Principle of DNA recognition by sporulation-regulatory protein (Spo0A) in Bacillus subtilis

Abstract

Master sporulation-regulatory protein Spo0A binds to the cognate DNA sequence 5′-TGTCGAA-3′ (0 A-box) and control transcription of hundreds of genes in sporulating Bacilli. Thus, discrimination of similar near-cognate 0 A-box sequences (differing by a single base pair) by Spo0A is critical for accurate transcriptional control. The thermodynamics underlying the 0 A-box recognition by Spo0A is unknown. Recent X-ray structure of Spo0A from Bacillus subtilis in complex with cognate 0 A-box DNA sequence not only revealed the intricate atomic interaction network related to transcription activation but also provide an opportunity of directly computing the energetics of 0 A-box selectivity by Spo0A. Using the X-ray structure of cognate Spo0A-DNA complex as a template, we report computer simulations that quantitatively estimated the relative binding free energies of Spo0A to cognate and near-cognate 0 A-box sequences in B. subtilis. The results show that the strength of Spo0A binding preference for cognate 0 A-box sequence relative to its near-cognate analogue varies drastically along the location of the mismatch (5′→ 3′) in the 0 A-box sequence. Spo0A selectivity in favour of the cognate sequence is ensured by the loss of protein-DNA major groove interactions and/solvent exposure of the hydrophobic pockets in the near-cognate Spo0A-DNA complexes. The calculations provide a clue about the energetics of Spo0A discrimination between cognate and near-cognate 0 A-box sequences and its link to 3 D structures, which ensure fidelity of transcription initiation in B. subtilis.

Communicated by Ramaswamy H. Sarma

Keywords:

• Spo0A
• 0A-box
• transcription
• molecular dynamics
• free energy

Acknowledgements

SS thank IIT Guwahati for funding. AK thanks MHRD, Govt. of India and BIF Facility, DBT, Govt. of India for funding. Biomolecular Simulation Lab (BSL), Bioinformatics Facility (BIF) and PARAM-ISHAN of IIT Guwahati are gratefully acknowledged for providing the computing facility.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

We acknowledge support from the Science and Engineering Research Board (SERB, Govt of India), Department of Biotechnology, Ministry of Science and Technology, and Ministry of Human Resource Development.