The growing family of photoactive yellow proteins and their presumed functional roles

Photochemical and Photobiological Sciences

Volumn 11, Issue 10, 2012, Pages 1495-1514

  Meyer, T E ^a   Kyndt, J A ^a   Memmi, S ^b   Moser, T ^a   Colon Acevedo B ^a   Devreese, B ^b   Van Beeumen, J J ^b  

^a University of Arizona   (United States)

^b GHENT UNIVERSITY   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS); HALOPHILA; HALORHODOSPIRA HALOPHILA;

BACTERIAL PROTEIN; PHOTOACTIVE YELLOW PROTEIN, BACTERIA; VISUAL PROTEINS AND PIGMENTS;

AMINO ACID SEQUENCE; CHEMISTRY; CLASSIFICATION; GENETICS; HALORHODOSPIRA HALOPHILA; METABOLISM; MOLECULAR GENETICS; PHYLOGENY; PHYSIOLOGY; PROTEIN ANALYSIS; REVIEW; RHODOBACTER; SEQUENCE ALIGNMENT;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; HALORHODOSPIRA HALOPHILA; MOLECULAR SEQUENCE DATA; PHOTORECEPTORS, MICROBIAL; PHYLOGENY; PROTEIN INTERACTION MAPPING; RHODOBACTER; SEQUENCE ALIGNMENT;

EID: 84871826062     PISSN: 1474905X     EISSN: 14749092     Source Type: Journal    
DOI: 10.1039/c2pp25090j     Document Type: Review

References (99)

1. T. E. Meyer Isolation and characterization of soluble cytochromes, ferredoxins and other chromophoric proteins from the halophilic phototrophic bacterium, Ectothiorhodospira halophila Biochim. Biophys. Acta 1985 806 175 183
2. T. E. Meyer E. Yakali M. A. Cusanovich G. Tollin Properties of a water soluble, yellow protein isolated from a halophilic phototrophic bacterium that has photochemical activity analogous to sensory rhodopsin Biochemistry 1987 26 418 423 (Pubitemid 17022111)
3. M. A. Cusanovich T. E. Meyer Photoactive yellow protein: A prototypic PAS domain sensory protein and development of a common signaling mechanism Biochemistry 2003 42 4759 4770 (Pubitemid 36532027)
4. W. W. Sprenger W. D. Hoff J. P. Armitage K. J. Hellingwerf The eubacterium Ectothiorhodospira halophila is negatively phototactic, with a wavelength dependence that fits the absorption spectrum of the photoactive yellow protein J. Bacteriol. 1993 175 3096 3104 (Pubitemid 23148746)
5. Z. Y. Jiang L. R. Swem B. G. Rushing S. Devanathan G. Tollin C. E. Bauer Bacterial photoreceptor with similarity to photoactive yellow protein and plant phytochromes Science 1999 285 406 409 (Pubitemid 29343962)
6. J. E. Berleman B. M. Hasselbring C. E. Bauer Hypercyst mutants in Rhodospirillum centenum identify regulatory loci involved in cyst cell differentiation J. Bacteriol. 2004 186 5834 5841 (Pubitemid 39128657)
7. Z. Y. Jiang C. E. Bauer Component of the Rhodospirillum centenum photosensory apparatus with structural and functional similarity to methyl-accepting chemotaxis protein chemoreceptors J. Bacteriol. 2001 183 171 177 (Pubitemid 32003121)
8. S. Kreutel A. Kuhn D. Kiefer The photosensor protein Ppr of Rhodocista centenaria is linked to the chemotaxic signaling pathway BMC Microbiol. 2010 10 281
9. J. A. Kyndt T. E. Meyer M. A. Cusanovich Photoactive yellow protein, bacteriophytochrome, and sensory rhodopsin in purple phototrophic bacteria Photochem. Photobiol. Sci. 2004 3 519 530 (Pubitemid 38968063)
