In cellulo serial crystallography of alcohol oxidase crystals inside yeast cells
Abstract
The possibility of using femtosecond pulses from an X-ray free-electron laser to collect diffraction data from protein crystals formed in their native cellular organelle has been explored. X-ray diffraction of submicrometre-sized alcohol oxidase crystals formed in peroxisomes within cells of genetically modified variants of the methylotrophic yeast Hansenula polymorpha is reported and characterized. Furthermore, the observations are supported by synchrotron radiation-based powder diffraction data and electron microscopy. Based on these findings, the concept of in cellulo serial crystallography on protein targets imported into yeast peroxisomes without the need for protein purification as a requirement for subsequent crystallization is outlined.
- Authors:
-
- Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); European Molecular Biology Lab. (EMBL), Heidelberg (Germany)
- Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)
- Univ. of Groningen, Groningen (The Netherlands)
- SLAC National Accelerator Lab., Menlo Park, CA (United States)
- Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Univ. of Hamburg, Hamburg (Germany); Center for Ultrafast Imaging, Hamburg (Germany)
- Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Univ. Medical Center Hamburg-Eppendorf, Hamburg (Germany)
- Publication Date:
- Research Org.:
- SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1244994
- Alternate Identifier(s):
- OSTI ID: 1307374
- Report Number(s):
- AC02-76SF00515
Journal ID: ISSN 2052-2525; IUCRAJ; PII: S2052252515022927
- Grant/Contract Number:
- AC02-76SF00515
- Resource Type:
- Accepted Manuscript
- Journal Name:
- IUCrJ
- Additional Journal Information:
- Journal Volume: 3; Journal Issue: 2; Journal ID: ISSN 2052-2525
- Publisher:
- International Union of Crystallography
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; protein structure; X-ray crystallography; femtosecond studies; nanocrystals; free-electron laser; 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Jakobi, Arjen J., Passon, Daniel M., Knoops, Kevin, Stellato, Francesco, Liang, Mengning, White, Thomas A., Seine, Thomas, Messerschmidt, Marc, Chapman, Henry N., and Wilmanns, Matthias. In cellulo serial crystallography of alcohol oxidase crystals inside yeast cells. United States: N. p., 2016.
Web. doi:10.1107/S2052252515022927.
Jakobi, Arjen J., Passon, Daniel M., Knoops, Kevin, Stellato, Francesco, Liang, Mengning, White, Thomas A., Seine, Thomas, Messerschmidt, Marc, Chapman, Henry N., & Wilmanns, Matthias. In cellulo serial crystallography of alcohol oxidase crystals inside yeast cells. United States. https://doi.org/10.1107/S2052252515022927
Jakobi, Arjen J., Passon, Daniel M., Knoops, Kevin, Stellato, Francesco, Liang, Mengning, White, Thomas A., Seine, Thomas, Messerschmidt, Marc, Chapman, Henry N., and Wilmanns, Matthias. Tue .
"In cellulo serial crystallography of alcohol oxidase crystals inside yeast cells". United States. https://doi.org/10.1107/S2052252515022927. https://www.osti.gov/servlets/purl/1244994.
@article{osti_1244994,
title = {In cellulo serial crystallography of alcohol oxidase crystals inside yeast cells},
author = {Jakobi, Arjen J. and Passon, Daniel M. and Knoops, Kevin and Stellato, Francesco and Liang, Mengning and White, Thomas A. and Seine, Thomas and Messerschmidt, Marc and Chapman, Henry N. and Wilmanns, Matthias},
abstractNote = {The possibility of using femtosecond pulses from an X-ray free-electron laser to collect diffraction data from protein crystals formed in their native cellular organelle has been explored. X-ray diffraction of submicrometre-sized alcohol oxidase crystals formed in peroxisomes within cells of genetically modified variants of the methylotrophic yeast Hansenula polymorpha is reported and characterized. Furthermore, the observations are supported by synchrotron radiation-based powder diffraction data and electron microscopy. Based on these findings, the concept of in cellulo serial crystallography on protein targets imported into yeast peroxisomes without the need for protein purification as a requirement for subsequent crystallization is outlined.},
doi = {10.1107/S2052252515022927},
journal = {IUCrJ},
number = 2,
volume = 3,
place = {United States},
year = {Tue Mar 01 00:00:00 EST 2016},
month = {Tue Mar 01 00:00:00 EST 2016}
}
Web of Science
Works referenced in this record:
The molecular organization of cypovirus polyhedra
journal, March 2007
- Coulibaly, Fasséli; Chiu, Elaine; Ikeda, Keiko
- Nature, Vol. 446, Issue 7131
Architecture of peroxisomal alcohol oxidase crystals from the methylotrophic yeast Hansenula polymorpha as deduced by electron microscopy.
journal, January 1992
- Vonck, J.; van Bruggen, E. F.
