Arun Malhotra

Assistant Professor of Biochemistry and Molecular Biology

Ph.D. (1989) University of Mississippi

Postdoctoral:
University of Alabama at Birmingham
The Rockefeller University

Structural biology: X-ray crystallography; Exoribonucleases; RNA modification enzymes; bacterial transcription initiation; axonal guidance proteins

Tel: (305) 243-2826, Fax: (305) 243-3065

My research interests lie in structural biology of macromolecules involved in a variety of basic cellular functions. Areas of major focus are bacterial nucleases involved in RNA maturation and degradation, enzymes involved in RNA modification, and molecules involved in axonal guidance and neuronal development. These macromolecules are being studied using the tools of X-ray crystallography and molecular biology.

Bacterial exoribonucleases

Ribonucleases play a central role in vital cellular RNA processes such as mRNA degradation and maturation & turnover of stable RNAs. Eight distinct exoribonucleases have been identified in E. coli. Of these, three (RNase T, RNase D, and oligoribonuclease) are members of a larger exonuclease superfamily (named the DEDD exonuclease family, after the four invariant acidic residues in these proteins) that includes the proof-reading domains of DNA polymerases.

While these proteins share similar sequence motifs, they are functionally quite different. RNase T is involved in tRNA turnover and maturation of tRNAs, 23S, and 5S rRNAs. RNase D is also involved in the maturation of tRNAs and small RNAs, but mainly as a backup enzyme. RNase D functions as a monomer, while RNase T and oligoribonuclease exist as dimers. Oligoribonuclease catalyzes the degradation of very short RNAs, and is the only exoribonuclease essential for cell viability in E. coli.

Our current work aims to obtain structures of these three exoribonucleases, and compare them to better understand differences in substrate specificities. The long term goals of this research are to understand the structures and mechanisms of action of all exoribonucleases in a single organism; these studies complement a parallel study, underway in the laboratory of Dr. Murray Deutscher (University of Miami), to completely characterize the physiological role of all the exoribonucleases in E. coli.

Pseudouridine Synthases

One of the most abundant post-transcriptional modification seen in RNA is the isomerization of uridine (U) to pseudouridine (5-ribosyluracil). While the physiological role of this modification in cells in not yet well understood, pseudouridines are often seen in functionally important regions of structural RNAs such as ribosomal RNAs, transfer RNAs and splicing RNAs.

The isomerization of uridines to pseudouridines is carried out by specialized enzymes called pseudouridine synthases. These enzymes fall into five different families, and crystallographic studies in a number of laboratories have shown that three of these families have very similar structures in spite of limited sequence homologies. This project focuses on the structural studies of pseudouridine synthases from the other two families (RluD from the RluA family, and the newly discovered TruD family), in collaboration with the laboratory of Dr. James Ofengand (University of Miami).

Structural Studies of axonal guidance molecules

This project aims to structurally characterize the interactions between ephrins and their receptors, a class of molecules involved in axonal guidance in the developing nervous system. Apart from axonal guidance, these receptors/ligands are also involved in cell migration, patterning of the nervous system, and angiogenesis. Given their critical roles in neuronal regeneration and angiogenesis, ephrins and their receptors are excellent targets for therapeutic intervention in a variety of cancers, injuries and diseases.

Eph receptors are the largest known family of receptor tyrosine kinases, with at least 16 members identified until now. The ligands for Eph receptors are the ephrins which have 8 members identified so far. The two classes of ephrins and their receptors, A and B, are defined by sequence homologies, mechanism of membrane anchorage, and by preferential binding of the ligands to their receptors. While within the same class, the ligand-receptor binding tends to be non-specific, there is no cross interaction between the two classes, except Eph A4 binds some of the B class ephrins. Ephrins-Eph interactions are also intriguing because these molecules often display bidirectional signaling: a forward signal (binding of ephrins to Eph receptor determines a response in a cell or axon) and a reverse/downstream signal (binding of Eph receptor to ephrin causes a change in the cell or axon to which ephrin molecule is bound).

This research aims to better understand the structural basis of ephrin/Eph ligand-receptor binding and specificity by crystallographic studies of the extra-cellular domains of several of these molecules. Residues identified as being critical for ephrin/Eph specificity will also be tested functionally using mutational approaches, in collaboration with the laboratory of Dr. Daniel Leibl (Miami Project to Cure Paralysis, University of Miami).

Malhotra Laboratory Home Page

Representative Publications

1.    Zuo, Y., Zheng, H., Wang, Y., Chruszcz, M., Cymborowski, M., Skarina, T., Savchenko, A., Malhotra, A., & Minor, W.  Crystal Structure of RNase T, an exoribonuclease involved in tRNA maturation and end-turnover. Structure, in press.

2.    Abaffy, T., Malhotra, A. & Luetje, C. W.  The molecular basis for ligand specificity in a mouse olfactory receptor: A network of functionally important residues. J. Biol. Chem., 282, 1216-1224, 2007. (Epub: Nov 17, 2006).

3.    Tolun A. A., Dickerson, I. M. & Malhotra, A.  Overexpression and purification of human calcitonin gene-related peptide-receptor component protein in Escherichia coli. Protein Expr. Purif., 52, 167-174, 2007. (Epub: Sept 20, 2006).

4.    Zuo Y., Vincent, H. A., Zhang, J., Wang, Y., Deutscher, M. P. & Malhotra, A.  Structural basis for processivity and single-strand specificity of RNase II. Mol. Cell, 24, 149-156, 2006.

5.    Suzuki, H., Zuo, Y., Wang, J., Zhang, M. Q., Malhotra, A. & Mayeda, A.  Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing. Nucl. Acids Res., 34, e63, 2006.

NCBI Pubmed Search

Honors and Professional Activities

• Member - AAAS

• Member - Protein Society

• Member - Biophysical Society