10. J. A. Kyndt J. C. Fitch T. E. Meyer M. A. Cusanovich Thermochromatium tepidum photoactive yellow protein/bacteriophytochrome/diguanylate cyclase: characterization of the PYP domain Biochemistry 2005 44 4755 4764 (Pubitemid 40396754)
11. J. A. Kyndt J. K. Hurley B. Devreese T. E. Meyer M. A. Cusanovich G. Tollin J. J. Van Beeumen Rhodobacter capsulatus photoactive yellow protein: genetic context, spectral and kinetics characterization, and mutagenesis Biochemistry 2004 43 1809 1820 (Pubitemid 38233244)
12. M. Kumauchi M. T. Hara P. Stalcup A. Xie W. D. Hoff Identification of six new photoactive yellow proteins - Diversity and Structure-function relationships in a bacterial blue light photoreceptor Photochem. Photobiol. 2008 84 956 969
13. J. J. Van Beeumen B. V. Devreese S. M. Van Bun W. D. Hoff K. J. Hellingwerf T. E. Meyer D. E. McRee M. A. Cusanovich Primary structure of a photoactive yellow protein from the phototrophic bacterium Ectothiorhodospira halophila, with evidence for the mass and the binding site of the chromophore Prot. Sci. 1993 2 1114 1125 (Pubitemid 23191752)
14. G. Borgstahl D. R. Williams E. D. Getzoff 1.4A Structure of photoactive yellow protein, a cytosolic photoreceptor: Unusual fold active site, and chromopore Biochemistry 1995 34 6278 6287
15. U. K. Genick S. Devanathan T. E. Meyer I. L. Canestrelli E. Williams M. A. Cusanovich G. Tollin E. D. Getzoff Active site mutants implicate key residues for control of color and light cycle kinetics of photoactive yellow protein Biochemistry 1997 36 8 14 (Pubitemid 27024672)
16. A. Xie K. Kelemen J. Hendriks B. J. White K. J. Hellingwerf W. D. Hoff Formation of a new buried charge drives a large-amplitude protein quake in photoreceptor activation Biochemistry 2001 40 1510 1517 (Pubitemid 32144019)
17. K. Mihara O. Hisatomi Y. Imamoto M. Kataoka F. Tokunaga Functional expression and site directed mutagenesis of photoactive yellow protein J. Biochem. 1997 121 876 880 (Pubitemid 27236905)
18. R. Brudler T. E. Meyer U. K. Genick S. Devanathan T. T. Woo D. P. Millar K. Gerwert M. A. Cusanovich G. Tollin E. D. Getzoff Coupling of hydrogen bonding to chromophore conformation and function in photoactive yellow protein Biochemistry 2000 39 13478 13486
19. C. P. Joshi H. Otto D. Hoersch T. E. Meyer M. A. Cusanovich M. P. Heyn Strong hydrogen bond between glutamic acid 46 and chromophore leads to the intermediate spectral form and excited state proton transfer in the Y42F mutant of the photoreceptor photoactive yellow protein Biochemistry 2009 48 9980 9993
20. S. Devanathan U. K. Genick I. L. Canestrelli T. E. Meyer M. A. Cusanovich E. D. Getzoff G. Tollin New insights into the photocycle of Ectothiorhodospira halophila photoactive yellow protein: photorecovery of the long-lived photobleached intermediate in the Met100Ala mutant Biochemistry 1998 37 11563 8 (Pubitemid 28388198)
21. M. Kumauchi N. Hamada J. Sasaki F. Tokunaga A role of methionine 100 in facilitating PYP(M)-decay process in the photocycle of photoactive yellow protein J. Biochem. 2002 132 205 210 (Pubitemid 34947881)
22. S. Rajagopal K. Moffat Crystal structure of a photoactive yellow protein from a sensor histidine kinase: conformational variability and signal transduction Proc. Natl. Acad. Sci. USA 2003 100 1649 1654 (Pubitemid 36254502)
