Skip to main content
Log in

Lights on and action! Controlling microbial gene expression by light

  • Mini-Review
  • Published:
Applied Microbiology and Biotechnology Aims and scope Submit manuscript

Abstract

Light-mediated control of gene expression and thus of any protein function and metabolic process in living microbes is a rapidly developing field of research in the areas of functional genomics, systems biology, and biotechnology. The unique physical properties of the environmental factor light allow for an independent photocontrol of various microbial processes in a noninvasive and spatiotemporal fashion. This mini review describes recently developed strategies to generate photo-sensitive expression systems in bacteria and yeast. Naturally occurring and artificial photoswitches consisting of light-sensitive input domains derived from different photoreceptors and regulatory output domains are presented and individual properties of light-controlled expression systems are discussed.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Arndt K, Fink GR (1986) GCN4 protein, a positive transcription factor in yeast, binds general control promoters at all 5′ TGACTC 3′ sequences. Proc Natl Acad Sci USA 83(22):8516–8520

    Article  CAS  Google Scholar 

  • Ávila-Pérez M, Hellingwerf KJ, Kort R (2006) Blue light activates the sigmaB-dependent stress response of Bacillus subtilis via YtvA. J Bacteriol 188(17):6411–6414

    Article  CAS  Google Scholar 

  • Ávila-Pérez M, Vreede J, Tang Y, Bende O, Losi A, Gärtner W, Hellingwerf K (2009) In vivo mutational analysis of YtvA from Bacillus subtilis: mechanism of light activation of the general stress response. J Biol Chem 284(37):24958–24964

    Article  CAS  Google Scholar 

  • Barends TR, Hartmann E, Griese JJ, Beitlich T, Kirienko NV, Ryjenkov DA, Reinstein J, Shoeman RL, Gomelsky M, Schlichting I (2009) Structure and mechanism of a bacterial light-regulated cyclic nucleotide phosphodiesterase. Nature 459(7249):1015–1018

    Article  CAS  Google Scholar 

  • Borgstahl GE, Williams DR, Getzoff ED (1995) 1.4 ºA structure of photoactive yellow protein, a cytosolic photoreceptor: unusual fold, active site, and chromophore. Biochemistry 34(19):6278–6287

    Article  CAS  Google Scholar 

  • Braatsch S, Gomelsky M, Kuphal S, Klug G (2002) A single flavoprotein, AppA, integrates both redox and light signals in Rhodobacter sphaeroides. Mol Microbiol 45(3):827–836

    Article  CAS  Google Scholar 

  • Briggs WR (2007) The LOV domain: a chromophore module servicing multiple photoreceptors. J Biomed Sci 14(4):499–504

    Article  CAS  Google Scholar 

  • Caamano AM, Vázquez ME, Martínez-Costas J, Castedo L, Mascarenas JL (2000) A light-modulated sequence-specific DNA-binding peptide. Angew Chem Int Ed 39(17):3104–3107

    Article  CAS  Google Scholar 

  • Cambridge SB, Geissler D, Keller S, Cürten B (2006) A caged doxycycline analogue for photoactivated gene expression. Angew Chem Int Ed 45:2229–2231

    Article  CAS  Google Scholar 

  • Cao Z, Buttani V, Losi A, Gärtner W (2008) A blue light inducible two-component signal transduction system in the plant pathogen Pseudomonas syringae pv. tomato. Biophys J 94(3):897–905

    Article  CAS  Google Scholar 

  • Cao Z, Livoti E, Losi A, Gärtner W (2010) A blue light-inducible phosphodiesterase activity in the cyanobacterium Synechococcus elongatus. Photochem Photobiol 86(3):606–611

    Article  CAS  Google Scholar 

  • Cashmore AR, Jarillo JA, Wu YJ, Liu D (1999) Cryptochromes: blue light receptors for plants and animals. Science 284(5415):760–765

    Article  CAS  Google Scholar 

  • Chen CH, Ringelberg CS, Gross RH, Dunlap JC, Loros JJ (2009) Genome-wide analysis of light-inducible responses reveals hierarchical light signalling in Neurospora. EMBO J 28(8):1029–1042

    Article  CAS  Google Scholar 

  • Chen CH, Demay BS, Gladfelter AS, Dunlap JC, Loros JJ (2010) Physical interaction between VIVID and white collar complex regulates photoadaptation in Neurospora. Proc Natl Acad Sci USA 107(38):16715–16720

    Article  CAS  Google Scholar 

  • Chou C, Young DD, Deiters A (2010) Photocaged T7 RNA polymerase for the light activation of transcription and gene function in pro- and eukaryontic cells. Chembiochem 11:972–977

