Rapid emergence of multi-drug resistance in Mycobacterium tuberculosis has necessitated the development of newer candidate drugs which can selectively inhibit the growth of the organism. Among the best targets available today, transcription machinery is, by far, the most important one and the antibiotic rifampicin binds to a specific site on the enzyme RNA polymerase. However, it is not very effective towards the stationary phase of the organism or the persistors. In order to address this problem, we report here a protocol for generating an affinity tagged RNA polymerase, which can be purified easily from different phases of growth of the organism. It allows exploring RNAP associated proteins, which may confer resistance to rifampicin, using the approach of functional proteomics. (c) 2008 Elsevier Inc. All rights reserved.