Research Projects
The research in the Hou lab is on understanding the system biology of tRNA. Many innovative projects are going on in the lab, but only a few of which are highlighted below. Please contact us if you are hungry for more.herefore emerging as an important regulator of protein expression and the composition of the proteome in each cell.
Epigenetic post-transcriptional modifications to tRNA
tRNA is extensively post-transcriptionally modified with epigenetic modifications, such as modification of A to m1A, U to cmo5U, and G to m1G. How do these epigenetic modifications in tRNA affect the quality of translating the codon bias of each gene in each genome and impact the fitness of each organism?
Why is tRNA methylation with m1G37 essential for life?
While each tRNA has several epigenetic modifications, only a very small number of them is essential for life. The N1-methylation of G37 at position 37 on the 3'-side of the anticodon (m1G37) is essential for life. It is catalyzed by the tRNA methyl transferase TrmD in bacteria.
We show that m1G37-tRNA is essential for life, because it is required throughout the entire elongation cycle of protein synthesis, which is coupled to cell growth and survival. It is required for reading the codon at the ribosome A site (the aminoacyl-tRNA binding site), for making the new peptide bond at the A site, for moving the tRNA to the P site (the peptidyl-tRNA binding site) after peptide bond formation, and for providing the nascent peptide from the P site to the A site for incorporation of the next amino acid that is entering the A site. Any cellular solution to rescue the loss of m1G37?
How does tRNA methylation with m1G37 confer resistance to antibiotics?
Gram-negative bacteria such as E. coli and Salmonella use m1G37-tRNA to translate genes for the cell envelope double-membrane structure.
Active cell envelope confers multidrug resistance and persistence to these bacteria, permitting regrowth upon removal of antibiotics. However, loss of m1G37 sensitizes these bacteria to antibiotic killing. We are screening for inhibitors that will target synthesis of m1G37. What is the best way to screen for them? What is the mechanism of action of these inhibitors?
Why are epigenetic modifications of mitochondrial tRNAs coupled to mitochondrial health?
Mitochondrial tRNAs (mt-tRNAs) are synthesized from the mitochondrial genome, separate from the nucleus-encoded tRNAs. Mt-tRNAs are frequently associated with mitochondrial mutations that cause human disease, mostly with neurological and metabolic disorders. One of the most common mitochondrial diseases is known as MELAS (mitochondrial myopathy, encephalopathy, lactic acidosis, stroke-like episodes). It is most frequently caused by the A3243G mutation in the mt-DNA and is mapped to the A14G mutation in mt-tRNALeu(UUR).
The MELAS mutation is adjacent to nucleotides in mt-tRNALeu(UUR) that are post-transcriptionally modified. Previous mass spectrometry data show that, while m1G9, m2G10, and m1A58 are all fully modified in the MELAS tRNA, the taurine modification at the normally wobble tm5U34 nucleotide is missing. Missing the taurine modification would affect translation of the Leu codons UUR in the mitochondrial genome. Why is the taurine modification lacking? Why is such a selective modification in the MELAS tRNA? What is the choice of the selection?
How to image tRNAs for trafficking?
The genetic code is degenerate and there are multiple tRNA species for each amino acid. Some of these tRNAs need to travel to organelles to support local protein synthesis. We are most interested in trafficking of tRNAs into synaptosomes, which regulate the plasticity of neurons and provide the basis for learning and memory. We have developed tools for imaging tRNAs. In these tools, we fuse an RNA aptamer, such as the Spinach aptamer into the V loop of a tRNA, and show that, when the aptamer is bound with a ligand, it lights up the tRNA, enabling us to track the location and trafficking of the tRNA inside the cell.
When does a tRNA travel? Does it travel alone or in groups or with protein partners? Is the tRNA trafficking impeded in a neurological disease? Using our imaging tools, we are addressing these important and interesting questions.
How does m1 G37 regulate gene expression in human cells?
We are investigating m1 G37 in human cells, which is synthesized by Trm5 –– a tRNA methyl transferase common to eukaryotic and archaeal cells that is fundamentally distinct from the bacterial TrmD enzyme. Why does the Nature use two different enzymes for m1 G37 synthesis?
From our work in bacterial TrmD, we know that genes that are biasedly dependent on translation of proline (Pro) codons, the leucine (Leu) CUA codon, and the arginine (Arg) CGG codon are dependent on m1 G37-tRNA. Are these the same codons in human cells? How does the codon bias of genes affect their expression in stress response? Is m1 G37 methylation regulated in the human disease state?