Publications

Invited reviews and book chapters

• Phytochrome cytoplasmic signaling.
  Hughes J. (2013)
  Ann. Rev. Pl. Biol., 63, 337-402 (PDF)

• Solid-state NMR spectroscopy to probe photoactivation in canonical phytochromes
  Song C., Rohmer T., Tiersch M., Zaanen J., Hughes J., Matysik J. (2013)
  Photochem. Photobiol., 89, 259–273

• On the structure and function of phytochromes.
  Hughes J. (2010)
  In "Plant photobiology and photosynthesis", Volotovski I.D., Ed., Natl. Acad. Sci. Belarus, Minsk. pp. 7-24 (PDF).
• Physcomitrella: the green yeast. (Book review: "The moss Physcomitrella patens", Knight C., Perroud P.F., Cove D., Annual Plant Reviews vol. 36, Wiley-Blackwell, Oxford)
  Hughes J. (2010)
  J Plant Physiol., 167, 1116-1117.
• Photomorphogenesis of mosses: physiology and molecular biology
  Hartmann E., Hughes J. (1999)
  In "Plant photobiology and photosynthesis", Volotovski I.D., Ed. Nat. Acad. Sci. Belarus, Minsk. pp. 49-77.

• Phytochromes and functions: studies using gene targeting in Physcomitrella
  Hughes J., Brücker G., Repp A., Zeidler M., Mittmann F. (2005). In "Light sensing in plants" Eds. Wada M., Shimazaki K. & Iino M. pp. 103-110. Springer Verlag / Botanical Society of Japan.
  ISBN: 4-431-24002-0
• Phytochromes and phytochrome-like proteins in cyanobacteria
  Lamparter T., Hughes J. (2003)
  In "Photoreceptors and light signalling" Ed. A. Batschauer (Comprehensive Series in Photochemical and Photobiological Sciences, Eds. Häder & Jori). RSC, pp 201 - 227.
• Photomorphogenesis in lower plants.
  Hughes J., Hartmann E. (1999)
  In "Concepts in photobiology: photosynthesis and photomorphogenesis" Eds. Singhal G., Renger W., Sopory S., Irrgang K.-D. & Govindjee. Narosa Publishing, pp. 805-837

Peer-reviewed research papers

• Ultrafast protein response in the Pfr state of Cph1 phytochrome.
  Yang Y, Stensitzki T, Lang Ch, Hughes J, Mroginski M-A, Heyne K (2023)
   Photochem Photobiol Sci. doi: 10.1007/s43630-023-00362-z
• Improved fluorescent phytochromes for in situ imaging.
  Nagano, S, Sadeghi, M, Balke, J, Fleck, M, Heckmann, N, Psakis, G, Alexiev, U. (2020)
  Sci. Rep. (Nature) 12:5587. doi: 10.1038/s41598-022-09169-x
• Multiplex CRISPR/Cas9 mutagenesis of the phytochrome gene family in Physcomitrella.
  Trogu S, Ermert AL, Stahl F, Nogué F, Gans T, Hughes J (2020)
  Plant Mol. Biol. doi: 10.1007/s11103-020-01103-x
• Phytochrome photoreceptors: Rapid response.
  Hughes J (2020)
  eLife 2020;9:e57105. doi: 10.7554/eLife.57105
• Structural insights into photoactivation and signalling in plant phytochromes.
  Nagano S, Guan K, Shenkutie S, Feiler Ch, Weiss M, Kraskov A, Buhrke D, Hildebrandt P, Hughes J (2020)
  Nature Plants, 6, 581-588 doi: 10.1038/s41477-020-0638-y
• Transient deprotonation of the chromophore affects protein dynamics proximal and distal to the linear tetrapyrrole chromophore in phytochrome Cph1.
  Sadeghi M, Balke J, Schneider C, Nagano S, Stellmacher J, Lochnit G, Lang C, Weise C, Hughes J, Alexiev U (2020)
  Biochemistry. 59:1051-1062. doi: 10.1021/acs.biochem.9b00967.
• CRISPR/Cas9-mediated knockout of Physcomitrella patens phytochromes.
  Ermert AL, Nogué F, Stahl F, Gans T, Hughes J (2019)Methods Mol Biol. 2026: 237-263. doi: 10.1007/978-1-4939-9612-4_20.3D structures of plant phytochrome A as Pr and Pfr from solid-state NMR: Implications for molecular function.
  Song C, Mroginski MA, Lang C, Kopycki J, Gärtner W, Matysik J, Hughes J (2018)
  Front Plant Sci 9: 498. doi: 10.3389/fpls.2018.00498.
• Structural communication between the chromophore binding pocket and the N-terminal extension in plant phytochrome phyB.
  Velázquez Escobar F, Buhrke D, Fernandez Lopez M, Shenkutie S, von Horsten S, Essen L-O, Hughes J, Hildebrandt P (2017)
  FEBS Letters, 591:1258-1265. doi: 10.1002/1873-3468.12642
• Influence of heterogeneity on the ultrafast photoisomerization dynamics of Pfr in Cph1 phytochrome.
  Stensitzki T, Yang Y, Wolke, AL, Knapp W, Hughes J, Mroginski MA, Heyne K (2017)
  Photochem Photobiol, 93:703-712. doi: 10.1111/php.12743.
• Protonation-dependent structural heterogeneity in the chromophore binding site of cyanobacterial phytochrome Cph1.
  Velázquez Escobar F, Lang C, Takiden A, Schneider C, Balke J, Hughes J, Alexiev U, Hildebrandt P, Mroginski MA (2017)
  J Phys Chem B. 121, 47-57, doi: 10.1021/acs.jpcb.6b09600.
• Dynamic nuclear polarization provides new insights into chromophore structure in phytochrome photoreceptors.
  Stöppler D, Song C, van Rossum BJ, Geiger MA, Lang C, Mroginski MA, Jagtap AP, Sigurdsson ST, Matysik J, Hughes J, Oschkinat H (2016)
  Angew Chem Intl Ed, 55, 16017-16020, doi: 10.1002/anie.201608119.
  
