Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Structural insights into the coordination of plastid division by the ARC6–PDV2 complex

Nature Plants volume 3, Article number: 17011 (2017) Cite this article

Subjects

Abstract

Chloroplasts divide by binary fission, which is accomplished by the simultaneous constriction of the FtsZ ring on the stromal side of the inner envelope membrane, and the ARC5 ring on the cytosolic side of the outer envelope membrane. The two rings are connected and coordinated mainly by the interaction between the inner envelope membrane protein ARC6 and the outer envelope membrane protein PDV2 in the intermembrane space. The underlying mechanism of this coordination is unclear to date. Here, we solved the crystal structure of the intermembrane space region of the ARC6–PDV2 complex. The results indicated that PDV2 inserts its carboxy terminus into a pocket formed in ARC6, and this interaction further induces the dimerization of the intermembrane space regions of two ARC6 molecules. A pdv2 mutant attenuating PDV2-induced ARC6 dimerization showed abnormal morphology of ARC6 rings and compromised chloroplast division in plant cells. Together, our data reveal that PDV2-induced dimerization of ARC6 plays a critical role in chloroplast division and provide insights into the coordination mechanism of the internal and external plastid division machineries.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: The IMS region of ARC6 binds to PDV2282–307.
Figure 2: PDV2282–307 induces the dimerization of the IMS region of ARC6.
Figure 3: The interaction between PDV2K299–G307 and ARC6 is essential for chloroplast division.
Figure 4: The PDV2V285–I291 is critical for PDV2-induced ARC6 dimerization and chloroplast division.
Figure 5: Suggested model of ARC6 dimerization induced by PDV2 in chloroplast division.

Similar content being viewed by others

References

  1. Osteryoung, K. W. & Pyke, K. A. Division and dynamic morphology of plastids. Annu. Rev. Plant Biol. 65, 443–472 (2014).

    Article  CAS  PubMed  Google Scholar 

  2. Yoshida, Y., Miyagishima, S. Y., Kuroiwa, H. & Kuroiwa, T. The plastid-dividing machinery: formation, constriction and fission. Curr. Opin. Plant Biol. 15, 714–721 (2012).

    Article  CAS  PubMed  Google Scholar 

  3. Miyagishima, S. Y., Nakanishi, H. & Kabeya, Y. Structure, regulation, and evolution of the plastid division machinery. Int. Rev. Cell Mol. Biol. 291, 115–153 (2011).

    Article  CAS  PubMed  Google Scholar 

  4. Miyagishima, S. Y. Mechanism of plastid division: from a bacterium to an organelle. Plant Physiol. 155, 1533–1544 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Yoshida, Y. et al. Isolated chloroplast division machinery can actively constrict after stretching. Science 313, 1435–1438 (2006).

    Article  CAS  PubMed  Google Scholar 

  6. Yoshida, Y. et al. Chloroplasts divide by contraction of a bundle of nanofilaments consisting of polyglucan. Science 329, 949–953 (2010).

    Article  CAS  PubMed  Google Scholar 

  7. Miyagishima, S. et al. Plastid division is driven by a complex mechanism that involves differential transition of the bacterial and eukaryotic division rings. Plant Cell 13, 2257–2268 (2001).

    Article  CAS  PubMed Central  Google Scholar 

  8. Vitha, S. et al. ARC6 is a J-domain plastid division protein and an evolutionary descendant of the cyanobacterial cell division protein Ftn2. Plant Cell 15, 1918–1933 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Maple, J. & Moller, S. G. Plastid division: evolution, mechanism and complexity. Ann. Bot. 99, 565–579 (2007).

    Article  CAS  PubMed  Google Scholar 

  10. Yang, Y., Glynn, J. M., Olson, B. J., Schmitz, A. J. & Osteryoung, K. W. Plastid division: across time and space. Curr. Opin. Plant Biol. 11, 577–584 (2008).

    Article  CAS  PubMed  Google Scholar 

  11. Osteryoung, K. W. & Pyke, K. A. Plastid division: evidence for a prokaryotically derived mechanism. Curr. Opin. Plant Biol. 1, 475–479 (1998).

