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Organelle DNA degradation contributes to the efficient use of phosphate in seed plants

Nature Plants volume 4, pages 1044–1055 (2018)Cite this article

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Abstract

Mitochondria and chloroplasts (plastids) both harbour extranuclear DNA that originates from the ancestral endosymbiotic bacteria. These organelle DNAs (orgDNAs) encode limited genetic information but are highly abundant, with multiple copies in vegetative tissues, such as mature leaves. Abundant orgDNA constitutes a substantial pool of organic phosphate along with RNA in chloroplasts, which could potentially contribute to phosphate recycling when it is degraded and relocated. However, whether orgDNA is degraded nucleolytically in leaves remains unclear. In this study, we revealed the prevailing mechanism in which organelle exonuclease DPD1 degrades abundant orgDNA during leaf senescence. The DPD1 degradation system is conserved in seed plants and, more remarkably, we found that it was correlated with the efficient use of phosphate when plants were exposed to nutrient-deficient conditions. The loss of DPD1 compromised both the relocation of phosphorus to upper tissues and the response to phosphate starvation, resulting in reduced plant fitness. Our findings highlighted that DNA is also an internal phosphate-rich reservoir retained in organelles since their endosymbiotic origin.

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Fig. 1: Exonuclease activity of DPD1.
Fig. 2: DPD1 is induced by leaf senescence and degrades orgDNA in vivo.
Fig. 3: Stay-green phenotype and prolonged leaf longevity in dpd1 leaves.
Fig. 4: Hydroponic culture of dpd1 mutants exhibited attenuated phosphorus response and reduced fitness in phosphate-deprived conditions.
Fig. 5: RNA-seq analysis showing compromised response of dpd1 to phosphate deprivation.
Fig. 6: CpDNA copy number decline and upregulation of DPD1 during leaf fall in a deciduous tree, P. alba.

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Data availability

Accession numbers of the genes used in this study are listed in Supplementary Table 9. Precise P values calculated by statistical tests in this study are listed in Supplementary Table 10. The raw data used to construct graphs in this study are presented as Supplementary Dataset. The raw transcriptomic data are deposited in the DDBJ with the accession number DRA007138, under the BioProject with the accession number PRJDB7233. All transcriptomic data used in Fig. 5 and Supplementary Figs. 10 and 11 are available in Supplementary Tables 1–8.

References

  1. Dyall, S. D., Brown, M. T. & Johnson, P. J. Ancient invasions: from endosymbionts to organelles. Science 304, 253–257 (2004).

    Article  CAS  Google Scholar 

  2. Gray, M. W. Evolution of organellar genomes. Curr. Opin. Genet. Dev. 9, 678–687 (1999).

    Article  CAS  Google Scholar 

  3. Sugiura, M. History of chloroplast genomics. Photosynth. Res. 76, 371–377 (2003).

    Article  CAS  Google Scholar 

  4. Wallace, D. C. Why do we still have a maternally inherited mitochondrial DNA? Insights from evolutionary medicine. Annu. Rev. Biochem. 76, 781–821 (2007).

    Article  CAS  Google Scholar 

  5. Sato, S., Nakamura, Y., Kaneko, T., Asamizu, E. & Tabata, S. Complete structure of the chloroplast genome of Arabidopsis thaliana. DNA Res. 6, 283–290 (1999).

    Article  CAS  Google Scholar 

  6. Jarvis, P. & Lopez-Juez, E. Biogenesis and homeostasis of chloroplasts and other plastids. Nat. Rev. Mol. Cell Biol. 14, 787–802 (2013).

    Article  CAS  Google Scholar 

  7. Sakamoto, W., Miyagishima, S. Y. & Jarvis, P. Chloroplast biogenesis: control of plastid development, protein import, division and inheritance. Arabidopsis Book 6, e0110 (2008).

    Article  Google Scholar 

  8. Gualberto, J. M. & Newton, K. J. Plant mitochondrial genomes: dynamics and mechanisms of mutation. Annu. Rev. Plant Biol. 68, 225–252 (2017).