• Holophytochrome-interacting proteins in Physcomitrella: putative actors in phytochrome cytoplasmic signaling.
  Ermert AL, Mailliet K, Hughes J (2016)
  Front. Plant Sci. 7:613, doi: 10.3389/fpls.2016.00613
• Dual-fluorescence pH probe for bio-labelling.
  Richter C, Schneider C, Quick MT, Volz P, Mahrwald R, Hughes J, Dick B, Alexiev U, Ernsting NP (2015) Phys. Chem. Chem. Phys.,17, 30590-30597.
  
• NMR chemical shift pattern changed by ammonium sulfate precipitation in cyanobacterial phytochrome Cph1.
  Song C., Lang C., Kopycki J., Hughes J., Matysik J. (2015)
  Front Mol Biosci., 2, 42, doi: 10.3389/fmolb.2015.00042

• Conformational heterogeneity of the Pfr chromophore in plant and cyanobacterial phytochromes.
  Velazquez Escobar F., von Stetten D., Günther-Lütkens M., Keidel A., Michael N., Lamparter T., Essen L.-O., Hughes J., Gärtner W., Yang Y., Heyne K., Mroginski M.A., Hildebrandt P. (2015)
  Front Mol Biosci., 2, 37, doi: 10.3389/fmolb.2015.00037.

• Nuclear phytochrome B regulates leaf flattening through Phytochrome Interacting Factors.
  Johansson H., Hughes J. (2014)
  Molecular Plant, doi: 10.1093/mp/ssu077
  
• Tyrosine 263 in cyanobacterial phytochrome Cph1 optimizes photochemistry at the prelumi-R → lumi-R step.
  Sineshchekov V., Mailliet J., Psakis G., Feilke K., Kopycki J., Zeidler M, Essen L.-O., Hughes J. (2014)
  Photochem Photobiol., 90, 786-795, doi: 10.1111/php.12263
• The D-ring, not the A-ring, rotates in Synechococcus OS-B' phytochrome.
  Song C., Psakis G., Kopycki J., Lang C., Matysik J., Hughes J. (2013)
  J. Biol. Chem., 289, 2552-2562, doi: 10.1074/jbc.M113.520031.10.1074/jbc.M113.520031.
  
