Abstract

Shoot meristems of plants are composed of stem cells that are continuously replenished through a classical feedback circuit involving the homeobox WUSCHEL (WUS) gene and the CLAVATA (CLV) gene signaling pathway. In CLV signaling, the CLV1 receptor complex is bound by CLV3, a secreted peptide modified with sugars. However, the pathway responsible for modifying CLV3 and its relevance for CLV signaling are unknown. Here we show that tomato inflorescence branching mutants with extra flower and fruit organs due to enlarged meristems are defective in arabinosyltransferase genes. The most extreme mutant is disrupted in a hydroxyproline O-arabinosyltransferase and can be rescued with arabinosylated CLV3. Weaker mutants are defective in arabinosyltransferases that extend arabinose chains, indicating that CLV3 must be fully arabinosylated to maintain meristem size. Finally, we show that a mutation in CLV3 increased fruit size during domestication. Our findings uncover a new layer of complexity in the control of plant stem cell proliferation.

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References

  1. 1.

    The classification of inflorescences. Bot. Rev. 10, 187–231 (1944).

  2. 2.

    , , , & Evolution and development of inflorescence architectures. Science 316, 1452–1456 (2007).

  3. 3.

    , & Meristem maturation and inflorescence architecture—lessons from the Solanaceae. Curr. Opin. Plant Biol. 17, 70–77 (2014).

  4. 4.

    , & Quantitative variation in maize kernel row number is controlled by the FASCIATED EAR2 locus. Nat. Genet. 45, 334–337 (2013).

  5. 5.

    The genetics of maize evolution. Annu. Rev. Genet. 38, 37–59 (2004).

  6. 6.

    Twenty years on: the inner workings of the shoot apical meristem, a developmental dynamo. Dev. Biol. 341, 95–113 (2010).

  7. 7.

    , & The CLAVATA1 gene encodes a putative receptor kinase that controls shoot and floral meristem size in Arabidopsis. Cell 89, 575–585 (1997).

  8. 8.

    , , , & Signaling of cell fate decisions by CLAVATA3 in Arabidopsis shoot meristems. Science 283, 1911–1914 (1999).

  9. 9.

    , , & A glycopeptide regulating stem cell fate in Arabidopsis thaliana. Nat. Chem. Biol. 5, 578–580 (2009).

  10. 10.

    & Plant primary meristems: shared functions and regulatory mechanisms. Curr. Opin. Plant Biol. 13, 53–58 (2010).

  11. 11.

    et al. The stem cell population of Arabidopsis shoot meristems in maintained by a regulatory loop between the CLAVATA and WUSCHEL genes. Cell 100, 635–644 (2000).

  12. 12.

    , , & Grass meristems I: shoot apical meristem maintenance, axillary meristem determinacy and the floral transition. Plant Cell Physiol. 54, 302–312 (2013).

  13. 13.

    , , , & In silico screening of a saturated mutation library of tomato. Plant J. 38, 861–872 (2004).

  14. 14.

    et al. The making of a compound inflorescence in tomato and related nightshades. PLoS Biol. 6, e288 (2008).

  15. 15.

    , & The Arabidopsis CLAVATA2 gene encodes a receptor-like protein required for the stability of the CLAVATA1 receptor-like kinase. Plant Cell 11, 1925–1934 (1999).

  16. 16.

    et al. Increase in tomato locule number is controlled by two single-nucleotide polymorphisms located near WUSCHEL. Plant Physiol. 156, 2244–2254 (2011).

  17. 17.

    , , & Microsurgical and laser ablation analysis of interactions between the zones and layers of the tomato shoot apical meristem. Development 130, 4073–4083 (2003).

  18. 18.

    , , & Genome-wide characterization, expression and functional analysis of CLV3/ESR gene family in tomato. BMC Genomics 15, 827 (2014).

  19. 19.

    et al. CLAVATA1 dominant-negative alleles reveal functional overlap between multiple receptor kinases that regulate meristem and organ development. Plant Cell 15, 1198–1211 (2003).

