• 1
    Ulijasz AT, Cornilescu G, von Stetten D, Cornilescu C, Velazquez Escobar F, Zhang J, Stankey RJ, Rivera M, Hildebrandt P & Vierstra RD (2009) The cyanochromes: blue-green photoreversible photoreceptors defined by a stable double cysteine linkage to a phycoviolobilin-type chromophore. J Biol Chem 284, 2975729772.
  • 2
    Auldridge ME & Forest KT (2011) Bacterial phytochromes: more than meets the light. Crit Rev Biochem Mol Biol 46, 6788.
  • 3
    Ikeuchi M & Ishizuka T (2008) Cyanobacteriochromes: a new superfamily of tetrapyrrole-binding photoreceptors in cyanobacteria. Photochem Photobiol Sci 7, 11591167.
  • 4
    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, 567577.
  • 5
    Narikawa R, Fukushima Y, Ishizuka T, Itoh S & Ikeuchi M (2008) A novel photoactive GAF domain of cyanobacteriochrome AnPixJ that shows reversible green/red photoconversion. J Mol Biol 380, 844855.
  • 6
    Okamoto S, Kasahara M, Kamiya A, Nakahira Y & Ohmori M (2004) A phytochrome-like protein AphC triggers the cAMP signaling induced by Far-red light in the cyanobacterium Anabaena sp. strain PCC7120. Photochem Photobiol 80, 429433.
  • 7
    Ng WO, Grossman AR & Bhaya D (2003) Multiple light inputs control phototaxis in Synechocystis sp. Strain PCC6803. J Bacteriol 185, 15991607.
  • 8
    Wilde A, Fiedler B & Börner T (2002) The cyanobacterial phytochrome Cph2 inhibits phototaxis towards blue light. Mol Microbiol 44, 981988.
  • 9
    Song JY, Cho HS, Cho JI, Jeon JS, Lagarias JC & Park YI (2011) Near-UV cyanobacteriochrome signaling system elicits negative phototaxis in the cyanobacterium Synechocystis sp. PCC 6803. Proc Natl Acad Sci USA 108, 1078010785.
  • 10
    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, 95289533.
  • 11
    Hirose Y, Narikawa R, Katayama M & Ikeuchi M (2010) Cyanobacteriochrome CcaS regulates phycoerythrin accumulation in Nostoc punctiforme, a group II chromatic adapter. Proc Natl Acd Sci USA 107, 90299030.
  • 12
    Rockwell NC, Su YS & Lagarias JC (2006) Phytochrome structure and signaling mechanisms. Annu Rev Plant Biol 57, 837858.
  • 13
    Gambetta GA & Lagarias JC (2001) Genetic engineering of phytochrome biosynthesis in bacteria. Proc Natl Acad Sci USA 98, 1056610571.
  • 14
    Tooley AJ, Cai YA & Glazer AN (2001) Biosynthesis of a fluorescent cyanobacterial C-phycocyanin holo-alpha subunit in a heterologous host. Proc Natl Acad Sci USA 98, 1056010565.
  • 15
    Kohchi T, Mukougawa K, Frankenberg N, Masuda M, Yokota A & Lagarias JC (2001) The Arabidopsis HY2 gene encodes phytochromobilin synthase, a ferredoxin-dependent biliverdin reductase. Plant Cell 13, 425436.
  • 16
    Rockwell NC, Martin SS, Feoktistova K & Lagarias JC (2011) Diverse two-cysteine photocycles in phytochromes and cyanobacteriochromes. Proc Natl Acad Sci USA 108, 1185411859.
  • 17
    Bishop JE, Rapoport H, Klotz AV, Chan CF, Glazer AN, Fuglistaller P & Zuber H (1987) Chromopeptides from phycoerythrocyanin. Structure and linkage of the three bilin groups. J Am Chem Soc 10, 875881.
  • 18
    Storf M, Parbel A, Meyer M, Strohmann B, Scheer H, Deng M, Zheng M, Zhou M & Zhao KH (2001) Chromophore attachment to biliproteins: specificity of PecE/PecF, a lyase/isomerase for the photoactive 31-Cys-α84-phycoviolobilin chromophore of phycoerythrocyanin. Biochemistry 40, 1244412456.
  • 19
    Ishizuka T, Narikawa R, Kohchi T, Katayama M & Ikeuchi M (2007) Cyanobacteriochrome TePixJ of Thermosynechococcus elongatus harbors phycoviolobilin as a chromophore. Plant Cell Physiol 48, 13851390.
  • 20
    Ishizuka T, Kamiya A, Suzuki H, Narikawa R, Noguchi T, Kohchi T, Inomata K & Ikeuchi M (2011) The cyanobacteriochrome, TePixJ, isomerizes its own chromophore by converting phycocyanobilin to phycoviolobilin. Biochemistry 50, 953961.
  • 21
    Fischer AJ & Lagarias JC (2004) Harnessing phytochrome’s glowing potential. Proc Natl Acad Sci USA 101, 1733417339.