- Journal of Bacteriology, Vol. 174, Issue 16
High Resolution Scanning Electron Microscopy of Protein Inclusions (Cores) purified from Peroxisomes of Sunflower (Helianthus annuus L.) Cotyledons
journal, July 2000
- Heinze, M.; Reichelt, R.; Kleff, S.
- Crystal Research and Technology, Vol. 35, Issue 6-7
The Nucleoids of rat Liver cell Microbodies
journal, March 1966
- Tsukada, Hideyuki; Mochizuki, Yohichi; Fujiwara, Seiki
- Journal of Cell Biology, Vol. 28, Issue 3
Isolation and properties of genetically defined strains of the methylotrophic yeast Hansenula polymorpha CBS4732
journal, November 2001
- Lahtchev, Kantcho L.; Semenova, Vika D.; Tolstorukov, Ilia I.
- Archives of Microbiology, Vol. 177, Issue 2
EVAL15 : a diffraction data integration method based on ab initio predicted profiles
journal, December 2009
- Schreurs, Antoine M. M.; Xian, Xinyi; Kroon-Batenburg, Loes M. J.
- Journal of Applied Crystallography, Vol. 43, Issue 1
Biochemistry of Mammalian Peroxisomes Revisited
journal, June 2006
- Wanders, Ronald J. A.; Waterham, Hans R.
- Annual Review of Biochemistry, Vol. 75, Issue 1
High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography
journal, May 2012
- Boutet, S.; Lomb, L.; Williams, G. J.
- Science, Vol. 337, Issue 6092
Structure of CPV17 polyhedrin determined by the improved analysis of serial femtosecond crystallographic data
journal, March 2015
- Ginn, Helen M.; Messerschmidt, Marc; Ji, Xiaoyun
- Nature Communications, Vol. 6, Issue 1
Femtosecond X-ray protein nanocrystallography
journal, February 2011
- Chapman, Henry N.; Fromme, Petra; Barty, Anton
- Nature, Vol. 470, Issue 7332, p. 73-77
Uricase: Localization in Hepatic Microbodies
journal, December 1964
- Hruban, Z.; Swift, H.
- Science, Vol. 146, Issue 3649
Dihydroxyacetone synthase is localized in the peroxisomal matrix of methanol-grown Hansenula polymorpha
journal, December 1985
- Douma, Anneke C.; Veenhuis, Marten; de Koning, Wim
- Archives of Microbiology, Vol. 143, Issue 3
Protein crystal structure obtained at 2.9 A resolution from injecting bacterial cells into an X-ray free-electron laser beam
journal, August 2014
- Sawaya, M. R.; Cascio, D.; Gingery, M.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 35
In cellulo structure determination of a novel cypovirus polyhedrin
journal, April 2014
- Axford, Danny; Ji, Xiaoyun; Stuart, David I.
- Acta Crystallographica Section D Biological Crystallography, Vol. 70, Issue 5
The atomic structure of baculovirus polyhedra reveals the independent emergence of infectious crystals in DNA and RNA viruses
journal, December 2009
- Coulibaly, Fasséli; Chiu, Elaine; Gutmann, Sascha
- Proceedings of the National Academy of Sciences, Vol. 106, Issue 52
Hansenula polymorpha pex11 cells are affected in peroxisome retention: A role of Pex11 in peroxisome retention in yeast
journal, January 2009
- Krikken, Arjen M.; Veenhuis, Marten; van der Klei, Ida J.
- FEBS Journal, Vol. 276, Issue 5
Electron microscopy and image analysis of two-dimensional crystals and single molecules of alcohol oxidase from Hansenula polymorpha
journal, March 1990
- Vonck, Janet; van Bruggen, Ernst F. J.
- Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology, Vol. 1038, Issue 1
Crystallization of a Globular Protein in Lipid Cubic Phase
journal, March 2004
- Tanaka, S.; Egelhaaf, S. U.; Poon, W. C. K.
- Physical Review Letters, Vol. 92, Issue 12
Freeze substitution in 3 hours or less: FREEZE SUBSTIUTION IN 3 HOURS OR LESS
journal, August 2011
- McDONALD, K. L.; Webb, R. I.
