1932

Abstract

Living organisms sense and respond to light, a crucial environmental factor, using photoreceptors, which rely on bound chromophores such as retinal, flavins, or linear tetrapyrroles for light sensing. The discovery of photoreceptors that sense light using 5′-deoxyadenosylcobalamin, a form of vitamin B that is best known as an enzyme cofactor, has expanded the number of known photoreceptor families and unveiled a new biological role of this vitamin. The prototype of these B-dependent photoreceptors, the transcriptional repressor CarH, is widespread in bacteria and mediates light-dependent gene regulation in a photoprotective cellular response. CarH activity as a transcription factor relies on the modulation of its oligomeric state by 5′-deoxyadenosylcobalamin and light. This review surveys current knowledge about these B-dependent photoreceptors, their distribution and mode of action, and the structural and photochemical basis of how they orchestrate signal transduction and control gene expression.

Loading

Article metrics loading...

/content/journals/10.1146/annurev-biochem-061516-044500
2017-06-20
2024-06-25
Loading full text...

Full text loading...

/deliver/fulltext/biochem/86/1/annurev-biochem-061516-044500.html?itemId=/content/journals/10.1146/annurev-biochem-061516-044500&mimeType=html&fmt=ahah

Literature Cited

  1. Croce R, van Amerongen H. 1.  2014. Natural strategies for photosynthetic light harvesting. Nat. Chem. Biol. 10:492–501 [Google Scholar]
  2. Palczewski K. 2.  2012. Chemistry and biology of vision. J. Biol. Chem. 287:1612–19 [Google Scholar]
  3. Wald G. 3.  1968. The molecular basis of visual excitation. Nature 219:800–7 [Google Scholar]
  4. Cohen SE, Golden SS. 4.  2015. Circadian rhythms in cyanobacteria. Microbiol. Mol. Biol. Rev. 79:373–85 [Google Scholar]
  5. Nagel DH, Kay SA. 5.  2012. Complexity in the wiring and regulation of plant circadian networks. Curr. Biol. 22:R648–57 [Google Scholar]
  6. Chaves I, Pokorny R, Byrdin M, Hoang N, Ritz T. 6.  et al. 2011. The cryptochromes: blue light photoreceptors in plants and animals. Annu. Rev. Plant Biol. 62:335–64 [Google Scholar]
  7. Sancar A, Lindsey-Boltz LA, Kang TH, Reardon JT, Lee JH, Ozturk N. 7.  2010. Circadian clock control of the cellular response to DNA damage. FEBS Lett 584:2618–25 [Google Scholar]
  8. Fankhauser C, Christie JM. 8.  2015. Plant phototropic growth. Curr. Biol. 25:R384–89 [Google Scholar]
  9. Ballaré CL. 9.  2014. Light regulation of plant defense. Annu. Rev. Plant Biol. 65:335–63 [Google Scholar]
  10. Swartz TE, Tseng TS, Frederickson MA, Paris G, Comerci DJ. 10.  et al. 2007. Blue-light-activated histidine kinases: two-component sensors in bacteria. Science 317:1090–93 [Google Scholar]
  11. Elías-Arnanz M, Padmanabhan S, Murillo FJ. 11.  2011. Light-dependent gene regulation in nonphototrophic bacteria. Curr. Opin. Microbiol. 14:128–35 [Google Scholar]
  12. Purcell EB, Crosson S. 12.  2008. Photoregulation in prokaryotes. Curr. Opin. Microbiol. 11:168–78 [Google Scholar]
  13. Crane BR, Young MW. 13.  2014. Interactive features of proteins composing eukaryotic circadian clocks. Annu. Rev. Biochem. 83:191–219 [Google Scholar]
  14. Ziegelhoffer EC, Donohue TJ. 14.  2009. Bacterial responses to photo-oxidative stress. Nat. Rev. Microbiol. 7:856–63 [Google Scholar]
  15. Li Z, Wakao S, Fischer BB, Niyogi KK. 15.  2009. Sensing and responding to excess light. Annu. Rev. Plant Biol. 60:239–60 [Google Scholar]
  16. Glaeser J, Nuss AM, Berghoff BA, Klug G. 16.  2011. Singlet oxygen stress in microorganisms. Adv. Microb. Physiol. 58:141–73 [Google Scholar]