23. A. Haker J. Hendriks T. Gensch K. Hellingwerf W. Crielaard Isolation, reconstitution and functional characterisation of the Rhodobacter sphaeroides photoactive yellow protein FEBS Lett. 2000 486 52 56
24. M. Kumauchi S. Kaledhonkar A. F. Philip J. Wycoff M. Hara Y. Li A. Xie W. D. Hoff A conserved helical capping hydrogen bond in PAS domains controls signaling kinetics in the superfamily prototype photoactive yellow protein J. Am. Chem. Soc. 2010 132 15820 15830
25. B. Borucki J. A. Kyndt C. P. Joshi H. Otto T. E. Meyer M. A. Cusanovich M. P. Heyn Effect of salt and pH on the activation of photoactive yellow protein and gateway mutants Y98Q and Y98F Biochemistry 2005 44 13650 13663 (Pubitemid 41507446)
26. J. A. Kyndt S. N. Savvides S. Memmi M. Koh J. C. Fitch T. E. Meyer M. P. Heyn J. J. Van Beeumen M. A. Cusanovich Structural role of Tyrosine 98 in photoactive yellow protein: effects on fluorescence, gateway and photocycle recovery Biochemistry 2007 46 95 105 (Pubitemid 46067740)
27. T. Morishita M. Harigai Y. Yamazaki H. Kamikubo M. Kataoka Y. Imamoto Array of aromatic amino acid side chains located near the chromophore of photoactive yellow protein Photochem. Photobiol. 2007 83 280 285 (Pubitemid 46623073)
28. M. Baca G. E. O. Borgstahl M. Boissinot P. M. Burke D. R. Williams K. A. Slater E. D. Getzoff Complete chemical structure of photoactive yellow protein: novel thioester-linked 4-hydroxycinnamyl chromophore and photocycle chemistry Biochemistry 1994 33 14369 14377
29. R. Kort W. D. Hoff M. Van West A. R. Kroon S. M. Hoffer K. H. Vlieg W. Crielaard J. J. Van Beeumen K. J. Hellingwerf The xanthopsins: a new family of eubacterial blue-light photoreceptors EMBO J. 1996 15 3209 3218 (Pubitemid 26231926)
30. J. A. Kyndt T. E. Meyer M. A. Cusanovich J. J. Van Beeumen Characterization of a bacterial tyrosine ammonia lyase, a biosynthetic enzyme for the photoactive yellow protein FEBS Lett. 2002 512 240 244 (Pubitemid 34164487)
31. J. A. Kyndt F. Vanrobaeys F. C. Fitch B. V. Devreese T. E. Meyer M. A. Cusanovich J. J. Van Beeumen Heterologous production of Halorhodospira halophila holo photoactive yellow protein through tandem expression of the postulated biosynthetic genes Biochemistry 2003 42 965 970 (Pubitemid 36159529)
32. J. S. Mattick Type IV pili and twitching motility Annu. Rev. Microbiol. 2002 56 289 314 (Pubitemid 35217457)
33. M. A. van der Horst W. Laan S. Yeremenko A. Wende P. Palm D. Oesterhelt K. J. Hellingwerf From primary photochemistry to biological function in the blue light photoreceptors PYP and AppA, Photochem Photobiol. Sci. 2005 4 688 693 (Pubitemid 41367018)
34. R. Narikawa Y. Fukushima T. Ishizuka S. Itoh M. Ikeuchi A novel photoactive GAF domain of cyanobacteriochrome AnPixJ that shows reversible green/red photoconversion J. Mol. Biol. 2008 380 844 855
35. S. Yoshihara F. Suzuki H. Fujita X. X. Geng M. Ikeuchi Novel putative photoreceptor and regulatory genes Required for the positive phototactic movement of the unicellular motile cyanobacterium Synechocystis sp. PCC 6803 Plant Cell Physiol. 2000 41 1299 1304 (Pubitemid 32099774)