- Journal of Microscopy, Vol. 243, Issue 3
In vivo crystallography at X-ray free-electron lasers: the next generation of structural biology?
journal, July 2014
- Gallat, François-Xavier; Matsugaki, Naohiro; Coussens, Nathan P.
- Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 369, Issue 1647
The membrane remodeling protein Pex11p activates the GTPase Dnm1p during peroxisomal fission
journal, May 2015
- Williams, Chris; Opalinski, Lukasz; Landgraf, Christiane
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 20
Microbodies in methanol-assimilating yeasts
journal, January 1975
- Van Dijken, J. P.; Veenhuis, M.; Kreger-Van Rij, N. J. W.
- Archives of Microbiology, Vol. 102, Issue 1
Assembly of alcohol oxidase in the cytosol of a peroxisome-deficient mutant ofHansenula polymorpha—properties of the protein and architecture of the crystals
journal, January 1991
- Van Der Klei, Ida J.; Sulter, Grietje J.; Harder, Wim
- Yeast, Vol. 7, Issue 1
Detection of Membrane Protein Two-Dimensional Crystals in Living Cells
journal, January 2011
- Gualtieri, E. J.; Guo, F.; Kissick, D. J.
- Biophysical Journal, Vol. 100, Issue 1
Characterization and use of the spent beam for serial operation of LCLS
journal, April 2015
- Boutet, Sébastien; Foucar, Lutz; Barends, Thomas R. M.
- Journal of Synchrotron Radiation, Vol. 22, Issue 3
Substructure of crystalline peroxisomes in methanol-grown Hansenula polymorpha: evidence for an in vivo crystal of alcohol oxidase.
journal, October 1981
- Veenhuis, M.; Harder, W.; van Dijken, J. P.
- Molecular and Cellular Biology, Vol. 1, Issue 10
Use of electron microscopy in the examination of lattice defects in crystals of alcohol oxidase
journal, February 1989
- Van der Klei, Ida J.; Lawson, Catherine L.; Rozeboom, Henriëtte
- FEBS Letters, Vol. 244, Issue 1
Hansenula polymorpha as a novel yeast system for the expression of heterologous genes
journal, December 1988
- Sudbery, P. E.; Gleeson, M. A.; Veale, R. A.
- Biochemical Society Transactions, Vol. 16, Issue 6
Protein Nanocrystallization
book, January 2006
- Georgieva, Dilyana; Abrahams, Jan Pieter; Kuil, Maxim E.
- Advanced Techniques in Biophysics
Peroxisomal Remnant Structures in Hansenula polymorpha pex5 Cells Can Develop into Normal Peroxisomes upon Induction of the PTS2 Protein Amine Oxidase
journal, October 2000
- Salomons, Florian A.; Nico Faber, Klaas; Veenhuis, Marten
- Journal of Biological Chemistry, Vol. 276, Issue 6
A Diffraction-Quality Protein Crystal Processed as an Autophagic Cargo
journal, April 2015
- Tsutsui, Hidekazu; Jinno, Yuka; Shoda, Keiko
- Molecular Cell, Vol. 58, Issue 1
Development of Microbodies in the yeast Kloeckera growing on methanol.
journal, January 1976
- Tanaka, A.; Yasuhara, S.; Kawamoto, S.
- Journal of Bacteriology, Vol. 126, Issue 2
Use of transmission electron microscopy to identify nanocrystals of challenging protein targets
journal, May 2014
- Stevenson, H. P.; Makhov, A. M.; Calero, M.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 23
Microcrystallization techniques for serial femtosecond crystallography using photosystem II from Thermosynechococcus elongatus as a model system
journal, July 2014
- Kupitz, Christopher; Grotjohann, Ingo; Conrad, Chelsie E.
- Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 369, Issue 1647
Crystal structure of pyridoxine 4-oxidase from Mesorhizobium loti
journal, June 2013
- Mugo, Andrew Njagi; Kobayashi, Jun; Yamasaki, Taiji
- Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Vol. 1834, Issue 6
Development of crystalline peroxisomes in methanol-grown cells of the yeast Hansenula polymorpha and its relation to environmental conditions
journal, May 1978
- Veenhuis, M.; van Dijken, J. P.; Pilon, S. A. F.
- Archives of Microbiology, Vol. 117, Issue 2
Protein crystallization in vivo
journal, April 2006
- Doye, J.; Poon, W.