    Article  CAS  PubMed  Google Scholar 

  12. Stokes, K. D., McAndrew, R. S., Figueroa, R., Vitha, S. & Osteryoung, K. W. Chloroplast division and morphology are differentially affected by overexpression of FtsZ1 and FtsZ2 genes in Arabidopsis. Plant Physiol. 124, 1668–1677 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Gao, H., Kadirjan-Kalbach, D., Froehlich, J. E. & Osteryoung, K. W. ARC5, a cytosolic dynamin-like protein from plants, is part of the chloroplast division machinery. Proc. Natl Acad. Sci. USA 100, 4328–4333 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Glynn, J. M., Froehlich, J. E. & Osteryoung, K. W. Arabidopsis ARC6 coordinates the division machineries of the inner and outer chloroplast membranes through interaction with PDV2 in the intermembrane space. Plant Cell 20, 2460–2470 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Miyagishima, S. Y., Froehlich, J. E. & Osteryoung, K. W. PDV1 and PDV2 mediate recruitment of the dynamin-related protein ARC5 to the plastid division site. Plant Cell 18, 2517–2530 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Maple, J., Aldridge, C. & Moller, S. G. Plastid division is mediated by combinatorial assembly of plastid division proteins. Plant J. 43, 811–823 (2005).

    Article  CAS  PubMed  Google Scholar 

  17. Sugase, K., Dyson, H. J. & Wright, P. E. Mechanism of coupled folding and binding of an intrinsically disordered protein. Nature 447, 1021–1025 (2007).

    Article  CAS  PubMed  Google Scholar 

  18. Krissinel, E. & Henrick, K. Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. 372, 774–797 (2007).

    Article  CAS  PubMed  Google Scholar 

  19. Kumar, N., Radhakrishnan, A., Su, C. C., Osteryoung, K. W. & Yu, E. W. Crystal structure of a conserved domain in the intermembrane space region of the plastid division protein ARC6. Protein Sci. 25, 523–529 (2016).

    Article  CAS  PubMed  Google Scholar 

  20. Handa, N. et al. Structure of the human Tim44 C-terminal domain in complex with pentaethylene glycol: ligand-bound form. Acta Crystallogr. D Biol. Crystallogr. 63, 1225–1234 (2007).

    Article  CAS  PubMed  Google Scholar 

  21. Bullock, T. L., Clarkson, W. D., Kent, H. M. & Stewart, M. The 1.6 angstroms resolution crystal structure of nuclear transport factor 2 (NTF2). J. Mol. Biol. 260, 422–431 (1996).

    Article  CAS  PubMed  Google Scholar 

  22. Rellos, P. et al. Structure of the CaMKIIdelta/calmodulin complex reveals the molecular mechanism of CaMKII kinase activation. PLoS Biol. 8, e1000426 (2010).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  23. Guo, F. et al. Structural insights into the tumor-promoting function of the MTDH-SND1 complex. Cell Rep. 8, 1704–1713 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Zhang, Q., Jia, N., Li, H. & Gao, H.-B. Identification and analysis of ARC6 gene in a chloroplast division mutant cpd44 in Arabidopsis thaliana. Plant Physiol. J. 51, 8 (2015).

    CAS  Google Scholar 

  25. Stewart, M., Kent, H. M. & McCoy, A. J. Structural basis for molecular recognition between nuclear transport factor 2 (NTF2) and the GDP-bound form of the Ras-family GTPase Ran. J. Mol. Biol. 277, 635–646 (1998).

    Article  CAS  PubMed  Google Scholar 

  26. Guo, F. et al. Structural basis of PP2A activation by PTPA, an ATP-dependent activation chaperone. Cell Res. 24, 190–203 (2014).

    Article  CAS  PubMed  Google Scholar 

  27. Du, D. et al. Structure of the AcrAB-TolC multidrug efflux pump. Nature 509, 512–515 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Hu, M. et al. Structural basis of competitive recognition of p53 and MDM2 by HAUSP/USP7: implications for the regulation of the p53-MDM2 pathway. PLoS Biol. 4, e27 (2006).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  29. Saredi, G. et al. H4k20me0 marks post-replicative chromatin and recruits the TONSL-MMS22L DNA repair complex. Nature 534, 714–718 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Zhang, M., Chen, C., Froehlich, J. E., TerBush, A. D. & Osteryoung, K. W. Roles of Arabidopsis PARC6 in coordination of the chloroplast division complex and negative regulation of FtsZ assembly. Plant Physiol. 170, 250–262 (2016).

    Article  CAS  PubMed  Google Scholar 

  31. Youle, R. J. & van der Bliek, A. M. Mitochondrial fission, fusion, and stress. Science 337, 1062–1065 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Marbouty, M., Saguez, C., Cassier-Chauvat, C. & Chauvat, F. Zipn, an FtsA-like orchestrator of divisome assembly in the model cyanobacterium synechocystis PCC6803. Mol. Microbiol. 74, 409–420 (2009).

    Article  CAS  PubMed  Google Scholar 

  33. Shiomi, D. & Margolin, W. Dimerization or oligomerization of the actin-like FtsA protein enhances the integrity of the cytokinetic Z ring. Mol. Microbiol. 66, 1396–1415 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  34. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Macromol. Crystallogr. Pt A, 307–326 (1997).