    Article  CAS  Google Scholar 

  • Christen M, Christen B, Folcher M, Schauerte A, Jenal U (2005) Identification and characterization of a cyclic di-GMP-specific phosphodiesterase and its allosteric control by GTP. J Biol Chem 280(35):30829–30837

    Article  CAS  Google Scholar 

  • Christie JM, Salomon M, Nozue K, Wada M, Briggs WR (1999) LOV (light, oxygen, or voltage) domains of the blue-light photoreceptor phototropin (nph1): binding sites for the chromophore flavin mononucleotide. Proc Natl Acad Sci USA 96(15):8779–8783

    Article  CAS  Google Scholar 

  • Christie JM, Corchnoy SB, Swartz TE, Hokenson M, Han IS, Briggs WR, Bogomolni RA (2007) Steric interactions stabilize the signaling state of the LOV2 domain of phototropin 1. Biochemistry 46(32):9310–9319

    Article  CAS  Google Scholar 

  • Crosson S, Moffat K (2002) Photoexcited structure of a plant photoreceptor domain reveals a light-driven molecular switch. Plant Cell 14(5):1067–1075

    Article  CAS  Google Scholar 

  • Cruz FG, Koh JT, Link KH (2000) Light-activated gene expression. J Am Chem Soc 122:8777–8778

    Article  CAS  Google Scholar 

  • D’Argenio DA, Miller SI (2004) Cyclic di-GMP as a bacterial second messenger. Microbiology 150:2497–2502

    Article  CAS  Google Scholar 

  • Deiters A (2010) Principles and applications of the photochemical control of cellular processes. Chembiochem 11:47–53

    Article  CAS  Google Scholar 

  • Dutta R, Qin L, Inouye M (1999) Histidine kinases: diversity of domain organization. Mol Microbiol 34(4):633–640

    Article  CAS  Google Scholar 

  • Ellenberger TE, Brandl CJ, Struhl K, Harrison SC (1992) The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted α helices: crystal structure of the protein–DNA complex. Cell 71(7):1223–1237

    Article  CAS  Google Scholar 

  • Elsen S, Jaubert M, Pignol D, Giraud E (2005) PpsR: a multifaceted regulator of photosynthesis gene expression in purple bacteria. Mol Microbiol 57(1):17–26

    Article  CAS  Google Scholar 

  • Fields S, Song O (1989) A novel genetic system to detect protein–protein interactions. Nature 340(6230):245–246

    Article  CAS  Google Scholar 

  • Fischer HM (1994) Genetic regulation of nitrogen fixation in Rhizobia. Microbiol Rev 58(3):352–386

    CAS  Google Scholar 

  • Forst SA, Roberts DL (1994) Signal transduction by the EnvZ–OmpR phosphotransfer system in bacteria. Res Microbiol 145(5–6):363–373

    Article  CAS  Google Scholar 

  • Gaidenko TA, Kim TJ, Weigel AL, Brody MS, Price CW (2006) The blue-light receptor YtvA acts in the environmental stress signaling pathway of Bacillus subtilis. J Bacteriol 188(17):6387–6395

    Article  CAS  Google Scholar 

  • Gambetta GA, Lagarias JC (2001) Genetic engineering of phytochrome biosynthesis in bacteria. Proc Natl Acad Sci USA 98(19):10566–10571

    Article  CAS  Google Scholar 

  • Gilles-Gonzalez MA, Ditta GS, Helinski DR (1991) A haemoprotein with kinase activity encoded by the oxygen sensor of Rhizobium meliloti. Nature 350(6314):170–172

    Article  CAS  Google Scholar 

  • Giraud E, Fardoux J, Fourrier N, Hannibal L, Genty B, Bouyer P, Dreyfus B, Vermeglio A (2002) Bacteriophytochrome controls photosystem synthesis in anoxygenic bacteria. Nature 417(6885):202–205

    Article  CAS  Google Scholar 

  • Gomelsky M, Kaplan S (1995) Genetic evidence that PpsR from Rhodobacter sphaeroides 2.4.1 functions as a repressor of puc and bchF expression. J Bacteriol 177(6):1634–1637

    CAS  Google Scholar 

  • Gomelsky M, Kaplan S (1997) Molecular genetic analysis suggesting interactions between AppA and PpsR in regulation of photosynthesis gene expression in Rhodobacter sphaeroides 2.4.1. J Bacteriol 179(1):128–134

    CAS  Google Scholar 

  • Gomelsky M, Klug G (2002) BLUF: a novel FAD-binding domain involved in sensory transduction in microorganisms. Trends Biochem Sci 27(10):497–500

    Article  CAS  Google Scholar 

  • Gong W, Hao B, Mansy SS, Gonzalez G, Gilles-Gonzalez MA, Chan MK (1998) Structure of a biological oxygen sensor: a new mechanism for heme-driven signal transduction. Proc Natl Acad Sci USA 95(26):15177–15182