  17. Latifi A, Ruiz M, Zhang CC. 17.  2009. Oxidative stress in cyanobacteria. FEMS Microbiol. Rev. 33:258–78 [Google Scholar]
  18. Setlow RB. 18.  1966. Cyclobutane-type pyrimidine dimers in polynucleotides. Science 153:379–86 [Google Scholar]
  19. Erickson E, Wakao S, Niyogi KK. 19.  2015. Light stress and photoprotection in Chlamydomonas reinhardtii. Plant J. 82:449–65 [Google Scholar]
  20. Christie JM, Arvai AS, Baxter KJ, Heilmann M, Pratt AJ. 20.  et al. 2012. Plant UVR8 photoreceptor senses UV-B by tryptophan-mediated disruption of cross-dimer salt bridges. Science 335:1492–96 [Google Scholar]
  21. Wu D, Hu Q, Yan Z, Chen W, Yan C. 21.  et al. 2012. Structural basis of ultraviolet-B perception by UVR8. Nature 484:214–19 [Google Scholar]
  22. Genick UK, Soltis SM, Kuhn P, Canestrelli IL, Getzoff ED. 22.  1998. Structure at 0.85 Å resolution of an early protein photocycle intermediate. Nature 392:206–9 [Google Scholar]
  23. Herrou J, Crosson S. 23.  2011. Function, structure and mechanism of bacterial photosensory LOV proteins. Nat. Rev. Microbiol. 9:713–23 [Google Scholar]
  24. Leverenz RL, Sutter M, Wilson A, Gupta S, Thurotte A. 24.  et al. 2015. A 12 Å carotenoid translocation in a photoswitch associated with cyanobacterial photoprotection. Science 348:1463–66 [Google Scholar]
  25. Losi A, Gärtner W. 25.  2012. The evolution of flavin-binding photoreceptors: an ancient chromophore serving trendy blue-light sensors. Annu. Rev. Plant Biol. 63:49–72 [Google Scholar]
  26. Masuda S. 26.  2013. Light detection and signal transduction in the BLUF photoreceptors. Plant Cell Physiol 54:171–79 [Google Scholar]
  27. Sancar A. 27.  2003. Structure and function of DNA photolyase and cryptochrome blue-light photoreceptors. Chem. Rev. 103:2203–37 [Google Scholar]
  28. Wilson A, Punginelli C, Gall A, Bonetti C, Alexandre M. 28.  et al. 2008. A photoactive carotenoid protein acting as light intensity sensor. PNAS 105:12075–80 [Google Scholar]
  29. Anders K, Essen LO. 29.  2015. The family of phytochrome-like photoreceptors: diverse, complex and multi-colored, but very useful. Curr. Opin. Struct. Biol. 35:7–16 [Google Scholar]
  30. Rockwell NC, Su Y-S, Lagarias JC. 30.  2006. Phytochrome structure and signaling mechanisms. Annu. Rev. Plant Biol. 57:837–58 [Google Scholar]
  31. Möglich A, Yang X, Ayers RA, Moffat K. 31.  2010. Structure and function of plant photoreceptors. Annu. Rev. Plant Biol. 61:21–47 [Google Scholar]
  32. Shcherbakova DM, Shemetov AA, Kaberniuk AA, Verkhusha VV. 32.  2015. Natural photoreceptors as a source of fluorescent proteins, biosensors, and optogenetic tools. Annu. Rev. Biochem. 84:519–50 [Google Scholar]
  33. Bhattacharyya RP, Reményi A, Yeh BJ, Lim WA. 33.  2006. Domains, motifs, and scaffolds: the role of modular interactions in the evolution and wiring of cell signaling circuits. Annu. Rev. Biochem. 75:655–80 [Google Scholar]
  34. Fenno L, Yizhar O, Deisseroth K. 34.  2011. The development and application of optogenetics. Annu. Rev. Neurosci. 34:389–412 [Google Scholar]
  35. Miesenböck G. 35.  2011. Optogenetic control of cells and circuits. Annu. Rev. Cell Dev. Biol. 27:731–58 [Google Scholar]
  36. Zhang K, Cui B. 36.  2015. Optogenetic control of intracellular signaling pathways. Trends Biotechnol 33:92–100 [Google Scholar]
  37. Ortiz-Guerrero JM, Polanco MC, Murillo FJ, Padmanabhan S, Elías-Arnanz M. 37.  2011. Light-dependent gene regulation by a coenzyme B12-based photoreceptor. PNAS 108:7565–70 [Google Scholar]
  38. Jost M, Fernández-Zapata J, Polanco MC, Ortiz-Guerrero JM, Chen PY. 38.  et al. 2015. Structural basis for gene regulation by a B12-dependent photoreceptor. Nature 526:536–41 [Google Scholar]
