Research in the Hammer Lab

The main focus of research in my lab is how bacteria sense and respond to extracellular chemical substances to regulate gene expression. Many harmful and beneficial bacteria produce and then respond to small molecules called autoinducers, a process called quorum sensing (QS). Populations of bacterial cells coordinate behaviors using autoinducers, and commonly integrate information provided by additional extracellular cues to tailor gene expression to a particular niche. Bacteria use information in the form of extracellular chemicals to control processes such as attachment (biofilm formation), virulence (toxin production), light production (bioluminescence), and competence (DNA uptake). To understand how chemical signals coordinate changes in gene expression, we measure processes controlled by cell signaling, with a goal to manipulate bacterial signaling system for beneficial purposes.  For example, disease outcome may be altered by disrupting signaling in harmful bacteria, while useful products may be produced by manipulating this process in benign bacteria. In Vibrio cholerae, a common inhabitant of marine ecosystems and the cause of the disease cholera, we are taking a “top-down” approach by dissecting the cell signaling network and the behaviors it controls. In the model organism, E. coli we are taking a bottom-up approach by engineering signaling systems into this microbe toward a goal of rationally designing molecular-based communication systems. We use complementary methods, including genetics, biochemistry, bioinformatics, and ecological approaches to achieve these ends.

Quorum-sensing small RNA regulation in pathogenic Vibrio cholerae. In V. cholerae, the response to secreted autoinducer signal molecules coordinates the expression of multiple non-coding small RNAs (sRNAs), called the Qrrs (quorum regulatory RNAs). Qrr sRNAs are predicted to base-pair with multiple mRNA targets and either promote or prevent translation depending on whether Qrr-mRNA duplex formation exposes or occludes the ribosome binding site in the mRNA. RNA chaperone Hfq is required for efficient base-pairing. We have used in vivo and in vitro methods to confirm Hfq-dependent base-pairing of Qrr RNA and the mRNA of QS transcription factor HapR, which regulates production of V. cholerae virulence factors such as the cholera toxin (Bardill, Zhao & Hammer, 2011). Genetic screens and computational methods have identified additional target genes under Qrr control. We are currently defining each Qrr-mRNA interaction and the consequence of pairing to the pathogenesis and ecology of V. cholerae.

Regulation of natural competence. In marine environments, V. cholerae often resides in biofilms on surfaces of zooplankton molts and crab shells, which are composed of the insoluble polysaccharide chitin. Prior studies demonstrated that chitin (via the TfoX regulator) and QS (via HapR) induce a genetically encoded state of natural competence in which V. cholerae can take up DNA from the environment. In other bacteria, acquired DNA may be for nutrition or genome repair, but may also recombine onto the chromosome resulting in transformation, one mechanism of horizontal gene transfer (HGT). We have shown that chitin-induced transformation is regulated not only by QS autoinducers (Antonova & Hammer, 2011), but also by a nucleoside scavenging response controlled by the CytR regulator (Antonova, Bernardy & Hammer, 2012). We are currently using computational and experimental methods to define the network of genes controlled by TfoX, HapR, and CytR. These studies will define the role that environment and genetics play in genome evolution for this important marine pathogen.

The role of Vibrio cholerae quorum sensing in microbial communities. Vibrio cholerae is an endemic member of aquatic environments in many regions of the world. Several Vibrio cholerae clinical isolates obtained during worldwide outbreaks encode non-functional QS systems due to mutations in transcription factor, HapR. That such strains are fully virulent supports the idea that QS is not required per se for V. cholerae to be a pandemic pathogen, however we and others have proposed that environmental niches likely exist where a functional QS system is maintained for it confers a fitness advantage. With collaborator Dr. Malka Halpern from Haifa University, we are currently quantifying QS functionality in V. cholerae isolates obtained from diverse marine habitats where QS-controlled gene products appear to play an important role in the microbial community.

Engineered signaling systems for bio-inspired molecular communication. There is interest in developing nano-scale communication systems capable of interfacing with biological systems. Bacterial QS is a tractable model system to initiate such research because autoinducer molecules convey information within a population of cells that serve as both senders and receivers of the signal. In an effort to understand the limits of chemical communication, we are engineering E. coli transmitter cells that make homoserine lactone (HSL) autoinducers, and also E. coli receiver cells that encode the HSL receptor and respond by producing green fluorescent protein. With our engineering colleagues in the School of Mechanical Engineering and School of Electrical and Computer Engineering we are designing synthetic QS circuits to manipulate chemical communication and to validate mathematical models of cell signaling within engineered microfluidic devices (see MoNaCo project on the links page).

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