36. S. Hou J. H. Saw K. S. Lee T. A. Freitas C. Belisle et al. Genome sequence of the deep-sea gamma-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy Proc. Natl. Acad. Sci. USA 2004 101 18036 18041 (Pubitemid 40054070)
37. S. P. Donachie S. Hou T. S. Gregory A. Malahoff M. Alam Idiomarina loihiensis sp. nov., a halophilic gamma-Proteobacterium from the Loihi submarine volcano, Hawaii Int. J. Syst. Evol. Microbiol. 2003 53 1873 1879 (Pubitemid 37483844)
38. M. A. van der Horst P. Stalcup S. Kaledhonkar M. Kumauchi M. Hara A. Xie K. J. Hellingwerf W. D. Hoff Locked chromophore analogs reveal that photoactive yellow protein regulates biofilm formation in the deep sea bacterium Idiomarina loihiensis J. Am. Chem. Soc. 2009 131 17443 17451
39. P. Peters E. Tel-Or H. G. Trueper Transport of glycine betaine in the extremely haloalkaliphilic sulphur bacterium Ectothiorhodospira halochloris J. Gen. Microbiol. 1992 138 1993 1998
40. J. L. Ramos M. Martinez-Bueno A. J. Molina-Henares W. Teran K. Watanabe X. Zhang M. T. Gallegos R. Brennan R. Tobes The TetR family of transcriptional repressors Microbiol. Mol. Biol. Rev. 2005 69 326 356 (Pubitemid 40847943)
41. D. S. Murray M. A. Schumacher R. G. Brennan Crystal structures of QacR-diamidine complexes reveal additional multidrug-binding modes and a novel mechanism of drug charge neutralization J. Biol. Chem. 2004 279 14365 14371 (Pubitemid 38468978)
42. M. Gomelsky W. D. Hoff Light helps bacteria make important lifestyle decisions Trends Microbiol 2011 19 441 448
43. T. E. Meyer J. C. Fitch R. G. Bartsch G. Tollin M. A. Cusanovich Soluble cytochromes and a photoactive yellow protein isolated from the moderately halophilic purple phototrophic bacterium, Rhodospirillum salexigens Biochim. Biophys. Acta 1990 1016 364 370
44. M. Koh G. Van Driessche B. Samyn W. D. Hoff T. E. Meyer M. A. Cusanovich J. J. Van Beeumen Sequence evidence for strong conservation of the photoactive yellow proteins from the halophilic phototrophic bacteria Chromatium salexigens and Rhodospirillum salexigens Biochemistry 1996 35 2526 2534 (Pubitemid 26099911)
45. S. S. Krishna I. Majumdar N. V. Grishin Structural classification of zinc fingers: survey and summary Nucleic Acids Res. 2003 31 532 550 (Pubitemid 36175942)
46. G. Meades Jr B. K. Benson A. Grove G. L. Waldrop A tale of two functions: enzymatic activity and translational repression by carboxyltransferase Nucleic Acids Res. 2010 38 1217 1227
47. T. Tamada K. Kitadokoro Y. Higuchi K. Inaka A. Yasui P. E. de Ruiter A. P. M. Eker K. Miki Crystal structure of DNA photolyase from Anacystis nidulans Nat. Struct. Mol. Biol. 1997 4 887 891 (Pubitemid 27479436)
48. H. Park S. Kim A. Sancar J. Deisenhofer Crystal structure of DNA photolyase from Escherichia coli Science 1995 268 1866 1872
49. R. Kort M. K. Phillips-Jones D. M. van Aalten A. Haker S. M. Hoffer K. J. Hellingwerf W. Crielaard Sequence, chromophore extraction and 3-D model of the photoactive yellow protein from Rhodobacter sphaeroides Biochim. Biophys. Acta 1998 1385 1 6 (Pubitemid 28277039)
50. H. Strnad A. Lapidus J. Paces P. Ulbrich C. Vlcek V. Paces R. Haselkorn Complete genome sequence of the photosynthetic purple nonsulfur bacterium Rhodobacter capsulatus SB 1003 J. Bacteriol. 2010 192 3545 3546
