Transcription is a key regulatory step for a specificset of gene expression, which in turn globally programs or reprograms the cellsin response to a variety of physiological or stress signals. In eukaryotecells, transcription factors as well as cofactors are centered on the specificenhancer regions of genes to form high-order regulatory assemblies. Themost, if not all, of these cofactors are histone modification enzymes thatconvey a variety of upstream signals to epigenetic marks. Our lab is taking a structuraland functional approach to unravel molecular mechanisms of the epigeneticmodifications and transcriptional regulation, in particular the histoneacetylation by p300/CBP and PCAF/GCN5. In prokaryotic cells, two-componentsystem (TCS), which typically consists of a histidine kinase (SK) and a cognateresponse regulator (RR), is a major signal transduction pathway responsible forstimuli induced reprogramming process. Our lab uses an essential TCS, VicRK, alsocalled YycFG or WalRK, in many gram+ bacteria as a model system tounderstand how the intra/extracellular signals regulate the transcription ofbacteria.


Epigenetic modifications deliver crucial informationbeyond genetic DNA. Their compositions,locations, dynamics and crosstalks are hypothesized in so-called ‘histonecodes’, which are complicated, sometimes very subtle and therefore challenging tostudy. While decoding is still in progress, we dedicateour efforts mainly on the regulation of acetylation and its crosstalk withhistone methylation. Modification enzymes of p300, CBP, PCAF andGCN5 are responsible for lysine acetylation while HDACs remove them. Theiractivities are always associated with specific transcription factors, forexample, myocyte enhancer factor 2 (MEF2) by forming high-order functionalcomplexes. We have made our greatest effort to build a series of architecturalpictures for those cofactors sitting on DNA that may reflect dynamic processesof molecular machineries in transcriptional regulation (Figure 1). We are also interestedin those underlying molecular mechanisms that regulate these assemblies andtheir enzymatic activities.

 
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Figure 1. A beautiful structureof p300 Cysteine-Histidine 3 (CH3) domain and MEF2/DNA complex, revealing threeasymmetric interfaces for high-order transcriptional enhancer assembly.

 
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Bacteria respond totransient environments via transmembrane-integrated sensor kinases (SK), whichact in concert with their intracellular cognate response regulators (RR) toelicit necessary adaptive responses that are critical for their survival andvirulence. The SK and RR are formulated into a concept of two-component signaltransduction systems (TCS), whereby upon detecting specific stimuli the SKautophosphorylates at a conserved histidine residue to initiate a signalingcascade of stress responses. Over 60% RRs serve transcriptional factors thatare activated upon aspartic acid phosphorylation by their cognate SKs. However,How the bacterial sensors perceive intracellular and environmental signals andfurther trigger autokinase activity is not well understood. We have determinedan entire intracellular region of a histidine kinase VicK by X-raycrystallography, a landmark progress in our exploration of signal sensing andtransduction (Figure 2). We are currently taking a combinatorial approach,including computational simulation and genome editing, to investigateconformational dynamics, signal transduction and cellular reprogramming of ahistidine kinase using VicK and its cognate response regulator VicR asexamples. Since this TCS is essential in many notorious pathogens, including Streptococci, Staphylococci and Enterococci, which have developed multipleantibioticresistances, VicKR system can be considered a potential drug target for newantibiotics.

 
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Figure 2. A dimeric structure ofan essential histidine kinase VicK from streptococci,providing a molecular base to better understand stress signal sensing andtransduction in bacteria.