  39. Jost M, Simpson JH, Drennan CL. 39.  2015. The transcription factor CarH safeguards use of adenosylcobalamin as a light sensor by altering the photolysis products. Biochemistry 54:3231–34 [Google Scholar]
  40. Kutta RJ, Hardman SJ, Johannissen LO, Bellina B, Messiha HL. 40.  et al. 2015. The photochemical mechanism of a B12-dependent photoreceptor protein. Nat. Commun. 6:7907 [Google Scholar]
  41. Whipple GH, Robscheit-Robbins FS. 41.  1925. Favourable influence of liver, heart and skeletal muscle in diet on blood regeneration in anemia. Am. J. Physiol. 72:408–18 [Google Scholar]
  42. Minot GR, Murphy WP. 42.  1926. Treatment of pernicious anemia by a special diet. J. Am. Med. Assoc 87470–76 [Google Scholar]
  43. Rickes EL, Brink NG, Koniuszy FR, Wood TR, Folkers K. 43.  1948. Crystalline vitamin B12. Science 107:396–97 [Google Scholar]
  44. Smith EL. 44.  1948. Purification of anti-pernicious anaemia factors from liver. Nature 161:638 [Google Scholar]
  45. Hodgkin DC, Kamper J, Mackay M, Pickworth J, Trueblood KN, White JG. 45.  1956. Structure of vitamin B12. Nature 178:64–66 [Google Scholar]
  46. Eschenmoser A, Wintner CE. 46.  1977. Natural product synthesis and vitamin B12. Science 196:1410–20 [Google Scholar]
  47. Croft MT, Lawrence AD, Raux-Deery E, Warren MJ, Smith AG. 47.  2005. Algae acquire vitamin B12 through a symbiotic relationship with bacteria. Nature 438:90–93 [Google Scholar]
  48. Roth JR, Lawrence JG, Bobik TA. 48.  1996. Cobalamin (coenzyme B12): synthesis and biological significance. Annu. Rev. Microbiol. 50:137–81 [Google Scholar]
  49. Taga ME, Larsen NA, Howard-Jones AR, Walsh CT, Walker GC. 49.  2007. BluB cannibalizes flavin to form the lower ligand of vitamin B12. Nature 446:449–53 [Google Scholar]
  50. Warren MJ, Raux E, Schubert HL, Escalante-Semerena JC. 50.  2002. The biosynthesis of adenosylcobalamin (vitamin B12). Nat. Prod. Rep. 19:390–412 [Google Scholar]
  51. Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS. 51.  2003. Comparative genomics of the vitamin B12 metabolism and regulation in prokaryotes. J. Biol. Chem. 278:41148–59 [Google Scholar]
  52. Zhang Y, Rodionov DA, Gelfand MS, Gladyshev VN. 52.  2009. Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization. BMC Genom 10:78 [Google Scholar]
  53. Degnan PH, Taga ME, Goodman AL. 53.  2014. Vitamin B12 as a modulator of gut microbial ecology. Cell Metab 20:769–78 [Google Scholar]
  54. Banerjee R, Ragsdale SW. 54.  2003. The many faces of vitamin B12: catalysis by cobalamin-dependent enzymes. Annu. Rev. Biochem. 72:209–47 [Google Scholar]
  55. Ludwig ML, Matthews RG. 55.  1997. Structure-based perspectives on B12-dependent enzymes. Annu. Rev. Biochem. 66:269–313 [Google Scholar]
  56. Lenhert PG, Hodgkin DC. 56.  1961. Structure of the 5,6-dimethyl-benzimidazolylcobamide coenzyme. Nature 192:937–38 [Google Scholar]
  57. Rossi R, Glusker JP, Randaccio L, Summers MF, Toscano PJ, Marzilli LG. 57.  1985. The structure of a B12 coenzyme: methylcobalamin studies by X-ray and NMR methods. J. Am. Chem. Soc. 107:1729–38 [Google Scholar]
  58. Hung RR, Grabowski JJ. 58.  1999. Listening to reactive intermediates: application of photoacoustic calorimetry to vitamin B12 compounds. J. Am. Chem. Soc. 121:1351–64 [Google Scholar]
  59. Hay BP, Finke RG. 59.  1986. Thermolysis of the cobalt-carbon bond of adenosylcobalamin. 2. Products, kinetics, and cobalt-carbon bond dissociation energy in aqueous solution. J. Am. Chem. Soc. 108:4820–29 [Google Scholar]