  20. 20.

    , & Identification of three hydroxyproline O-arabinosyltransferases in Arabidopsis thaliana. Nat. Chem. Biol. 9, 726–730 (2013).

  21. 21.

    & Extensin: repetitive motifs, functional sites, post-translational codes, and phylogeny. Plant J. 5, 157–172 (1994).

  22. 22.

    , , & Role of the extensin superfamily in primary cell wall architecture. Plant Physiol. 156, 11–19 (2011).

  23. 23.

    et al. Self-assembly of the plant cell wall requires an extensin scaffold. Proc. Natl. Acad. Sci. USA 105, 2226–2231 (2008).

  24. 24.

    Small post-translationally modified peptide signals in. Arabidopsis. Arabidopsis Book 9, e0150 (2011).

  25. 25.

    , , & The sequence flanking the N-terminus of the CLV3 peptide is critical for its cleavage and activity in stem cell regulation in Arabidopsis. BMC Plant Biol. 13, 225 (2013).

  26. 26.

    & Chemical synthesis of Arabidopsis CLV3 glycopeptide reveals the impact of hydroxyproline arabinosylation on peptide conformation and activity. Plant Cell Physiol. 54, 369–374 (2013).

  27. 27.

    & Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science 346, 1258096 (2014).

  28. 28.

    , , , & Editing plant genomes with CRISPR/Cas9. Curr. Opin. Biotechnol. 32, 76–84 (2015).

  29. 29.

    , , & Efficient gene editing in tomato in the first generation using the clustered regularly interspaced short palindromic repeats/CRISPR-associated9 system. Plant Physiol. 166, 1292–1297 (2014).

  30. 30.

    , & An evolutionarily conserved pseudokinase mediates stem cell production in plants. Plant Cell 23, 851–854 (2011).

  31. 31.

    , , & Identification of plant cell wall mutants by means of a forward chemical genetic approach using hydrolases. Proc. Natl. Acad. Sci. USA 106, 14699–14704 (2009).

  32. 32.

    et al. O-glycosylated cell wall proteins are essential in root hair growth. Science 332, 1401–1403 (2011).

  33. 33.

    et al. Molecular characterization of two Arabidopsis thaliana glycosyltransferase mutants, rra1 and rra2, which have a reduced residual arabinose content in a polymer tightly associated with the cellulosic wall residue. Plant Mol. Biol. 64, 439–451 (2007).

  34. 34.

    The genetic, developmental, and molecular bases of fruit size and shape variation in tomato. Plant Cell 16 (suppl.), S181–S189 (2004).

  35. 35.

    & Evaluating the genetic basis of multiple-locule fruit in a broad cross section of tomato cultivars. Theor. Appl. Genet. 109, 669–679 (2004).

  36. 36.

    & Dissecting the genetic pathway to extreme fruit size in tomato using a cross between the small-fruited wild species Lycopersicon pimpinellifolium and L. esculentum var. Giant Heirloom. Genetics 158, 413–422 (2001).

  37. 37.

    et al. What lies beyond the eye: the molecular mechanisms regulating tomato fruit weight and shape. Front. Plant Sci. 5, 227 (2014).

  38. 38.

    , & Regulatory change in YABBY-like transcription factor led to evolution of extreme fruit size during tomato domestication. Nat. Genet. 40, 800–804 (2008).

  39. 39.

    & Tomato fruit weight 11.3 maps close to fasciated on the bottom of chromosome 11. Theor. Appl. Genet. 123, 465–474 (2011).

  40. 40.

    , , , & The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 42, D490–D495 (2014).

  41. 41.

    , , , & in Annual Plant Reviews: Plant Polysaccharides: Biosynthesis and Bioengineering (ed. Ulvskov, P.) (Wiley-Black, 2011).

  42. 42.

    , & in Annual Plant Reviews: Plant Polysaccharides: Biosynthesis and Bioengineering (ed. Ulvskov, P.) (Wiley-Black, 2011).

