Detailed map of a cis-regulatory input function - PubMed (original) (raw)
Detailed map of a cis-regulatory input function
Y Setty et al. Proc Natl Acad Sci U S A. 2003.
Abstract
Most genes are regulated by multiple transcription factors that bind specific sites in DNA regulatory regions. These cis-regulatory regions perform a computation: the rate of transcription is a function of the active concentrations of each of the input transcription factors. Here, we used accurate gene expression measurements from living cell cultures, bearing GFP reporters, to map in detail the input function of the classic lacZYA operon of Escherichia coli, as a function of about a hundred combinations of its two inducers, cAMP and isopropyl beta-d-thiogalactoside (IPTG). We found an unexpectedly intricate function with four plateau levels and four thresholds. This result compares well with a mathematical model of the binding of the regulatory proteins cAMP receptor protein (CRP) and LacI to the lac regulatory region. The model is also used to demonstrate that with few mutations, the same region could encode much purer AND-like or even OR-like functions. This possibility means that the wild-type region is selected to perform an elaborate computation in setting the transcription rate. The present approach can be generally used to map the input functions of other genes.
Figures
Fig. 1.
Simple mathematical model of the lac region, protein–DNA level reactions. Transcription occurs from states where RNAP is bound (large open arrows). The activity of the promoter in these states is α and β. An additional parameter γ describes transcription from other states (leakiness). The K parameters are the equilibrium dissociation constants of the various reactions.
Fig. 2.
Growth and GFP fluorescence of the _lac_-reporter strain for 20 different IPTG and cAMP concentrations. (a) OD at 600 nm. (b) GFP fluorescence (535 nm). (c) Promoter activity, _d_[GFP]/dt/OD600 (proportional to mRNA production rate). Cell cycles = log2(OD/OD0).
Fig. 3.
lac cis-regulatory input function (promoter activity) as function of cAMP and IPTG concentrations measured by using the GFP-plasmid system. The promoter activity was taken as the mean over two cell cycles in midexponential phase; to help visualize the lowest plateau there are two rows that represent data at low IPTG. Note the logarithmic scales. (a) Promoter activity. (b) Smoothed surface plot of the promoter activity. (c) Smoothed contour plot of the promoter activity, with the four thresholds and the interdependency diagonal. (d) Schematic form of the input function of the lac promoter. The four plateaus are designated as follows: I, low cAMP, low IPTG; II, high cAMP, low IPTG; III, low cAMP, high IPTG; IV, high cAMP, high IPTG.
Fig. 4.
(a) Assay of chromosomally encoded β-galactosidase activity as a function of cAMP and IPTG concentrations by the ONPG colorimetric method. To help visualize the lowest plateau there are two rows that represent data at low IPTG. (b) Smoothed promoter activity as a function of lactose and cAMP concentration measured by using the GFP-plasmid system. Promoter activity was taken as the mean over two cell cycles in midexponential phase.
Fig. 5.
Input function (promoter activity) in the mathematical model of the lac promoter. (a) Input function with best-fit parameters to the GFP measurements. (b) Input function with parameters for AND-like function. (c) Input function with parameters for OR-like function.
Similar articles
- lac operon induction in Escherichia coli: Systematic comparison of IPTG and TMG induction and influence of the transacetylase LacA.
Marbach A, Bettenbrock K. Marbach A, et al. J Biotechnol. 2012 Jan;157(1):82-8. doi: 10.1016/j.jbiotec.2011.10.009. Epub 2011 Nov 3. J Biotechnol. 2012. PMID: 22079752 - Evolving Lac repressor for enhanced inducibility.
Satya Lakshmi O, Rao NM. Satya Lakshmi O, et al. Protein Eng Des Sel. 2009 Feb;22(2):53-8. doi: 10.1093/protein/gzn069. Epub 2008 Nov 21. Protein Eng Des Sel. 2009. PMID: 19029094 - Towards a circuit engineering discipline.
McAdams HH, Arkin A. McAdams HH, et al. Curr Biol. 2000 Apr 20;10(8):R318-20. doi: 10.1016/s0960-9822(00)00440-1. Curr Biol. 2000. PMID: 10801411 Review.
Cited by
- Fibration symmetry uncovers minimal regulatory networks for logical computation in bacteria.
Álvarez-García LA, Liebermeister W, Leifer I, Makse HA. Álvarez-García LA, et al. ArXiv [Preprint]. 2023 Oct 17:arXiv:2310.10895v1. ArXiv. 2023. PMID: 37904746 Free PMC article. Preprint. - Deduction of signaling mechanisms from cellular responses to multiple cues.
Saha S, Moon HR, Han B, Mugler A. Saha S, et al. NPJ Syst Biol Appl. 2022 Nov 30;8(1):48. doi: 10.1038/s41540-022-00262-5. NPJ Syst Biol Appl. 2022. PMID: 36450797 Free PMC article. - Understanding the Genome-Wide Transcription Response To Various cAMP Levels in Bacteria Using Phenomenological Models.
Chakraborty S, Singh P, Seshasayee ASN. Chakraborty S, et al. mSystems. 2022 Dec 20;7(6):e0090022. doi: 10.1128/msystems.00900-22. Epub 2022 Nov 21. mSystems. 2022. PMID: 36409084 Free PMC article. - Shared cis-regulatory modules control expression of the tandem paralogs midline and H15 in the follicular epithelium.
Stevens CA, Stott HL, Desai SV, Yakoby N. Stevens CA, et al. Development. 2022 Nov 15;149(22):dev201016. doi: 10.1242/dev.201016. Epub 2022 Nov 16. Development. 2022. PMID: 36278857 Free PMC article. - Modulating gene regulation function by chemically controlled transcription factor clustering.
Wu J, Chen B, Liu Y, Ma L, Huang W, Lin Y. Wu J, et al. Nat Commun. 2022 May 13;13(1):2663. doi: 10.1038/s41467-022-30397-2. Nat Commun. 2022. PMID: 35562359 Free PMC article.
References
- Jacob, F. & Monod, J. (1961) J. Mol. Biol. 3, 318-356. - PubMed
- Beckwith, J. & Zipser, D., eds. (1970) The Lactose Operon (Cold Spring Harbor Lab. Press, Plainview, NY).
- Muller-Hill, B. (1996) The lac Operon (de Gruyter, Berlin).
- Savageau, M. A. (1976) Biochemical Systems Analysis: A Study of Function and Design in Molecular Biology (Addison–Wesley, Reading, MA).
- Hartwell, L. H., Hopfield, J. J., Leibler, S. & Murray, A. W. (1999) Nature 402, C47-C52. - PubMed
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources
Research Materials
Miscellaneous