    Article  CAS  Google Scholar 

  9. Marechal, A. & Brisson, N. Recombination and the maintenance of plant organelle genome stability. New Phytol. 186, 299–317 (2010).

    Article  CAS  Google Scholar 

  10. Oldenburg, D. J. & Bendich, A. J. DNA maintenance in plastids and mitochondria of plants. Front. Plant Sci. 6, 883 (2015).

    Article  Google Scholar 

  11. Rauwolf, U., Golczyk, H., Greiner, S. & Herrmann, R. G. Variable amounts of DNA related to the size of chloroplasts III. Biochemical determinations of DNA amounts per organelle. Mol. Genet. Genomics 283, 35–47 (2010).

    Article  CAS  Google Scholar 

  12. Fujie, M., Kuroiwa, H., Kawano, S., Mutoh, S. & Kuroiwa, T. Behavior of organelles and their nucleoids in the shoot apical meristem during leaf development in Arabidopsis thaliana L. Planta 194, 395–405 (1994).

    Article  CAS  Google Scholar 

  13. Zoschke, R., Liere, K. & Borner, T. From seedling to mature plant: Arabidopsis plastidial genome copy number, RNA accumulation and transcription are differentially regulated during leaf development. Plant J. 50, 710–722 (2007).

    Article  CAS  Google Scholar 

  14. Dean, C. & Leech, R. M. Genome expression during normal leaf development: I. Cellular and chloroplast numbers and DNA, RNA, and protein levels in tissues of different ages within a seven-day-old wheat leaf. Plant Physiol. 69, 904–910 (1982).

    Article  CAS  Google Scholar 

  15. Veneklaas, E. J. et al. Opportunities for improving phosphorus-use efficiency in crop plants. New Phytol. 195, 306–320 (2012).

    Article  CAS  Google Scholar 

  16. Golczyk, H. et al. Chloroplast DNA in mature and senescing leaves: a reappraisal. Plant Cell 26, 847–854 (2014).

    Article  CAS  Google Scholar 

  17. Oldenburg, D. J., Rowan, B. A., Kumar, R. A. & Bendich, A. J. On the fate of plastid DNA molecules during leaf development: response to the Golczyk et al. commentary. Plant Cell 26, 855–861 (2014).

    Article  CAS  Google Scholar 

  18. Sato, M. & Sato, K. Maternal inheritance of mitochondrial DNA by diverse mechanisms to eliminate paternal mitochondrial DNA. Biochim. Biophys. Acta 1833, 1979–1984 (2013).

    Article  CAS  Google Scholar 

  19. Kuroiwa, T. Review of cytological studies on cellular and molecular mechanisms of uniparental (maternal or paternal) inheritance of plastid and mitochondrial genomes induced by active digestion of organelle nuclei (nucleoids). J. Plant Res. 123, 207–230 (2010).

    Article  CAS  Google Scholar 

  20. Zhou, Q. et al. Mitochondrial endonuclease G mediates breakdown of paternal mitochondria upon fertilization. Science 353, 394–399 (2016).

    Article  CAS  Google Scholar 

  21. Nishimura, Y. et al. An mt + gamete-specific nuclease that targets mt − chloroplasts during sexual reproduction in C. reinhardtii. Genes Dev. 16, 1116–1128 (2002).

    Article  CAS  Google Scholar 

  22. Matsushima, R. et al. A conserved, Mg2+-dependent exonuclease degrades organelle DNA during Arabidopsis pollen development. Plant Cell 23, 1608–1624 (2011).

    Article  CAS  Google Scholar 

  23. Sakamoto, W. & Takami, T. Nucleases in higher plants and their possible involvement in DNA degradation during leaf senescence. J. Exp. Bot. 65, 3835–3843 (2014).

    Article  Google Scholar 

  24. Portis, A. R. Jr & Heldt, H. W. Light-dependent changes of the Mg2+ concentration in the stroma in relation to the Mg2+ dependency of CO2 fixation in intact chloroplasts. Biochim. Biophys. Acta 449, 434–436 (1976).

