William Shafer, PhD
William Shafer received his PhD degree in Microbiology from Kansas State University in 1979 where he studied the genetics of enterotoxin synthesis by Staphylococcus aureus. After postdoctoral studies with P.F. Sparling at the University of North Carolina where he studied the genetics of antibiotic resistance expressed by Neisseria gonorrhoeae, he moved to Emory University School of Medicine where he now Full Professor. He is also a Senior Research Career Scientist at the Atlanta VA Medical Center. He has been continually funded by the NIH and VA since 1984, has published over 115 manuscripts, serves on multiple Editorial Boards and served on several NIH, VA and international study sections.
Ribosomal RNA (rRNA) modification is important for correct ribosome assembly, can alter ribosome function, and can confer resistance to many clinically important ribosome-targeting antibiotics in pathogenic bacteria. Unlike other ribosome-targeting antibiotics, such as macrolides and aminoglycosides, whose activity is blocked by methylation of the ribosome, the tuberactinomycn antibiotic capreomycin requires methylation at position C1409 of the 16S rRNA within the small ribosome subunit (30S) and C1920 of the 23S rRNA within the large ribosome subunit (50S). TlyA is the 2’-O-methyltransferase that modifies the ribose 2’- OH of C1409 and C1920 using S-adenosyl-methionine (SAM) as a methyl group donor. The X-ray crystal structure of the C-terminal domain (CTD) of TlyA showed that the domain adopts a Class I methyltransferase fold while homology modeling suggests the N-terminal domain (NTD) adopts an S4 ribosomal protein fold. Additionally, the structural studies of the CTD revealed that the short interdomain linker was able to adopt two different conformations and was unexpectedly critical for SAM binding within the CTD. These observations lead to a proposal that the interdomain linker might be able to act a “molecular switch” by altering the interaction between the NTD and the CTD and controlling TlyA activity upon correct substrate recognition. However, TlyA’s mechanism of recognition and modification of its target sites located in structurally distinct contexts is currently not known. In this project, he will test the hypothesis that TlyA is structurally and functionally divided: the NTD directs specific ribosome subunit recognition, the CTD performs catalysis of methylation, and the flexible linker controls essential communication between these two domains. The goal is to determine the mechanism of TlyA 30S/50S recognition and site-specific methylation of two distinct target nucleotides. He will accomplish this through the following two Specific Aims. The first aim is to define TlyA NTD surfaces and critical residues for recognition of the distinct 30S and 50S ribosomal subunit binding sites using site-directed mutagenesis followed by binding and methyltransferase assays. In my second aim, he will determine the molecular mechanism by which TlyA recognizes then methylates its target sites on the ribosome using studies of protein dynamics using hydrogen-deuterium exchange coupled to mass spectrometry, and high- resolution structures using X-ray crystallography and cryo-EM. This project will increase our understanding of not only TlyA’s mechanism of binding and modification but also those of other ribosome-modifying enzymes, expanding our limited understanding of how RNA modification enzymes control substrate specificity.
Graeme Conn, PhD
Graeme Conn is an Associate Professor in the Biochemistry Department, Emory University School of Medicine. His lab uses modern biochemical and biophysical methods to study the structures, interactions and biological functions of biomedically important RNA and protein molecules. Current topics include mechanisms of bacterial
Aimee Paulk, BS
Acinetobacter baumannii is a multidrug-resistant (MDR), Gram-negative nosocomial pathogen that exhibits two forms, distinguished by their opaque (O) and translucent (T) colony phenotypes. The two variants have different patterns of gene expression, and notably, only the O variant is capable of infection. Additionally, the O variant exhibits significantly greater resistance to host antimicrobial peptides, reactive oxygen species, hospital disinfectants, and to certain antibiotics including colistin. The enhanced resistances of the O variant are especially worrisome as the MDR nature of A. baumannii already poses a considerable problem in treating infections, and colistin is often reserved as the last line option for treatment. Colonies of the O and T variants rapidly interconvert, and therefore our group has focused on identifying and characterizing genes involved in this switch. My thesis objective is to thoroughly characterize ABUW_1132, a gene I recently discovered where loss of function mutations reduce O to T switching by 35-fold. ABUW_1132 is predicted to encode a LysR-family transcriptional regulator, and preliminary data indicates it to be a major component of the O to T switch. This work will provide a more complete picture of the regulation of A. baumannii’s phenotypic switch, which is crucial to understanding infection by this pathogen and thereby formulating new methods of treatment.