    Article  Google Scholar 

  35. CP Collaborative. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50, 760–763 (1994).

  36. Schneider, T. R. & Sheldrick, G. M. Substructure solution with SHELXD. Acta Crystallogr. D Biol. Crystallogr. 58, 1772–1779 (2002).

    Article  PubMed  CAS  Google Scholar 

  37. McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Cowtan, K. D. & Zhang, K. Y. Density modification for macromolecular phase improvement. Prog. Biophys. Mol. Biol. 72, 245–270 (1999).

    Article  CAS  PubMed  Google Scholar 

  39. Cowtan, K. The Buccaneer software for automated model building. 1. Tracing protein chains. Acta Crystallogr. D Biol. Crystallogr. 62, 1002–1011 (2006).

    Article  PubMed  CAS  Google Scholar 

  40. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004).

    Article  CAS  PubMed  Google Scholar 

  41. Adams, P. D. et al. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr. D Biol. Crystallogr. 58, 1948–1954 (2002).

    Article  PubMed  CAS  Google Scholar 

  42. Gao, Y. et al. Arabidopsis FRS4/CPD25 and FHY3/CPD45 work cooperatively to promote the expression of the chloroplast division gene ARC5 and chloroplast division. Plant J. 75, 795–807 (2013).

    Article  CAS  PubMed  Google Scholar 

  43. Lukowitz, W., Gillmor, C. S. & Scheible, W. R. Positional cloning in Arabidopsis. Why it feels good to have a genome initiative working for you. Plant Physiol. 123, 795–805 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Li, Y., Sun, Q., Feng, Y., Liu, X. & Gao, H. An improved immunofluorescence staining method for chloroplast proteins. Plant Cell Rep. 35, 2285–2293 (2016).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We would like to thank the staff at beamline BL17U of the Shanghai Synchrotron Radiation Facility for their assistance with data collection, and J. Wang at Tsinghua University for crystallographic data analysis. This work was supported by the National Natural Science Foundation of China (31400635 and 30971439), the Beijing Natural Science Foundation (5154031) and the Fundamental Research Funds for the Central Universities (JD1609).

Author information

Author notes

  1. Wenhe Wang, Jinyu Li, Qingqing Sun and Xiaoyu Yu: These authors contributed equally to this work.

Authors and Affiliations

  1. Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China

    Wenhe Wang, Xiaoyu Yu, Weiwei Zhang, Yanan Dong, Fengjiao Han, Zhiling Zhu, Shi-zhong Luo & Yue Feng

  2. College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China

    Jinyu Li, Qingqing Sun, Ning Jia, Chuanjing An, Yiqiong Li, Ning Chang, Xiaomin Liu & Hongbo Gao

  3. Ministry of Education Key Laboratory of Protein Science, Center for Structural Biology, School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China

    You Yu, Shilong Fan & Maojun Yang

Authors
  1. Wenhe Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jinyu Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Qingqing Sun
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Xiaoyu Yu
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Weiwei Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Ning Jia
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Chuanjing An
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Yiqiong Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Yanan Dong
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Fengjiao Han
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Ning Chang
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Xiaomin Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Zhiling Zhu
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. You Yu
    View author publications

    You can also search for this author in PubMed Google Scholar

  15. Shilong Fan
    View author publications

    You can also search for this author in PubMed Google Scholar

  16. Maojun Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  17. Shi-zhong Luo
    View author publications

    You can also search for this author in PubMed Google Scholar

  18. Hongbo Gao
    View author publications

    You can also search for this author in PubMed Google Scholar

  19. Yue Feng
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Y.F. and H.G. designed the project. W.W., X.Y., W.Z., Y.D., F.H., Y.Y., S.F., M.Y., N.C., Z.Z. and S.L. purified the proteins, grew the crystals, collected data, solved the crystal structures and performed the in vitro pull-down and gel filtration assays. J.L., N.J., X.L. and N.C. performed the yeast two-hybrid assays. J.L., Q.S., C.A., X.L. and N.C. identified the Arabidopsis mutants, generated transgenic plants and did the microscopy and other analyses. Q.S. and Y.L. performed the immunofluorescence staining experiments. Y.F. analysed the data and wrote the paper with the help of all the authors.

Corresponding authors

Correspondence to Hongbo Gao or Yue Feng.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

Supplementary Methods, Supplementary Figures 1–10, Supplementary Table 1. (PDF 1790 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Wang, W., Li, J., Sun, Q. et al. Structural insights into the coordination of plastid division by the ARC6–PDV2 complex. Nature Plants 3, 17011 (2017). https://doi.org/10.1038/nplants.2017.11

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1038/nplants.2017.11

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing