Mycobacterium tuberculosis H37 Rv1222: structural insight in transcription inhibition

Eradication of multidrug resistant (MDR) Mycobacterium tuberculosis is a world-wide focus. A recent study by Fakhar et al is successful to elicit the structural information of a potent drug target of M. tuberculosis involved in the peptidoglycan biosynthesis (Fakhar et al., 2016). The computational virtual screening and molecular docking study suggested that bioactive compounds can be a target inhibitor molecule against the MDR pathogen (Skariyachan et al., 2015). Location of specific amino acids in some of the protein is a useful link to predict their function in order to identify the molecular targets for the development of new drugs (Saidijam & Patching, 2015). RNA polymerase is a proven target for anti-tuberculosis drug development. RNA polymerase (RNAP) together with the various sigma factors plays the major role in controlling transcription and thus the gene expression. Sigma factors are further controlled by anti-sigma factors inhibiting promoter recognition process and thereby interfere in transcription initiation (Rodrigue, Provvedi, Jacques, Gaudreau, & Manganelli, 2006; Betts, Lukey, Robb, McAdam, & Duncan, 2002). These anti-sigma factors are regulated by several downstream protein factors called anti-anti-sigma factors (Betts et al., 2002). Hence, the entire biochemical cascade is orchestrated to maintain proper homoeostasis within the host. The complex transcriptional regulation of Mtb-SigE is well regulated by a ZAS family protein, Rv1222, located immediately downstream to the former (Dona et al., 2008). It has been proposed that the interaction of Rv1222 with Mtb-SigE takes place under reducing conditions (Barik, Sureka, Mukherjee, Basu, & Kundu, 2010). However, recent studies have denied the fact of anti-sigma properties of Rv1222. On the contrary, it prompts that Rv1222 is a potent transcription inhibitor that can bind with the RNAP core rather than the sigma factor to paralyse the entire gene regulation process. It has stated that Rv1222 anchors RNAP onto DNA to inhibit transcription (Rudra, Prajapati, Banerjee, Sengupta, & Mukhopadhyay, 2015). This study is first to delineate the structural prediction of Rv1222 and to study its nature of transcription inhibition under multiple mutually exclusive circumstances. Rv1222 is allowed to interact with Mtb-SigE through molecular docking studies and found to behave differentially, like, (1) when only Rv1222 is allowed to interact with the Mtb-SigE and β subunit of Mtb-RNAP complex (Rv1222-SigE::β) (2) if Rv1222 and Mtb-SigE complex binds with the β subunit of Mtb-RNAP (Rv1222::SigE-β) (3) Rv1222 docked with Mtb-SigE and Phsp20 promoter binding complex Rv1222-SigE::Phsp20 (4) the Mtb-SigE and Rv1222 complex interacts with its cognate promoter Phsp20 (Rv1222::SigE-Phsp20). It is well noted from all these interactions that Rv1222 binds efficiently with sigma factor, rather than binding to core RNAP and inhibit transcription. Rv1222 can interact with promoter DNA but this interaction is much weaker than that of sigma factor. Thus, it provides us a great means to analyse the inhibition of gene expression of Rv1222 through RNAP or promoter-mediated pathway. Strenuous molecular simulations have given enough vividness on the validity of the structure of each of the macromolecules.