Conditional cooperativity in toxin–antitoxin regulation prevents random toxin activation and promotes fast translational recovery

Many toxin–antitoxin (TA) loci are known to strongly repress their own transcription. This auto-inhibition is often called ‘conditional cooperativity’ as it relies on cooperative binding of TA complexes to operator DNA that occurs only when toxins are in a proper stoichiometric relationship with antitoxins. There has recently been an explosion of interest in TA systems due to their role in bacterial persistence, however the role of conditional cooperativity is still unclear. We reveal the biological function of conditional cooperativity by constructing a mathematical model of the well studied TA system, relBE of Escherichia coli. We show that the model with the in vivo and in vitro established parameters reproduces experimentally observed response to nutritional stress. We further demonstrate that conditional cooperativity stabilizes the level of antitoxin in rapidly growing cells such that random induction of relBE is minimized. At the same time it enables quick removal of free toxin when the starvation is terminated.

[1]  T. Hwa,et al.  Interdependence of Cell Growth and Gene Expression: Origins and Consequences , 2010, Science.

[2]  D. Gillespie Exact Stochastic Simulation of Coupled Chemical Reactions , 1977 .

[3]  N. Shoresh,et al.  Regulation of phenotypic variability by a threshold-based mechanism underlies bacterial persistence , 2010, Proceedings of the National Academy of Sciences.

[4]  T. Hwa,et al.  Growth Rate-Dependent Global Effects on Gene Expression in Bacteria , 2009, Cell.

[5]  D. Lane,et al.  Autoregulation of the ccd operon in the F plasmid , 1989, Molecular and General Genetics MGG.

[6]  K. Gerdes,et al.  The Escherichia coli relBE genes belong to a new toxin–antitoxin gene family , 1998, Molecular microbiology.

[7]  K. Gerdes,et al.  Toxin–antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes , 2005, Nucleic acids research.

[8]  Martin Overgaard,et al.  Messenger RNA interferase RelE controls relBE transcription by conditional cooperativity , 2008, Molecular microbiology.

[9]  J. Elf,et al.  Probing Transcription Factor Dynamics at the Single-Molecule Level in a Living Cell , 2007, Science.

[10]  Chunbo Lou,et al.  A molecular model for persister in E. coli. , 2008, Journal of theoretical biology.

[11]  Mark Ptashne,et al.  Gene regulation by proteins acting nearby and at a distance , 1986, Nature.

[12]  K. Gerdes,et al.  Prokaryotic toxin–antitoxin stress response loci , 2005, Nature Reviews Microbiology.

[13]  N. Balaban,et al.  The importance of being persistent: heterogeneity of bacterial populations under antibiotic stress. , 2009, FEMS microbiology reviews.

[14]  Kim Sneppen,et al.  Physics in molecular biology , 2005 .

[15]  B. Séraphin,et al.  Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion , 2001, The EMBO journal.

[16]  Ertugrul M. Ozbudak,et al.  Multistability in the lactose utilization network of Escherichia coli , 2004, Nature.

[17]  L. Mirny,et al.  Diffusion in correlated random potentials, with applications to DNA. , 2004, Physical review. E, Statistical, nonlinear, and soft matter physics.

[18]  Martin Overgaard,et al.  RelB and RelE of Escherichia coli Form a Tight Complex That Represses Transcription via the Ribbon–Helix–Helix Motif in RelB , 2009, Journal of molecular biology.

[19]  K. Gerdes,et al.  Regulation of Enteric vapBC Transcription: Induction by VapC Toxin Dimer-Breaking , 2012, Nucleic acids research.

[20]  Mitsuhiko Ikura,et al.  Structural mechanism of transcriptional autorepression of the Escherichia coli RelB/RelE antitoxin/toxin module. , 2008, Journal of molecular biology.

[21]  I. Tanaka,et al.  Crystal structure of archaeal toxin-antitoxin RelE–RelB complex with implications for toxin activity and antitoxin effects , 2005, Nature Structural &Molecular Biology.

[22]  M. Yarmolinsky,et al.  Corepression of the P1 Addiction Operon by Phd and Doc , 1998, Journal of bacteriology.

[23]  Måns Ehrenberg,et al.  The Bacterial Toxin RelE Displays Codon-Specific Cleavage of mRNAs in the Ribosomal A Site , 2003, Cell.

[24]  U. Zabel,et al.  Purified human IκB can rapidly dissociate the complex of the NF-κB transcription factor with its cognate DNA , 1990, Cell.

[25]  Lode Wyns,et al.  Allostery and Intrinsic Disorder Mediate Transcription Regulation by Conditional Cooperativity , 2010, Cell.

[26]  Uri Alon,et al.  Invariant Distribution of Promoter Activities in Escherichia coli , 2009, PLoS Comput. Biol..

[27]  J. Friesen,et al.  Functional mRNA half lives in E. coli , 1978, Molecular and General Genetics MGG.

[28]  T. Hwa,et al.  Growth-rate-dependent partitioning of RNA polymerases in bacteria , 2008, Proceedings of the National Academy of Sciences.

[29]  K. Gerdes,et al.  Rapid induction and reversal of a bacteriostatic condition by controlled expression of toxins and antitoxins , 2002, Molecular microbiology.

[30]  K. Gerdes,et al.  Bacterial persistence by RNA endonucleases , 2011, Proceedings of the National Academy of Sciences.

[31]  K. Gerdes,et al.  RelE, a global inhibitor of translation, is activated during nutritional stress , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[32]  A Kornberg,et al.  Role of Inorganic Polyphosphate in Promoting Ribosomal Protein Degradation by the Lon Protease in E. coli , 2001, Science.