About Us

William Shafer, Ph.D.DIRECTOR:
William Shafer, PhD

wshafer@emory.edu

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.

Zane Laughlin

TRAINEE:
Zane Laughlin
Graduate Student
zane.timothy.laughlin@emory.edu

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. 

Dr. Conn

MENTOR:
Graeme Conn, PhD

Associate Professor
gconn@emory.edu

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 antibiotic resistance that arise through ribosomal RNA modification and non-coding RNA-mediated pathogen evasion of host cell innate immune responses.

Dr. Conn received his B.Sc. and Ph.D. at the University of Edinburgh, UK, and followed this with postdoctoral research as a Wellcome Trust International Fellow at the Johns Hopkins University, Baltimore, MD. Graeme was a faculty member at UMIST/ The University of Manchester, UK, from 2000 and joined the Department of Biochemistry at Emory as an Associate Professor in September 2008.

Aimee Paulk

TRAINEE:
Aimee Paulk, BS
Graduate Student
arpaulk@emory.edu

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

MENTOR:
Philip Rather, PhD

Professor
prather@emory.edu

Philip N. Rather is a Professor in Microbiology and Immunology. His lab studies the mechanisms of virulence and intrinsic antibiotic resistance in the nosocomial pathogen Acinetobacter baumannii. Dr. Rather's lab is studying cell-to-cell signaling in the human pathogen Acinetobacter baumannii with the goal of understanding the role of this process in virulence. These studies involve: (i) purification and structural characterization of extracellular signaling molecules, (ii) identification of genes involved in signal response, (iii) identification of genes involved in signal production, and (iv) the use of RNA-Seq to identify genes activated/repressed by extracellular signals.

A second area of study addresses the mechanisms that allow the urinary tract pathogen Proteus mirabilis to differentiate to swarmer cells. The role of a regulatory molecule, phenethylamine, in controlling the activity of a key transcriptional regulator (FlhDC) is being investigated.  In addition the Rather Lab is investigating the mechanisms that allow P. mirabilis to sense surfaces and transmit these signals to the regulation of gene expression.

 

Sherman

TRAINEE:
Edgar Sherman, BS
Graduate Student
edgar.sherman@emory.edu

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. 

Dr. Weiss

MENTOR:
David S. Weiss, PhD

Associate Professor
david.weiss@emory.edu

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 mechanisms of antibiotic resistance employed by Gram-negative nosocomial pathogens such as Acinetobacter baumannii and Enterobacter cloacae.

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.

Michelle Su

TRAINEE:
Michelle Su
Graduate Student
michelle.su@emory.edu

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

MENTOR:
Timothy Read, PhD

Professor
tread@emory.edu

Dr. Read is Professor of Infectious Diseases with Secondary Appointment in Human Genetics. Dr. Read's research interests center around the application of genomics technologies to understanding infectious diseases. In particular, he is interested in trying to frame the questions that only become possible to answer as new and even better instruments for generating DNA sequence information come online. Genomics for infectious disease detection and clinical diagnosis. The rapidly decreasing cost of sequencing offers the opportunity in the near future to rapidly acquire large portions of the genome sequence of pathogens, either from DNA extracted from pure cultures or directly from clinical samples (metagenomics).

Dr. Read is interested in applying new technologies to determine their limits of sensitivity and to develop software to extract clinically useful information from the sequence data. Bacterial Pathogen Genome Evolution. The availability of multiple high quality genomes of pathogens such as Bacillus anthracis (etiologic agent of anthrax) and its less pathogenic close relatives affords the opportunity to ask questions about the evolution of virulence in these lineages. His particular interest is the extrachromosomal elements such as plasmids and bacteriophage, and intergenic repeat sequences. These extraneous genetic entities often carry vital virulence genes (like the anthrax toxin and plague virulence genes). They are also potent factors for short term genome change, through insertion, expansion and movement in the genomes and through the selection pressure they presumably exert on the genome for resistance.

Dr. Read seeks to find out how (and why) pathogens evolve to infect humans. What are the species that recent ancestors of B. anthracis were infecting before they developed virulence for mammals? What are the danger signs to look for in predicting the source of new emerging diseases? A genome based understanding of pathogen evolution will be vital for interpreting genetic variation in clinical sequence data (see above). The same knowledge can also be applied to vaccine and drug target selection.

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.