  60. Randaccio L, Geremia S, Demitri N, Wuerges J. 60.  2010. Vitamin B12: unique metalorganic compounds and the most complex vitamins. Molecules 15:3228–59 [Google Scholar]
  61. Kozlowski PM, Garabato BD, Lodowski P, Jaworska M. 61.  2016. Photolytic properties of cobalamins: a theoretical perspective. Dalton Trans 45:4457–70 [Google Scholar]
  62. Rury AS, Wiley TE, Sension RJ. 62.  2015. Energy cascades, excited state dynamics, and photochemistry in cob(III)alamins and ferric porphyrins. Acc. Chem. Res. 48:860–67 [Google Scholar]
  63. Gruber K, Puffer B, Kräutler B. 63.  2011. Vitamin B12-derivatives—enzyme cofactors and ligands of proteins and nucleic acids. Chem. Soc. Rev. 40:4346–63 [Google Scholar]
  64. Drennan CL, Huang S, Drummond JT, Matthews RG, Ludwig ML. 64.  1994. How a protein binds B12: a 3.0 Å X-ray structure of B12-binding domains of methionine synthase. Science 266:1669–74 [Google Scholar]
  65. Liptak MD, Brunold TC. 65.  2006. Spectroscopic and computational studies of Co1+cobalamin: spectral and electronic properties of the “superreduced” B12 cofactor. J. Am. Chem. Soc. 128:9144–56 [Google Scholar]
  66. Stich TA, Brooks AJ, Buan NR, Brunold TC. 66.  2003. Spectroscopic and computational studies of Co3+-corrinoids: spectral and electronic properties of the B12 cofactors and biologically relevant precursors. J. Am. Chem. Soc. 125:5897–914 [Google Scholar]
  67. Stich TA, Buan NR, Brunold TC. 67.  2004. Spectroscopic and computational studies of Co2+corrinoids: spectral and electronic properties of the biologically relevant base-on and base-off forms of Co2+cobalamin. J. Am. Chem. Soc. 126:9735–49 [Google Scholar]
  68. Shell TA, Lawrence DS. 68.  2011. A new trick (hydroxyl radical generation) for an old vitamin (B12). J. Am. Chem. Soc. 133:2148–50 [Google Scholar]
  69. Wiley TE, Miller WR, Miller NA, Sension RJ, Lodowski P. 69.  et al. 2016. Photostability of hydroxocobalamin: ultrafast excited state dynamics and computational studies. J. Phys. Chem. Lett. 7:143–47 [Google Scholar]
  70. Schwartz PA, Frey PA. 70.  2007. 5′-Peroxyadenosine and 5′-peroxyadenosylcobalamin as intermediates in the aerobic photolysis of adenosylcobalamin. Biochemistry 46:7284–92 [Google Scholar]
  71. Hogenkamp HP. 71.  1963. A cyclic nucleoside derived from coenzyme B12. J. Biol. Chem. 238:477–80 [Google Scholar]
  72. Hogenkamp HP. 72.  1966. The photolysis of methylcobalamin. Biochemistry 5:417–22 [Google Scholar]
  73. Law PY, Wood JM. 73.  1973. The photolysis of 5′-deoxyadenosylcobalamin under anaerobic conditions. Biochim. Biophys. Acta 331:451–54 [Google Scholar]
  74. Chen E, Chance MR. 74.  1990. Nanosecond transient absorption spectroscopy of coenzyme B12. Quantum yields and spectral dynamics. J. Biol. Chem. 265:12987–94 [Google Scholar]
  75. Endicott JF, Netzel TL. 75.  1979. Early events and transient chemistry in the photohomolysis of alkylcobalamins. J. Am. Chem. Soc. 101:4000–2 [Google Scholar]
  76. Jones AR, Russell HJ, Greetham GM, Towrie M, Hay S, Scrutton NS. 76.  2012. Ultrafast infrared spectral fingerprints of vitamin B12 and related cobalamins. J. Phys. Chem. A 116:5586–94 [Google Scholar]
  77. Walker LA, Jarett JT, Anderson NA, Pullen SH, Matthews RG, Sension RJ. 77.  1998. Time-resolved spectroscopic studies of B12 coenzymes: the identification of a metastable cob(III)alamin photoproduct in the photolysis of methylcobalamin. J. Am. Chem. Soc. 120:3597–603 [Google Scholar]
  78. Walker LA, Shiang JJ, Anderson NA, Pullen SH, Sension RJ. 78.  1998. Time-resolved spectroscopic studies of B12 coenzymes: the photolysis and geminate recombination of adenosylcobalamin. J. Am. Chem. Soc. 120:7286–92 [Google Scholar]
