in

DNA demethylases are required for myo-inositol-mediated mutualism between plants and beneficial rhizobacteria

  • 1.

    Lugtenberg, L. & Kamilova, F. Plant-growth-promoting rhizobacteria. Annu. Rev. Microbiol. 63, 541–556 (2009).

    CAS  PubMed  Google Scholar 

  • 2.

    Nobori, T., Mine, A. & Tsuda, K. Molecular networks in plant–pathogen holobiont. FEBS Lett. 592, 1937–1953 (2018).

    CAS  PubMed  Google Scholar 

  • 3.

    Sasse, J., Martinoia, E. & Northen, T. Feed your friends: do plant exudates shape the root microbiome? Trends Plant Sci. 23, 25–41 (2018).

    CAS  PubMed  Google Scholar 

  • 4.

    Zhang, H., Lang, Z. & Zhu, J.-K. Dynamics and function of DNA methylation in plants. Nat. Rev. Mol. Cell Biol. 19, 489–506 (2018).

    CAS  PubMed  Google Scholar 

  • 5.

    Lang, Z. et al. Critical roles of DNA demethylation in the activation of ripening-induced genes and inhibition of ripening-repressed genes in tomato fruit. Proc. Natl Acad. Sci. USA 114, E4511–E4519 (2017).

    CAS  PubMed  Google Scholar 

  • 6.

    Liu, R. et al. A DEMETER-like DNA demethylase governs tomato fruit ripening. Proc. Natl Acad. Sci. USA 112, 10804–10809 (2015).

    CAS  PubMed  Google Scholar 

  • 7.

    Zhu, J.-K. Active DNA demethylation mediated by DNA glycosylases. Annu. Rev. Genet. 43, 143–166 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 8.

    Le, T.-N. et al. DNA demethylases target promoter transposable elements to positively regulate stress responsive genes in Arabidopsis. Genome Biol. 15, 458 (2014).

    PubMed  PubMed Central  Google Scholar 

  • 9.

    Qian, W. et al. A histone acetyltransferase regulates active DNA demethylation in Arabidopsis. Science 336, 1445–1448 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 10.

    Vilchez, J. I. et al. Genome sequence of Bacillus megaterium strain YC4-R4, a plant growth-promoting rhizobacterium isolated from a high-salinity environment. Genome Announc. 6, e00527-18 (2018).

    PubMed  PubMed Central  Google Scholar 

  • 11.

    Onodera, Y. et al. Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation. Cell 120, 613–622 (2005).

    CAS  PubMed  Google Scholar 

  • 12.

    Wierzbicki, A. T., Haag, J. R. & Pikaard, C. S. Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes. Cell 135, 635–648 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 13.

    Pini, F. et al. Bacterial biosensors for in vivo spatiotemporal mapping of root secretion. Plant Physiol. 174, 1289–1306 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 14.

    Sannino, A., Demitri, C. & Madaghiele, M. Biodegradable cellulose-based hydrogels: design and applications. Materials 2, 353–373 (2009).

    CAS  PubMed Central  Google Scholar 

  • 15.

    Torabinejad, J., Donahue, J. L., Gunesekera, B. N., Allen-Daniels, M. J. & Gillaspy, G. E. VTC4 is a bifunctional enzyme that affects myoinositol and ascorbate biosynthesis in plants. Plant Physiol. 150, 951–961 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 16.

    Morcillo, R. J. et al. Rhizobacterium-derived diacetyl modulates plant immunity in a phosphate-dependent manner. EMBO J. 39, e102602 (2019).

    PubMed  PubMed Central  Google Scholar 

  • 17.

    Vilchez, J. I. et al. Complete genome sequence of Bacillus megaterium strain TG1-E1, a plant drought tolerance-enhancing bacterium. Microbiol. Resour. Announc. 7, e00842-18 (2018).

    PubMed  PubMed Central  Google Scholar 

  • 18.

    Bais, H. P., Fall, R. & Vivanco, J. M. Biocontrol of Bacillus subtilis against infection of Arabidopsis roots by Pseudomonas syringae is facilitated by biofilm formation and surfactin production. Plant Physiol. 134, 307–319 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 19.

    Yu, A. et al. Dynamics and biological relevance of DNA demethylation in Arabidopsis antibacterial defense. Proc. Natl Acad. Sci. USA 110, 2389–2394 (2013).

    CAS  PubMed  Google Scholar 

  • 20.

    López Sánchez, A., Stassen, J. H., Furci, L., Smith, L. M. & Ton, J. The role of DNA (de)methylation in immune responsiveness of Arabidopsis. Plant J. Cell Mol. Biol. 88, 361–374 (2016).

