Journal of Biosciences

, Volume 24, Issue 4, pp 453–459 | Cite as

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


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.


ω subunit ω-less RNA polymerase interaction promoter foot-printing 


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Copyright information

© Indian Academy of Sciences 1999

Authors and Affiliations

  1. 1.Centre for Cellular and Molecular BiologyHyderabadIndia
  2. 2.The Swedish Institute for Infectious Disease ControlSweden

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