    Article  CAS  Google Scholar 

  25. Parent, J. S., Lepage, E. & Brisson, N. Divergent roles for the two PolI-like organelle DNA polymerases of Arabidopsis. Plant Physiol. 156, 254–262 (2011).

    Article  CAS  Google Scholar 

  26. Moriyama, T. & Sato, N. Enzymes involved in organellar DNA replication in photosynthetic eukaryotes. Front. Plant Sci. 5, 480 (2014).

    Article  Google Scholar 

  27. Wang, D. Y. et al. The levels of male gametic mitochondrial DNA are highly regulated in angiosperms with regard to mitochondrial inheritance. Plant Cell 22, 2402–2416 (2010).

    Article  CAS  Google Scholar 

  28. Preuten, T. et al. Fewer genes than organelles: extremely low and variable gene copy numbers in mitochondria of somatic plant cells. Plant J. 64, 948–959 (2010).

    Article  CAS  Google Scholar 

  29. Arimura, S. I. Fission and fusion of plant mitochondria, and genome maintenance. Plant Physiol. 176, 152–161 (2018).

    Article  CAS  Google Scholar 

  30. Conn, S. J. et al. Protocol: optimising hydroponic growth systems for nutritional and physiological analysis of Arabidopsis thaliana and other plants. Plant Methods 9, 4 (2013).

    Article  CAS  Google Scholar 

  31. Rubio, V. et al. A conserved MYB transcription factor involved in phosphate starvation signaling both in vascular plants and in unicellular algae. Genes Dev. 15, 2122–2133 (2001).

    Article  CAS  Google Scholar 

  32. Castrillo, G. et al. Root microbiota drive direct integration of phosphate stress and immunity. Nature 543, 513–518 (2017).

    Article  CAS  Google Scholar 

  33. Krapp, A. et al. Arabidopsis roots and shoots show distinct temporal adaptation patterns toward nitrogen starvation. Plant Physiol. 157, 1255–1282 (2011).

    Article  CAS  Google Scholar 

  34. Peng, M., Bi, Y. M., Zhu, T. & Rothstein, S. J. Genome-wide analysis of Arabidopsis responsive transcriptome to nitrogen limitation and its regulation by the ubiquitin ligase gene NLA. Plant Mol. Biol. 65, 775–797 (2007).

    Article  CAS  Google Scholar 

  35. Keskitalo, J., Bergquist, G., Gardestrom, P. & Jansson, S. A cellular timetable of autumn senescence. Plant Physiol. 139, 1635–1648 (2005).

    Article  CAS  Google Scholar 

  36. Kurita, Y. et al. Establishment of a shortened annual cycle system; a tool for the analysis of annual re-translocation of phosphorus in the deciduous woody plant (Populus alba L.). J. Plant Res. 127, 545–551 (2014).

    Article  CAS  Google Scholar 

  37. Kurita, Y. et al. Inositol hexakis phosphate is the seasonal phosphorus reservoir in the deciduous woody plant Populus alba L. Plant Cell Physiol. 58, 1477–1485 (2017).

    Article  CAS  Google Scholar 

  38. Fulgosi, H. et al. Degradation of chloroplast DNA during natural senescence of maple leaves. Tree Physiol. 32, 346–354 (2012).

    Article  CAS  Google Scholar 

  39. Sodmergen, Kawano, S., Tano, S. & Kuroiwa, T. Preferential digestion of chloroplast nuclei (nucleoids) during senescence of the coleoptile of Oryza sativa. Protoplasma 152, 65–68 (1989).

    Article  Google Scholar 

  40. Inada, N., Sakai, A., Kuroiwa, H. & Kuroiwa, T. Three-dimensional analysis of the senescence program in rice (Oryza sativa L.) coleoptiles. Planta 206, 585–597 (1998).

    Article  CAS  Google Scholar 

  41. Sakamoto, W. & Takami, T. Chloroplast DNA dynamics: copy number, quality control and degradation. Plant Cell Physiol. 59, 1120–1127 (2018).

