How do SorC proteins recognize their DNA operators?

M. Šoltysová¹, J. Škerlová¹, P. Pachl¹, J. Brynda^1,2, I. Sieglová^1,2, M. Fábry², M. Babiak³, J. Nováček³, P. Řezáčová^1,2

¹Institute of Organic Chemistry and Biochemistry, CAS, v.v.i., Flemingovo nám. 2, 16610 Prague, Czech Republic
²Institute of Molecular Genetics CAS, v.v.i., Vídeňská 1083, Praha 4, 142 20, Czech Republic

³ Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic

rezacova@uochb.cas.cz

The SorC family is a large family of bacterial transcription regulators involved in the control of carbohydrate metabolism and quorum-sensing (1,2). SorC protomers constitute an N‑terminal helix‑turn‑helix DNA‑binding domain (DBD) and a C‑terminal effector‑binding domain (EBD) that perceives a change in the environment by binding a phosphor‑sugar molecule which affects oligomerization state and subsequently the affinity to the DNA operator.

We have studied the mechanism of how these proteins recognize their DNA and determined crystal structures of DBDs of two representatives, bsCggR and bsDeoR from Bacillus subtilis in complex with their DNA operators (3). In previous studies, EBDs of these two proteins was also determined in their free form and in complex with their effector molecules (4,5). Our next question was how these proteins bind DNA in their full‑length forms and what structural mechanism underlies the affinity change. To unveil this, we have combined methods of X‑ray crystallography and cryogenic electron microscopy (cryo‑EM), thus completing the partial structural information about separated EBDs and DBDs (3-5). To gain an overall picture of bsCggR and bsDeoR in complex with their cognate DNA duplexes, we determined 4.5 Å cryo‑EM structure and 3.6 Å resolution crystal structure of bsCggR and bsDeoR DNA complexes, respectively. These models represent the first comprehensive insight into the DNA recognition by the SorC protein family.

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3.         Šoltysová, M.S., I.; Fábry, M.; Brynda, J.; Škerlová, J.; Řezáčová, P. (2021) Structural insight into DNA recognition by bacterial transcriptional regulators of the SorC/DeoR family. Acta Crystallographica D Structural Biology, 77, 1411-1424.

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