  • 22
    Shu X, Royant A, Lin MZ, Aguilera TA, Lev-Ram V, Steinbach PA & Tsien RY (2009) Mammalian expression of infrared fluorescent proteins engineered from a bacterial phytochrome. Science 324, 804807.
  • 23
    Zhang J, Wu XJ, Wang ZB, Chen Y, Wang X, Zhou M, Scheer H & Zhao KH (2010) Fused-gene approach to photoswitchable and fluorescent biliproteins. Angew Chem Int Ed 49, 54565458.
  • 24
    Kaneko T, Sato S, Kotani H, Tanaka A, Asamizu E, Nakamura Y, Miyajima N, Hirosawa M, Sugiura M, Sasamoto S et al. (1996) Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res 3, 109136.
  • 25
    Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR et al. (2011) CDD: a conserved domain database for the functional annotation of proteins. Nucleic Acids Res 39(Suppl. 1), D225D229.
  • 26
    Hofmann K & Stoffel W (1993) TMbase – a database of membrane spanning proteins segments. Biol Chem Hoppe-Seyler 374, 166.
  • 27
    Martinez-Argudo I, Martin-Nieto J, Salinas P, Maldonado R, Drummond M & Contreras A (2001) Two-hybrid analysis of domain interactions involving NtrB and NtrC two-component regulators. Mol Microbiol 40, 169178.
  • 28
    Monds RD, Silby MW & Mahanty HK (2001) Expression of the Pho regulon negatively regulates biofilm formation by Pseudomonas aureofaciens PA147-2. Mol Microbiol 42, 415426.
  • 29
    Zhao KH, Su P, Tu JM, Wang X, Liu H, Plöscher M, Eichacker L, Yang B, Zhou M & Scheer H (2007) Phycobilin:cystein-84 biliprotein lyase, a near-universal lyase for cysteine-84 binding sites in cyanobacterial biliproteins. Proc Natl Acad Sci USA 104, 1430014305.
  • 30
    Glazer AN & Fang S (1973) Chromophore content of blue-green algal phycobiliproteins. J Biol Chem 248, 659662.
  • 31
    Zhao KH, Zhang J, Tu JM, Böhm S, Plöscher M, Eichacker L, Bubenzer C, Scheer H, Wang X & Zhou M (2007) Lyase activities of CpcS and CpcT-like proteins from Nostoc PCC7120, and sequential reconstitution of binding sites of phycoerythrocyanin and phycocyanin β-subunits. J Biol Chem 282, 3409334103.
  • 32
    Zhao KH, Ran Y, Li M, Sun YF, Zhou M, Storf M, Kupka M, Böhm S, Bubenzer C & Scheer H (2004) Photochromic biliproteins from the cyanobacterium Anabaena PCC 7120: lyase activities, chromophore exchange, and photochromism in phytochrome AphA. Biochemistry 43, 1157611588.
  • 33
    Rockwell NC, Shang L, Martin SS & Lagarias JC (2009) Distinct classes of red/far-red photochemistry within the phytochrome superfamily. Proc Natl Acad Sci USA 106, 61236127.
  • 34
    Rüdiger W & Thümmler F (1991) Phytochrome, the visual pigment of plants. Angew Chem Int Ed Engl 30, 12161228.
  • 35
    Rohmer T, Lang C, Hughes J, Essen LO, Gärtner W & Matysik J (2008) Light-induced chromophore activity and signal transduction in phytochromes observed by 13C and 15N magic-angle spinning NMR. Proc Natl Acad Sci USA 105, 1522915234.
  • 36
    Song C, Psakis G, Lang C, Mailliet J, Gärtner W, Hughes J & Matysik J (2011) Two ground state isoforms and a chromophore D-ring photoflip triggering extensive intramolecular changes in a canonical phytochrome. Proc Natl Acad Sci USA 108, 38423847.
  • 37
    Schmidt M, Patel A, Zhao Y & Reuter W (2007) Structural basis for the photochemistry of α-Phycoerythrocyanin. Biochemistry 46, 416423.
  • 38
    Ulijasz AT, Cornilescu G, Cornilescu CC, Zhang J, Rivera M, Markley JL & Vierstra RD (2010) Structural basis for the photoconversion of a phytochrome to the activated Pfr form. Nature 463, 250254.
  • 39
    Zhao KH & Scheer H (1995) Type I and type II reversible photochemistry of phycoerythrocyanin α-subunit from Mastigocladus laminosus both involve Z, E isomerization of phycoviolobilin chromophore and are controlled by sulfhydryls in apoprotein. Biochim Biophys Acta. 1228, 244253.
  • 40
    Wu SH & Lagarias JC (2000) Defining the bilin lyase domain: lessons from the extended phytochrome superfamily. Biochemistry 39, 1348713495.
  • 41
    Scheer H & Zhao KH (2008) Biliprotein maturation: the chromophore attachment. Mol Microbiol 68, 263276.
  • 42
    Sidler WA (1994) Phycobilisome and phycobiliprotein structures. In The Molecular Biology of Cyanobacteria (Bryant DA, ed.), pp. 139216. Kluwer, Dordrecht.