- Current Opinion in Colloid & Interface Science, Vol. 11, Issue 1
Computer Visualization of Three-Dimensional Image Data Using IMOD
journal, January 1996
- Kremer, James R.; Mastronarde, David N.; McIntosh, J. Richard
- Journal of Structural Biology, Vol. 116, Issue 1
In vivo protein crystallization opens new routes in structural biology
journal, January 2012
- Koopmann, Rudolf; Cupelli, Karolina; Redecke, Lars
- Nature Methods, Vol. 9, Issue 3
Gas dynamic virtual nozzle for generation of microscopic droplet streams
journal, September 2008
- DePonte, D. P.; Weierstall, U.; Schmidt, K.
- Journal of Physics D: Applied Physics, Vol. 41, Issue 19, Article No. 195505
How proteins penetrate peroxisomes
journal, November 1995
- Rachubinski, Richard A.; Subramani, Suresh
- Cell, Vol. 83, Issue 4
Natively Inhibited Trypanosoma brucei Cathepsin B Structure Determined by Using an X-ray Laser
journal, November 2012
- Redecke, L.; Nass, K.; DePonte, D. P.
- Science, Vol. 339, Issue 6116
Cheetah : software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction data
journal, May 2014
- Barty, Anton; Kirian, Richard A.; Maia, Filipe R. N. C.
- Journal of Applied Crystallography, Vol. 47, Issue 3
Serial crystallography on in vivo grown microcrystals using synchrotron radiation
journal, February 2014
- Gati, Cornelius; Bourenkov, Gleb; Klinge, Marco
- IUCrJ, Vol. 1, Issue 2
Femtosecond protein nanocrystallography—data analysis methods
journal, January 2010
- Kirian, Richard A.; Wang, Xiaoyu; Weierstall, Uwe
- Optics Express, Vol. 18, Issue 6
An anti-settling sample delivery instrument for serial femtosecond crystallography
journal, July 2012
- Lomb, Lukas; Steinbrener, Jan; Bari, Sadia
- Journal of Applied Crystallography, Vol. 45, Issue 4
New Python-based methods for data processing
journal, June 2013
- Sauter, Nicholas K.; Hattne, Johan; Grosse-Kunstleve, Ralf W.
- Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 7
Room-temperature macromolecular serial crystallography using synchrotron radiation
journal, May 2014
- Stellato, Francesco; Oberthür, Dominik; Liang, Mengning
- IUCrJ, Vol. 1, Issue 4, p. 204-212
CrystFEL : a software suite for snapshot serial crystallography
journal, March 2012
- White, Thomas A.; Kirian, Richard A.; Martin, Andrew V.
- Journal of Applied Crystallography, Vol. 45, Issue 2
Crystal structure of pyridoxine 4-oxidase from Mesorhizobium loti
journal, August 2014
- Mugo, Andrew; Kobayashi, Jun; Yamasaki, Taiji
- Acta Crystallographica Section A Foundations and Advances, Vol. 70, Issue a1
Arbuscular cell invasion coincides with extracellular vesicles and membrane tubules.
text, January 2019
- Roth, Ronelle; Hillmer, Stefan; Funaya, Charlotta
- Apollo - University of Cambridge Repository
Substructure of crystalline peroxisomes in methanol-grown Hansenula polymorpha: evidence for an in vivo crystal of alcohol oxidase
journal, October 1981
- Veenhuis, M.; Harder, W.; van Dijken, J. P.
- Molecular and Cellular Biology, Vol. 1, Issue 10
Works referencing / citing this record:
Protein phase separation and determinants of in cell crystallization
journal, November 2019
- Mudogo, Celestin N.; Falke, Sven; Brognaro, Hévila
- Traffic, Vol. 21, Issue 2
Protein crystallization in living cells
journal, June 2018
- Schönherr, Robert; Rudolph, Janine Mia; Redecke, Lars
- Biological Chemistry, Vol. 399, Issue 7
The New Era of Microcrystallography
journal, July 2018
- Banerjee, Sanchari; Montaville, Pierre; Chavas, Leonard M. G.
- Journal of the Indian Institute of Science, Vol. 98, Issue 3
Towards in cellulo virus crystallography
journal, February 2018
- Duyvesteyn, Helen M. E.; Ginn, Helen M.; Pietilä, Maija K.
- Scientific Reports, Vol. 8, Issue 1
An outlook on using serial femtosecond crystallography in drug discovery
journal, May 2019
- Mishin, Alexey; Gusach, Anastasiia; Luginina, Aleksandra
- Expert Opinion on Drug Discovery, Vol. 14, Issue 9
Protein phase separation and determinants of in cell crystallization
text, January 2019
- Mudogo, Celestin Nzanzu; Falke, Sven; Brognaro dos Santos, Hevila
- Deutsches Elektronen-Synchrotron, DESY, Hamburg