51. M. Choudhary X. Zanhua Y. X. Fu S. Kaplan Genome analyses of three strains of Rhodobacter sphaeroides: Evidence of rapid evolution of chromosome II J. Bacteriol. 2007 189 1914 1921 (Pubitemid 46446155)
52. S. K. Lim S. J. Kim S. H. Cha Y. K. Oh H. J. Rhee M. S. Kim J. K. Lee Complete genome sequence of Rhodobacter sphaeroides KD131 J. Bacteriol. 2009 191 1118 1119
53. S. Yooseph G. Sutton D. B. Rusch A. L. Halpern S. J. Williamson et al. The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families PLoS Biol. 2007 5 e16
54. J. F. Imhoff B. J. Tindall W. D. Grant H. G. Trueper Ectothiorhodospira vacuolata sp.: nov., a new phototrophic bacterium from Soda Lakes Arch. Microbiol. 1981 130 238 242
55. A. E. Walsby Gas vesicles Microbiol. Rev. 1994 58 94 144
56. D. O. Jung L. A. Achenbach E. A. Karr S. Takaichi M. T. Madigan A gas vesiculate planktonic strain of the purple non-sulfur bacterium Rhodoferax antarcticus isolated from Lake Fryxell, Dry Valleys, Antarctica Arch. Microbiol. 2004 182 236 243 (Pubitemid 39361999)
57. G. van Keulen D. A. Hopwood L. Dijkhuizen R. G. Sawers Gas vesicles in actinomycetes: old buoys in novel habitats? Trends Micobiol. 2005 13 350 354 (Pubitemid 41073804)
58. A. E. Walsby P. G. Dunton Gas vesicles in actinomycetes? Trends Microbiol. 2006 14 99 100 (Pubitemid 43376045)
59. M. Jaubert J. Lavergne J. Fardoux L. Hannibal L. Vuillet J. M. Adriano P. Bouyer D. Pignol E. Giraud A. Verméglio A singular bacteriophytochrome acquired by lateral gene transfer J. Biol. Chem. 2007 282 7320 7328 (Pubitemid 47093685)
60. Y. K. Lu J. Marden M. Han W. D. Swingley S. D. Mastrian S. R. Chowdhury J. Hao T. Helmey S. Kim A. A. Kurdoglu H. J. Matthies D. Rollo P. Stothard R. E. Blankenship C. E. Bauer J. E. Touchman Metabolic flexibility revealed in the genome of the cyst forming alpha-1 proteobacterium Rhodospirillum centenum BMC Genomics 2010 11 325
61. J. E. Berleman C. E. Bauer Involvement of a Che-like signal transduction cascade in regulating cyst cell development in Rhodospirillum centenum Mol. Biol. 2005 56 457 466
62. D. Segura T. Cruz G. Espin Encystment and alkylresorcinol production by Azotobacter vinelandii strains impaired in poly-beta-hydroxybutyrate synthesis Arch. Microbiol. 2003 179 437 443 (Pubitemid 36745688)
63. N. Funa H. Ozawa A. Hirata S. Horinouchi Phenolic lipid synthesis by type III polyketide synthases is essential for cyst formation in Azotobacter vinelandii Proc. Natl. Acad. Sci. USA 2006 103 6356 6361
64. J. A. Kyndt J. C. Fitch T. E. Meyer M. A. Cusanovich The photoactivated PYP domain of Rhodospirillum centenum Ppr accelerates the recovery of the bacteriophytochrome domain after white light illumination Biochemistry 2007 46 8256 8262 (Pubitemid 47075965)
65. J. A. Kyndt J. C. Fitch S. Seibeck B. Borucki M. P. Heyn T. E. Meyer M. A. Cusanovich Regulation of the Ppr histidine kinase by light-induced interactions between its photoactive yellow protein and bacteriophytochrome domains Biochemistry 2010 49 17344 17354
66. J. B. Jaftha B. W. Strijdom P. L. Steyn Characterization of pigmented methylotrophic bacteria which nodulate Lotononis bainesii Syst. Appl. Microbiol. 2002 25 440 449 (Pubitemid 35204129)
