A Novel Feedback Loop That Controls Bimodal Expression of Genetic Competence
Gene expression can be highly heterogeneous in clonal cell populations. An extreme type of heterogeneity is the so-called bistable or bimodal expression, whereby a cell can differentiate into two alternative expression states, and consequently a population will be composed of cells that are ‘ON’ and cells that are ‘OFF’. Stochastic fluctuations of protein levels, also referred to as noise, provide the necessary source of heterogeneity that must be amplified by autostimulatory feedback regulation to obtain the bimodal response. A classical model of bistable differentiation is the development of genetic competence in Bacillus subtilis. Noise in expression of the transcription factor ComK ultimately determines the fraction of cells that enter the competent state. Due to its intrinsic random nature, noise is difficult to investigate. We adapted an artificial autostimulatory loop that bypasses all known ComK regulators, to screen for possible factors that affect noise in the bimodal regulation of ComK. This led to the discovery of Kre, a novel factor that controls the bimodal expression of ComK. Kre appears to affect the stability of comK mRNA. Interestingly, ComK itself represses the expression of kre, adding a new double negative feedback loop to the intricate ComK regulation circuit. Our data emphasize that mRNA stability is an important factor in bimodal regulation.
Vyšlo v časopise:
A Novel Feedback Loop That Controls Bimodal Expression of Genetic Competence. PLoS Genet 11(6): e32767. doi:10.1371/journal.pgen.1005047
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1005047
Souhrn
Gene expression can be highly heterogeneous in clonal cell populations. An extreme type of heterogeneity is the so-called bistable or bimodal expression, whereby a cell can differentiate into two alternative expression states, and consequently a population will be composed of cells that are ‘ON’ and cells that are ‘OFF’. Stochastic fluctuations of protein levels, also referred to as noise, provide the necessary source of heterogeneity that must be amplified by autostimulatory feedback regulation to obtain the bimodal response. A classical model of bistable differentiation is the development of genetic competence in Bacillus subtilis. Noise in expression of the transcription factor ComK ultimately determines the fraction of cells that enter the competent state. Due to its intrinsic random nature, noise is difficult to investigate. We adapted an artificial autostimulatory loop that bypasses all known ComK regulators, to screen for possible factors that affect noise in the bimodal regulation of ComK. This led to the discovery of Kre, a novel factor that controls the bimodal expression of ComK. Kre appears to affect the stability of comK mRNA. Interestingly, ComK itself represses the expression of kre, adding a new double negative feedback loop to the intricate ComK regulation circuit. Our data emphasize that mRNA stability is an important factor in bimodal regulation.
Zdroje
1. Lopez D, Kolter R (2010) Extracellular signals that define distinct and coexisting cell fates in Bacillus subtilis. FEMS Microbiol Rev 34: 134–149. doi: 10.1111/j.1574-6976.2009.00199.x 20030732
2. Veening JW, Smits WK, Kuipers OP (2008) Bistability, epigenetics, and bet-hedging in bacteria. Annu Rev Microbiol 62: 193–210. doi: 10.1146/annurev.micro.62.081307.163002 18537474
3. van Sinderen D, Luttinger A, Kong L, Dubnau D, Venema G, et al. (1995) comK encodes the competence transcription factor, the key regulatory protein for competence development in Bacillus subtilis. Mol Microbiol 15: 455–462. 7783616
4. Hamoen LW, Smits WK, de Jong A, Holsappel S, Kuipers OP (2002) Improving the predictive value of the competence transcription factor (ComK) binding site in Bacillus subtilis using a genomic approach. Nucleic Acids Res 30: 5517–5528. 12490720
5. Ogura M, Yamaguchi H, Kobayashi K, Ogasawara N, Fujita Y, et al. (2002) Whole-genome analysis of genes regulated by the Bacillus subtilis competence transcription factor ComK. J Bacteriol 184: 2344–2351. 11948146
6. Berka RM, Hahn J, Albano M, Draskovic I, Persuh M, et al. (2002) Microarray analysis of the Bacillus subtilis K-state: genome-wide expression changes dependent on ComK. Mol Microbiol 43: 1331–1345. 11918817