• A phytochrome-phototropin light signaling complex at the plasma membrane.
  Jaedicke K, Lichtenthäler AL, Meyberg R, Zeidler M, Hughes J. (2012)
  Proc. Natl. Acad. Sci. USA, 109, 12231-12236.
• Solid-state NMR spectroscopic study of chromophore-protein interactions in the Pr ground state of plant phytochrome A.
  Song C., Essen L.-O., Gärtner W., Hughes J., Matysik J. (2012)
  Mol. Plant, 5, 698-715.
• On the collective nature of phytochrome photoactivation.
  Song C., Psakis G., Lang C., Mailliet J., Zaanen J., Gaertner W., Hughes J., Matysik J. (2011)
  Biochemisty, 50, 10987-10989.
• Spectroscopy and a high-resolution crystal structure of Tyr-263 mutants of cyanobacterial phytochrome Cph1.
  Mailliet J., Psakis G., Feilke, K., Sineshchekov V., Essen L.-O., & Hughes J. (2011)
  J. Mol. Biol., 413, 115-27.
• Signalling kinetics of cyanobacterial phytochrome Cph1, a light regulated histidine kinase.
  Psakis G., Mailliet J, Lang C., Teufel L., Essen L.-O., Hughes J. (2011)
  Biochemistry, 50, 6178-6188.
• Two ground state isoforms and a chromophore D-ring photoflip triggering extensive intramolecular changes in a canonical phytochrome.
  Song C., Psakis G., Lang C., Mailliet J., Gärtner W., Hughes J., Matysik J. (2011)
  Proc. Natl. Acad. Sci. USA, 108, 15229–15234.
• Spectroscopic and photochemical characterization of the red-light sensitive photosensory module of Cph2 from Synechocystis PCC 6803.
  Anders K., von Stetten D., Mailliet J., Kiontke S., Sineshchekov V.A., Hildebrandt P., Hughes J., Essen L.-O. (2011)
  Photochem. Photobiol., 87, 160–173.
• Role of the protein cavity in chromoprotein assembly and double-bond isomerization in phytochrome: a comparison with model compounds.
  Rohmer T., Lang C., Gärtner W., Hughes J., Matysik J. (2010)
  Photochem. Photobiol., 86, 856-861.
• NMR spectroscopic investigation of mobility and hydrogen bonding of the chromophore in the binding pocket of phytochrome proteins.
  Röben M., Hahn J., Klein E., Lamparter T., Psakis G., Hughes J., Schmieder P. (2010)
  ChemPhysChem, 11, 1248-1257.
• Phytochrome as molecular machine: Revealing chromophore action during the Pfr->Pr photoconversion by magic-angle spinning NMR.
  Rohmer T., Lang C., Bongards C., Gupta S., Hughes J., Gärtner W. & Matysik, J. (2010)
  J. Am. Chem. Soc., 132, 4431–4437.
• Phytochrome 3D structures and functions.
  Hughes J. (2010)
  Biochemical Society Transactions, 38, 710-716.
• Dwelling in the dark: procedures for the crystallography of phytochromes and other photochromic proteins.
  Mailliet J., Psakis G., Schröder, C., Kaltofen S., Dürrwang U., Hughes J. & Essen L.-O. (2009)
  Acta Crystallogr D, 65, 1232-1235.
• Chromophore structure of cyanobacterial phytochrome Cph1 in the Pr state: reconciling structural and spectroscopic data by QM/MM calculations.
  Mroginski M.A., von Stetten D., Escobar F.V., Strauss H.M., Kaminski S., Scheerer P., Günther M., Murgida D.H., Schmieder P., Bongards C., Gärtner W., Mailliet J., Hughes J., Essen L.-O., Hildebrandt P. (2009)
  Biophys J., 96, 4153-4163.
• The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants.
  Rensing et al. [Hughes J. as one of 70 co-authors] (2008)
  Science, 319, 64-69.
• The structure of a complete phytochrome sensory module in the Pr ground state.
  Essen L.-O., Mailliet J., Hughes J. (2008)
  Proc. Natl. Acad. Sci. USA, 105, 14709–14714.