    Article  CAS  Google Scholar 

  • Greber D, Fussenegger M (2007) Mammalian synthetic biology: engineering of sophisticated gene networks. J Biotechnol 130(4):329–345

    Article  CAS  Google Scholar 

  • Grünberg R, Serrano L (2010) Strategies for protein synthetic biology. Nucleic Acids Res 38(8):2663–2675

    Article  CAS  Google Scholar 

  • Gunsalus RP, Yanofsky C (1980) Nucleotide sequence and expression of Escherichia coli trpR, the structural gene for the trp aporepressor. Proc Natl Acad Sci USA 77(12):7117–7121

    Article  CAS  Google Scholar 

  • Hagiwara D, Sugiura M, Oshima T, Mori H, Aiba H, Yamashino T, Mizuno T (2003) Genome-wide analyses revealing a signaling network of the RcsC–YojN–RcsB phosphorelay system in Escherichia coli. J Bacteriol 185(19):5735–5746

    Article  CAS  Google Scholar 

  • Heckel A, Mayer G (2010) Light-responsive nucleic acids for the spatiotemporal control of biological processes. In: Mayer G (ed) The chemical biology of nucleic acids. Wiley, pp 279–306

  • Hecker M, Pane-Farre J, Volker U (2007) SigB-dependent general stress response in Bacillus subtilis and related gram-positive bacteria. Annu Rev Microbiol 61:215–236

    Article  CAS  Google Scholar 

  • Hengge R (2009) Principles of c-di-GMP signalling in bacteria. Nat Rev Microbiol 7(4):263–273

    Article  CAS  Google Scholar 

  • Hiltbrunner A, Tscheuschler A, Viczian A, Kunkel T, Kircher S, Schäfer E (2006) FHY1 and FHL act together to mediate nuclear accumulation of the phytochrome A photoreceptor. Plant Cell Physiol 47(8):1023–1034

    Article  CAS  Google Scholar 

  • Hirose Y, Shimada T, Narikawa R, Katayama M, Ikeuchi M (2008) Cyanobacteriochrome CcaS is the green light receptor that induces the expression of phycobilisome linker protein. Proc Natl Acad Sci USA 105(28):9528–9533

    Article  CAS  Google Scholar 

  • Hoff WD, van der Horst MA, Nudel CB, Hellingwerf KJ (2009) Prokaryotic phototaxis. Methods Mol Biol 571:25–49

    Article  CAS  Google Scholar 

  • Hori Y, Ueno H, Mizukami S, Kikuchi K (2009) Photoactive yellow protein-based protein labeling system with turn-on fluorescence intensity. J Am Chem Soc 131(46):16610–16611

    Article  CAS  Google Scholar 

  • Hübschmann T, Yamamoto H, Gieler T, Murata N, Börner T (2005) Red and far-red light alter the transcript profile in the cyanobacterium Synechocystis sp. PCC 6803: impact of cyanobacterial phytochromes. FEBS Lett 579(7):1613–1618

    Article  CAS  Google Scholar 

  • Hughes J (2010) Phytochrome three-dimensional structures and functions. Biochem Soc Trans 38(2):710–716

    Article  CAS  Google Scholar 

  • Hunt SM, Thompson S, Elvin M, Heintzen C (2010) VIVID interacts with the WHITE COLLAR complex and FREQUENCY-interacting RNA helicase to alter light and clock responses in Neurospora. Proc Natl Acad Sci USA 107(38):16709–16714

    Article  CAS  Google Scholar 

  • Imamoto Y, Kataoka M (2007) Structure and photoreaction of photoactive yellow protein, a structural prototype of the PAS domain superfamily. Photochem Photobiol 83(1):40–49

    Article  CAS  Google Scholar 

  • Iseki M, Matsunaga S, Murakami A, Ohno K, Shiga K, Yoshida K, Sugai M, Takahashi T, Hori T, Watanabe M (2002) A blue-light-activated adenylyl cyclase mediates photoavoidance in Euglena gracilis. Nature 415(6875):1047–1051

    Article  CAS  Google Scholar 

  • Ishikawa M, Takahashi F, Nozaki H, Nagasato C, Motomura T, Kataoka H (2009) Distribution and phylogeny of the blue light receptors aureochromes in eukaryotes. Planta 230(3):543–552

    Article  CAS  Google Scholar 

  • Jarillo JA, Capel J, Tang RH, Yang HQ, Alonso JM, Ecker JR, Cashmore AR (2001) An Arabidopsis circadian clock component interacts with both CRY1 and phyB. Nature 410(6827):487–490