7. Smits WK, Eschevins CC, Susanna KA, Bron S, Kuipers OP, et al. (2005) Stripping Bacillus: ComK auto-stimulation is responsible for the bistable response in competence development. Mol Microbiol 56: 604–614. 15819618
8. Maamar H, Dubnau D (2005) Bistability in the Bacillus subtilis K-state (competence) system requires a positive feedback loop. Mol Microbiol 56: 615–624. 15819619
9. Leisner M, Stingl K, Radler JO, Maier B (2007) Basal expression rate of comK sets a 'switching-window' into the K-state of Bacillus subtilis. Mol Microbiol 63: 1806–1816. 17367397
10. Maamar H, Raj A, Dubnau D (2007) Noise in gene expression determines cell fate in Bacillus subtilis. Science 317: 526–529. 17569828
11. Ferrell JE Jr. (2002) Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability. Curr Opin Cell Biol 14: 140–148. 11891111
12. Losick R, Desplan C (2008) Stochasticity and cell fate. Science 320: 65–68. doi: 10.1126/science.1147888 18388284
13. Kearns DB, Losick R (2005) Cell population heterogeneity during growth of Bacillus subtilis. Genes Dev 19: 3083–3094. 16357223
14. Veening JW, Igoshin OA, Eijlander RT, Nijland R, Hamoen LW, et al. (2008) Transient heterogeneity in extracellular protease production by Bacillus subtilis. Mol Syst Biol 4: 184. doi: 10.1038/msb.2008.18 18414485
15. Veening JW, Stewart EJ, Berngruber TW, Taddei F, Kuipers OP, et al. (2008) Bet-hedging and epigenetic inheritance in bacterial cell development. Proc Natl Acad Sci U S A 105: 4393–4398. doi: 10.1073/pnas.0700463105 18326026
16. Diard M, Garcia V, Maier L, Remus-Emsermann MN, Regoes RR, et al. (2013) Stabilization of cooperative virulence by the expression of an avirulent phenotype. Nature 494: 353–356. doi: 10.1038/nature11913 23426324
17. Mikeladze-Dvali T, Wernet MF, Pistillo D, Mazzoni EO, Teleman AA, et al. (2005) The growth regulators warts/lats and melted interact in a bistable loop to specify opposite fates in Drosophila R8 photoreceptors. Cell 122: 775–787. 16143107
18. Elowitz MB, Levine AJ, Siggia ED, Swain PS (2002) Stochastic gene expression in a single cell. Science 297: 1183–1186. 12183631
19. Haijema BJ, Hahn J, Haynes J, Dubnau D (2001) A ComGA-dependent checkpoint limits growth during the escape from competence. Mol Microbiol 40: 52–64. 11298275
20. Briley K Jr., Prepiak P, Dias MJ, Hahn J, Dubnau D (2011) Maf acts downstream of ComGA to arrest cell division in competent cells of B. subtilis. Mol Microbiol 81: 23–39. doi: 10.1111/j.1365-2958.2011.07695.x 21564336
21. Hoa TT, Tortosa P, Albano M, Dubnau D (2002) Rok (YkuW) regulates genetic competence in Bacillus subtilis by directly repressing comK. Mol Microbiol 43: 15–26. 11849533
22. Hamoen LW, Kausche D, Marahiel MA, van Sinderen D, Venema G, et al. (2003) The Bacillus subtilis transition state regulator AbrB binds to the -35 promoter region of comK. FEMS Microbiol Lett 218: 299–304. 12586407
23. Serror P, Sonenshein AL (1996) CodY is required for nutritional repression of Bacillus subtilis genetic competence. J Bacteriol 178: 5910–5915. 8830686
24. Mirouze N, Desai Y, Raj A, Dubnau D (2012) Spo0A~P imposes a temporal gate for the bimodal expression of competence in Bacillus subtilis. PLoS Genet 8: e1002586. doi: 10.1371/journal.pgen.1002586 22412392
25. Hamoen LW, Van Werkhoven AF, Venema G, Dubnau D (2000) The pleiotropic response regulator DegU functions as a priming protein in competence development in Bacillus subtilis. Proc Natl Acad Sci U S A 97: 9246–9251. 10908654
26. Hamoen LW, Venema G, Kuipers OP (2003) Controlling competence in Bacillus subtilis: shared use of regulators. Microbiology 149: 9–17. 12576575
27. Smits WK, Hoa TT, Hamoen LW, Kuipers OP, Dubnau D (2007) Antirepression as a second mechanism of transcriptional activation by a minor groove binding protein. Mol Microbiol 64: 368–381. 17493123
28. Ogura M, Tanaka T (1996) Bacillus subtilis DegU acts as a positive regulator for comK expression. FEBS Lett 397: 173–176. 8955341
29. Turgay K, Hahn J, Burghoorn J, Dubnau D (1998) Competence in Bacillus subtilis is controlled by regulated proteolysis of a transcription factor. Embo J 17: 6730–6738. 9890793