    Google Scholar 

  • 21.

    Ma, L. et al. Arabidopsis FHY3 and FAR1 regulate light-induced myo-inositol biosynthesis and oxidative stress responses by transcriptional activation of MIPS1. Mol. Plant 9, 541–557 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 22.

    Glawischnig, E. Camalexin. Phytochemistry 68, 401–406 (2007).

    CAS  PubMed  Google Scholar 

  • 23.

    Tang, K., Lang, Z., Zhang, H. & Zhu, J.-K. The DNA demethylase ROS1 targets genomic regions with distinct chromatin modifications. Nat. Plants 2, 16169 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 24.

    Bacete, L., Mélida, H., Miedes, E. & Molina, A. Plant cell wall-mediated immunity: cell wall changes trigger disease resistance responses. Plant J. Cell Mol. Biol. 93, 614–636 (2018).

    CAS  Google Scholar 

  • 25.

    Schulze-Lefert, P. Knocking on the heaven’s wall: pathogenesis of and resistance to biotrophic fungi at the cell wall. Curr. Opin. Plant Biol. 7, 377–383 (2004).

    CAS  PubMed  Google Scholar 

  • 26.

    Bulgarelli, D., Schlaeppi, K., Spaepen, S., Ver Loren van Themaat, E. & Schulze-Lefert, P. Structure and functions of the bacterial microbiota of plants. Annu. Rev. Plant Biol. 64, 807–838 (2013).

    CAS  PubMed  Google Scholar 

  • 27.

    Busby, P. E. et al. Research priorities for harnessing plant microbiomes in sustainable agriculture. PLoS Biol. 15, e2001793 (2017).

    PubMed  PubMed Central  Google Scholar 

  • 28.

    Finkel, O. M., Castrillo, G., Herrera Paredes, S., Salas González, I. & Dangl, J. L. Understanding and exploiting plant beneficial microbes. Curr. Opin. Plant Biol. 38, 155–163 (2017).

    PubMed  PubMed Central  Google Scholar 

  • 29.

    Martin, F. M., Uroz, S. & Barker, D. G. Ancestral alliances: plant mutualistic symbioses with fungi and bacteria. Science 356, eaad4501 (2017).

    PubMed  Google Scholar 

  • 30.

    Gillaspy, G. E. The cellular language of myo-inositol signaling. New Phytol. 192, 823–839 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 31.

    Yoshida, K. I., Aoyama, D., Ishio, I., Shibayama, T. & Fujita, Y. Organization and transcription of the myo-inositol operon, iol, of Bacillus subtilis. J. Bacteriol. 179, 4591–4598 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 32.

    Vives-Peris, V., de Ollas, C, Gómez-Cadenas, A. & Pérez-Clemente, R. M. Root exudates: from plant to rhizosphere and beyond. Plant Cell Rep. 39, 3–17 (2020).

    CAS  PubMed  Google Scholar 

  • 33.

    Lung, S. C. et al. Phytase activity in tobacco (Nicotiana tabacum) root exudates is exhibited by a purple acid phosphatase. Phytochemistry 69, 365–373 (2008).

    CAS  PubMed  Google Scholar 

  • 34.

    Jones, P., Garcia, B. J., Furches, A., Tuskan, G. A. & Jacobson, D. Plant host-associated mechanisms for microbial selection. Front. Plant Sci. 10, 862 (2019).

    PubMed  PubMed Central  Google Scholar 

  • 35.

    Kohler, P. R. A., Zheng, J. Y., Schoffers, E. & Rossbach, S. Inositol catabolism, a key pathway in Sinorhizobium meliloti for competitive host nodulation. Appl. Environ. Microbiol. 76, 7972–7980 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 36.

    Donahue, J. L. et al. The Arabidopsis thaliana myo-inositol 1-phosphate synthase1 gene is required for myo-inositol synthesis and suppression of cell death. Plant Cell 22, 888–903 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 37.

    Kanter, U. et al. The inositol oxygenase gene family of Arabidopsis is involved in the biosynthesis of nucleotide sugar precursors for cell-wall matrix polysaccharides. Planta 221, 243–254 (2005).

    CAS  PubMed  Google Scholar 

  • 38.

    Lei, M. et al. Regulatory link between DNA methylation and active demethylation in Arabidopsis. Proc. Natl Acad. Sci. USA 112, 3553–3557 (2015).

    CAS  PubMed  Google Scholar 

  • 39.

    Williams, B. P., Pignatta, D., Henikoff, S. & Gehring, M. Methylation-sensitive expression of a DNA demethylase gene serves as an epigenetic rheostat. PLoS Genet. 11, e1005142 (2015).

