Abstract
Photoactive yellow protein (PYP) is a photoreceptor that has been isolated from three halophilic phototrophic purple bacteria. The PYP from Ectothiorhodospira halophila BN9626 is the only member for which the sequence has been reported at the DNA level. Here we describe the cloning and sequencing of the genes encoding the PYPs from E.halophila SL-1 (type strain) and Rhodospirillum salexigens. The latter protein contains, like the E.halophila PYP, the chromophore trans p-coumaric acid, as we show here with high performance capillary zone electrophoresis. Additionally, we present evidence for the presence of a gene encoding a PYP homolog in Rhodobacter sphaeroides, the first genetically well-characterized bacterium in which this photoreceptor has been identified. An ORF downstream of the pyp gene from E.halophila encodes an enzyme, which is proposed to be involved in the biosynthesis of the chromophore of PYP. The pyp gene from E.halophila was used for heterologous overexpression in both Escherichia coli and R.sphaeroides, aimed at the development of a holoPYP overexpression system (an intact PYP, containing the p-coumaric acid chromophore and displaying the 446 nm absorbance band). In both organisms the protein could be detected immunologically, but its yellow color was not observed. Molecular genetic construction of a histidine-tagged version of PYP led to its 2500-fold overproduction in E.coli and simplified purification of the heterologously produced apoprotein. HoloPYP could be reconstituted by the addition of p-coumaric anhydride to the histidine-tagged apoPYP (PYP lacking its chromophore). We propose to call the family of photoactive yellow proteins the xanthopsins, in analogy with the rhodopsins.
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- Armitage J. P. Behavioral responses in bacteria. Annu Rev Physiol. 1992;54:683–714. doi: 10.1146/annurev.ph.54.030192.003343. [DOI] [PubMed] [Google Scholar]
- Armitage J. P., Macnab R. M. Unidirectional, intermittent rotation of the flagellum of Rhodobacter sphaeroides. J Bacteriol. 1987 Feb;169(2):514–518. doi: 10.1128/jb.169.2.514-518.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Baca M., Borgstahl G. E., Boissinot M., Burke P. M., Williams D. R., Slater K. A., Getzoff E. D. Complete chemical structure of photoactive yellow protein: novel thioester-linked 4-hydroxycinnamyl chromophore and photocycle chemistry. Biochemistry. 1994 Dec 6;33(48):14369–14377. doi: 10.1021/bi00252a001. [DOI] [PubMed] [Google Scholar]
- Bader J., Rauschenbach P., Simon H. On a hitherto unknown fermentation path of several amino acids by proteolytic clostridia. FEBS Lett. 1982 Apr 5;140(1):67–72. doi: 10.1016/0014-5793(82)80522-x. [DOI] [PubMed] [Google Scholar]
- Becker-André M., Schulze-Lefert P., Hahlbrock K. Structural comparison, modes of expression, and putative cis-acting elements of the two 4-coumarate: CoA ligase genes in potato. J Biol Chem. 1991 May 5;266(13):8551–8559. [PubMed] [Google Scholar]
- Black P. N., DiRusso C. C., Metzger A. K., Heimert T. L. Cloning, sequencing, and expression of the fadD gene of Escherichia coli encoding acyl coenzyme A synthetase. J Biol Chem. 1992 Dec 15;267(35):25513–25520. [PubMed] [Google Scholar]
- Borgstahl G. E., Williams D. R., Getzoff E. D. 1.4 A structure of photoactive yellow protein, a cytosolic photoreceptor: unusual fold, active site, and chromophore. Biochemistry. 1995 May 16;34(19):6278–6287. doi: 10.1021/bi00019a004. [DOI] [PubMed] [Google Scholar]
- Duronio R. J., Knoll L. J., Gordon J. I. Isolation of a Saccharomyces cerevisiae long chain fatty acyl:CoA synthetase gene (FAA1) and assessment of its role in protein N-myristoylation. J Cell Biol. 1992 May;117(3):515–529. doi: 10.1083/jcb.117.3.515. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Eggen R. I., Geerling A. C., Boshoven A. B., de Vos W. M. Cloning, sequence analysis, and functional expression of the acetyl coenzyme A synthetase gene from Methanothrix soehngenii in Escherichia coli. J Bacteriol. 1991 Oct;173(20):6383–6389. doi: 10.1128/jb.173.20.6383-6389.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Engler-Blum G., Meier M., Frank J., Müller G. A. Reduction of background problems in nonradioactive northern and Southern blot analyses enables higher sensitivity than 32P-based hybridizations. Anal Biochem. 1993 May 1;210(2):235–244. doi: 10.1006/abio.1993.1189. [DOI] [PubMed] [Google Scholar]
