Drosophila CTP synthase can form distinct substrate- and product-bound filaments

Xian Zhou; Chen-Jun Guo; Huan-Huan Hu; Jiale Zhong; Qianqian Sun; Dandan Liu; Shuang Zhou; Chia Chun Chang; Ji-Long Liu

doi:10.1016/j.jgg.2019.11.006

Volume 46 Issue 11

Nov. 2019

Turn off MathJax

Article Contents

Article Navigation > Journal of Genetics and Genomics > 2019 > 46(11): 537-545

PDF( 4065 KB)

Drosophila CTP synthase can form distinct substrate- and product-bound filaments

doi: 10.1016/j.jgg.2019.11.006

Xian Zhou^{a, #},
Chen-Jun Guo^{a, #},
Huan-Huan Hu^{a, b, c},
Jiale Zhong^{a, b, c},
Qianqian Sun^{a, d},
Dandan Liu^{a, d},
Shuang Zhou^{a, b, c},
Chia Chun Chang^a,
Ji-Long Liu^a

a
School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
b
Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
c
University of Chinese Academy of Sciences, Beijing, 100049, China
d
iHuman Institute, ShanghaiTech University, Shanghai, 201210, China

More Information

Corresponding author: E-mail address: liujl3@shanghaitech.edu.cn (Ji-Long Liu)
Received Date: 2019-10-22
Accepted Date: 2019-11-10
Rev Recd Date: 2019-11-07

Available Online: 2019-11-29

Publish Date: 2019-11-20

Abstract

Abstract

Intracellular compartmentation is a key strategy for the functioning of a cell. In 2010, several studies revealed that the metabolic enzyme CTP synthase (CTPS) can form filamentous structures termed cytoophidia in prokaryotic and eukaryotic cells. However, recent structural studies showed that CTPS only forms inactive product-bound filaments in bacteria while forming active substrate-bound filaments in eukaryotic cells. In this study, using negative staining and cryo-electron microscopy, we demonstrate that Drosophila CTPS, whether in substrate-bound or product-bound form, can form filaments. Our results challenge the previous model and indicate that substrate-bound and product-bound filaments can coexist in the same species. We speculate that the ability to switch between active and inactive cytoophidia in the same cells provides an additional layer of metabolic regulation.
- CTP synthase,
- Cytoophidium,
- Cryo-EM

These authors contributed to this work equally.

FullText(HTML)

References(28)