Philip Rather, PhD
Philip N. Rather is a Professor in Microbiology and Immunology. His lab studies the mechanisms of virulence and intrinsic
Edgar Sherman, BS
Edgar Sherman received his BS from The University of Texas at San Antonio (UTSA) in 2014. Edgar developed a strong interest in microbial genetics following two research internships where he investigated the role of mitochondrial gene function in eukaryotic respiration at The University of Texas at Austin and studied how protein turnover affects aging in rodents at The University of Texas Health Science Center in San Antonio. At UTSA, Edgar’s research focused on mechanisms of biofilm formation in the nosocomial pathogen Acinetobacter baumannii by targeting genes involved in bacterial cell signaling. After graduating, Edgar was accepted into the Microbiology and Molecular Genetics (MMG) program at Emory University where his research interest in antimicrobial resistance led him to join Dr. David Weiss’ lab and focus on studying antibiotic resistance mechanisms in Multi-drug resistant Gram-Negative pathogens. Specifically, Edgar’s research focuses on understanding the underlying genetic pathways facilitating resistance to aminoglycosides, an important class of antibiotics, in A. baumannii and how these mechanisms lead to treatment failure in a patient. Under the Antimicrobial Resistance and Therapeutic Discovery Training Program, Edgar seeks to characterize novel resistance mechanisms to ultimately improve patient outcome and expand our understanding on how bacteria evolve to combat our clinical therapeutics.
David S. Weiss, PhD
David S. Weiss is an Associate Professor in the Division of Infectious Diseases and Co-Director of the Emory Antibiotic Resistance Center. His lab's research is focused on understanding
His lab has identified and mechanistically characterized several novel genes that contribute to resistance to the last-line, cationic polymyxin antibiotics in diverse bacteria. Furthermore, this research has shown that the development of polymyxin resistance in treated patients leads to cross-resistance to cationic antimicrobial peptides of the host innate immune system. Thus, polymyxin treatment may select for bacterial strains with increased virulence. In addition to how antibiotics may alter bacterial susceptibility to the immune system, his lab is very interested in exploring the causes of unexplained treatment failures in which antibiotic therapy is ineffective despite bacterial strains appearing to be susceptible to a given antibiotic.
I am interested in how the Gram-positive pathogen Staphylococcus aureus develops intermediate resistance to vancomycin; these strains are called VISA. My project tests the hypothesis that different VISA mutations have different fitness in two clinically important genetic backgrounds and are compensated by different mutations. Aim 1. Interaction of genetic background, mutation and fitness costs for vancomycin resistance level. I will determine how single nucleotide polymorphisms (SNPs) in candidate genes modulate vancomycin resistance to characterize mutations found in VISA strains by using isogenic USA100 and USA300 mutants and testing for a phenotypic effect on vancomycin resistance. Validated VISA determinants will be introduced into USA100 and USA300 MRSA lineages to investigate how vancomycin resistance alters the fitness and virulence of strains and ultimately the fitness landscape between lineages. Aim 2. Parallel evolution of vancomycin resistance and subsequent divergence. I will determine the convergent mutation in candidate genes of USA100 and USA300 by generating and sequencing laboratory VISA strains at different bottlenecking pressures. Maintenance of these VISA strains at sub-MIC antibiotic concentrations will allow for the study of divergence in evolution that will occur after selection pressures have decreased and more evolutionary pathways have opened. Together, these two approaches will be a comprehensive study of the evolution of vancomycin intermediate resistance in S. aureus and its effects on the fitness landscape.
Timothy Read, PhD
Dr. Read received a BSc in Biological Sciences from the University of London and then studied Microbial Genetics at the University of Leicester with Prof Brian Wilkins.