67. M. Tarutina D. A. Ryjenkov M. Gomelsky An unorthodox bacteriophytochrome from Rhodobacter sphaeroides involved in turnover of the second messenger c-di-GMP J. Biol. Chem. 2006 281 34751 8 (Pubitemid 46036515)
68. R. Tal H. C. Wong R. Calhoon D. Gelfand A. L. Fear G. Volman R. Mayer P. Ross D. Amikam H. Weinhouse A. Cohen S. Sapir P. Ohana M. Benziman Three cdg operons control cellular turnover of cyclic di-GMP in Acetobacter xylinum: genetic organization and occurrence of conserved domains in isoenzymes J. Bacteriol. 1998 180 4416 4425 (Pubitemid 28405564)
69. A. D. Tischler A. Camilli Cyclic diguanylate (c-di-GMP) regulates Vibrio cholerae biofilm formation Mol. Microbiol. 2004 53 857 869 (Pubitemid 39036965)
70. U. Romling M. Gomelsky M. Y. Galperin C-di-GMP: the dawning of a novel bacterial signaling system Mol. Microbiol. 2005 57 629 639 (Pubitemid 41025947)
71. R. P. Ryan T. Tolker-Nielsen J. M. Dow When the PilZ don't work: effectors for cyclic di-GMPaction in bacteria Trends Microbiol 2012 20 235 242
72. N. Sudarsan E. R. Lee Z. Weinberg R. H. Moy J. N. Kim K. H. Link R. R. Breaker Riboswitches in eubacteria sense the second messenger cyclic di-GMP Science 2008 321 411 413 (Pubitemid 352029978)
73. E. F. Mongodin K. E. Nelson S. Daugherty R. T. DeBoy J. Wister H. Khouri J. Weidman D. A. Walsh R. T. Papke G. Sanchez Perezs A. K. Sharma C. L. Nesbo D. MacLeod E. Bapteste W. F. Doolittle R. T. L. Charlebois B. Legault F. Rodriguez-Valera The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea Proc. Natl. Acad. Sci. USA 2005 102 18147 18152 (Pubitemid 41798516)
74. S. Memmi J. A. Kyndt T. E. Meyer B. Devreese M. A. Cusanovich J. J. Van Beeumen Photoactive yellow protein from the halophilic bacterium Salinibacter ruber Biochemistry 2008 47 2014 2024 (Pubitemid 351287127)
75. A. Pena et al. Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting salinibacter ruber strains ISME J. 2010 4 882 895
76. Y. Oda F. W. Larimer P. S. Chain S. Malfatti M. V. Shin L. M. Vergez L. Hauser M. L. Land S. Braatsch J. T. Beatty D. A. Pelletier A. L. Schaefer C. S. Harwood Multiple genome sequences reveal adaptations of a phototrophic bacterium to sediment microenvironments Proc. Natl. Acad. Sci. USA 2008 105 18543 8
77. P. J. B. Brown D. T. Kysela A. Buechlein C. Hemmerich Y. V. Brun Genome sequences of eight morphologically diverse alphaproteobacteria J. Bacteriol. 2011 193 4567 4568
78. A. Weilharter B. Mitter M. V. Shin P. S. G. Chain J. Nowak A. Sessitsch Complete genome sequence of the plant growth-promoting endophyte, Burkholderia phytofirmans strain PsJN J. Bacteriol. 2011 193 3383 3384
79. W. Kittichotirat N. M. Good R. Hall F. Bringel A. Lajus C. Medigue N. E. Smalley D. Beck R. Bumgarner S. Vuilleummier M. G. Kalyushnaya Genome sequence of Methyloversatilis universalis FASM5, a methylotrophic representative of the order Rhodocyclales J. Bacteriol. 2011 193 4541 4542
80. I. M. Oh K. Lee Y. Jang I. Kang I. J. Kim T. W. Kang S. Y. Kim J. C. Cho Genome sequence of strain IMCC9480, a xanthorhodopsin-bearing betaproteobacterim isolated from the Arctic Ocean J. Bacteriol. 2011 193 3421
81. J. A. Chapman E. F. Kirkness O. Simakov S. E. Hampson T. Mitros et al. The dynamic genome of Hydra Nature 2010 464 592 596