    Article  CAS  Google Scholar 

  • Jaubert M, Zappa S, Fardoux J, Adriano JM, Hannibal L, Elsen S, Lavergne J, Vermeglio A, Giraud E, Pignol D (2004) Light and redox control of photosynthesis gene expression in Bradyrhizobium: dual roles of two PpsR. J Biol Chem 279(43):44407–44416

    Article  CAS  Google Scholar 

  • Jeeves M, Evans PD, Parslow RA, Jaseja M, Hyde EI (1999) Studies of the Escherichia coli Trp repressor binding to its five operators and to variant operator sequences. Eur J Biochem 265(3):919–928

    Article  CAS  Google Scholar 

  • Jentzsch K, Wirtz A, Circolone F, Drepper T, Losi A, Gärtner W, Jaeger KE, Krauss U (2009) Mutual exchange of kinetic properties by extended mutagenesis in two short LOV domain proteins from Pseudomonas putida. Biochemistry 48(43):10321–10333

    Article  CAS  Google Scholar 

  • Jorns MS (1990) DNA photorepair: chromophore composition and function in two classes of DNA photolyases. Biofactors 2(4):207–211

    CAS  Google Scholar 

  • Kaplan JH, Forbush B III, Hoffmann JF (1978) Rapid photolytic release of adenosine 5′-triphosphate from a protected analog: utilization by the sodium:potassium pump of human red blood cell ghosts. Biochemistry 17:1929–1935

    Article  CAS  Google Scholar 

  • Kasahara M, Swartz TE, Olney MA, Onodera A, Mochizuki N, Fukuzawa H, Asamizu E, Tabata S, Kanegae H, Takano M, Christie JM, Nagatani A, Briggs WR (2002) Photochemical properties of the flavin mononucleotide-binding domains of the phototropins from Arabidopsis, rice, and Chlamydomonas reinhardtii. Plant Physiol 129(2):762–773

    Article  CAS  Google Scholar 

  • Kaupp UB, Seifert R (2002) Cyclic nucleotide-gated ion channels. Physiol Rev 82(3):769–824

    CAS  Google Scholar 

  • Kehoe DM, Grossman AR (1996) Similarity of a chromatic adaptation sensor to phytochrome and ethylene receptors. Science 273(5280):1409–1412

    Article  CAS  Google Scholar 

  • Kehoe DM, Grossman AR (1997) New classes of mutants in complementary chromatic adaptation provide evidence for a novel four-step phosphorelay system. J Bacteriol 179(12):3914–3921

    CAS  Google Scholar 

  • Kehoe DM, Gutu A (2006) Responding to color: the regulation of complementary chromatic adaptation. Annu Rev Plant Biol 57:127–150

    Article  CAS  Google Scholar 

  • Khalil AS, Collins JJ (2010) Synthetic biology: applications come of age. Nat Rev Genet 11(5):367–379

    Article  CAS  Google Scholar 

  • Kim WY, Fujiwara S, Suh SS, Kim J, Kim Y, Han L, David K, Putterill J, Nam HG, Somers DE (2007) ZEITLUPE is a circadian photoreceptor stabilized by GIGANTEA in blue light. Nature 449(7160):356–360

    Article  CAS  Google Scholar 

  • Kolb A, Busby S, Buc H, Garges S, Adhya S (1993) Transcriptional regulation by cAMP and its receptor protein. Annu Rev Biochem 62:749–795

    Article  CAS  Google Scholar 

  • Koldin B, Suckow M, Seydel A, von Wilcken-Bergmann B, Müller-Hill B (1995) A comparison of the different DNA binding specificities of the bZip proteins C/EBP and GCN4. Nucleic Acids Res 23(20):4162–4169

    Article  CAS  Google Scholar 

  • Kort R, Hoff WD, Van West M, Kroon AR, Hoffer SM, Vlieg KH, Crielaand W, Van Beeumen JJ, Hellingwerf KJ (1996) The xanthopsins: a new family of eubacterial blue-light photoreceptors. EMBO J 15(13):3209–3218

    CAS  Google Scholar 

  • Krauss U, Minh BQ, Losi A, Gärtner W, Eggert T, von Haeseler A, Jaeger K-E (2009) Distribution and phylogeny of light–oxygen–voltage-blue-light-signaling proteins in the three kingdoms of life. J Bacteriol 191(23):7234–7242

    Article  CAS  Google Scholar 

  • Kyndt JA, Vanrobaeys F, Fitch JC, Devreese BV, Meyer TE, Cusanovich MA, Van Beeumen JJ (2003) Heterologous production of Halorhodospira halophila holo-photoactive yellow protein through tandem expression of the postulated biosynthetic genes. Biochemistry 42(4):965–970