  79. Stickrath AB, Carroll EC, Dai X, Harris DA, Rury A. 79.  et al. 2009. Solvent-dependent cage dynamics of small nonpolar radicals: lessons from the photodissociation and geminate recombination of alkylcobalamins. J. Phys. Chem. A 113:8513–22 [Google Scholar]
  80. Yamada R, Shimizu S, Fukui S. 80.  1966. Factors affecting the anaerobic photolysis of the cobalt-carbon bond of cobalt-methylcobalamin. Biochim. Biophys. Acta 124:195–97 [Google Scholar]
  81. Deery E, Schroeder S, Lawrence AD, Taylor SL, Seyedarabi A. 81.  et al. 2012. An enzyme-trap approach allows isolation of intermediates in cobalamin biosynthesis. Nat. Chem. Biol. 8:933–40 [Google Scholar]
  82. Hazra AB, Han AW, Mehta AP, Mok KC, Osadchiy V. 82.  et al. 2015. Anaerobic biosynthesis of the lower ligand of vitamin B12. PNAS 112:10792–97 [Google Scholar]
  83. Moore SJ, Lawrence AD, Biedendieck R, Deery E, Frank S. 83.  et al. 2013. Elucidation of the anaerobic pathway for the corrin component of cobalamin (vitamin B12). PNAS 110:14906–11 [Google Scholar]
  84. Yin L, Bauer CE. 84.  2013. Controlling the delicate balance of tetrapyrrole biosynthesis. Philos. Trans. R. Soc. B 368:20120262 [Google Scholar]
  85. Banerjee R, Gherasim C, Padovani D. 85.  2009. The tinker, tailor, soldier in intracellular B12 trafficking. Curr. Opin. Chem. Biol. 13:484–91 [Google Scholar]
  86. Cracan V, Banerjee R. 86.  2013. Cobalt and corrinoid transport and biochemistry. Met. Ions Life Sci. 12:333–74 [Google Scholar]
  87. Fedosov SN. 87.  2012. Physiological and molecular aspects of cobalamin transport. Subcell. Biochem. 56:347–67 [Google Scholar]
  88. Nielsen MJ, Rasmussen MR, Andersen CB, Nexø E, Moestrup SK. 88.  2012. Vitamin B12 transport from food to the body's cells—a sophisticated, multistep pathway. Nat. Rev. Gastroenterol. Hepatol. 9:345–54 [Google Scholar]
  89. Yamanishi M, Vlasie M, Banerjee R. 89.  2005. Adenosyltransferase: an enzyme and an escort for coenzyme B12?. Trends Biochem. Sci. 30:304–8 [Google Scholar]
  90. Jost M, Cracan V, Hubbard PA, Banerjee R, Drennan CL. 90.  2015. Visualization of a radical B12 enzyme with its G-protein chaperone. PNAS 112:2419–24 [Google Scholar]
  91. Gherasim C, Lofgren M, Banerjee R. 91.  2013. Navigating the B12 road: assimilation, delivery, and disorders of cobalamin. J. Biol. Chem. 288:13186–93 [Google Scholar]
  92. Johnson CL, Pechonick E, Park SD, Havemann GD, Leal NA, Bobik TA. 92.  2001. Functional genomic, biochemical, and genetic characterization of the Salmonella pduO gene, an ATP:cob(I)alamin adenosyltransferase gene. J. Bacteriol. 183:1577–84 [Google Scholar]
  93. Dowling DP, Croft AK, Drennan CL. 93.  2012. Radical use of Rossmann and TIM barrel architectures for controlling coenzyme B12 chemistry. Annu. Rev. Biophys. 41:403–27 [Google Scholar]
  94. Giedyk M, Goliszewska K, Gryko D. 94.  2015. Vitamin B12 catalysed reactions. Chem. Soc. Rev. 44:3391–404 [Google Scholar]
  95. Ludwig ML, Drennan CL, Matthews RG. 95.  1996. The reactivity of B12 cofactors: The proteins make a difference. Structure 4:505–12 [Google Scholar]
  96. Jones AR, Levy C, Hay S, Scrutton NS. 96.  2013. Relating localized protein motions to the reaction coordinate in coenzyme B12-dependent enzymes. FEBS J 280:2997–3008 [Google Scholar]
  97. Sukumar N. 97.  2013. Crystallographic studies on B12 binding proteins in eukaryotes and prokaryotes. Biochimie 95:976–88 [Google Scholar]
  98. Bommer M, Kunze C, Fesseler J, Schubert T, Diekert G, Dobbek H. 98.  2014. Structural basis for organohalide respiration. Science 346:455–58 [Google Scholar]