    Article  Google Scholar 

  42. Zhang, Q., Liu, Y. & Sodmergen. Examination of the cytoplasmic DNA in male reproductive cells to determine the potential for cytoplasmic inheritance in 295 angiosperm species. Plant Cell Physiol. 44, 941–951 (2003).

    Article  CAS  Google Scholar 

  43. Mogensen, H. L. The hows and whys of cytoplasmic inheritance in seed plants. Am. J. Bot. 83, 383–404 (1996).

    Article  Google Scholar 

  44. Corriveau, J. L. & Coleman, A. W. Rapid screening method to detect potential biparental inheritance of plastid DNA and results for over 200 angiosperm species. Am. J. Bot. 75, 1443–1458 (1988).

    Article  Google Scholar 

  45. Tang, L. Y., Matsushima, R. & Sakamoto, W. Mutations defective in ribonucleotide reductase activity interfere with pollen plastid DNA degradation mediated by DPD1 exonuclease. Plant J. 70, 637–649 (2012).

    Article  CAS  Google Scholar 

  46. Lim, P. O., Kim, H. J. & Nam, H. G. Leaf senescence. Annu. Rev. Plant Biol. 58, 115–136 (2007).

    Article  CAS  Google Scholar 

  47. Gregersen, P. L., Culetic, A., Boschian, L. & Krupinska, K. Plant senescence and crop productivity. Plant Mol. Biol. 82, 603–622 (2013).

    Article  CAS  Google Scholar 

  48. Krupinska, K. in The Structure and Function of Plastids (eds Wise, R. R. & Hoober, J. K.) 433–449 (Springer, Dordrecht, 2006).

  49. Makino, A. & Osmond, B. Effects of nitrogen nutrition on nitrogen partitioning between chloroplasts and mitochondria in pea and wheat. Plant Physiol. 96, 355–362 (1991).

    Article  CAS  Google Scholar 

  50. Smith, D. W., Fontenot, E. B., Zhahraeifard, S. & DiTusa, S. F. Molecular components that drive phosphorus-remobilization during leaf senescence. Annu. Plant Rev. 48, 159–186 (2015).

    CAS  Google Scholar 

  51. Stigter, K. A. & Plaxton, W. C. Molecular mechanisms of phosphorus metabolism and transport during leaf senescence. Plants (Basel) 4, 773–798 (2015).

    Article  CAS  Google Scholar 

  52. Robinson, W. D., Carson, I., Ying, S., Ellis, K. & Plaxton, W. C. Eliminating the purple acid phosphatase AtPAP26 in Arabidopsis thaliana delays leaf senescence and impairs phosphorus remobilization. New Phytol. 196, 1024–1029 (2012).

    Article  CAS  Google Scholar 

  53. Bariola, P. A., MacIntosh, G. C. & Green, P. J. Regulation of S-like ribonuclease levels in Arabidopsis. Antisense inhibition of RNS1 or RNS2 elevates anthocyanin accumulation. Plant Physiol. 119, 331–342 (1999).

    Article  CAS  Google Scholar 

  54. Perez-Amador, M. A. et al. Identification of BFN1, a bifunctional nuclease induced during leaf and stem senescence in Arabidopsis. Plant Physiol. 122, 169–180 (2000).

    Article  CAS  Google Scholar 

  55. Matallana-Ramirez, L. P. et al. NAC transcription factor ORE1 and senescence-induced BIFUNCTIONAL NUCLEASE1 (BFN1) constitute a regulatory cascade in Arabidopsis. Mol. Plant 6, 1432–1452 (2013).

    Article  CAS  Google Scholar 

  56. Liere, K. & Borner, T. in Plastid Development in Leaves During Growth and Senescence. Advances in Photosynthesis and Respiration Vol. 36 (eds Biswal, B. et al.) 215–237 (Springer, Dordrecht, 2013).

  57. Chiou, T. J. & Lin, S. I. Signaling network in sensing phosphate availability in plants. Annu. Rev. Plant Biol. 62, 185–206 (2011).