    Article  CAS  Google Scholar 

  • Lee J, Natarajan M, Nashine VC, Socolich M, Vo T, Russ WP, Benkovic SJ, Ranganathan R (2008) Surface sites for engineering allosteric control in proteins. Science 322(5900):438–442

    Article  CAS  Google Scholar 

  • Lee MM, Larson DR, Lawrence DS (2009) Illuminating the chemistry of life: design, synthesis, and applications of ‘caged’ and related photoresponsive compounds. ACS Chem Biol 4:409–427

    Article  CAS  Google Scholar 

  • Leivar P, Quail PH (2010) PIFs: pivotal components in a cellular signaling hub. Trends Plant Sci 16(1):19–28

    Article  CAS  Google Scholar 

  • Levskaya A, Chevalier AA, Tabor JJ, Simpson ZB, Lavery LA, Levy M, Davidson EA, Scouras A, Ellington AD, Marcotte EM, Voigt CA (2005) Synthetic biology: engineering Escherichia coli to see light. Nature 438(7067):441–442

    Article  CAS  Google Scholar 

  • Lin W, Albanese C, Pestell RG, Lawrence DS (2002) Spatially discrete, light-driven protein expression. Chem Biol 9:1347–1353

    Article  CAS  Google Scholar 

  • Link KH, Shi Y, Koh JT (2005) Light activated recombination. J Am Chem Soc 127:13088–13089

    Article  CAS  Google Scholar 

  • Liu H, Yu X, Li K, Klejnot J, Yang H, Lisiero D, Lin C (2008) Photoexcited CRY2 interacts with CIB1 to regulate transcription and floral initiation in Arabidopsis. Science 322(5907):1535–1539

    Article  CAS  Google Scholar 

  • Losi A (2004) The bacterial counterparts of plant phototropins. Photochem Photobiol Sci 3(6):566–574

    Article  CAS  Google Scholar 

  • Losi A (2007) Flavin-based blue-light photosensors: a photobiophysics update. Photochem Photobiol 83(6):1283–1300

    Article  CAS  Google Scholar 

  • Losi A, Gärtner W (2008) Bacterial bilin- and flavin-binding photoreceptors. Photochem Photobiol Sci 7(10):1168–1178

    Article  CAS  Google Scholar 

  • Losi A, Polverini E, Quest B, Gärtner W (2002) First evidence for phototropin-related blue-light receptors in prokaryotes. Biophys J 82(5):2627–2634

    Article  CAS  Google Scholar 

  • Malzahn E, Ciprianidis S, Káldi K, Schafmeier T, Brunner M (2010) Photoadaptation in Neurospora by competitive interaction of activating and inhibitory LOV domains. Cell 142(5):762–772

    Article  CAS  Google Scholar 

  • Marmorstein RQ, Sigler PB (1989) Stereochemical effects of l-tryptophan and its analogues on trp repressor’s affinity for operator-DNA. J Biol Chem 264(16):9149–9154

    CAS  Google Scholar 

  • Masuda S, Bauer CE (2002) AppA is a blue light photoreceptor that antirepresses photosynthesis gene expression in Rhodobacter sphaeroides. Cell 110(5):613–623

    Article  CAS  Google Scholar 

  • Mayer G, Heckel A (2006) Biologically active molecules with a ‘light switch’. Angew Chem Int Ed 45:4900–4921

    Article  CAS  Google Scholar 

  • Mitrophanov AY, Groisman EA (2008) Signal integration in bacterial two-component regulatory systems. Genes Dev 22(19):2601–2611

    Article  CAS  Google Scholar 

  • Möglich A, Ayers RA, Moffat K (2009a) Design and signaling mechanism of light-regulated histidine kinases. J Mol Biol 385(5):1433–1444

    Article  CAS  Google Scholar 

  • Möglich A, Ayers RA, Moffat K (2009b) Structure and signaling mechanism of Per-ARNT-Sim domains. Structure 17(10):1282–1294

    Article  CAS  Google Scholar 

  • Möglich A, Ayers RA, Moffat K (2010) Addition at the molecular level: signal integration in designed Per-ARNT-Sim receptor proteins. J Mol Biol 400(3):477–486

    Article  CAS  Google Scholar 

  • Möglich A, Moffat K (2010) Engineered photoreceptors as novel optogenetic tools. Photochem Photobiol Sci 9(10):1286–1300

    Google Scholar 

  • Morgan SA, Woolley GA (2010) A photoswitchable DNA-binding protein based on a truncated GCN4-photoactive yellow protein chimera. Photochem Photobiol Sci 9(10):1320–1326

    Article  CAS  Google Scholar 

  • Morgan SA, Al-Abdul-Wahid S, Woolley GA (2010) Structure-based design of a photocontrolled DNA binding protein. J Mol Biol 399(1):94–112