  99. Payne KA, Quezada CP, Fisher K, Dunstan MS, Collins FA. 99.  et al. 2015. Reductive dehalogenase structure suggests a mechanism for B12-dependent dehalogenation. Nature 517:513–16 [Google Scholar]
  100. Dowling DP, Miles ZD, Kohrer C, Maiocco SJ, Elliott SJ. 100.  et al. 2016. Molecular basis of cobalamin-dependent RNA modification. Nucleic Acids Res 44:9965–76 [Google Scholar]
  101. Payne KA, Fisher K, Sjuts H, Dunstan MS, Bellina B. 101.  et al. 2015. Epoxyqueuosine reductase structure suggests a mechanism for cobalamin-dependent tRNA modification. J. Biol. Chem. 290:27572–81 [Google Scholar]
  102. Goulding CW, Postigo D, Matthews RG. 102.  1997. Cobalamin-dependent methionine synthase is a modular protein with distinct regions for binding homocysteine, methyltetrahydrofolate, cobalamin, and adenosylmethionine. Biochemistry 36:8082–91 [Google Scholar]
  103. Matthews RG, Koutmos M, Datta S. 103.  2008. Cobalamin-dependent and cobamide-dependent methyltransferases. Curr. Opin. Struct. Biol. 18:658–66 [Google Scholar]
  104. Jarrett JT, Drennan CL, Amaratunga M, Scholten JD, Ludwig ML, Matthews RG. 104.  1996. A protein radical cage slows photolysis of methylcobalamin in methionine synthase from Escherichia coli. Bioorg. Med. Chem 41237–46 [Google Scholar]
  105. Mandal M, Breaker RR. 105.  2004. Gene regulation by riboswitches. Nat. Rev. Mol. Cell Biol. 5:451–63 [Google Scholar]
  106. Serganov A, Patel DJ. 106.  2012. Metabolite recognition principles and molecular mechanisms underlying riboswitch function. Annu. Rev. Biophys. 41:343–70 [Google Scholar]
  107. Nahvi A, Barrick JE, Breaker RR. 107.  2004. Coenzyme B12 riboswitches are widespread genetic control elements in prokaryotes. Nucleic Acids Res 32:143–50 [Google Scholar]
  108. Johnson JE Jr, Reyes FE, Polaski JT, Batey RT. 108.  2012. B12 cofactors directly stabilize an mRNA regulatory switch. Nature 492:133–37 [Google Scholar]
  109. Peselis A, Serganov A. 109.  2012. Structural insights into ligand binding and gene expression control by an adenosylcobalamin riboswitch. Nat. Struct. Mol. Biol. 19:1182–84 [Google Scholar]
  110. Elías-Arnanz M, Fontes M, Padmanabhan S. 110.  2008. Carotenogenesis in Myxococcus xanthus: a complex regulatory network. Myxobacteria: Multicellularity and Differentiation DE Whitworth 211–25 Washington, DC: ASM Press [Google Scholar]
  111. Armstrong GA. 111.  1997. Genetics of eubacterial carotenoid biosynthesis: a colorful tale. Annu. Rev. Microbiol. 51:629–59 [Google Scholar]
  112. Galbis-Martínez M, Padmanabhan S, Murillo FJ, Elías-Arnanz M. 112.  2012. CarF mediates signaling by singlet oxygen, generated via photoexcited protoporphyrin IX, in Myxococcus xanthus light-induced carotenogenesis. J. Bacteriol. 194:1427–36 [Google Scholar]
  113. Cervantes M, Murillo FJ. 113.  2002. Role for vitamin B12 in light induction of gene expression in the bacterium Myxococcus xanthus. J. Bacteriol. 184:2215–24 [Google Scholar]
  114. Chang CC, Lin LY, Zou XW, Huang CC, Chan NL. 114.  2015. Structural basis of the mercury(II)-mediated conformational switching of the dual-function transcriptional regulator MerR. Nucleic Acids Res 43:7612–23 [Google Scholar]
  115. Heldwein EE, Brennan RG. 115.  2001. Crystal structure of the transcription activator BmrR bound to DNA and a drug. Nature 409:378–82 [Google Scholar]
  116. Philips SJ, Canalizo-Hernandez M, Yildirim I, Schatz GC, Mondragón A, O'Halloran TV. 116.  2015. Allosteric transcriptional regulation via changes in the overall topology of the core promoter. Science 349:877–81 [Google Scholar]
  117. Martell DJ, Joshi CP, Gaballa A, Santiago AG, Chen TY. 117.  et al. 2015. Metalloregulator CueR biases RNA polymerase's kinetic sampling of dead-end or open complex to repress or activate transcription. PNAS 112:13467–72 [Google Scholar]