  • 43
    Lamparter T & Michael N (2005) Agrobacterium phytochrome as an enzyme for the production of ZZE bilins. Biochemistry 44, 84618469.
  • 44
    Zhao KH, Haessner R, Cmiel E & Scheer H (1995) Type I reversible of phycoerythrocyanin involves Z/E-isomerization of α-84 phycoviolobilin chromophore. Biochim Biophys Acta 1228, 235243.
  • 45
    Falk H (1989) The Chemistry of Linear Oligopyrroles and Bile Pigments. Springer, Wien, New York.
  • 46
    Hübschmann T, Börner T, Hartmann E & Lamparter T (2001) Characterization of the Cph1 holo-phytochrome from Synechocystis sp. PCC 6803. Eur J Biochem 268, 20552063.
  • 47
    Yeh KC, Wu SH, Murphy JT & Lagarias JC (1997) A cyanobacterial phytochrome two-component light sensory system. Science 277, 15051508.
  • 48
    Yang X, Stojkovic EA, Kuk J & Moffat K (2007) Crystal structure of the chromophore binding domain of an unusual bacteriophytochrome, RpBphP3, reveals residues that modulate photoconversion. Proc Natl Acad Sci USA 104, 1257112576.
  • 49
    Dürring M, Huber R, Bode W, Rümbeli R & Zuber H (1990) Refined three-dimensional structure of Phycoerythrocyanin from the cyanobacterium Mastigocladus laminosus at 2.7 A. J Mol Biol 211, 633644.
  • 50
    Micura R & Grubmayr K (1994) Long-wavelength absorbing derivatives of phycocyanobilin: new structural aspects on phytochrome. Bioorg Med Chem Lett 4, 25172522.
  • 51
    Parker W, Goebel P, Ross CR II, Song PS & Stezowski JS (1994) Molecular modeling of phytochrome using constitutive C-phycocyanin from Fremyella diplosiphon as a putative structural template. Bioconjug Chem 5, 2130.
  • 52
    Jorissen HJ, Quest B, Lindner I, Tandeau de Marsac N & Gärtner W (2002) Phytochromes with noncovalently bound chromophores: the ability of apophytochromes to direct tetrapyrrole photoisomerization. Photochem Photobiol 75, 554559.
  • 53
    Eichenberg K, Bäurle I, Paulo N, Sharrock RA, Rüdiger W & Schäfer E (2000) Arabidopsis phytochromes C and E have different spectral characteristics from those of phytochromes A and B. FEBS Lett 470, 107112.
  • 54
    Elich TD & Chory J (1997) Biochemical characterization of Arabidopsis wild-type and mutant phytochrome B holoproteins. Plant Cell 9, 22712280.
  • 55
    Giraud E, Zappa S, Vuillet L, Adriano JM, Hannibal L, Fardoux J, Berthomieu C, Bouyer P, Pignol D & Vermeglio A (2005) A new type of bacteriophytochrome acts in tandem with a classical bacteriophytochrome to control the antennae synthesis in Rhodopseudomonas palustris. J Biol Chem 280, 3238932397.
  • 56
    Hennig L & Schäfer E (2001) Both subunits of the dimeric plant photoreceptor phytochrome require chromophore for stability of the far-red light-absorbing form. J Biol Chem 276, 79137918.
  • 57
    Oesterhelt D, Tittor J & Bamberg E (1992) A unifying concept for ion translocation by retinal proteins. J Bioenerg Biomembr 24, 181191.
  • 58
    Narikawa R, Kohchi T & Ikeuchi M (2008) Characterization of the photoactive GAF domain of the CikA homolog (SyCikA, Slr1969) of the cyanobacterium Synechocystis sp. PCC 6803. Photochem Photobiol Sci 7, 12531259.
  • 59
    Sato S, Shimoda Y, Muraki A, Nakamura Y, Kohara M & Tabata S (2007) A Large-scale protein–protein interaction analysis in Synechocystis sp. PCC 6803. DNA Res 14, 207216.
  • 60
    Gärtner W (2010) Lights on: a switchable fluorescent biliprotein. ChemBioChem 11, 16491652.
  • 61
    Möglich A & Moffat K (2010) Engineered photoreceptors as novel optogenetic tools. Photochem Photobiol Sci 9, 12861300.
  • 62
    Rust MJ, Bates M & Zhuang X (2006) Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat Methods 3, 793796.
  • 63
    Sambrook J, Fritsch E & Maniatis T (1989) Molecular Cloning: A Laboratory Manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
  • 64
    Bradford M (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72, 248254.
  • 65
    Laemmli U (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227, 680685.
  • 66
    Berkelman T & Lagarias JC (1986) Visualization of bilin-linked peptides and proteins in polyacrylamide gels. Anal Biochem 156, 194201.
  • 67
    Cai YA, Murphy JT, Wedemayer G & Glazer AN (2001) Recombinant phycobiliproteins. Recombinant C-phycocyanins equipped with affinity tags, oligomerization, and biospecific recognition domains. Anal Biochem 290, 186204.