
    A Yeast-Based Genetic System for Functional Analysis of Viral mRNA Capping Enzymes.
    J. Virol. 74: 5486-5494. [Abstract|PDF ]

  • Ho CK and Shuman S. (2001)
    A Yeast-like mRNA Capping Apparatus in Plasmodium falciparum.
    Proc. Natl. Acad. Sci. USA 98: 3050-3055 [Abstract|PDF ]

  • Chiu YL, Coronel E, Ho CK, Shuman S, and Rana TM. (2001)
    HIV-1 Tat Protein Interacts with Mammalian Capping Enzyme and Stimulates Capping of TAR RNA.
    J. Biol. Chem. 276: 12959-12966 [Abstract|PDF ]

  • Changela A, Ho CK, Martins A, Shuman S, and Mondragon A. (2001)
    Structure and Mechanism of the RNA Triphosphatase Component of Mammalian mRNA Capping Enzyme.
    EMBO J. 20: 2575-2586 [Abstract|PDF]

  • Ho CK and Shuman S. (2001)
    Trypanosoma brucei RNA Triphosphatase: Anti-Protozoal Drug Target and Guide to Eukaryotic Phylogeny.
    J. Biol. Chem. 276: 46182-46186 [Abstract|PDF]

  • Ho CK and Shuman S. (2002)
    Bacteriophage T4 RNA ligase 2 (gp24.1) Exemplifies a Family of RNA Ligases Found in All Phylogenic Domains.
    Proc. Natl. Acad. Sci. USA 99: 12709-12714 [Abstract|PDF]

  • Chiu YL, Ho CK, Saha N, Schwer B, Shuman S, and Rana TM. (2002)
    Tat Stimulates Cotranscriptional Capping of HIV-1 mRNA.
    Molecular Cell 10: 585-597 [Abstract|PDF]

  • Yin S, Ho CK and Shuman S. (2003)
    Structure-Function Analysis of T4 RNA Ligase 2.
    J. Biol. Chem. 278: 17601-17608 [Abstract|PDF]

  • Ho CK, Wang LK, Lima CD and Shuman S. (2004)
    Structure and Mechanism of RNA Ligase.
    Structure 12: 327-339 [Abstract |PDF] [Commentary]

  • Schwer B, Sawaya R, Ho CK and Shuman S. (2004)
    Portability and Fidelity of RNA-Repair Systems
    Proc. Natl. Acad. Sci. USA 101: 2788-2793 [Abstract|PDF]

  • Pfeffer S, Sewer A, Lagos-Quintana M, Sheridan R, Sander C, Grässer FA, van Dyk LF, Shuman S, Ho CK, Chien M, Russo JJ, Ju J, Randall G, Lindenbach BD, Rice CM, Simon V, Ho DD, Zavolan M, and Tuschl T. (2005)
    Identification of the MicroRNAs of the Herpesvirus Family.
    Nature Method 2: 269-276

  • Hall MP and Ho CK. (2006)
    Characterization of a Trypanosoma brucei a mRNA Cap (Guanine N-7) Methyltransferase.
    RNA 12:488-497 [Abstract|PDF]

  • Hall MP and Ho CK. (2006)
    Functional characterization of a 48 kDa Trypanosoma brucei cap 2 RNA methyltransferase.
    Nucleic Acid Research (in press) [Abstract|PDF]

Click here for complete list of publication

Kiong Ho
Department of Biological Sciences
648 Cooke Hall, Norrth Campus
State University of New York at Buffalo
Buffalo, NY 14260

Phone: (716) 645-2363 Ext. 174

Email: kiongho@buffalo.edu

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