  43. 43.

    et al. The ROOT DETERMINED NODULATION1 gene regulates nodule number in roots of Medicago truncatula and defines a highly conserved, uncharacterized plant gene family. Plant Physiol. 157, 328–340 (2011).

  44. 44.

    , , , & Dynamic and compensatory responses of Arabidopsis shoot and floral meristems to CLV3 signaling. Plant Cell 18, 1188–1198 (2006).

  45. 45.

    et al. Mitogen-activated protein kinase regulated by the CLAVATA receptors contributes to shoot apical meristem homeostasis. Plant Cell Physiol. 52, 14–29 (2011).

  46. 46.

    et al. The CLAVATA1-related BAM1, BAM2 and BAM3 receptor kinase-like proteins are required for meristem function in. Arabidopsis. Plant J. 45, 1–16 (2006).

  47. 47.

    & BAM receptors regulate stem cell specification and organ development through complex interactions with CLAVATA signaling. Genetics 180, 895–904 (2008).

  48. 48.

    et al. RPK2 is an essential receptor-like kinase that transmits the CLV3 signal in Arabidopsis. Development 137, 3911–3920 (2010).

  49. 49.

    , & The receptor kinase CORYNE of Arabidopsis transmits the stem cell–limiting signal CLAVATA3 independently of CLAVATA1. Plant Cell 20, 934–946 (2008).

  50. 50.

    , , , & Plant stem cell maintenance by transcriptional cross-regulation of related receptor kinases. Development 142, 1043–1049 (2015).

  51. 51.

    et al. A novel single-nucleotide mutation in a CLAVATA3 gene homolog controls a multilocular silique trait in Brassica rapa L. Mol. Plant 7, 1788–1792 (2014).

  52. 52.

    , , & Rate of meristem maturation determines inflorescence architecture in tomato. Proc. Natl. Acad. Sci. USA 109, 639–644 (2012).

  53. 53.

    Tomato Genome Consortium. The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485, 635–641 (2012).

  54. 54.

    in Molecular Plant Pathology: A Practical Approach (eds. Gurr, S.J., Bowles, D.J. & McPherson, M.J.) 163–174 (Oxford University Press, 1992).

  55. 55.

    et al. Plant N-glycan processing enzymes employ different targeting mechanisms for their spatial arrangement along the secretory pathway. Plant Cell 18, 3182–3200 (2006).

  56. 56.

    et al. Subcompartment localization of the side chain xyloglucan-synthesizing enzymes within Golgi stacks of tobacco suspension-cultured cells. Plant J. 64, 977–989 (2010).

  57. 57.

    , & A multicolored set of in vivo organelle markers for co-localization studies in Arabidopsis and other plants. Plant J. 51, 1126–1136 (2007).

  58. 58.

    et al. Degradation of MONOCULM 1 by APC/CTAD1 regulates rice tillering. Nat. Commun. 3, 750 (2012).

  59. 59.

    , & Arabidopsis mesophyll protoplasts: a versatile cell system for transient gene expression analysis. Nat. Protoc. 2, 1565–1572 (2007).

  60. 60.

    , & Xylan O-acetylation impacts xylem development and enzymatic recalcitrance as indicated by the Arabidopsis mutant tbl29. Mol. Plant 6, 1373–1375 (2013).

  61. 61.

    , , & 3-deoxy-D-manno-2-octulosonic acid (KDO) is a component of rhamnogalacturonan II, a pectic polysaccharide in the primary cell walls of plants. Carbohydr. Res. 138, 109–126 (1985).

  62. 62.

    et al. The CLAVATA3/ESR motif of CLAVATA3 is functionally independent from the nonconserved flanking sequences. Plant Physiol. 141, 1284–1292 (2006).