    Article  CAS  Google Scholar 

  • Neiss A, Schafmeier T, Brunner M (2008) Transcriptional regulation and function of the Neurospora clock gene white collar 2 and its isoforms. EMBO Rep 9(8):788–794

    Article  CAS  Google Scholar 

  • Newell PD, Monds RD, O’Toole GA (2009) LapD is a bis-(3′, 5′)-cyclic dimeric GMP-binding protein that regulates surface attachment by Pseudomonas fluorescens Pf0–1. Proc Natl Acad Sci USA 106(9):3461–3466

    Article  CAS  Google Scholar 

  • Ntefidou M, Iseki M, Watanabe M, Lebert M, Hader DP (2003) Photoactivated adenylyl cyclase controls phototaxis in the flagellate Euglena gracilis. Plant Physiol 133(4):1517–1521

    Article  CAS  Google Scholar 

  • Ogura Y, Komatsu A, Zikihara K, Nanjo T, Tokutomi S, Wada M, Kiyosue T (2008) Blue light diminishes interaction of PAS/LOV proteins, putative blue light receptors in Arabidopsis thaliana, with their interacting partners. J Plant Res 121(1):97–105

    Article  CAS  Google Scholar 

  • Oshima T, Aiba H, Masuda Y, Kanaya S, Sugiura M, Wanner BL, Mori H, Mizuno T (2002) Transcriptome analysis of all two-component regulatory system mutants of Escherichia coli K-12. Mol Microbiol 46(1):281–291

    Article  CAS  Google Scholar 

  • Pawson T, Nash P (2003) Assembly of cell regulatory systems through protein interaction domains. Science 300(5618):445–452

    Article  CAS  Google Scholar 

  • Pellequer JL, Wager-Smith KA, Kay SA, Getzoff ED (1998) Photoactive yellow protein: a structural prototype for the three-dimensional fold of the PAS domain superfamily. Proc Natl Acad Sci USA 95(11):5884–5890

    Article  CAS  Google Scholar 

  • Petersohn A, Bernhardt J, Gerth U, Hoper D, Koburger T, Volker U, Hecker M (1999) Identification of sigma(B)-dependent genes in Bacillus subtilis using a promoter consensus-directed search and oligonucleotide hybridization. J Bacteriol 181(18):5718–5724

    CAS  Google Scholar 

  • Purcell EB, Crosson S (2008) Photoregulation in prokaryotes. Curr Opin Microbiol 11(2):168–178

    Article  CAS  Google Scholar 

  • Purcell EB, Siegal-Gaskins D, Rawling DC, Fiebig A, Crosson S (2007) A photosensory two-component system regulates bacterial cell attachment. Proc Natl Acad Sci USA 104(46):18241–18246

    Article  CAS  Google Scholar 

  • Purcell EB, McDonald CA, Palfey BA, Crosson S (2010) An analysis of the solution structure and signaling mechanism of LovK, a sensor histidine kinase integrating light and redox signals. Biochemistry 49(31):6761–6770

    Article  CAS  Google Scholar 

  • Rajagopal S, Key JM, Purcell EB, Boerema DJ, Moffat K (2004) Purification and initial characterization of a putative blue light-regulated phosphodiesterase from Escherichia coli. Photochem Photobiol 80(3):542–547

    Article  CAS  Google Scholar 

  • Riggsbee CW, Deiters A (2010) Recent advances in the photochemical control of protein function. Trends Biotech 28:468–475

    Article  CAS  Google Scholar 

  • Rockwell NC, Lagarias JC (2010) A brief history of phytochromes. Chemphyschem 11(6):1172–1180

    Article  CAS  Google Scholar 

  • Ryu MH, Moskvin OV, Siltberg-Liberles J, Gomelsky M (2010) Natural and engineered photoactivated nucleotidyl cyclases for optogenetic applications. J Biol Chem 285(53):41501–41508

    Article  CAS  Google Scholar 

  • Sauers DJ, Temburni MK, Biggins JB, Ceo LM, Galileo DS, Loh JT (2010) Light-activated gene expression directs segregation of co-cultured cells in vitro. ACS Chem Biol 5(3):313–320

    Article  CAS  Google Scholar 

  • Sawa M, Nusinow DA, Kay SA, Imaizumi T (2007) FKF1 and GIGANTEA complex formation is required for day-length measurement in Arabidopsis. Science 318(5848):261–265

    Article  CAS  Google Scholar 

  • Schaper K, Etinski M, Fleig T (2009) Theoretical investigation on the excited states of 2-nitrobenzyl and 4, 5-methylendioxy-2-nitrobenzyl caging groups. Photochem Photobiol 85:1075–1081

    Article  CAS  Google Scholar 

  • Schirmer T, Jenal U (2009) Structural and mechanistic determinants of c-di-GMP signalling. Nat Rev Microbiol 7(10):724–735