  118. Botella JA, Murillo FJ, Ruiz-Vázquez R. 118.  1995. A cluster of structural and regulatory genes for light-induced carotenogenesis in Myxococcus xanthus. Eur. J. Biochem. 233:238–48 [Google Scholar]
  119. Navarro-Avilés G, Jiménez MA, Pérez-Marín MC, González C, Rico M. 119.  et al. 2007. Structural basis for operator and antirepressor recognition by Myxococcus xanthus CarA repressor. Mol. Microbiol. 63:980–94 [Google Scholar]
  120. Pérez-Marín MC, López-Rubio JJ, Murillo FJ, Elías-Arnanz M, Padmanabhan S. 120.  2004. The N terminus of Myxococcus xanthus CarA repressor is an autonomously folding domain that mediates physical and functional interactions with both operator DNA and antirepressor protein. J. Biol. Chem. 279:33093–103 [Google Scholar]
  121. Pérez-Marín MC, Padmanabhan S, Polanco MC, Murillo FJ, Elías-Arnanz M. 121.  2008. Vitamin B12 partners the CarH repressor to downregulate a photoinducible promoter in Myxococcus xanthus. Mol. Microbiol. 67:804–19 [Google Scholar]
  122. López-Rubio JJ, Elías-Arnanz M, Padmanabhan S, Murillo FJ. 122.  2002. A repressor-antirepressor pair links two loci controlling light-induced carotenogenesis in Myxococcus xanthus. J. Biol. Chem. 277:7262–70 [Google Scholar]
  123. López-Rubio JJ, Padmanabhan S, Lázaro JM, Salas M, Murillo FJ, Elías-Arnanz M. 123.  2004. Operator design and mechanism for CarA repressor-mediated down-regulation of the photoinducible carB operon in Myxococcus xanthus. J. Biol. Chem. 279:28945–53 [Google Scholar]
  124. Whitworth DE, Hodgson DA. 124.  2001. Light-induced carotenogenesis in Myxococcus xanthus: evidence that CarS acts as an anti-repressor of CarA. Mol. Microbiol. 42:809–19 [Google Scholar]
  125. León E, Navarro-Avilés G, Santiveri CM, Flores-Flores C, Rico M. 125.  et al. 2010. A bacterial antirepressor with SH3 domain topology mimics operator DNA in sequestering the repressor DNA recognition helix. Nucleic Acids Res 38:5226–41 [Google Scholar]
  126. Takano H, Obitsu S, Beppu T, Ueda K. 126.  2005. Light-induced carotenogenesis in Streptomyces coelicolor A3(2): identification of an extracytoplasmic function sigma factor that directs photodependent transcription of the carotenoid biosynthesis gene cluster. J. Bacteriol. 187:1825–32 [Google Scholar]
  127. Díez AI, Ortiz-Guerrero JM, Ortega A, Elías-Arnanz M, Padmanabhan S, García de la Torre J. 127.  2013. Analytical ultracentrifugation studies of oligomerization and DNA-binding of TtCarH, a Thermus thermophilus coenzyme B12-based photosensory regulator. Eur. Biophys. J. 42:463–76 [Google Scholar]
  128. Takano H, Kondo M, Usui N, Usui T, Ohzeki H. 128.  et al. 2011. Involvement of CarA/LitR and CRP/FNR family transcriptional regulators in light-induced carotenoid production in Thermus thermophilus. J. Bacteriol. 193:2451–59 [Google Scholar]
  129. Takano H, Mise K, Hagiwara K, Hirata N, Watanabe S. 129.  et al. 2015. Role and function of LitR, an adenosyl B12-bound light-sensitive regulator of Bacillus megaterium QM B1551, in regulation of carotenoid production. J. Bacteriol. 197:2301–15 [Google Scholar]
  130. Cheng Z, Li K, Hammad LA, Karty JA, Bauer CE. 130.  2014. Vitamin B12 regulates photosystem gene expression via the CrtJ antirepressor AerR in Rhodobacter capsulatus. Mol. Microbiol. 91:649–64 [Google Scholar]
  131. Vermeulen AJ, Bauer CE. 131.  2015. Members of the PpaA/AerR antirepressor family bind cobalamin. J. Bacteriol. 197:2694–703 [Google Scholar]