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Acknowledgements

We thank members of the Lippman laboratory, especially S. Thomain for her initial finding of FAB2 and for invaluable conversations that helped shape this work. We thank D. Zamir (Hebrew University of Jerusalem) for providing mutants and also Y. Eshed (Weizmann Institute of Science) for providing mutants and comments on the manuscript. We thank S. Hearn at the Cold Spring Harbor Laboratory St. Giles Advanced Microscopy Center for providing technical service for transmission electron microscopy. We thank W. Wang for assistance with tomato transformation, X. Song for advice on peptide assays, DuPont Pioneer for research support, and T. Mulligan, A. Krainer and staff from Cornell University's Long Island Horticultural Research and Extension Center in Riverhead, New York, for assistance with plant care. This research was supported by the Energy Biosciences Institute and the Fred Dickinson Chair for M.P., a National Science Foundation Graduate Research Fellowship (DGE-0914548) to K.L.L., a Gordon and Betty Moore Foundation Fellowship from the Life Sciences Research Foundation to C.A.M., grants from the National Science Foundation Plant Genome Research Program to E.v.d.K. (0922661) and to J.V.E. and Z.B.L. (1237880), and an Agriculture and Food Research Initiative competitive grant (2015-67013-22823) of the US Department of Agriculture National Institute of Food and Agriculture to Z.B.L.

Author information

Author notes

    • Katie L Liberatore
    • , Cora A MacAlister
    • , Zejun Huang
    • , Ke Jiang
    •  & Guangyan Xiong

    Present addresses: Cereal Disease Laboratory, US Department of Agriculture, Agriculture Research Service, St. Paul, Minnesota, USA (K.L.L.), Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA (C.A.M.), Chinese Academy of Agricultural Sciences, Institute of Vegetables and Flowers, Beijing, China (Z.H.), Dow AgroSciences, LLC, Indianapolis, Indiana, USA (K.J.) and Department of Anatomical Sciences and Neurobiology, University of Louisville, Louisville, Kentucky, USA (G.X.).

    • Cao Xu
    •  & Katie L Liberatore

    These authors contributed equally to this work.

Affiliations

  1. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.

    • Cao Xu
    • , Katie L Liberatore
    • , Cora A MacAlister
    • , Ke Jiang
    • , Christopher Brooks
    •  & Zachary B Lippman
  2. Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.

    • Katie L Liberatore
    •  & Zachary B Lippman
  3. Department of Horticulture and Crop Science, Ohio State University, Wooster, Ohio, USA.

    • Zejun Huang
    • , Yi-Hsuan Chu
    •  & Esther van der Knaap
  4. Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan.

    • Mari Ogawa-Ohnishi
    •  & Yoshikatsu Matsubayashi
  5. Energy Biosciences Institute, University of California, Berkeley, Berkeley, California, USA.

    • Guangyan Xiong
    •  & Markus Pauly
  6. Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA.

    • Markus Pauly
  7. Boyce Thompson Institute for Plant Science, Ithaca, New York, USA.

    • Joyce Van Eck

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Contributions

C.X., K.L.L., C.A.M., Z.H., Y.-H.C., M.P., J.V.E., Y.M., E.v.d.K. and Z.B.L. designed and planned experiments. C.X., K.L.L., C.A.M., Z.H., Y.-H.C., C.B., M.O.-O., G.X. and Z.B.L. performed experiments and collected the data. C.X., K.L.L., C.A.M., Z.H., Y.-H.C., K.J., C.B., M.O.-O., G.X., M.P., Y.M., E.v.d.K. and Z.B.L. analyzed the data. K.L.L., C.X., Y.M., E.v.d.K. and Z.B.L. designed the research. C.X., K.L.L. and Z.B.L. wrote the manuscript.

Competing interests

The authors (C.A.M., K.L.L. and Z.B.L., on behalf of Cold Spring Harbor Laboratory and DuPont Pioneer) have filed a PCT patent application based in part on this work with the US Patent and Trademark Office.

Corresponding author

Correspondence to Zachary B Lippman.

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    Differentially expressed (DE) gene list for fin and fab vegetative meristem transcriptome profiling compared to WT.

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https://doi.org/10.1038/ng.3309

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