 Manal A. Swairjo, Assistant Professor of Biochemistry
| Background |
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| Education |
1988 B.Sc. Physics and Mathematics,
Kuwait University.
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1996 Ph.D. Cellular Biophysics Program,
Department of Physics and Chemistry,
Boston University, and Department of
Physiology, Boston University School of
Medicine
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| Ongoing and Future Research Interest |
| My research focuses on tRNA biogenesis processes and their links to human disease. tRNA is an ancient molecule that evolved to be the adapter between amino acids and codons, thus mediating the translation of the genetic code. In its life and times in the cell, a tRNA molecule undergoes extensive processing and handling by diverse enzymes and protein factors. After transcription and removal of introns, the nascent tRNA molecule is trimmed at the 3' and 5' ends and a CCA tri-nucleotide is added to the 3' end. It is also edited, modified and aminoacylated. In eukaryotes, these steps occur in the nucleolus. The fully modified and aminoacylated tRNA is then transported to the cytoplasm through the nuclear pore complex and is "channeled" to the ribosome. Three steps of tRNA biogenesis constitute the core of my ongoing and future research interests: aminoacylation, modification, and nucleocytoplasmic export. Each of these cell-biochemical processes critically depends on specificity of tRNA recognition. |
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Translational control by tRNA in cancer and other human diseases
In recent years, we have witnessed the unraveling of new molecular links between the deregulation in eukaryotic cells of mRNA translation and ribosome biogenesis on the one hand and tumor-suppressive and oncogenic pathways on the other. Three major developments support the notion that aberrant translational control could be a driving force of the oncogenic process: 1) Human cancer susceptibility syndromes have been attributed to mutations in tumor suppressor genes that control protein synthesis. 2) The oncogenic effect of deregulated expression of protein translational  regulators has been demonstrated in vivo in animal models. 3) Effective anticancer drugs have been shown to impact key regulators of the protein synthesis machinery.
Although a key molecule of the translation machinery, tRNA has been overlooked in ongoing research on translational control in cancer. Several tRNA biogenesis processes have been implicated in human disease: 1) The hypermodified nucleosides of tRNA are excreted at high levels in the urine of cancer patients, and have been promoted for decades as sensitive diagnostic and prognostic markers of cancer. 2) Autoantibodies against several aminoacyl-tRNA synthetases are found at high levels in the blood serum of autoimmune-disease patients. 3) Proteolytic fragments of human tyrosyl- and tryptophanyl-tRNA synthetases are potent cytokines that are actively secreted from apoptotic cells to act as angiogenic and angiostatic factors. 4) Mutations in alanyl-tRNA synthetase and glycyl-tRNA synthetase genes have been linked to symptomatic neuropathies in mice and humans, respectively. 5) Lack of anticodon-loop modifications in mutant human mitochondrial tRNAs are causally linked to hereditary mitochondrial disease such as MELAS and MERRF. 6) The levels of many modified nucleosides of tRNA are altered in cancer tissue, and several tRNA modification enzymes (e.g. dihydrouridine synthase and IRIP) are overproduced in tumor cells. 7) tRNA modifications are essential in cellular metabolism and regulation, and have thus been targeted in anti-infectives research (e.g. anti-Shigellosis).
Limited knowledge of the pathophysiology of most of these health conditions points to mistranslation of proteins (mediated by a malfunctioning tRNA) as a possible mechanism. However, evidence is only emerging and - for most cases - it is not known whether a tRNA malfunction induces disease-causing cellular transformation or is a passive result of cellular changes associated with disease. These physiological changes (upstream or downstream of the tRNA) may involve other cell functions such as the unfolded protein response (e.g., in neurodegenerative disease), and the oxygen signal (e.g., in tumor cells). Certainly, a thorough in vitro characterization of functionally compromised tRNAs and of the responsible enzymes is only starting.
With the long-term goal of understanding tRNA-mediated translational control in eukaryotic cells and its role in human cancer and other diseases, I have set out to study newly identified, disease-linked pathways of tRNA aminoacylation and nucleoside modification and to characterize their components functionally and structurally. I started studying the fundamental biochemical pathways involved both in model microbial systems and in mammals. The approach I use combines X-ray crystallography, biochemical analysis and bioinformatics, and a variety of biophysical and spectroscopic methods. This approach is complemented by collaborations with geneticists and organic chemists.
tRNA modification / function and biosynthesis of modified nucleosides
The coding properties of a tRNA molecule do not reside only in its primary sequence. Post-transcriptional nucleoside modifications, particularly in the anticodon loop, alters cognate codon  recognition, aminoacylation properties, or stabilize the codon-anticodon wobble base pairing to prevent ribosomal frameshifting. Typically, about 10% of the nucleosides in a particular tRNA are modified. Over 90 modified nucleosides have been characterized, many of which are conserved across great phylogenetic distances. Reflecting the importance of post-transcriptional modifications in "fine tuning" gene expression, organisms devote more genetic information to the modification than to the encoding of tRNAs. The nature of nucleoside modifications varies from simple methylation of the base or ribose ring to extensive "hypermodification" of the canonical bases that can result in radical structural changes and involve multiple enzymatic steps. Consistent with their role in translation, hypermodified nucleosides cluster in the tRNA anticodon region.