References

[1]	Adams, P.D., Grosse-Kunstleve, R.W., Hung, L.W., Ioerger, T.R., McCoy, A.J., Moriarty, N.W., Read, R.J., Sacchettini, J.C., Sauter, N.K., and Terwilliger, T.C., 2002. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr D. Biol. Crystallogr. 58, 1948-1954.
[2]	Aughey, G.N., Grice, S.J., Shen, Q.J., Xu, Y., Chang, C.C., Azzam, G., Wang, P.Y., Freeman-Mills, L., Pai, L.M., Sung, L.Y., Yan, J., and Liu, J.L., 2014. Nucleotide synthesis is regulated by cytoophidium formation during neurodevelopment and adaptive metabolism. Biol. Open. 3, 1045-1056.
[3]	Barry, R.M., Bitbol, A.F., Lorestani, A., Charles, E.J., Habrian, C.H., Hansen, J.M., Li, H.J., Baldwin, E.P., Wingreen, N.S., Kollman, J.M., and Gitai, Z., 2014. Large-scale filament formation inhibits the activity of CTP synthetase. eLife. 3, e03638.
[4]	Carcamo, W.C., Satoh, M., Kasahara, H., Terada, N., Hamazaki, T., Chan, J.Y., Yao, B., Tamayo, S., Covini, G., von Muhlen, C.A., and Chan, E.K., 2011. Induction of cytoplasmic rods and rings structures by inhibition of the CTP and GTP synthetic pathway in mammalian cells. PLoS One. 6, e29690.
[5]	Chen, K., Zhang, J., Tastan, O.Y., Deussen, Z.A., Siswick, M.Y., and Liu, J.L., 2011. Glutamine analogs promote cytoophidium assembly in human and Drosophila cells. J. Genet. Genomics. 38, 391-402.
[6]	Daumann, M., Hickl, D., Zimmer, D., DeTar, R.A., Kunz, H.H., and Mohlmann, T., 2018. Characterization of filament-forming CTP synthases from Arabidopsis thaliana. Plant J. 96, 316-328.
[7]	DiMaio, F., and Chiu, W., 2016. Tools for model building and optimization into near-atomic resolution electron cryo-microscopy density maps. Methods Enzymol. 579, 255-276.
[8]	Endrizzi, J.A., Kim, H., Anderson, P.M., and Baldwin, E.P., 2004. Crystal structure of Escherichia coli cytidine triphosphate synthetase, a nucleotide-regulated glutamine amidotransferase/ATP-dependent amidoligase fusion protein and homologue of anticancer and antiparasitic drug targets. Biochemistry. 43, 6447-6463.
[9]	Goto, M., Omi, R., Nakagawa, N., Miyahara, I., and Hirotsu, K., 2004. Crystal structures of CTP synthetase reveal ATP, UTP, and glutamine binding sites. Structure. 12, 1413-1423.
[10]	Gou, K.M., Chang, C.C., Shen, Q.J., Sung, L.Y., and Liu, J.L., 2014. CTP synthase forms cytoophidia in the cytoplasm and nucleus. Exp. Cell Res. 323, 242-253.
[11]	Hunkeler, M., Hagmann, A., Stuttfeld, E., Chami, M., Guri, Y., Stahlberg, H., and Maier, T., 2018. Structural basis for regulation of human acetyl-CoA carboxylase. Nature. 558, 470-474.
[12]	Ingerson-Mahar, M., Briegel, A., Werner, J.N., Jensen, G.J., and Gitai, Z., 2010. The metabolic enzyme CTP synthase forms cytoskeletal filaments. Nat. Cell Biol. 12, 739-746.
[13]	Ji, Y., Gu, J., Makhov, A.M., Griffith, J.D., and Mitchell, B.S., 2006. Regulation of the interaction of inosine monophosphate dehydrogenase with mycophenolic Acid by GTP. J. Biol. Chem. 281, 206-212.
[14]	Kleinschmidt, A.K., Moss, J., and Lane, D.M., 1969. Acetyl coenzyme A carboxylase: filamentous nature of the animal enzymes. Science. 166, 1276-1278.
[15]	Lewis, D.A., and Villafranca, J.J., 1989. Investigation of the mechanism of CTP synthetase using rapid quench and isotope partitioning methods. Biochemistry. 28, 8454-8459.
[16]	Liu, J.L., 2010. Intracellular compartmentation of CTP synthase in Drosophila. J. Genet. Genomics. 37, 281-296.
[17]	Lynch, E.M., Hicks, D.R., Shepherd, M., Endrizzi, J.A., Maker, A., Hansen, J.M., Barry, R.M., Gitai, Z., Baldwin, E.P., and Kollman, J.M., 2017. Human CTP synthase filament structure reveals the active enzyme conformation. Nat. Struct. Mol. Biol. 24, 507-514.
[18]	McCluskey, G.D., and Bearne, S.L., 2018. "Pinching" the ammonia tunnel of CTP synthase unveils coordinated catalytic and allosteric-dependent control of ammonia passage. Biochim. Biophys. Acta Gen. Subj. 1862, 2714-2727.
[19]	Noree, C., Monfort, E., Shiau, A.K., and Wilhelm, J.E., 2014. Common regulatory control of CTP synthase enzyme activity and filament formation. Mol. Biol. Cell 25, 2282-2290.
[20]	Noree, C., Sato, B.K., Broyer, R.M., and Wilhelm, J.E., 2010. Identification of novel filament-forming proteins in Saccharomyces cerevisiae and Drosophila melanogaster. J. Cell Biol. 190, 541-551.
[21]	Petrovska, I., Nuske, E., Munder, M.C., Kulasegaran, G., Malinovska, L., Kroschwald, S., Richter, D., Fahmy, K., Gibson, K., Verbavatz, J.M., and Alberti, S., 2014. Filament formation by metabolic enzymes is a specific adaptation to an advanced state of cellular starvation. eLife. 3, e02409
[22]	Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., and Ferrin, T.E., 2004. UCSF Chimera--a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605-1612.
[23]	Shen, Q.J., Kassim, H., Huang, Y., Li, H., Zhang, J., Li, G., Wang, P.Y., Yan, J., Ye, F., and Liu, J.L., 2016. Filamentation of metabolic enzymes in Saccharomyces cerevisiae. J. Genet. and Genomics. 43, 393-404.
[24]	Strochlic, T.I., Stavrides, K.P., Thomas, S.V., Nicolas, E., O'Reilly, A.M., and Peterson, J.R., 2014. Ack kinase regulates CTP synthase filaments during Drosophila oogenesis. EMBO Rep. 15, 1184-1191.
[25]	Wang, P.Y., Lin, W.C., Tsai, Y.C., Cheng, M.L., Lin, Y.H., Tseng, S.H., Chakraborty, A., and Pai, L.M., 2015. Regulation of CTP synthase filament formation during DNA endoreplication in Drosophila. Genetics. 201, 1511-1523.
[26]	Weng, M.L., and Zalkin, H., 1987. Structural role for a conserved region in the CTP synthetase glutamine amide transfer domain. J. Bacteriol. 169, 3023-3028.
[27]	Wu, Z., and Liu, J.L., 2019. Cytoophidia respond to nutrient stress in Drosophila. Exp. Cell Res. 376, 159-167.
[28]	Zhang, J., Hulme, L., and Liu, J.L., 2014. Asymmetric inheritance of cytoophidia in Schizosaccharomyces pombe. Biol. Open. 3, 1092-1097.