- Ferrando-May E., Krah M., Marwan W., Oesterhelt D. The methyl-accepting transducer protein HtrI is functionally associated with the photoreceptor sensory rhodopsin I in the archaeon Halobacterium salinarium. EMBO J. 1993 Aug;12(8):2999–3005. doi: 10.1002/j.1460-2075.1993.tb05968.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Fulda M., Heinz E., Wolter F. P. The fadD gene of Escherichia coli K12 is located close to rnd at 39.6 min of the chromosomal map and is a new member of the AMP-binding protein family. Mol Gen Genet. 1994 Feb;242(3):241–249. doi: 10.1007/BF00280412. [DOI] [PubMed] [Google Scholar]
- Hoff W. D., Sprenger W. W., Postma P. W., Meyer T. E., Veenhuis M., Leguijt T., Hellingwerf K. J. The photoactive yellow protein from Ectothiorhodospira halophila as studied with a highly specific polyclonal antiserum: (intra)cellular localization, regulation of expression, and taxonomic distribution of cross-reacting proteins. J Bacteriol. 1994 Jul;176(13):3920–3927. doi: 10.1128/jb.176.13.3920-3927.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hoff W. D., van Stokkum I. H., van Ramesdonk H. J., van Brederode M. E., Brouwer A. M., Fitch J. C., Meyer T. E., van Grondelle R., Hellingwerf K. J. Measurement and global analysis of the absorbance changes in the photocycle of the photoactive yellow protein from Ectothiorhodospira halophila. Biophys J. 1994 Oct;67(4):1691–1705. doi: 10.1016/S0006-3495(94)80643-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Imamoto Y., Ito T., Kataoka M., Tokunaga F. Reconstitution photoactive yellow protein from apoprotein and p-coumaric acid derivatives. FEBS Lett. 1995 Oct 30;374(2):157–160. doi: 10.1016/0014-5793(95)01096-w. [DOI] [PubMed] [Google Scholar]
- Jones M. R., Fowler G. J., Gibson L. C., Grief G. G., Olsen J. D., Crielaard W., Hunter C. N. Mutants of Rhodobacter sphaeroides lacking one or more pigment-protein complexes and complementation with reaction-centre, LH1, and LH2 genes. Mol Microbiol. 1992 May;6(9):1173–1184. doi: 10.1111/j.1365-2958.1992.tb01556.x. [DOI] [PubMed] [Google Scholar]
- Karger B. L., Cohen A. S., Guttman A. High-performance capillary electrophoresis in the biological sciences. J Chromatogr. 1989 Aug 11;492:585–614. doi: 10.1016/s0378-4347(00)84480-1. [DOI] [PubMed] [Google Scholar]
- Kim M., Mathies R. A., Hoff W. D., Hellingwerf K. J. Resonance Raman evidence that the thioester-linked 4-hydroxycinnamyl chromophore of photoactive yellow protein is deprotonated. Biochemistry. 1995 Oct 3;34(39):12669–12672. doi: 10.1021/bi00039a024. [DOI] [PubMed] [Google Scholar]
- Koh M., Van Driessche G., Samyn B., Hoff W. D., Meyer T. E., Cusanovich M. A., Van Beeumen J. J. Sequence evidence for strong conservation of the photoactive yellow proteins from the halophilic phototrophic bacteria Chromatium salexigens and Rhodospirillum salexigens. Biochemistry. 1996 Feb 27;35(8):2526–2534. doi: 10.1021/bi951494t. [DOI] [PubMed] [Google Scholar]
- Laemmli U. K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970 Aug 15;227(5259):680–685. doi: 10.1038/227680a0. [DOI] [PubMed] [Google Scholar]
- McRee D. E., Meyer T. E., Cusanovich M. A., Parge H. E., Getzoff E. D. Crystallographic characterization of a photoactive yellow protein with photochemistry similar to sensory rhodopsin. J Biol Chem. 1986 Oct 15;261(29):13850–13851. [PubMed] [Google Scholar]
- Messing J., Vieira J. A new pair of M13 vectors for selecting either DNA strand of double-digest restriction fragments. Gene. 1982 Oct;19(3):269–276. doi: 10.1016/0378-1119(82)90016-6. [DOI] [PubMed] [Google Scholar]