30. Turgay K, Hamoen LW, Venema G, Dubnau D (1997) Biochemical characterization of a molecular switch involving the heat shock protein ClpC, which controls the activity of ComK, the competence transcription factor of Bacillus subtilis. Genes Dev 11: 119–128. 9000055
31. D'Souza C, Nakano MM, Zuber P (1994) Identification of comS, a gene of the srfA operon that regulates the establishment of genetic competence in Bacillus subtilis. Proc Natl Acad Sci U S A 91: 9397–9401. 7937777
32. Hamoen LW, Eshuis H, Jongbloed J, Venema G, van Sinderen D (1995) A small gene, designated comS, located within the coding region of the fourth amino acid-activation domain of srfA, is required for competence development in Bacillus subtilis. Mol Microbiol 15: 55–63. 7752896
33. van Sinderen D, Venema G (1994) comK acts as an autoregulatory control switch in the signal transduction route to competence in Bacillus subtilis. J Bacteriol 176: 5762–5770. 8083168
34. Hamoen LW, Van Werkhoven AF, Bijlsma JJ, Dubnau D, Venema G (1998) The competence transcription factor of Bacillus subtilis recognizes short A/T-rich sequences arranged in a unique, flexible pattern along the DNA helix. Genes Dev 12: 1539–1550. 9585513
35. Le Breton Y, Mohapatra NP, Haldenwang WG (2006) In vivo random mutagenesis of Bacillus subtilis by use of TnYLB-1, a mariner-based transposon. Appl Environ Microbiol 72: 327–333. 16391061
36. Mirouze N, Prepiak P, Dubnau D (2011) Fluctuations in spo0A transcription control rare developmental transitions in Bacillus subtilis. PLoS Genet 7: e1002048. doi: 10.1371/journal.pgen.1002048 21552330
37. Ben-Yehuda S, Rudner DZ, Losick R (2003) RacA, a bacterial protein that anchors chromosomes to the cell poles. Science 299: 532–536. 12493822
38. Nicolas P, Mader U, Dervyn E, Rochat T, Leduc A, et al. (2012) Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis. Science 335: 1103–1106. doi: 10.1126/science.1206848 22383849
39. Charoensawan V, Wilson D, Teichmann SA (2010) Genomic repertoires of DNA-binding transcription factors across the tree of life. Nucleic Acids Res 38: 7364–7377. doi: 10.1093/nar/gkq617 20675356
40. Fukushima T, Ishikawa S, Yamamoto H, Ogasawara N, Sekiguchi J (2003) Transcriptional, functional and cytochemical analyses of the veg gene in Bacillus subtilis. J Biochem 133: 475–483. 12761295
41. Hahn J, Bylund J, Haines M, Higgins M, Dubnau D (1995) Inactivation of mecA prevents recovery from the competent state and interferes with cell division and the partitioning of nucleoids in Bacillus subtilis. Mol Microbiol 18: 755–767. 8817496
42. Suel GM, Garcia-Ojalvo J, Liberman LM, Elowitz MB (2006) An excitable gene regulatory circuit induces transient cellular differentiation. Nature 440: 545–550. 16554821
43. Konkol MA, Blair KM, Kearns DB (2013) Plasmid-encoded ComI inhibits competence in the ancestral 3610 strain of Bacillus subtilis. J Bacteriol 195: 4085–4093. doi: 10.1128/JB.00696-13 23836866
44. Oussenko IA, Abe T, Ujiie H, Muto A, Bechhofer DH (2005) Participation of 3'-to-5' exoribonucleases in the turnover of Bacillus subtilis mRNA. J Bacteriol 187: 2758–2767. 15805522
45. Luttinger A, Hahn J, Dubnau D (1996) Polynucleotide phosphorylase is necessary for competence development in Bacillus subtilis. Mol Microbiol 19: 343–356. 8825779
46. Lehnik-Habrink M, Pfortner H, Rempeters L, Pietack N, Herzberg C, et al. (2010) The RNA degradosome in Bacillus subtilis: identification of CshA as the major RNA helicase in the multiprotein complex. Mol Microbiol 77: 958–971. doi: 10.1111/j.1365-2958.2010.07264.x 20572937
47. Wurtmann EJ, Ratushny AV, Pan M, Beer KD, Aitchison JD, et al. (2014) An evolutionarily conserved RNase-based mechanism for repression of transcriptional positive autoregulation. Mol Microbiol 92: 369–382. doi: 10.1111/mmi.12564 24612392
48. Klumpp S, Zhang Z, Hwa T (2009) Growth rate-dependent global effects on gene expression in bacteria. Cell 139: 1366–1375. doi: 10.1016/j.cell.2009.12.001 20064380
49. Anagnostopoulos C, Spizizen J (1961) Requirements for Transformation in Bacillus subtilis. J Bacteriol 81: 741–746. 16561900
50. Commichau FM, Rothe FM, Herzberg C, Wagner E, Hellwig D, et al. (2009) Novel activities of glycolytic enzymes in Bacillus subtilis: interactions with essential proteins involved in mRNA processing. Mol Cell Proteomics 8: 1350–1360. doi: 10.1074/mcp.M800546-MCP200 19193632