• Light-induced chromophore activity and signal transduction in phytochromes observed by ¹³C and ¹⁵N magic-angle spinning NMR.
  Rohmer T., Lang C., Hughes J., Essen L.-O., Gärtner W., Matysik J. (2008)
  Proc. Natl. Acad. Sci. USA, 105, 15229–15234.
• ¹⁵N MAS-NMR studies of Cph1 phytochrome: chromophore dynamics and intramolecular signal transduction.
  Rohmer T., Strauss H., Hughes J., Gärtner W., de Groot H., Schmieder P., Matysik J. (2006)
  J. Phys. Chem. B, 110, 20580-20585.
• Probing protein-chromophore interactions in Cph1 phytochrome via mutagenesis.
  Hahn J., Strauss H., Landgraf F., Faus Gimenèz H., Lochnit G., Schmieder P., Hughes J. (2006)
  FEBS J. 273: 1415–1429
• Real time spectral analysis during phytochrome chromophore and chromoprotein purification.
  Zeidler M, Lang C, Hahn J, Hughes J. (2006).
  Int J Biol Macromol. 39: 100-3.
• A chimeric photoreceptor gene, NEOCHROME, has arisen twice during plant evolution
  Suetsugu N., Mittmann F., Wagner G., Hughes J., Wada M. (2005)
  Proc. Nat. Acad. Sci. USA: 102, 13705-13709
• Heteronuclear solution-state NMR studies of the chromophore in cyanobacterial phytochrome Cph1
  Strauss HM, Hughes J & Schmieder P (2005)
  Biochemistry, 44, 8244-8250.
• Light-dependent dimerisation in the N-terminal sensory module
  Strauss, H., Schmieder, P., Hughes, J. (2005)
  FEBS Letters: 579, 3970-3974
• Targeted knockout in Physcomitrella reveals direct actions of phytochrome in the cytoplasm
  Mittmann F., Brücker G., Zeidler M., Repp A., Abts T., Hartmann E., Hughes J. (2004)
  Proc. Nat. Acad. Sci. USA 101: 13939–13944
• Dimerization and inter-chromphore distance of Cph1 phytochrome from Synechocystis, as monitored by fluorescence homo and hetero energy transfer.
  Otto H., Lamparter T., Borucki B., Hughes J., Heyn M. (2003)
  Biochemistry, 42, 5885-95
• Mechanism of Cph1 phytochrome assembly from stopped-flow kinetics and circular dichroism.
  Borucki B., Otto H., Rottwinkel G., Hughes J., Heyn M., Lamparter T. (2003)
  Biochemistry, 42: 13684-97.
• Fluorescence and photochemical investigations of the full-length (Cph1) and C-terminally truncated (Cph1D2) recombinant phytochrome from the cyanobacterium Synechocystis.
  Sineshchekov V., Koppel' L., Esteban B., Hughes J., Lamparter T. (2002)
  J Photochem Photobiol B., 67, 39-50.
• Ultrafast dynamics of recombinant phytochrome from the cyanobacterium Synechocystis reconstituted with phycocyanobilin and phycoerythrobilin.
  Heyne J., Stehlik D., Esteban B., Lamparter T., Hughes J., Diller R. (2002)
  Biophysical J., 82, 1004 - 1016.
• The phototropin family of photoreceptors.
  Briggs W.R., Beck C.F., Cashmore A.R., Christie J.M., Hughes J., Jarillo J.A., Kagawa T., Kanegae H., Liscum E., Nagatani A., Okada K., Salomon M., Rüdiger W., Sakai T., Takano M., Wada M., Watson J.C. (2001)
  Plant Cell, 13, 993-997.
• Light-induced proton release and uptake reactions in the cyanobacterial phytochrome, Cph1.
  van Thor J., Borucki B., Lamparter T., Hughes J., Hellingwerf K., Heyn, M. (2001)
  Biochemistry, 40, 11460-71.
• Phytochrome Cph1 from the cyanobacterium Synechocystis PCC6803: purification, assembly, and quarternary structure.
  Lamparter T., Esteban B. & Hughes, J. (2001)
  Eur. J. Biochem., 268, 4720-30.
• Recombinant Holophytochrome in Escherichia coli.
  Landgraf, F.T., Forreiter, C., Hurtado Picó, A., Lamparter, T., Hughes, J. (2001)
  FEBS-Letters 508, 459-462
