Modelling and analysis of a gene-regulatory feed-forward loop with basal expression of the second regulator

Journal of Theoretical Biology

Volumn 363, Issue , 2014, Pages 290-299

  Roselius, Louisa ^a   Langemann, Dirk ^a   Müller, Johannes ^b,c   Hense, Burkhard A ^c   Filges, Stefan ^a   Jahn, Dieter ^a   Münch, Richard ^a  

^a TECHNICAL UNIVERSITY OF BRAUNSCHWEIG   (Germany)

^b TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^c INSTITUTE OF EPIDEMIOLOGY   (Germany)

Author keywords

Energy metabolism; Environmental adaptation; Gene regulation; Mathematical modelling

Indexed keywords

NITRATE; NITRATE REDUCTASE; OXYGEN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR ANR; TRANSCRIPTION FACTOR NAR; TRANSCRIPTION FACTOR NARXL; UNCLASSIFIED DRUG;

ADAPTATION; BACTERIUM; ENVIRONMENTAL CHANGE; GENE; GENE EXPRESSION; METABOLISM; NUMERICAL MODEL; PATHOGEN; PATHOGENICITY;

ANAEROBIC CAPACITY; ARTICLE; BACTERIAL GROWTH; BACTERIAL METABOLISM; BACTERIAL SURVIVAL; BACTERIAL VIRULENCE; COST BENEFIT ANALYSIS; ENVIRONMENTAL STRESS; EVOLUTIONARY ADAPTATION; GENE ACTIVITY; GENE CONTROL; GENE EXPRESSION; MATHEMATICAL MODEL; NONHUMAN; NONLINEAR SYSTEM; OPERON; POSITIVE FEEDBACK; PROMOTER REGION; PROTEIN MOTIF; PSEUDOMONAS AERUGINOSA; REGULATOR GENE; RESPONSE TIME; SIGNAL PROCESSING; SIGNAL TRANSDUCTION; STATISTICAL MODEL; ADAPTATION; ANAEROBIC GROWTH; BIOLOGICAL MODEL; ENVIRONMENT; GENE REGULATORY NETWORK; GENETICS; PHYSIOLOGY;

ADAPTATION, BIOLOGICAL; ANAEROBIOSIS; COST-BENEFIT ANALYSIS; ENVIRONMENT; GENE REGULATORY NETWORKS; MODELS, BIOLOGICAL; PSEUDOMONAS AERUGINOSA;

EID: 84907531585     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2014.08.043     Document Type: Article

References (30)

