Steric occlusion regulates proximal interactions of acyl carrier protein domain in fungal fatty acid synthase.


Journal

Communications biology
ISSN: 2399-3642
Titre abrégé: Commun Biol
Pays: England
ID NLM: 101719179

Informations de publication

Date de publication:
29 05 2020
Historique:
received: 15 01 2020
accepted: 06 05 2020
entrez: 31 5 2020
pubmed: 31 5 2020
medline: 16 6 2021
Statut: epublish

Résumé

The acyl carrier protein (ACP) domain shuttles substrates and reaction intermediates in type I fungal fatty acid synthases via transient protein-protein interactions. Here, using electron cryo-microscopy (cryoEM), we report the structure of a fungal FAS stalled at the dehydration reaction, which precedes the final enoyl reduction in the fatty acid biosynthesis cycle. This conformation revealed multiple contact sites between ACP and the dehydratase (DH) and enoyl reductase (ER) domains that occluded the ACP binding to the adjacent ER domain. Our data suggests a minimal path from the DH to the ER reaction site that requires minute changes in the coordinates of the structured N- and C- termini of the ACP domain.

Identifiants

pubmed: 32471977
doi: 10.1038/s42003-020-0997-y
pii: 10.1038/s42003-020-0997-y
pmc: PMC7260205
doi:

Substances chimiques

Acyl Carrier Protein 0
Fatty Acid Synthases EC 2.3.1.85

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

274

Subventions

Organisme : CIHR
ID : 419240
Pays : Canada

Références

Röhrig, F. & Schulze, A. The multifaceted roles of fatty acid synthesis in cancer. Nat. Rev. Cancer 16, 732–749 (2016).
doi: 10.1038/nrc.2016.89
Menendez, J. A., Vazquez-Martin, A., Ortega, F. J. & Fernandez-Real, J. M. Fatty acid synthase: association with insulin resistance, type 2 diabetes, and cancer. Clin. Chem. 55, 425–438 (2009).
doi: 10.1373/clinchem.2008.115352
Pan, J., Hu, C. & Yu, J.-H. Lipid biosynthesis as an antifungal target. J. Fungi 4, 50 (2018).
doi: 10.3390/jof4020050
Grininger, M. Perspectives on the evolution, assembly and conformational dynamics of fatty acid synthase type I (FAS I) systems. Curr. Opin. Struct. Biol. 25, 49–56 (2014).
doi: 10.1016/j.sbi.2013.12.004
White, S. W., Zheng, J., Zhang, Y.-M. & Rock, C. O. The structural biology of type ii fatty acid biosynthesis. Annu. Rev. Biochem. 74, 791–831 (2005).
doi: 10.1146/annurev.biochem.74.082803.133524
Maier, T., Leibundgut, M., Boehringer, D. & Ban, N. Structure and function of eukaryotic fatty acid synthases. Q. Rev. Biophys. 43, 373–422 (2010).
doi: 10.1017/S0033583510000156
Leibundgut, M., Jenni, S., Frick, C. & Ban, N. Structural basis for substrate delivery by acyl carrier protein in the yeast fatty acid synthase. Science 316, 288–290 (2007).
doi: 10.1126/science.1138249
Lomakin, I. B., Xiong, Y. & Steitz, T. A. The crystal structure of yeast fatty acid synthase, a cellular machine with eight active sites working together. Cell 129, 319–332 (2007).
doi: 10.1016/j.cell.2007.03.013
Jenni, S. et al. Structure of fungal fatty acid synthase and implications for iterative substrate shuttling. Science 316, 254–261 (2007).
doi: 10.1126/science.1138248
Elad, N. et al. Structure of type-I mycobacterium tuberculosis fatty acid synthase at 3.3 Å resolution. Nat. Commun. 9, 3886 (2018).
doi: 10.1038/s41467-018-06440-6
Anselmi, C., Grininger, M., Gipson, P. & Faraldo-Gómez, J. D. Mechanism of substrate shuttling by the acyl-carrier protein within the fatty acid mega-synthase. J. Am. Chem. Soc. 132, 12357–12364 (2010).
doi: 10.1021/ja103354w
Gipson, P. et al. Direct structural insight into the substrate-shuttling mechanism of yeast fatty acid synthase by electron cryomicroscopy. Proc. Natl Acad. Sci. USA 107, 9164–9169 (2010).
doi: 10.1073/pnas.0913547107
D’Imprima, E. et al. Protein denaturation at the air-water interface and how to prevent it. Elife 8, 42747 (2019).
Lou, J. W., Iyer, K. R., Hasan, S. M. N., Cowen, L. E. & Mazhab-Jafari, M. T. Electron cryomicroscopy observation of acyl carrier protein translocation in type I fungal fatty acid synthase. Sci. Rep. 9, 12987 (2019).
doi: 10.1038/s41598-019-49261-3
Kastritis, P. L. et al. Capturing protein communities by structural proteomics in a thermophilic eukaryote. Mol. Syst. Biol. 13, 936 (2017).
doi: 10.15252/msb.20167412
Qiu, S., Liu, S., Zaoti, Z. F., Wang, X. & Cai, G. Modulation of fatty acid synthase by ATR checkpoint kinase Rad3. J. Mol. Cell Biol. https://doi.org/10.1093/jmcb/mjz096 (2019).
doi: 10.1093/jmcb/mjz096 pubmed: 31509190 pmcid: 6934155
Fischer, M. et al. Cryo-EM structure of fatty acid synthase (FAS) from Rhodosporidium toruloides provides insights into the evolutionary development of fungal FAS. Protein Sci. 24, 987–995 (2015).
doi: 10.1002/pro.2678
Enderle, M., McCarthy, A., Paithankar, K. S. & Grininger, M. Crystallization and X-ray diffraction studies of a complete bacterial fatty-acid synthase type I. Acta Crystallogr. F. Struct. Biol. Commun. 71, 1401–1407 (2015).
doi: 10.1107/S2053230X15018336
Fischer, M. et al. Molecular mechanisms in fungal fatty acid synthase (FAS) assembly. bioRxiv https://doi.org/10.1101/336578 (2018).
Scheres, S. H. W. Processing of structurally heterogeneous Cryo-EM data in RELION. Methods Enzymol. 579, 125–157 (2016).
doi: 10.1016/bs.mie.2016.04.012
Nguyen, C. et al. Trapping the dynamic acyl carrier protein in fatty acid biosynthesis. Nature 505, 427–431 (2014).
doi: 10.1038/nature12810
Johnson, M. N. R., Londergan, C. H. & Charkoudian, L. K. Probing the phosphopantetheine arm conformations of acyl carrier proteins using vibrational spectroscopy. J. Am. Chem. Soc. 136, 11240–11243 (2014).
doi: 10.1021/ja505442h
Perez, D. R., Leibundgut, M. & Wider, G. Interactions of the acyl chain with the Saccharomyces cerevisiae acyl carrier protein. Biochemistry 54, 2205–2213 (2015).
doi: 10.1021/bi5014563
Bryksin, A. & Matsumura, I. Overlap extension PCR cloning. in. Methods Mol. Biol. 1073, 31–42 (2013).
doi: 10.1007/978-1-62703-625-2_4
Johansson, P. et al. Inhibition of the fungal fatty acid synthase type I multienzyme complex. Proc. Natl Acad. Sci. USA 105, 12803–12808 (2008).
doi: 10.1073/pnas.0805827105
Marr, C. R., Benlekbir, S. & Rubinstein, J. L. Fabrication of carbon films with ∼500nm holes for cryo-EM with a direct detector device. J. Struct. Biol. 185, 42–47 (2014).
doi: 10.1016/j.jsb.2013.11.002
Kremer, J. R., Mastronarde, D. N. & McIntosh, J. R. Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 116, 71–76 (1996).
doi: 10.1006/jsbi.1996.0013
Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).
doi: 10.1038/nmeth.4169
Rubinstein, J. L. & Brubaker, M. A. Alignment of cryo-EM movies of individual particles by optimization of image translations. J. Struct. Biol. 192, 188–195 (2015).
doi: 10.1016/j.jsb.2015.08.007
Rohou, A. & Grigorieff, N. CTFFIND4: fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015).
doi: 10.1016/j.jsb.2015.08.008
Pettersen, E. F. et al. UCSF Chimera? A visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).
doi: 10.1002/jcc.20084
Smith, J. M. XIMDISP—a visualization tool to aid structure determination from electron microscope images. J. Struct. Biol. 125, 223–228 (1999).
doi: 10.1006/jsbi.1998.4073
Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. Elife 7, 42166 (2018).
Kimanius, D., Forsberg, B. O., Scheres, S. H. & Lindahl, E. Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2. Elife 5, 18722 (2016).
The PyMOL Molecular Graphics System, Version 2.0 Schrödinger, LLC.
Altschul, S. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997).
doi: 10.1093/nar/25.17.3389
Sievers, F. et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7, 539–539 (2014).
doi: 10.1038/msb.2011.75
Crooks, G. E., Hon, G., Chandonia, J.-M. & Brenner, S. E. WebLogo: a sequence logo generator. Genome Res. 14, 1188–1190 (2004).
doi: 10.1101/gr.849004

Auteurs

Jennifer W Lou (JW)

Department of Medical Biophysics, University of Toronto, Toronto, Canada.
Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada.

Mohammad T Mazhab-Jafari (MT)

Department of Medical Biophysics, University of Toronto, Toronto, Canada. Mohammad.Mazhab-Jafari@uhnresearch.ca.
Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada. Mohammad.Mazhab-Jafari@uhnresearch.ca.

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Classifications MeSH