Biography: Dr. Adhya received his Ph.D. from the University of Calcutta and also from the University of Wisconsin. He was a Research Associate at University of Rochester and Stanford University. He joined the Laboratory of Molecular Biology in 1971. In 1994, Dr. Adhya was elected a member of the National Academy of Sciences. Dr. Adhya has also been an Adjunct Professor in the Department of Genetics at George Washington University since 1987.
Research: Virtually every adaptation and developmental process originates at the level of gene regulation by transduction of extra- or intracellular signals. Transcription is the major target of regulation of gene expression. Our research interest covers modulation of transcription by DNA control elements and regulatory proteins--for example, repressors, activators, terminators, and antiterminators and their signals. We have previously demonstrated transcriptional regulation both at the level of initiation by activators and repressors and at the level of elongation by terminators and antiterminators in the gal operon which encodes enzymes of D-galactose metabolism in Escherichia coli. Presumably because of the amphibiotic nature of the biochemical pathway in carbon metabolism, the operon shows a multitude of controls even at the level of transcription initiation and has been a paradigm system for studying control of transcription initiation. The operon is transcribed from two promoters which are subject to both negative and positive control by at least four proteins, Gal repressor, Gal isorepressor, cyclic AMP receptor protein, and bacterial liestone like protein, HU.
The major highlight of our work in the past two years is the revelation that GalR alone exerts control on the two promoters in a multivalent way.
Regulation by DNA Looping: Synergistic repressor binding to two operators, OE and OI encompassing the promoters, P1 and P2, creates a DNA loop which inhibits transcription initiation from the gal promoters. A topologically closed loop of 11 helical turns, which is inflexible to torsional changes, disables the promoters by resisting DNA unwinding by RNA polymerase needed for open complex formation. Interaction between two proteins bound to different sites on DNA modulating the activity of the intervening segment toward other proteins may be a common mechanism of regulation in DNA-multiprotein complexes.
Requirement of HU: Concurrent repression of the gal promoter by GalR needs another factor, which has been purified and identified to be the bacterial histone-like protein HU, and a supercoiled DNA template. Footprinting experiments show that HU binds to gal DNA in a site- specific way and HU binding is entirely dependent upon binding of GalR to both OE and OI. HU, in concert with GalR, forms a specific nucleoprotein higher order complex containing a DNA loop. This way, while remaining sensitive to inducer, HU deforms the promoter to make the latter inactive. The gal repression system provides a model for studying how a "condensed" DNA becomes available for transcription.
Atomic Force Microscopic observation of DNA loop: We successfully applied atomic force microscopy (AFM) imaging to visualize gal DNA loops when complexed with GalR and HU. Supecoiling of DNA, which is critical for GalR action, stabilizes the DNA loops by providing an energetically favorable geometry of DNA.
Regulation by DNA unlooping: Repressor binding to the upstream operator OE alone, in the absence of DNA looping, represses one promoter P1 and activates the other P2. We have shown that both inhibition and stimulation of transcription requires the presence of specific regions of the alpha subunit of RNA polymerase. Our results suggest that Gal repressor inhibits or stimulates transcription initiation by disabling or stimulating RNA polymerase activity at a postbinding step by directly or indirectly altering the specific domain of alpha to an unfavorable or to a more favorable state, respectively.
A new enzyme: We have discovered a new enzyme, aldose-1-epimerase, which interconverts the two optical anomers of the inducer, D-galactose.
Inducer-repressor interaction: By genetic and biochemical studies, we have identified several residues in the Gal repressor which interact with the inducer.
Currently, we are (1) studying the biochemical nature of the different nucleoprotein complexes that control transcription initiation in gal in different ways; (2) investigating the role of HU in repression, (3) detecting both genetically and biochemically various protein-protein and DNA protein contacts in the different complexes; and (4) identifying whether one or both of the optional anomers of the D-galactose is the real inducer.