1. Achbergerová L., Nahálka J. Polyphosphate-an ancient energy source and active metabolic regulator. Microb. Cell. Factories 2011, 10:63. http://dx.doi.org/10.1186/1475-2859-10-63.
2. Alon U. Network motifs. theory and experimental approaches. Nat. Rev. Genet. 2007, 8(6):450-461. http://dx.doi.org/10.1038/nrg2102.
3. Chan P.-L., Yu V., Wai L., Yu H.-F. Production of medium-chain-length polyhydroxyalkanoates by Pseudomonas aeruginosa with fatty acids and alternative carbon sources. Appl. Biochem. Biotechnol. 2006, 129-132:933-941.
4. Davidson C.J., Surette M.G. Individuality in bacteria. Annu. Rev. Genet. 2008, 42:253-268. http://dx.doi.org/10.1146/annurev.genet.42.110807.091601.
5. Dekel E., Mangan S., Alon U. Environmental selection of the feed-forward loop circuit in gene-regulation networks. Phys. Biol. 2005, 2(2):81-88. http://dx.doi.org/10.1088/1478-3975/2/2/001.
6. Eichenberger P., Fujita M., Jensen S.T., Conlon E.M., Rudner D.Z., Wang S.T., Ferguson C., Haga K., Sato T., Liu J.S., Losick R. The program of gene transcription for a single differentiating cell type during sporulation in Bacillus subtilis. PLoS Biol. 2004, 2(10):e328. http://dx.doi.org/10.1371/journal.pbio.0020328.
7. Engelstädter J., Moradigaravand D. Adaptation through genetic time travel? Fluctuating selection can drive the evolution of bacterial transformation. Proc. Biol. Sci. 2014, 281(1775). 20132609. http://dx.doi.org/10.1098/rspb.2013.2609.
8. Gomes A.L.C., Galagan J.E., Segrè D. Resource competition may lead to effective treatment of antibiotic resistant infections. PLoS One 2013, 8(12):e80775. http://dx.doi.org/10.1371/journal.pone.0080775.
9. Görke B., Stülke J. Carbon catabolite repression in bacteria. many ways to make the most out of nutrients. Nat. Rev. Microbiol. 2008, 6:613-624.
10. Heuer H., Abdo Z., Smalla K. Patchy distribution of flexible genetic elements in bacterial populations mediates robustness to environmental uncertainty. FEMS Microbiol. Ecol. 2008, 65(3):361-371. http://dx.doi.org/10.1111/j.1574-6941.2008.00539.x.
11. Kalir, S., Mangan, S., Alon, U., 2005. A coherent feed-forward loop with a SUM input function prolongs flagella expression in Escherichia coli. Mol. Syst. Biol. 1, 2005.0006. http://dx.doi.org/10.1038/msb4100010.
12. Lan G., Tu Y. The cost of sensitive response and accurate adaptation in networks with an incoherent type-1 feed-forward loop. J. R. Soc. Interface 2013, 10(87):20130489. http://dx.doi.org/10.1098/rsif.2013.0489.
13. Langemann D., Rehberg M. Unbuffered and buffered supply chains in human metabolism. J. Biol. Phys. 2010, 36(3):227-244. http://dx.doi.org/10.1007/s10867-009-9178-4.
14. Lieleg O., Caldara M., Baumgärtel R., Ribbeck K. Mechanical robustness of Pseudomonas aeruginosa biofilms. Soft Matter 2011, 7(7):3307-3314. http://dx.doi.org/10.1039/c0sm01467b.
15. Macia J., Widder S., Solé R. Specialized or flexible feed-forward loop motifs. a question of topology. BMC Syst. Biol. 2009, 3:84. http://dx.doi.org/10.1186/1752-0509-3-84.
16. Mangan S., Alon U. Structure and function of the feed-forward loop network motif. Proc. Natl. Acad. Sci. USA 2003, 100(21):11980-11985. http://dx.doi.org/10.1073/pnas.2133841100.
17. Mangan S., Itzkovitz S., Zaslaver A., Alon U. The incoherent feed-forward loop accelerates the response-time of the gal system of Escherichia coli. J. Mol. Biol. 2006, 356(5):1073-1081. http://dx.doi.org/10.1016/j.jmb.2005.12.003.
18. Mangan S., Zaslaver A., Alon U. The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks. J. Mol. Biol. 2003, 334(2):197-204.
19. Salathé M., Van Cleve J., Feldman M.W. Evolution of stochastic switching rates in asymmetric fitness landscapes. Genetics 2009, 182(4):1159-1164. http://dx.doi.org/10.1534/genetics.109.103333.
20. Schobert M., Jahn D. Anaerobic physiology of Pseudomonas aeruginosa in the cystic fibrosis lung. Int. J. Med. Microbiol. 2010, 300(8):549-556. http://dx.doi.org/10.1016/j.ijmm.2010.08.007.
21. Schreiber K., Krieger R., Benkert B., Eschbach M., Arai H., Schobert M., Jahn D. The anaerobic regulatory network required for Pseudomonas aeruginosa nitrate respiration. J. Bacteriol. 2007, 189(11):4310-4314. http://dx.doi.org/10.1128/JB.00240-07.
22. Shachrai I., Zaslaver A., Alon U., Dekel E. Cost of unneeded proteins in E. coli is reduced after several generations in exponential growth. Mol. Cell. 2010, 38(5):758-767. http://dx.doi.org/10.1016/j.molcel.2010.04.015.
23. Shen-Orr S.S., Milo R., Mangan S., Alon U. Network motifs in the transcriptional regulation network of Escherichia coli. Nat. Genet. 2002, 31(1):64-68. http://dx.doi.org/10.1038/ng881.
24. Silva-Rocha R., de Lorenzo V. A composite feed-forward loop I4-FFL involving IHF and Crc stabilizes expression of the XylR regulator of Pseudomonas putida mt-2 from growth phase perturbations. Mol. Biosyst. 2011, 7(11):2982-2990. http://dx.doi.org/10.1039/c1mb05264k.
25. Strohm T.O., Griffin B., Zumft W.G., Schink B. Growth yields in bacterial denitrification and nitrate ammonification. Appl. Environ. Microbiol. 2007, 73(5):1420-1424. http://dx.doi.org/10.1128/AEM.02508-06.
26. Turrientes M.-C., Baquero F., Levin B.R., Martínez J.-L., Ripoll A., González-Alba J.-M., Tobes R., Manrique M., Baquero M.-R., Rodríguez-Domínguez M.-J., Cantón R., Galán J.-C. Normal mutation rate variants arise in a mutator (mut s) Escherichia coli population. PLoS One 2013, 8(9):e72963. http://dx.doi.org/10.1371/journal.pone.0072963.
27. Wall M.E., Dunlop M.J., Hlavacek W.S. Multiple functions of a feed-forward-loop gene circuit. J. Mol. Biol. 2005, 349(3):501-514. http://dx.doi.org/10.1016/j.jmb.2005.04.022.
28. Widder S., Solé R., Macía J. Evolvability of feed-forward loop architecture biases its abundance in transcription networks. BMC Syst. Biol. 2012, 6(1):7. http://dx.doi.org/10.1186/1752-0509-6-7.
29. Wolf D.M., Fontaine-Bodin L., Bischofs I., Price G., Keasling J., Arkin A.P. Memory in microbes. quantifying history-dependent behavior in a bacterium. PLoS One 2008, 3(2):e1700. http://dx.doi.org/10.1371/journal.pone.0001700.
30. Xu K.D., Stewart P.S., Xia F., Huang C.T., McFeters G.A. Spatial physiological heterogeneity in Pseudomonas aeruginosa biofilm is determined by oxygen availability. Appl. Environ. Microbiol. 1998, 64(10):4035-4039.