82. K. Cho D. R. Zusman AsgD, a new two-component regulator required for A signaling and nutrient sensing during early development of Myxococcus xanthus Mol. Microbiol. 1999 34 268 281 (Pubitemid 29486245)
83. D. Kaiser Signaling in myxobacteria Annu. Rev. Microbiol. 2004 58 75 98 (Pubitemid 39551979)
84. S. Inouye D. White M. Inouye Development of Stigmatella aurantiaca: effects of light and gene expression J. Bacteriol. 1980 141 1360 1365 (Pubitemid 10076165)
85. G. T. Qualls K. Stephens D. White Light-stimulated morphogenesis in the fruiting myxobacterium Stigmatella aurantiaca Science 1978 201 444 445 (Pubitemid 9016238)
86. D. White W. Shropshire Jr K. Stephens Photocontrol of development by Stigmatella aurantiaca J. Bacteriol. 1980 142 1023 1024 (Pubitemid 11230357)
87. C. Benda C. Scheufler N. Tandeau de Marsac W. Gärtner Crystal structures of two cyanobacterial response regulators in apo- and phosphorylated form reveal a novel dimerization motif of phytochrome-associated response regulators Biophys. J. 2004 87 476 487 (Pubitemid 38880101)
88. S. Schneiker O. Perlova O. Kaiser K. Gerth A. Alici et al. Complete genome sequence of the myxobacterium Sorangium cellulosum Nat. Biotechnol. 2007 25 1281 1289 (Pubitemid 350076516)
89. D. Guzman A. Balderrama-Subieta C. Cardona-Orturo M. Guevara-Martinez N. Callisaya-Quispe J. Quillaguaman Evolutionary patterns of carbohydrate transport and metabolism in Halomonas boliviensis as derived from its genome sequence: influences on polyester production Aquat. Biosyst. 2012 8 9
90. J. K. Gupta R. D. Gupta A. Singh N. S. Chauhan R. Sharma Genome sequence of Rheinheimera sp. strain A13L, isolated from Pangong Lake, India J. Bacteriol. 2011 193 5873 5874
91. J. Valdes R. Quatrini K. Hallberg M. Dopson P. D. T. Valenzuela D. S. Holmes Draft genome sequence of the extremely acidophilic bacterium Acidithiobacillus caldus ATCC 51756 reveals metabolic versatility in the genus Acidithiobacillus J. Bacteriol. 2009 191 5877 5878
92. S. Vuilleumier L. Chistoserdova M. C. Lee F. Bringel A. Lajus et al. Methylobacterium genome sequences: a reference blueprint to investigate microbial metabolism of C1 compounds from natural and industrial sources PLoS One 2009 4 E5584
93. L. Vuillet M. Kojadinovic S. Zappa M. Jaubert J. M. Adriano J. Fardoux L. Hannibal D. Pignol A. Verméglio E. Giraud Evolution of a bacteriophytochrome from light to redox sensor EMBO J. 2007 26 3322 3331 (Pubitemid 47123535)
94. S. Vuilleumier et al. Genome sequence of the haloalkaliphilic methanotrophic bacterium Methylomicrobium alcaliphilum 20Z J. Bacteriol. 2012 194 551 552
95. T. Weissgerber et al. Complete genome sequence of Allochromatium vinosum DSM180 Stand. Gen. Sci. 2011 5 311 330
96. S. Huntley et al. Comparative genomic analysis of fruiting body formation in Myxococcales Mol. Biol. Evol. 2010 28 1083 1097
97. N. Ivanova et al. Complete genome sequence of Haliangium ochraceum type strain (SMP-2) Stand. Gen. Sci. 2010 2 96 106
98. A. Lapidus et al. Genomes of three methylotrophs from a single niche reveal the genetic and metabolic divergence of the Methylophilaceae J. Bacteriol. 2011 193 3757 3764
99. T) Stand. Gen. Sci. 2010 2 176 185