    Article  CAS  Google Scholar 

  • Schünke S, Stoldt M, Novak K, Kaupp UB, Willbold D (2009) Solution structure of the Mesorhizobium loti K1 channel cyclic nucleotide-binding domain in complex with cAMP. EMBO Rep 10(7):729–735

    Article  CAS  Google Scholar 

  • Shao Q, Xing B (2010) Photoactive molecules for applications in molecular imaging and cell biology. Chem Soc Rev 39:2835–2846

    Article  CAS  Google Scholar 

  • Sharrock RA (2008) The phytochrome red/far-red photoreceptor superfamily. Genome Biol 9(8):230

    Article  CAS  Google Scholar 

  • Shimizu-Sato S, Huq E, Tepperman JM, Quail PH (2002) A light-switchable gene promoter system. Nat Biotechnol 20(10):1041–1044

    Article  CAS  Google Scholar 

  • Shin DH, Cho MH, Kim TL, Yoo J, Kim JI, Han YJ, Song PS, Jeon JS, Bhoo SH, Hahn TR (2010) A small GTPase activator protein interacts with cytoplasmic phytochromes in regulating root development. J Biol Chem 285(42):32151–32159

    Article  CAS  Google Scholar 

  • Somers DE (2001) Clock-associated genes in Arabidopsis: a family affair. Philos Trans R Soc Lond B Biol Sci 356(1415):1745–1753

    Article  CAS  Google Scholar 

  • Sorokina O, Kapus A, Terecskei K, Dixon LE, Kozma-Bognar L, Nagy F, Millar AJ (2009) A switchable light-input, light-output system modelled and constructed in yeast. J Biol Eng 3:15

    Article  CAS  Google Scholar 

  • Sprenger WW, Hoff WD, Armitage JP, Hellingwerf KJ (1993) The eubacterium Ectothiorhodospira halophila is negatively phototactic, with a wavelength dependence that fits the absorption spectrum of the photoactive yellow protein. J Bacteriol 175(10):3096–3104

    CAS  Google Scholar 

  • Stierl M, Stumpf P, Udwari D, Gueta R, Hagedorn R, Losi A, Gärtner W, Petereit L, Efetova M, Schwarzel M, Oertner TG, Nagel G, Hegemann P (2011) Light-modulation of cellular cAMP by a small bacterial photoactivated adenylyl cyclase, bPAC, of the soil bacterium Beggiatoa. J Biol Chem 286:1181–1188

    Google Scholar 

  • Strickland D, Moffat K, Sosnick TR (2008) Light-activated DNA binding in a designed allosteric protein. Proc Natl Acad Sci USA 105(31):10709–10714

    Article  CAS  Google Scholar 

  • Strickland D, Yao X, Gawlak G, Rosen MK, Gardner KH, Sosnick TR (2010) Rationally improving LOV domain-based photoswitches. Nat Methods 7(8):623–626

    Article  CAS  Google Scholar 

  • Swartz TE, Wenzel PJ, Corchnoy SB, Briggs WR, Bogomolni RA (2002) Vibration spectroscopy reveals light-induced chromophore and protein structural changes in the LOV2 domain of the plant blue-light receptor phototropin 1. Biochemistry 41(23):7183–7189

    Article  CAS  Google Scholar 

  • Swartz TE, Tseng TS, Frederickson MA, Paris G, Comerci DJ, Rajashekara G, Kim JG, Mudgett MB, Splitter GA, Ugalde RA, Goldbaum FA, Briggs WR, Bogomolni RA (2007) Blue-light-activated histidine kinases: two-component sensors in bacteria. Science 317(5841):1090–1093

    Article  CAS  Google Scholar 

  • Tabor JJ, Salis HM, Simpson ZB, Chevalier AA, Levskaya A, Marcotte EM, Voigt CA, Ellington AD (2009) A synthetic genetic edge detection program. Cell 137(7):1272–1281

    Article  Google Scholar 

  • Tabor JJ, Levskaya A, Voigt CA (2011) Multichromatic control of gene expression in Escherichia coli. J Mol Biol 405:315–324

    Google Scholar 

  • Takahashi F, Yamagata D, Ishikawa M, Fukamatsu Y, Ogura Y, Kasahara M, Kiyosue T, Kikuyama M, Wada M, Kataoka H (2007) AUREOCHROME, a photoreceptor required for photomorphogenesis in stramenopiles. Proc Natl Acad Sci USA 104(49):19625–19630

    Article  CAS  Google Scholar 

  • Tarutina M, Ryjenkov DA, Gomelsky M (2006) An unorthodox bacteriophytochrome from Rhodobacter sphaeroides involved in turnover of the second messenger c-di-GMP. J Biol Chem 281(46):34751–34758

