Projects
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RNA-Binding Proteins
We study in particular an RNA-binding domain called ANTAR, which binds a two-hairpin element to prevent transcription termination.
RNA-binding proteins
Our laboratory investigates different mechanisms of transcription attenuation in bacteria. In these mechanisms, a transcription termination site is controlled in a signal-dependent manner by a cis-acting regulatory RNA. In particular, we are studying the structure and function of an RNA-binding protein domain called ANTAR. We investigate the determinants for ANTAR-RNA recognition and use this information to predict ANTAR-based regulons.
Processive Antitermination
The transcription elongation protein NusG is present in all cells; we discovered a discrete phylogenetic subfamily called LoaP, which affects transcription elongation of secondary metabolite pathways
Processive Antitermination
Processive antitermination (PA) occurs when RNA polymerase is modified to become resistant to downstream pause and termination sites. There are only a few classes of PA mechanisms that have been discovered. We discovered and are investigating two new classes: (1) an RNA element called ‘EAR’, which alone promotes PA of operons encoding expolysaccharides, and (2) a subclass of specialized NusG paralogs called LoaP, which promote PA of gene clusters encoding secondary metabolites and polysaccharides.
Bacterial Microcompartments
Microcompartments house specific cargo enzymes, such as those that are responsible for ethanolamine catabolism
Bacterial microcompartments
Microcompartments are organelle-like structures, which package specific enzymes inside the microcompartment lumen. They allow exchange of substrates, products and cofactors through surface-associated pores and are assembled and disassembled under specific cellular conditions. In particular, we study microcompartments for ethanolamine utilization.
Riboswitch Reporters
When coupled to fluorescent output platforms, riboswitches can provide single-cell information about metabolite dynamics
Riboswitches
Riboswitches are cis-acting, signal-responsive regulatory RNAs. We have longstanding interests in: (1) their structural characteristics, (2) the genes that they regulate, and (3) their synthetic applications. For the latter, we are currently exploring how riboswitches can be used for live-cell imaging of metabolite dynamics.
Nramp Proteins
NrmT proteins comprise a discrete, deep-branching outgroup of the Nramp family of proteins. Some or all of NrmT proteins transport magnesium.
Magnesium homeostasis
As a result of our efforts in studying metal-sensing riboswitches, we discovered a class of transport proteins called NrmT, which may act as magnesium transporters. These proteins are evolutionarily related to Nramp transport proteins, which are not traditionally assumed to transport this metal. Furthermore, they are widely used among bacteria. Also, we believe this transporter interacts with additional cytoplasmic proteins that affect its activity. For all of these reasons, we are studying the structure and function of these magnesium transporters.
Dinucleotidase Enzymes
ome enzymes appear to specialize in the recycling of dinucleotides, which is an activity that affects nucleotide signaling pathways.
Signaling nucleotides
There are many types of noncoding RNAs that have been discovered to regulate bacterial gene expression. However, another increasingly large category of RNA-based regulatory factors are signaling nucleotides, including but definitely not limited to cyclic nucleotides (e.g., cAMP), and cyclic dinucleotides (e.g., cyclic di-GMP, cyclic di-AMP). In a collaborative project with Drs. Vincent Lee and Holger Sondermann, we are investigating some of the RNase enzymes that affect recycling of these ribonucleotide signals.