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
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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
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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
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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
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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.

 

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TRAINEE:
Pooja Srivanas
Graduate Student/Trainee
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Pooja is a graduate student in the Molecular and Systems Pharmacology Program in the laboratory of Dr. Christine M. Dunhan. She earned her B.A. Molecular & Cell Biology, University of California, Berkeley.

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MENTOR:
Christine M. Dunham, PhD
Associate Professor
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Dr. Christine M. Dunham is Associate Professor of Biochemistry and an Associated Faculty Member in the Department of Chemistry in the Emory College of Arts and Sciences. She earned her B.A. in Biochemistry at Barnard College, Columbia University. She earned her Ph.D. in the Department of Chemistry and Biochemistry, University of California, Santa Cruz, Laboratory of Prof. William G. Scott, with the thesis entitled, "Structure and Function of an RNA enzyme".

Dr. Dunham was an American Cancer Society Postdoctoral Fellow, MRC Laboratory of Molecular Biology, Cambridge, England, in the Laboratory of Dr. Venki Ramakrishnan.

 

German Vargas-Cuebas

TRAINEE:
Germán Vargas-Cuebas
Graduate Student/Trainee
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Germán Vargas-Cuebas earned his BS in Industrial Microbiology at the University of Puerto Rico – Mayagüez.Later, he trained as a post-baccalaureate under the mentorship of Dr. Ralph R. Isberg at Tufts University, where he employed Tn-seq to identify targets to potentiate antibiotics against the nosocomial pathogen Acinetobacter baumannii. Currently, he is a Ph.D. candidate and an ARTDTP fellow at Emory University, studying Clostridioides difficile response to the host antimicrobial peptide LL-37 under the mentorship of Dr. Shonna M. McBride. With his project, he aims to expand our knowledge of how C. difficile is able to survive within the host, and determine which molecular mechanisms this pathogen uses to adapt to this antimicrobial peptide.

Dr. McBride

MENTOR:
Shonna M. McBride, PhD
Assistant Professor
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Shonna McBride, PhD, is Assisant Professor in the Department of Microbiology and Immunology at Emory University School of Medicine. Her research laboratory centers on the emerging pathogen, Clostridium difficile. C. difficile causes chronic intestinal disease that is difficult and costly to treat. The focus of her laboratory is to identify mechanisms that C. difficile uses to colonize the host and disseminate in the environment, with the intent of opening new avenues for treatment of infections. These studies employ a combination of molecular genetic, genomic, biochemical and in vivo approaches to tease apart these mechanisms and their regulation in C. difficile. To colonize the intestine and cause persistent disease, the bacterium must be able to circumvent killing by host innate immune mechanisms. The production of antimicrobial peptides (AMPs) by the innate immune system represents a critical component of host defense against infections that bacteria must overcome to cause persistent disease.  Resistance to these peptides is a demonstrated virulence factor for many bacterial pathogens.  They hypothesize that resistance of C. difficile to antimicrobial peptides plays a major role in the ability of the bacterium to colonize the human intestine and cause disease.  As such, the laboratory is focused on identifying and understanding the mechanisms that C. difficile utilizes to resist AMPs produced by the host and the indigenous microbiota of the intestine. To date, they have identified multiple AMP resistance mechanisms employed by C. difficile, including the novel bacteriocin resistance mechanism, CprABC. By uncovering the bacterial resistance mechanisms that influence disease progression, it is expected that this research will generate knowledge that can be used to manipulate the interactions between the bacteria and the host to prevent and treat infections.

Dr. McBride joined the Emory faculty in June 2012.  She received her Ph.D. degree from the University of Texas Health Science Center at San Antonio in 2005 and a Bachelor of Science degree from McNeese State University in 1999.  She trained as a postdoctoral fellow in the field of bacterial pathogenesis at the Schepens Eye Research Institute of Harvard Medical School from 2005 to 2008 and at the Tufts University School of Medicine from 2008 to 2012.  Dr. McBride’s research is supported by a K01 Career Development Award and an R03 Research grant from the NIDDK/NIH.  

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TRAINEE:
Cassie Zaremba
Graduate Student
/Trainee
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Cassie is a graduate student in the Department of Chemistry in the Emory University College of Arts and Sciences.

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MENTOR:
Bill Wuest, PhD
Associate Professor/Mentor
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Dr. Wuest is a GRA Distinguished Investigator and Associate Professor in the Department of Chemistry in the Emory College of Arts and Sciences.