    Article  CAS  Google Scholar 

  • Terauchi K, Montgomery BL, Grossman AR, Lagarias JC, Kehoe DM (2004) RcaE is a complementary chromatic adaptation photoreceptor required for green and red light responsiveness. Mol Microbiol 51(2):567–577

    Article  CAS  Google Scholar 

  • Tschowri N, Busse S, Hengge R (2009) The BLUF-EAL protein YcgF acts as a direct anti-repressor in a blue-light response of Escherichia coli. Genes Dev 23(4):522–534

    Article  CAS  Google Scholar 

  • Utsumi R, Brissette RE, Rampersaud A, Forst SA, Oosawa K, Inouye M (1989) Activation of bacterial porin gene expression by a chimeric signal transducer in response to aspartate. Science 245(4923):1246–1249

    Article  CAS  Google Scholar 

  • van der Horst MA, Hellingwerf KJ (2004) Photoreceptor proteins, star actors of modern times: a review of the functional dynamics in the structure of representative members of six different photoreceptor families. Acc Chem Res 37(1):13–20

    Article  CAS  Google Scholar 

  • van der Horst MA, Key J, Hellingwerf KJ (2007) Photosensing in chemotrophic, non-phototrophic bacteria: let there be light sensing too. Trends Microbiol 15(12):554–562

    Article  CAS  Google Scholar 

  • Wang L, Xie J, Schultz PG (2006) Expanding the genetic code. Annu Rev Biophys Biomol Struct 35:225–249

    Article  CAS  Google Scholar 

  • Wang W, Shu D, Chen L, Jiang W, Lu Y (2009) Cross-talk between an orphan response regulator and a noncognate histidine kinase in Streptomyces coelicolor. FEMS Microbiol Lett 294(2):150–156

    Article  CAS  Google Scholar 

  • Wilson CJ, Zhan H, Swint-Kruse L, Matthews KS (2007) The lactose repressor system: paradigms for regulation, allosteric behavior and protein folding. Cell Mol Life Sci 64(1):3–16

    Article  CAS  Google Scholar 

  • Won HS, Lee YS, Lee SH, Lee BJ (2009) Structural overview on the allosteric activation of cyclic AMP receptor protein. Biochim Biophys Acta 1794(9):1299–1308

    CAS  Google Scholar 

  • Woolley GA, Jaikaran AS, Berezovski M, Calarco JP, Krylov SN, Smart OS, Kumita JR (2006) Reversible photocontrol of DNA binding by a designed GCN4-bZIP protein. Biochemistry 45(19):6075–6084

    Article  CAS  Google Scholar 

  • Yao X, Rosen MK, Gardner KH (2008) Estimation of the available free energy in a LOV2-J alpha photoswitch. Nat Chem Biol 4(8):491–497

    Article  CAS  Google Scholar 

  • Yasuhara M, Mitsui S, Hirano H, Takanabe R, Tokioka Y, Ihara N, Komatsu A, Seki M, Shinozaki K, Kiyosue T (2004) Identification of ASK and clock-associated proteins as molecular partners of LKP2 (LOV kelch protein 2) in Arabidopsis. J Exp Bot 55(405):2015–2027

    Article  CAS  Google Scholar 

  • Yazawa M, Sadaghiani AM, Hsueh B, Dolmetsch RE (2009) Induction of protein–protein interactions in live cells using light. Nat Biotechnol 27(10):941–945

    Article  CAS  Google Scholar 

  • Yeh KC, Wu SH, Murphy JT, Lagarias JC (1997) A cyanobacterial phytochrome two-component light sensory system. Science 277(5331):1505–1508

    Article  CAS  Google Scholar 

  • Young DD, Deiters A (2007a) Photochemical activation of protein expression in bacterial cells. Angew Chem Int Ed 46:4290–4292

    Article  CAS  Google Scholar 

  • Young DD, Deiters A (2007b) Photochemical control of biological processes. Org Biomol Chem 5:999–1005

    Article  CAS  Google Scholar 

  • Young DD, Garner RA, Yoder JA, Deiters A (2009) Light-activation of gene function in mammalian cells via ribozymes. Chem Commun 568–570

  • Zoltowski BD, Vaccaro B, Crane BR (2009) Mechanism-based tuning of a LOV domain photoreceptor. Nat Chem Biol 5(11):827–834

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Thomas Drepper.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Drepper, T., Krauss, U., Meyer zu Berstenhorst, S. et al. Lights on and action! Controlling microbial gene expression by light. Appl Microbiol Biotechnol 90, 23–40 (2011). https://doi.org/10.1007/s00253-011-3141-6

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00253-011-3141-6

Keywords

Navigation