    PubMed  PubMed Central  Google Scholar 

  • 40.

    Kawakatsu, T. et al. Epigenomic diversity in a global collection of Arabidopsis thaliana accessions. Cell 166, 492–505 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 41.

    Satgé, C. et al. Reprogramming of DNA methylation is critical for nodule development in Medicago truncatula. Nat. Plants 2, 16166 (2016).

    PubMed  Google Scholar 

  • 42.

    Huang, A. C. et al. A specialized metabolic network selectively modulates Arabidopsis root microbiota. Science 364, eaau6389 (2019).

    CAS  PubMed  Google Scholar 

  • 43.

    Stringlis, I. A. et al. MYB72-dependent coumarin exudation shapes root microbiome assembly to promote plant health. Proc. Natl Acad. Sci. USA 115, E5213–E5222 (2018).

    CAS  PubMed  Google Scholar 

  • 44.

    Voges, M. J. E. E. E., Bai, Y., Schulze-Lefert, P. & Sattely, E. S. Plant-derived coumarins shape the composition of an Arabidopsis synthetic root microbiome. Proc. Natl Acad. Sci. USA 116, 12558–12565 (2019).

    PubMed  Google Scholar 

  • 45.

    Hamon, M. A. & Lazazzera, B. A. The sporulation transcription factor Spo0A is required for biofilm development in Bacillus subtilis. Mol. Microbiol. 42, 1199–1209 (2001).

    CAS  PubMed  Google Scholar 

  • 46.

    López, A. & Alippi, A. Phenotypic and genotypic diversity of Bacillus cereus isolates recovered from honey. Int. J. Food Microbiol. 117, 175–184 (2007).

    PubMed  Google Scholar 

  • 47.

    Heras, J., Domínguez, C., Mata, E. & Pascual, V. GelJ—a tool for analyzing DNA fingerprint gel images. BMC Bioinformatics 16, 270 (2015).

    PubMed  PubMed Central  Google Scholar 

  • 48.

    Hu, L. et al. Root exudate metabolites drive plant–soil feedbacks on growth and defense by shaping the rhizosphere microbiota. Nat. Commun. 9, 2738 (2018).

    PubMed  PubMed Central  Google Scholar 

  • 49.

    Walker, T. S., Bais, H. P., Grotewold, E. & Vivanco, J. M. Root exudation and rhizosphere biology. Plant Physiol. 132, 44–51 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 50.

    Roessner, U., Wagner, C., Kopka, J., Trethewey, R. N. & Willmitzer, L. Technical advance: simultaneous analysis of metabolites in potato tuber by gas chromatography–mass spectrometry. Plant J. Cell Mol. Biol. 23, 131–142 (2000).

    CAS  Google Scholar 

  • 51.

    Barsch, A., Carvalho, H. G., Cullimore, V. J. & Niehaus, K. GC–MS based metabolite profiling implies three interdependent ways of ammonium assimilation in Medicago truncatula root nodules. J. Biotechnol. 127, 79–83 (2006).

    CAS  PubMed  Google Scholar 

  • 52.

    Gorzolka, K., Lissel, M., Kessler, N., Loch-Ahring, S. & Niehaus, K. Metabolite fingerprinting of barley whole seeds, endosperms, and embryos during industrial malting. J. Biotechnol. 159, 177–187 (2012).

    CAS  PubMed  Google Scholar 

  • 53.

    Kopka, J. et al. GMD@CSB.DB: the Golm Metabolome Database. Bioinformatics 21, 1635–1638 (2005).

    CAS  PubMed  Google Scholar 

  • 54.

    Ge, S. X., Son, E. W. & Yao, R. iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data. BMC Bioinformatics 19, 534 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 55.

    Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498–2504 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 56.

    Maere, S., Heymans, K. & Kuiper, M. BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in biological networks. Bioinformatics 21, 3448–3449 (2005).

    CAS  PubMed  Google Scholar 

  • 57.

    Xi, Y. & Li, W. BSMAP: whole genome bisulfite sequence MAPping program. BMC Bioinformatics 10, 232 (2009).

    PubMed  PubMed Central  Google Scholar 

  • 58.

    Cox, M. P., Peterson, D. A. & Biggs, P. J. SolexaQA: at-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics 11, 485 (2010).

    PubMed  PubMed Central  Google Scholar 

  • 59.

    Juhling, F. et al. Metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data. Genome Res. 26, 256–262 (2016).

    PubMed  PubMed Central  Google Scholar 


  • Source: Ecology - nature.com

    Gainers and losers of surface and terrestrial water resources in China during 1989–2016

    Time to revise the Sustainable Development Goals