51. Newman JA, Hewitt L, Rodrigues C, Solovyova AS, Harwood CR, et al. (2012) Dissection of the network of interactions that links RNA processing with glycolysis in the Bacillus subtilis degradosome. J Mol Biol 416: 121–136. doi: 10.1016/j.jmb.2011.12.024 22198292
52. Lehnik-Habrink M, Lewis RJ, Mader U, Stulke J (2012) RNA degradation in Bacillus subtilis: an interplay of essential endo- and exoribonucleases. Mol Microbiol 84: 1005–1017. doi: 10.1111/j.1365-2958.2012.08072.x 22568516
53. Nurmohamed S, McKay AR, Robinson CV, Luisi BF (2010) Molecular recognition between Escherichia coli enolase and ribonuclease E. Acta Crystallogr D Biol Crystallogr 66: 1036–1040. doi: 10.1107/S0907444910030015 20823555
54. Hahn J, Luttinger A, Dubnau D (1996) Regulatory inputs for the synthesis of ComK, the competence transcription factor of Bacillus subtilis. Mol Microbiol 21: 763–775. 8878039
55. Kaltwasser M, Wiegert T, Schumann W (2002) Construction and application of epitope- and green fluorescent protein-tagging integration vectors for Bacillus subtilis. Appl Environ Microbiol 68: 2624–2628. 11976148
56. Gamba P, Veening JW, Saunders NJ, Hamoen LW, Daniel RA (2009) Two-step assembly dynamics of the Bacillus subtilis divisome. J Bacteriol 191: 4186–4194. doi: 10.1128/JB.01758-08 19429628
57. Murray H, Errington J (2008) Dynamic control of the DNA replication initiation protein DnaA by Soj/ParA. Cell 135: 74–84. doi: 10.1016/j.cell.2008.07.044 18854156
58. Vagner V, Dervyn E, Ehrlich SD (1998) A vector for systematic gene inactivation in Bacillus subtilis. Microbiology 144 (Pt 11): 3097–3104. 9846745
59. Feucht A, Lewis PJ (2001) Improved plasmid vectors for the production of multiple fluorescent protein fusions in Bacillus subtilis. Gene 264: 289–297. 11250085
60. Morimoto T, Loh PC, Hirai T, Asai K, Kobayashi K, et al. (2002) Six GTP-binding proteins of the Era/Obg family are essential for cell growth in Bacillus subtilis. Microbiology 148: 3539–3552. 12427945
61. Lewis PJ, Marston AL (1999) GFP vectors for controlled expression and dual labelling of protein fusions in Bacillus subtilis. Gene 227: 101–110. 9931458
62. Itaya M (1992) Construction of a novel tetracycline resistance gene cassette useful as a marker on the Bacillus subtilis chromosome. Biosci Biotechnol Biochem 56: 685–686. 1368214
63. Steinmetz M, Richter R (1994) Plasmids designed to alter the antibiotic resistance expressed by insertion mutations in Bacillus subtilis, through in vivo recombination. Gene 142: 79–83. 8181761
64. Kearns DB, Chu F, Branda SS, Kolter R, Losick R (2005) A master regulator for biofilm formation by Bacillus subtilis. Mol Microbiol 55: 739–749. 15661000
65. Schneider CA, Rasband WS, Eliceiri KW (2012) NIH Image to ImageJ: 25 years of image analysis. Nat Methods 9: 671–675. 22930834
66. Daniel RA, Williams AM, Errington J (1996) A complex four-gene operon containing essential cell division gene pbpB in Bacillus subtilis. J Bacteriol 178: 2343–2350. 8636036
67. Miller JH (1972) Experiments in molecular genetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
68. Surdova K, Gamba P, Claessen D, Siersma T, Jonker MJ, et al. (2013) The conserved DNA-binding protein WhiA is involved in cell division in Bacillus subtilis. J Bacteriol 195: 5450–5460. doi: 10.1128/JB.00507-13 24097947
69. de Knegt GJ, Bruning O, ten Kate MT, de Jong M, van Belkum A, et al. (2013) Rifampicin-induced transcriptome response in rifampicin-resistant Mycobacterium tuberculosis. Tuberculosis (Edinb) 93: 96–101.
70. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, et al. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249–264. 12925520
71. Smyth GK (2004) Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3: Article3.
72. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society Series B 57: 289–300.
73. Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25: 402–408. 11846609
74. Yuan JS, Reed A, Chen F, Stewart CN Jr. (2006) Statistical analysis of real-time PCR data. BMC Bioinformatics 7: 85. 16504059
75. Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, et al. (2011) The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res 39: D561–568. doi: 10.1093/nar/gkq973 21045058
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Genetika Reprodukčná medicínaČlánok vyšiel v časopise
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