- Meyer T. E. Isolation and characterization of soluble cytochromes, ferredoxins and other chromophoric proteins from the halophilic phototrophic bacterium Ectothiorhodospira halophila. Biochim Biophys Acta. 1985 Jan 23;806(1):175–183. doi: 10.1016/0005-2728(85)90094-5. [DOI] [PubMed] [Google Scholar]
- Meyer T. E., Yakali E., Cusanovich M. A., Tollin G. Properties of a water-soluble, yellow protein isolated from a halophilic phototrophic bacterium that has photochemical activity analogous to sensory rhodopsin. Biochemistry. 1987 Jan 27;26(2):418–423. doi: 10.1021/bi00376a012. [DOI] [PubMed] [Google Scholar]
- Olsiewski P. J., Kaczorowski G. J., Walsh C. Purification and properties of D-amino acid dehydrogenase, an inducible membrane-bound iron-sulfur flavoenzyme from Escherichia coli B. J Biol Chem. 1980 May 25;255(10):4487–4494. [PubMed] [Google Scholar]
- Priefert H., Steinbüchel A. Identification and molecular characterization of the acetyl coenzyme A synthetase gene (acoE) of Alcaligenes eutrophus. J Bacteriol. 1992 Oct;174(20):6590–6599. doi: 10.1128/jb.174.20.6590-6599.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Raymond J. C., Sistrom W. R. ctothiorhodospira halophila: a new species ofthe genus Ectothiorhodospira. Arch Mikrobiol. 1969;69(2):121–126. doi: 10.1007/BF00409756. [DOI] [PubMed] [Google Scholar]
- Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Saraste M., Sibbald P. R., Wittinghofer A. The P-loop--a common motif in ATP- and GTP-binding proteins. Trends Biochem Sci. 1990 Nov;15(11):430–434. doi: 10.1016/0968-0004(90)90281-f. [DOI] [PubMed] [Google Scholar]
- Schägger H., von Jagow G. Tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the separation of proteins in the range from 1 to 100 kDa. Anal Biochem. 1987 Nov 1;166(2):368–379. doi: 10.1016/0003-2697(87)90587-2. [DOI] [PubMed] [Google Scholar]
- Sprenger W. W., Hoff W. D., Armitage J. P., Hellingwerf K. J. The eubacterium Ectothiorhodospira halophila is negatively phototactic, with a wavelength dependence that fits the absorption spectrum of the photoactive yellow protein. J Bacteriol. 1993 May;175(10):3096–3104. doi: 10.1128/jb.175.10.3096-3104.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Spudich J. L. Protein-protein interaction converts a proton pump into a sensory receptor. Cell. 1994 Dec 2;79(5):747–750. doi: 10.1016/0092-8674(94)90064-7. [DOI] [PubMed] [Google Scholar]
- Studier F. W., Moffatt B. A. Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. J Mol Biol. 1986 May 5;189(1):113–130. doi: 10.1016/0022-2836(86)90385-2. [DOI] [PubMed] [Google Scholar]
- Towbin H., Staehelin T., Gordon J. Electrophoretic transfer of proteins from polyacrylamide gels to nitrocellulose sheets: procedure and some applications. Proc Natl Acad Sci U S A. 1979 Sep;76(9):4350–4354. doi: 10.1073/pnas.76.9.4350. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Van Beeumen J. J., Devreese B. V., Van Bun S. M., Hoff W. D., Hellingwerf K. J., Meyer T. E., McRee D. E., Cusanovich M. A. 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. Protein Sci. 1993 Jul;2(7):1114–1125. doi: 10.1002/pro.5560020706. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Woese C. R. Bacterial evolution. Microbiol Rev. 1987 Jun;51(2):221–271. doi: 10.1128/mr.51.2.221-271.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Yao V. J., Spudich J. L. Primary structure of an archaebacterial transducer, a methyl-accepting protein associated with sensory rhodopsin I. Proc Natl Acad Sci U S A. 1992 Dec 15;89(24):11915–11919. doi: 10.1073/pnas.89.24.11915. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Zhao Y., Kung S. D., Dube S. K. Nucleotide sequence of rice 4-coumarate:CoA ligase gene, 4-CL.1. Nucleic Acids Res. 1990 Oct 25;18(20):6144–6144. doi: 10.1093/nar/18.20.6144. [DOI] [PMC free article] [PubMed] [Google Scholar]
- van Niel C. B. THE CULTURE, GENERAL PHYSIOLOGY, MORPHOLOGY, AND CLASSIFICATION OF THE NON-SULFUR PURPLE AND BROWN BACTERIA. Bacteriol Rev. 1944 Mar;8(1):1–118. doi: 10.1128/br.8.1.1-118.1944. [DOI] [PMC free article] [PubMed] [Google Scholar]