Demirci H, Murphy IV FM, Murphy E, Gregory S, Dahlberg AE, Jogl G*; A structural basis for streptomycin-induced misreading of the genetic code. Nature Comms. 10.1038/ncomms2364 (2013).
Larsen LH, Rasmussen A, Giessing AM, Jogl G*, Kirpekar F*; Identification and characterization of the Thermus thermophilus m5C methyltransferase modifying 23S rRNA base C1942. J. Biol. Chem. 287, 27593-27600 (2012).
Li H and Jogl G*; Crystal structure of decaprenylphosphoryl-β-D-ribose 2'-epimerase from Mycobacterium smegmatis. Proteins, 81(3), 538-543 (2012).
Jogl G, Wang X, Mason SA, Kovalevsky A, Mustyakimov M, Fisher Z, Hoffman C, Kratky C, Langan P; High-resolution neutron crystallographic studies of the hydration of the coenzyme cob(II)alamin. Acta Cryst. D 67, 584-591 (2011).
Demirci H, Larsen HGL, Hansen T, Rasmussen A, Cadambi A, Gregory ST, Kirpekar F, Jogl G; Multi-site specific 16S rRNA methyltransferase RsmF from Thermus thermophilus. RNA 16, 1584-1596 (2010)
Demirci H, Murphy IV FM, Belardinelli R, Kelley AC, Ramakrishnan V, Gregory ST, Dahlberg AE, Jogl G; Modification of 16S ribosomal RNA by the KsgA methyltransferase restructures the 30S subunit to optimize ribosome function. RNA 16, 2319-2324.
Demirci H, Belardinelli R, Seri E, Gregory ST, Gualerzi C, Dahlberg AE, Jogl G; Structural rearrangements in the active site of the Thermus thermophilus 16S rRNA methyltransferase KsgA in a binary complex with 5'-methylthioadenosine. J. Mol. Biol. 388, 271-282 (2009).
Li H and Jogl G; Structural and biochemical studies of TIGAR (TP53-Induced Glycolysis and Apoptosis Regulator). J. Biol. Chem. 284, 1748-1754 (2009).
Gregory ST, Demirci H, Belardinelli R, Monshupanee T, Gualerzi C, Dahlberg AE, Jogl G; Structural and functional studies of the Thermus thermophilus 16S rRNA methyltransferase RsmG. RNA 15, 1693-1704 (2009).
Demirci H, Gregory S, Dahlberg AE, Jogl G; Multiple site trimethylation of ribosomal protein L11 by the PrmA methyltransferase. Structure, 16, 1059-1066 (2008).
Demirci H, Gregory S, Dahlberg AE, Jogl G; Crystal structure of the Thermus thermophilus 16S rRNA methyltransferase RsmC in complex with cofactor and substrate guanosine. J. Biol. Chem. 283, 26548-26556 (2008).
Demirci H, Gregory S, Dahlberg A, Jogl G; Recognition of Ribosomal Protein L11 by the Protein Trimethyltransferase PrmA. EMBO J., 26, 567-577 (2007).
Li H and Jogl G; Crystal Structure of the Zinc-binding Transport Protein ZnuA from Escherichia coli Reveals an Unexpected Variation in Metal Coordination. JMB, 368, 1358-1366 (2007).
You Z, Omura S, Ikeda H, Cane DE, Jogl G; Crystal Structure of the Non-heme Iron Dioxygenase PtlH in Penatlenolactone Biosynthesis. J. Biol. Chem. 282, 36552-36560 (2007).
Holmes W and Jogl G; Crystal Structure of Inositol Phosphate Multikinase 2 and Implications for Substrate Specificity. J. Biol. Chem., 281, 38109-38116 (2006)
Jogl G, Hsiao Y, Tong L: Crystal structure of mouse carnitine octanoyltransferase and molecular determinants of substrate selectivity. J. Biol. Chem., 280, 738-744 (2005).
Jogl G, Tong, L: Crystal structure of yeast acetyl-coenzyme A synthetase in complex with AMP. Biochemistry, 43, 1425-1431 (2004).
Jogl G, Tong, L: Crystal structure of carnitine acetyltransferase and implications for the catalytic mechanism and fatty acid transport. Cell, 112, 113-122 (2003).
Jogl G, Rozovsky S, McDermott AE, Tong, L: Optimal alignment for enzymatic proton transfer: Structure of the Michaelis complex of triosephosphate isomerase at 1.2Å resolution. Proc. Natl. Acad. Sci. USA, 100, 1, 50-55 (2003).
We use X-ray crystallography as our main research tool (together with biochemical and biophysical approaches) to study the structure and function of proteins and macromolecular complexes such as the ribosome.