• Recombinant phytochrome A in yeast differs by its spectroscopic and photochemical properties from the major phyA' and is close to the minor phyA'': evidence for post-translational modification of the pigment in plants.
  Sineshchekov V., Hennig T, Lamparter T., Hughes J., Gärtner W., Schäfer E. (2001)
  Photochem. Photobiol., 73, 692-6.
• Phytochrome chromophor deficent mutants of the moss Ceratodon purpureus can be rescued by microinjecting heme oxygenase genes.
  Brücker G, Zeidler M, Kohchi T, Hartmann E, Lamparter T (2000) Phytochrome chromophor deficent mutants of the moss Ceratodon purpureus can be rescued by microinjecting heme oxygenase genes.
  Planta 210:529-535.
• Recombinant phytochrome of the moss Ceratodon purpureus (CP2): fluorescence spectroscopy and photochemistry.
  Sineshchekov V, Koppel L, Hughes J, Lamparter T, Zeidler M.(2000) Recombinant phytochrome of the moss Ceratodon purpureus (CP2): fluorescence spectroscopy and photochemistry.
  J Photochem Photobiol B. 2000 56:145-53.
• The photoreactions of recombinant phytochrome from the cyanobacterium Synechocystis: A low temperature UV-Vis and FT-IR spectroscopic study.
  Foerstendorf H., Lamparter T., Hughes J., Gärtner W., Siebert F. (2000)
  Photochem. Photobiol., 71, 655-661.
• Prokaryotes and phytochrome: the connection to chromophores and signaling.
  Hughes J., Lamparter T. (1999)
  Plant Physiol., 121, 1059-1068.
• Transgene Expression in the moss Ceratodon purpureus.
  Zeidler M., Hartmann E., Hughes J. (1999)
  J. Plant Phys. 154:641-650.
• Blue light- and genetically-reversed gravitropic response in protonemata of the moss Ceratodon purpureus.
  Lamparter T., Hughes J., Hartmann E. (1998)
  Planta, 206, 95-102.
• Fluorescence and photochemistry of recombinant phytochrome from the cyanobacterium Synechocystis.
  Sineshchekov V., Hughes J., Lamparter T. (1998)
  Photochem. Photobiol., 67: 263-267.
• Non-angiosperm phytochromes and the evolution of vascular plants.
  Schneider-Poetsch H.A.W., Kolukisaoglu Ü, Clapham D., Hughes J., Lamparter T. (1998)
  Physiol. Plantarum, 102, 612-622.
• Recombinant phytochrome of the moss Ceratodon purpureus: heterologous expression and kinetic analysis of Pr -> Pfr conversion.
  Zeidler M, Lamparter T, Hughes J, Hartmann E, Remberg A, Braslavsky SE, Schaffner K, Gärtner W (1998) Recombinant phytochrome of the moss Ceratodon purpureus: heterologous expression and kinetic analysis of Pr -> Pfr conversion.
  Photochem Photobiol 68:857-863.
• Somatic hybridisation with aphotopropic mutants of the moss Ceratodon purpureus: genome size, phytochrome photoreversibility, tip-cell phototropism and chlorophyll regulation.
  Lamparter T., Brücker G., Esch H., Hughes J., Meister A., Hartmann E. (1998)
  J. Plant Physiol., 153: 394-400.
• A prokaryotic phytochrome.
  Hughes J., Lamparter T., Mittmann F., Hartmann E., Gärtner W., Wilde A., Börner T. (1997)
  Nature, 386: 663 (PDF).
• Characterization of recombinant phytochrome from the cyanobacterium Synechocystis.
  Lamparter T., Mittmann F., Gärtner W., Börner T., Hartmann E., Hughes J. (1997)
  Proc. Natl. Acad. Sci. USA., 94: 11792-11797.
• Raman spectroscopic and light-induced kinetic characterization of a recombinant phytochrome of the cyanobacterium Synechocystis.
  Remberg A., Lindner I., Lamparter T., Hughes J., Kneip K., Hildebrandt P., Braslavsky S.E., Gärtner W., Schaffner, K. (1997).
  Biochemistry, 36: 13389-13395