Despite a wealth of chemical, biophysical and structural knowledge of the tRNA modifications themselves, their biosynthesis pathways remain highly uncharacterized. This discrepancy is mainly due to lack of knowledge of the genes involved. However, the availability of hundreds of whole-genome sequences has now allowed the identification of several missing tRNA-modification genes by combining comparative genomic approaches with experimental validations. Studies of the complex chemical reactions entailed in hypermodification of nucleosides will uncover new enzymatic mechanisms and unprecedented chemistries.
In the past two years, and with the help of several collaborators, I advanced a number of projects on the biosynthesis of several modified tRNA nucleosides implicated in cancer. Using a combination of bioinformatics and crystallographic tools, biochemical characterization and in vivo genetic manipulation, we will attempt to characterize the biosynthetic pathways of some of these cancer markers.
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| Selected Publications |
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Swairjo M.A., Roberts M.F., Campos M. B., Dedman J.R. & Seaton B.A. (1994). 31P- and 1H NMR studies of the interaction of annexin V with small phosphatidic acid containing unilamellar vesicles. Biochemistry 33: 10944 50.
Swairjo M.A., Concha N.O., Kaetzel M.A., Dedman J.R. & Seaton B.A. (1995). Crystal structures at 1.9 Å resolution of rat annexin V in complex with glycerophosphoserine or glycerophosphoethanolamine: modes of binding to phospholipid polar moieties. Nature Structural Biology 2: 968-74.
Swairjo M.A., Towler E.M., Debouck C. & Abdel-Meguid S.S. (1998). Structural Role of the 30's Loop in Determining the Ligand Specificity of the Human Immunodeficiency Virus protease. Biochemistry 31: 10928-36.
Morales A.J., Swairjo M.A., & Schimmel P. (1999). Structure-Specific tRNA Binding Protein From the Extreme Thermophile Aquifex aeolicus. EMBO J. 18: 3475-83.
Swairjo, M.A.*, Morales A.J., Wang C.-C., Ortiz A.R., & Schimmel P. (2000). Crystal Structure of Trbp111: a Structure-Specific tRNA Binding Protein. EMBO J. 19: 6287-98.
Swairjo M.A., Otero F.J., Yang X.-L., Lovato M.A., et al., Schimmel P. (2004). Alanyl-tRNA synthetase crystal structure and design for acceptor-stem recognition. Mol. Cell. 13: 829-41.
Lovato M.A., Swairjo M.A., Schimmel P. (2004). Positional recognition of a tRNA determinant dependent on a peptide insertion. Mol. Cell. 13: 843-51.
Swairjo M.A. and Schimmel P. (2005). Breaking sieve for steric exclusion of a noncognate amino acid from active site of a tRNA synthetase. Proc. Natl. Acad. Sci. USA. 102: 988-93.
Van Lanen S.G., Reader J.S., Swairjo M.A., de Crécy-Lagard V., Lee B., Iwata-Reuyl D. (2005). From cyclohydrolase to oxido-reductase: Discovery of nitrile reductase activity in a common fold. Proc. Natl. Acad. Sci. USA. 102:12, 4264-9.
Swairjo M.A.*, Reddy R.R., Lee B., Van Lanen S.G., Brown S., de Crécy-Lagard V., Iwata-Reuyl D., Schimmel P. (2005). Crystallization and preliminary X-ray characterization of the nitrile reductase QueF - a queuosine biosynthesis enzyme. Acta Crystallogr. F61: 945-8.
Swairjo M.A. and Schimmel P. Structural evidence of the associative mechanism of amino acid activation by a class II synthetase. In preparation.
Swairjo M.A. and Seaton B.A. (1994). Annexin structure and membrane interactions: a molecular perspective. Annual Reviews for Biophysics and Biomolecular Structure. 23: 193 213. Swairjo M.A. (1998) Anti-Factor IX Fab Fragment Crystal Structure and Methods of Use for Peptidomimetic Design. U.S.A. Patent.
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| Invited Talks |
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"Adaptive evolution in translation." Hauptman-Woodward Institute, Buffalo, N.Y. September 2005.
"Transfer-RNA recognition codes in aminoacylation, modification and transport." Prof. S. Yokoyama's Satellite Workshop at the 2004 International Conference on Aminoacyl-tRNA Synthetases: Ancient Molecules for Future Biology and Medicine. July 2004.
"Inhibitor specificity of HIV proteases: the structural role of residues outside the active site cavity." The National Cancer Institute, Frederick, Maryland . April 1998.
"HIV protease - structural insights into drug resistance." The Scripps Research Institute, La Jolla, CA. January, 1998. "NMR and crystallographic studies of membrane binding by Annexin V." Boston College, Department of Chemistry, Boston, MA. April 1995.
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| Honors and Awards |
- Honor from Kuwait University, 1988.
- NATO award to Photobiological Techniques Advanced Study Institute, 1990.
- Boston University School of Medicine Graduate Student Meritorious Recognition Award, July 1994.
- Boston University School of Medicine Annual Henry I. Russek Award, April 1995.
- National Research Service Award, NIH, "Crystal Structure Determination of HIV-1 Vpu Protein," December 1997. |
| Press Review |
| Old molecules yield new secrets, by Jason S. Bardi. TSRI News and Views, vol. 4, issue 11 Mar. 29, 2004. |
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