• Dipankar Chatterji

      Articles written in Journal of Biosciences

    • Promoter search and strength of a promoter: two important means for regulation of gene expression inEscherichia coli

      Rakesh K Mishra Dipankar Chatterji

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      Search for a promoter element by RNA polymerase from the extremely large DNA base sequence is thought to be the slowest and rate-determining for the regulation of transcription process. Few direct experiments we described here which have tried to follow the mechanistic implications of this promoter search. However, once the promoter is located, transcription complex, constituting mainly the RNA polymerase molecule and few transcription factors has to unidirectionally clear the promoter and elongate the RNA chain through a series of steps which altogether define the initiation of transcription process. Thus, it appears that the promoter sequence acts as a trap for RNA polymerase associated with a large binding constant, although to clear the promoter and to elongate the transcript such energy barrier has to be overcome. Topological state of the DNA, particularly in the neighbourhood of the promoter plays an important role in the energetics of the whole process

    • Alteration in template recognition byEscherichia coli RNA polymerase lacking the ω subunit: A mechanistic analysis through gel retardation and foot-printing studies

      Kakoli Mukherjee Dipankar Chatterji

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      The ω subunit ofEscherichia coli RNA polymerase is a 91 amino acid polypeptide which co-purifies with the enzyme and is thought to help in maturing the rest of the enzyme to its full functionality. Purified ω when added externally was found to inhibit general transcriptional activity of ω-less RNA polymerase as well as promoter-specific single-round transcriptional activity at all the promoters tested. In this study we have tried to analyse the observed inhibition of transcription using gel retardation assays and KMnO4 foot-printing. Further, through protein foot-printing we have attempted to identify alterations in the interaction of the ω-less core enzyme with the σ70 subunit.

      Our results suggest that the ω-less holoenzyme has lesser affinity towards the DNA template and external addition of ω destabilizes the open complex for both the wild-type and ω-less enzyme. The ω-less core enzyme interacts with the σ70 subunit to expose the — 35 recognition domain (domain 4.2) unlike that observed in the wild-type interaction. Thus the absence of the ω subunit leads to the formation of an enzyme which has altered DNA binding and σ70binding properties. Circular dichroic measurements also indicate a major conformational alteration of both holo and core RNA polymerase in the presence and absence of the ω subunit.

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