The overall goal of our research is to understand the molecular mechanism of antibiotic resistance caused by mutations in bacterial ribosomes and to evaluate the contribution of post-transcriptional rRNA modifications for ribosome function and antibiotic resistance.
The ribosome is a large molecular machine that translates the genetic code in messenger RNA (mRNA) molecules into proteins. The structure and the function of the ribosome is highly conserved in all domains of life. Despite this high conservation, however, bacterial ribosomes are targets for a large number of antibiotic compounds used to treat human diseases. 70S ribosomes consist of two subunits: the small subunit (30S) contains the function site for decoding messenger RNAs (the decoding center); the large subunit (50S) contains the site catalyzing peptide bond formation (the peptidyltransferase center). Proteins are synthesized in a cyclic process that extends a growing polypeptide chain by one amino acid during each cycle. At the beginning of the cycle, a codon of the messenger RNA is placed in the decoding center. The ribosome then selects a matching transfer RNA (tRNA) molecule delivering the correct amino acid. This process is enhanced by a protein, elongation factor Tu, that delivers the tRNA and leaves after the ribosome signals that the correct tRNA is bound. In the next step, the tRNA is accommodated into the peptidyltransferase center in the large subunit and the growing protein chain is extended by one amino acid. The ribosome then translocates bound tRNA molecules in a ratcheting motion and places the next mRNA codon in the decoding center to initiate the subsequent cycle of protein chain elongation.
We study how the antibiotic streptomycin interferes with the decoding process in ribosomes and how streptomycin causes the wrong tRNAs to be accepted for protein chain elongation. When streptomycin binds close to the decoding center, the ribosome continues to synthesize proteins but inserts incorrect amino acids in the growing protein chain. Newly made proteins are therefore dysfunctional and cause cell death. Previously, it was thought that streptomycin stabilizes a ribosome conformation signaling that the correct tRNA is bound in the decoding center regardless of identity of the bound tRNA. In our studies, however, we found that streptomycin also induces a surprising structural reorganization of the decoding center in the absence of tRNAs. This observation showed that streptomycin directly impacts the organization of the decoding center, in addition to its global effects on the conformation of the small ribosomal subunit. Our study also revealed that the decoding center is more dynamic than had been appreciated previously. Our experiments have focused on the impact of streptomycin on the small subunit using small tRNA analogues. Continuing this work, we are now studying how streptomycin affects the decoding center in the 70S ribosome in the presence of full-length tRNAs in order to better understand the functional relationship between global stabilization and local reorganization induced by streptomycin.
Related to this work, we have studied two mutations in a ribosomal protein (S12) that inactivate the ribosome, unless, surprisingly, the antibiotic streptomycin is bound as well. We found that these mutations also induce surprisingly large rearrangements of the decoding center although different than those induced by streptomycin. Studying structures of mutant ribosomes in complex with streptomycin, we could show that the rearrangements induced by the mutations and by streptomycin neutralize each other, restoring the function of the decoding center.
In a third study, we investigated how streptomycin-resistance mutations in ribosomal RNA neutralize the miscoding effects of streptomycin. We examined five different resistance mutations located in the vicinity of the streptomycin binding site. Three of these affected RNA bases in the small subunit that interact with each other in a hydrogen bond triplet interaction. Our studies showed that in all five cases, the mutation of an RNA base caused structural changes in the streptomycin binding site that were likely to reduce the binding affinity of streptomycin to the ribosome. We also found that changing any of the three bases in the base triplet induced a similar structural rearrangement of this region regardless of which base was replaced. Thus we were able to show how the ribosome structure tolerates smaller changes in local structure (resulting in streptomycin resistance) and yet retains a functional overall structure.
In current work, we now extend this approach to examine the structural basis for resistance to the antibiotic compounds capreomycin and hygromycin. We are also developing methods to enable structural studies of dominant lethal mutations that will provide new insights into the details of protein synthesis by the ribosome.
NIH R01GM094157-01, 9/15/10 - 8/31/15,
Structural robustness of ribosome functional centers
MPI grant with Dr. Steven Gregory
2015: Brown University Seed Award (with Steven Gregory, MCB)
Engineering orthogonal ribosomes to study ribosome function.
2008: Brown University Salomon Faculty Research Award
2006: Medical Research Award, Rhode Island Foundation
2006: Brown University Research Seed Fund (with Rebecca Page)
Structural Biology and Function of Macromolecular Complexes: Using Light Scattering to Initiate the Establishment of a Brown University Facility for State-of-the-Art Protein Biophysical Characterization