• A chloroplast transcript lacking the 3' inverted repeat is degraded by 3'-->5' exoribonuclease activity.
  Drager RG, Zeidler M, Simpson CL, Stern DB (1996) A chloroplast transcript lacking the 3' inverted repeat is degraded by 3'-->5' exoribonuclease activity.
  RNA 2:652-63
• Aphototropic mutants of the moss Ceratodon purpureus with spectrally-normal and with spectrally dysfunctional phytochrome.
  Lamparter T., Esch H., Cove D., Hughes J., Hartmann E. (1996)
  Plant, Cell & Environ., 19: 560-568.
• Cerpu;PHY0;2, a "normal" phytochrome in Ceratodon (Accession No. U56698)
  Hughes J., Lamparter T., Mittmann F. (1996)
  Plant Physiol., 112: 446 (PGR 96-067)
• pIDDLE6: A system for ligation and expression-cloning in E. coli.
  Hughes J. (1996)
  Biotech. Techniques, 10: 831-838.
• Tetracycline-regulated reporter gene expression in the moss Physcomitrella patens.
  Zeidler M., Gatz C., Hartmann E., Hughes J. (1996)
  Plant Mol Biol 30:199-205.
• Phytochrome from protonemal tissue of the moss Ceratodon purpureus.
  Lamparter T., Podlowski S., Mittmann F., Schneider-Poetsch H. A. W., Hartmann E., Hughes J. (1995)
  J. Plant Physiol., 147: 426-434
• A fully automated dual-wavelength photometer for phytochrome measurements and its application to phytochrome from chlorophyll-containing extracts.
  Lamparter T., Hughes J., Hartmann E. (1994)
  Photochem. Photobiol., 60: 179-183.
• Sequencing of double-stranded nucleic acid with thionucleotide triphosphates.
  Bisztray G. D., Hughes J. E., Qoronfleh M. W. (1994)
  BioTechniques, 16: 817-818.
• PIDDLE: PCR-based, in-frame, directional DNA ligation and expression.
  Hughes J. E., Qoronfleh M. W., Bizstray G., Pratt L. H. (1993)
  Biotech. Techniques, 7: 91-98.
• Perspectives in plant genetic engineering and biopharmacy.
  Hughes J. E., Qoronfleh M. W. (1991)
  Biopharmacy, 4: 18-28
• Photoregulation of psbA transcript levels in mustard cotyledons.
  Hughes J. E., Link G. (1988)
  Photosynth. Res., 17: 57-73.
  Also in: "Molecular biology of photosynthesis", Govindjee, Bohnert, Bottomly, Bryant, Mullet, Ogren, Pakrasi, Somerville, Eds. Kluwer, Dortrecht, pp 423-439.
• Photomorphogenesis in Chenopodium album: effects of supplimentary far-red light on stem extension kinetics.
  Hughes J. E., Wagner E. (1987)
  Planta, 172: 131-138.
• Transcripts of two adjacent chloroplast genes during mustard (Sinapis alba L.) seedling development are under differential temporal and light control.
  Hughes J. E., Neuhaus H., Link G. (1987)
  Plant Mol. Biol., 9: 355-363.
• The dark side of sunlight - the facts about UV in sunlight.
  Hughes J. E., Beggs C. J. (1986)
  New Scientist, #1522 (August 21): 31-35.
• Transmission properties of an oak canopy in relation to photoperception.
  Hughes J. E., Morgan D. C., Black C. R. (1985).
  Plant, Cell & Environ., 8: 509-516.
• A growth cabinet providing variable spectral photon distributions at high fluence rates.
  Hughes J. E., Heathcote L., Bambridge K., Black C. R. (1984)
  New Phytol., 98: 211-219.
• Photoperiodic time-signals during twilight.
  Hughes J. E., Morgan D. C., Lambton P. A., Black C. R., Smith H. (1984)
  Plant, Cell, Environ., 7: 269-277

Habilitation thesis

• Molekulare und physiologische Ansätze zum Phytochromsystem.
  Hughes J. (1998)
  Habilitation thesis, Free University of Berlin, Germany.

PhD thesis

• Natural daylight and the simulation of its effects upon stomata.
  Hughes J. E. (1983)
  PhD Thesis, University of Nottingham, UK.