pH modulates the role of SP6 RNA polymerase in transcription process: an in silico study

Abstract

SP6 RNA polymerase (SP6 RNAP) is an essential enzyme for the transcription process in SP6 bacteriophage. SP6 RNAP plays a vital role in mRNA vaccine designing technology and other translational biotechnology research due to the high specificity towards its promoter. The self-replicating performance also put this polymerase to study extensively. Despite of the reports emphasizing the function of this enzyme, a detailed structural and functional understanding of RNA polymerase is not reported so far. Here, we report the first-ever information about SP6RNAP structure and its effect on promoter binding at different pH environments using molecular docking and molecular dynamics simulation (MDS) study. We also report the changes in polymerase conformations in different pH conditions using in-silico approach. The docking study was also performed for SP6 RNAP with SP6 promoter at different pH environments using the in-silico docking tools and conducted the MDS study for complexes. MM/PBSA and per residue energy contribution has been performed at three different pH environments. The structural aspects confirmed that the pH 7.9 state favors the polymerase functional activity in the transcription process which was in the range reported using transcription assay. This polymerase’s unique features may play its emerging role as an efficient transcription factor in translational biological research.

Communicated by Ramaswamy H. Sarma

The PRL and PBL of polymerase maintain a minimum distance from the promoter site at pH 7.9, leading to a possible transcription model for SP6 bacteriophage.

HIGHLIGHTS

• The structure of SP6 RNA polymerase (SP6RNAP) was modelled using in silico tools. This model is essential as no structure was solved for this enzyme using any of the standard structural biology techniques.

• The modelled structure was used to understand the interactions between SP6 RNAP and its promoter.

• The structure of the SP6 RNAP-SP6 promoter was subjected to various pH states to analyze the stability of the complex using in silico tools.

• The model was successfully able to explain the pH-dependent activity of the polymerase reported in the literature.

• A possible mechanism for the change in the activity of the polymerase was proposed.

Keywords:

• SP6 RNA polymerase
• pH-based MD simulation
• SP6 promoter
• transcription
• MM/PBSA

Acknowledgments

SRS is thankful to Pondicherry University for providing a UGC fellowship. The authors acknowledge the computational facility of the Department of Bioinformatics supported by the Department of Biotechnology, Govt. of India, New Delhi.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Funding

No funding was received for conducting this study.

Data availability statement

The data is available with the authors and shall be provided upon request.

Author contributions

SRS: Conceptualization, Methodology, Software, Validation, Investigation, Writing - Original Draft, Visualization

AM: Conceptualization, Writing - Review & Editing, Resources, Supervision, Project administration,