  132. Ponnampalam SN, Bauer CE. 132.  1997. DNA binding characteristics of CrtJ. A redox-responding repressor of bacteriochlorophyll, carotenoid, and light harvesting-II gene expression in Rhodobacter capsulatus. J. Biol. Chem. 272:18391–96 [Google Scholar]
  133. Ponnampalam SN, Buggy JJ, Bauer CE. 133.  1995. Characterization of an aerobic repressor that coordinately regulates bacteriochlorophyll, carotenoid, and light harvesting-II expression in Rhodobacter capsulatus. J. Bacteriol. 177:2990–97 [Google Scholar]
  134. Edayathumangalam R, Wu R, Garcia R, Wang Y, Wang W. 134.  et al. 2013. Crystal structure of Bacillussubtilis GabR, an autorepressor and transcriptional activator of gabT. PNAS 110:17820–25 [Google Scholar]
  135. Al-Zyoud WA, Hynson RM, Ganuelas LA, Coster AC, Duff AP. 135.  et al. 2016. Binding of transcription factor GabR to DNA requires recognition of DNA shape at a location distinct from its cognate binding site. Nucleic Acids Res 44:1411–20 [Google Scholar]
  136. Ohlendorf R, Schumacher CH, Richter F, Möglich A. 136.  2016. Library-aided probing of linker determinants in hybrid photoreceptors. ACS Synth. Biol. 5:1117–26 [Google Scholar]
  137. Katz RN, Vickrey TM, Schrauzer GN. 137.  1976. Detection of 4′,5′-anhydroadenosine as the cleavage product of coenzyme B12 in functional holoenzymes. Angew. Chem. Int. Ed. Engl. 15:542–43 [Google Scholar]
  138. Krouwer JS, Schultz RM, Babior BM. 138.  1978. The mechanism of action of ethanolamine ammonia-lyase, an adenosylcobalamin-dependent enzyme. Reaction of the enzyme cofactor complex with 2-aminoacetaldehyde. J. Biol. Chem. 253:1041–47 [Google Scholar]
  139. Garr CD, Finke RG. 139.  1993. Adocobalamin (AdoCbl or coenzyme B12) cobalt-carbon bond homolysis radical-cage effects: product, kinetic, mechanistic, and cage efficiency factor (Fc) studies, plus the possibility that coenzyme B12-dependent enzymes function as “ultimate radical cages” and “ultimate radical traps.”. Inorg. Chem. 32:4414–21 [Google Scholar]
  140. Sension RJ, Cole AG, Harris AD, Fox CC, Woodbury NW. 140.  et al. 2004. Photolysis and recombination of adenosylcobalamin bound to glutamate mutase. J. Am. Chem. Soc. 126:1598–99 [Google Scholar]
  141. Sension RJ, Harris DA, Stickrath A, Cole AG, Fox CC, Marsh EN. 141.  2005. Time-resolved measurements of the photolysis and recombination of adenosylcobalamin bound to glutamate mutase. J. Phys. Chem. B 109:18146–52 [Google Scholar]
  142. Gruber K, Kräutler B. 142.  2016. Coenzyme B12 repurposed for photoregulation of gene expression. Angew. Chem. Int. Ed. Engl. 55:5638–40 [Google Scholar]
  143. Cheng Z, Yamamoto H, Bauer CE. 143.  2016. Cobalamin's (vitamin B12) surprising function as a photoreceptor. Trends Biochem. Sci. 41:647–50 [Google Scholar]
  144. Martinkova M, Kitanishi K, Shimizu T. 144.  2013. Heme-based globin-coupled oxygen sensors: linking oxygen binding to functional regulation of diguanylate cyclase, histidine kinase, and methyl-accepting chemotaxis. J. Biol. Chem. 288:27702–11 [Google Scholar]
  145. García-Moreno D, Polanco MC, Navarro-Avilés G, Murillo FJ, Padmanabhan S, Elías-Arnanz M. 145.  2009. A vitamin B12-based system for conditional expression reveals dksA to be an essential gene in Myxococcus xanthus. J. Bacteriol. 191:3108–19 [Google Scholar]
  146. Kainrath S, Stadler M, Reichhart E, Distel M, Janovjak H. 146.  2017. Green-light-induced inactivation of receptor signaling using cobalamin-binding domains. Angew. Chem. Int. Ed. Engl. 56:4608–11 [Google Scholar]
/content/journals/10.1146/annurev-biochem-061516-044500
Loading
/content/journals/10.1146/annurev-biochem-061516-044500
Loading

Data & Media loading...

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error