    Article  CAS  Google Scholar 

  58. Versaw, W. K. & Garcia, L. R. Intracellular transport and compartmentation of phosphate in plants. Curr. Opin. Plant Biol. 39, 25–30 (2017).

    Article  CAS  Google Scholar 

  59. Liu, T. Y., Lin, W. Y., Huang, T. K. & Chiou, T. J. MicroRNA-mediated surveillance of phosphate transporters on the move. Trends Plant Sci. 19, 647–655 (2014).

    Article  CAS  Google Scholar 

  60. Ishida, H., Izumi, M., Wada, S. & Makino, A. Roles of autophagy in chloroplast recycling. Biochim. Biophys. Acta 1837, 512–521 (2014).

    Article  CAS  Google Scholar 

  61. Bendich, A. J. Circular chloroplast chromosomes: the grand illusion. Plant Cell 16, 1661–1666 (2004).

    Article  CAS  Google Scholar 

  62. Sears, B. B. & VanWinkle-Swift, K. The salvage/turnover/repair (STOR) model for uniparental inheritance in Chlamydomonas: DNA as a source of sustenance. J. Hered. 85, 366–376 (1994).

    Article  CAS  Google Scholar 

  63. Yang, Y. G., Lindahl, T. & Barnes, D. E. Trex1 exonuclease degrades ssDNA to prevent chronic checkpoint activation and autoimmune disease. Cell 131, 873–886 (2007).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank R. Hijiya (Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan) for technical support, H. Kanegae (Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan) for assisting mtDNA sequence alignment in Populus species and K. Baba (Research Institute for Sustainable Humanosphere, Kyoto University, Kyoto, Japan) for supporting poplar leaf sampling. This work was supported by KAKENHI grants from JSPS (16H06554 and 17H03699 to W.S.) and from the Oohara Foundation (to W.S.).

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  1. Yuko Kurita

    Present address: Faculty of Agriculture, Ryukoku University, Otsu, Japan

Authors and Affiliations

  1. Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan

    Tsuneaki Takami, Norikazu Ohnishi & Wataru Sakamoto

  2. Department of Biology, Graduate School of Science, Kobe University, Kobe, Japan

    Yuko Kurita, Shoko Iwamura, Miwa Ohnishi & Tetsuro Mimura

  3. Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Japan

    Makoto Kusaba

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Contributions

W.S. designed the project. T.T. performed all qPCR and qRT–PCR measurements for various environments, in addition to photosynthetic activity measurements and RNA-seq analysis. N.O. performed the nuclease assays. Y.K., S.I., M.O. and T.M. prepared the poplar samples and conducted primary work related to poplar. T.T., M.K. and W.S. analysed the data. W.S. wrote the manuscript with consultation among all co-authors.

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Correspondence to Wataru Sakamoto.

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Supplementary information

Supplementary Information

Supplementary Figures 1–15 and Supplementary Table 9.

Reporting Summary

Supplementary Tables 1–8

Supplementary Table 1: Differential expression analysis of Col under P deprivation by edgeR. Supplementary Table 2: Differential expression analysis of dpd1-1 under P deprivation by edgeR. Supplementary Table 3: Expression profile of literature-curated phosphate starvation marker genes. Supplementary Table 4: Expression profile of PHR1 regulon genes. Supplementary Table 5: Differential expression analysis of Col under N deprivation by edgeR. Supplementary Table 6: Differential expression analysis of dpd1-1 under N deprivation by edgeR. Supplementary Table 7: Comparative analysis between Krapp et al. (ref. 32) and this study on upregulated gene profile under long term nitrogen starvation. Supplementary Table 8: Comparative analysis between Peng et al. (ref. 34) and this study on upregulated gene profile under long term nitrogen starvation.

Supplementary Supplementary Table 10

Precise P values in this study.

Supplementary Dataset

Raw data used to construct bar graphs.

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Takami, T., Ohnishi, N., Kurita, Y. et al. Organelle DNA degradation contributes to the efficient use of phosphate in seed plants. Nature Plants 4, 1044–1055 (2018). https://doi.org/10.1038/s41477-018-0291-x

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