Molecular mechanism governing ratio-dependent transcription regulation in the ccdAB operon.
Bacteria can become transiently tolerant to several classes of antibiotics. This phenomenon known as persistence is regulated by small genetic elements called toxin-antitoxin modules with intricate yet often poorly understood self-regulatory features. Here, we describe the structures of molecular complexes and interactions that drive the transcription regulation of the ccdAB toxin-antitoxin module. Low specificity and affinity of the antitoxin CcdA2 for individual binding sites on the operator are enhanced by the toxin CcdB2, which bridges the CcdA2 dimers. This results in a unique extended repressing complex that spirals around the operator and presents equally spaced DNA binding sites. The multivalency of binding sites induces a digital on-off switch for transcription, regulated by the toxin:antitoxin ratio. The ratio at which this switch occurs is modulated by non-specific interactions with the excess chromosomal DNA. Altogether, we present the molecular mechanisms underlying the ratio-dependent transcriptional regulation of the ccdAB operon.
Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium.|Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050 Brussel, Belgium.
Alexandra
A
Vandervelde
Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna pot 113, 1000 Ljubljana, Slovenia.
Igor
I
Drobnak
Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium.|Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050 Brussel, Belgium.|Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia.
San
S
Hadži
Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050 Brussel, Belgium.|Research Unit for Cellular and Molecular Immunology (CMIM), VUB, Pleinlaan 2, B-1050 Brussel, Belgium.
Yann G-J
YG
Sterckx
Dynamic Biosensors GmbH, Lochhamer Strasse 15, D-82152 Martinsried, Germany.
Thomas
T
Welte
Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium.|Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050 Brussel, Belgium.
Henri
H
De Greve
Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium.
Daniel
D
Charlier
Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium.|Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050 Brussel, Belgium.
Rouslan
R
Efremov
Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium.|Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050 Brussel, Belgium.
Remy
R
Loris
Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna pot 113, 1000 Ljubljana, Slovenia.
Jurij
J
Lah
D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001427:Bacterial Toxins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D004269:DNA, Bacterial / Q000737:chemistry / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D008958:Models, Molecular; D009875:Operator Regions, Genetic; D009876:Operon; D011485:Protein Binding; D000072417:Protein Domains; D055503:Protein Multimerization; D012097:Repressor Proteins / Q000737:chemistry* / Q000378:metabolism; D014158:Transcription, Genetic
D001426:Bacterial Proteins; D001427:Bacterial Toxins; C068355:CcdA protein, Bacteria; D004269:DNA, Bacterial; D012097:Repressor Proteins