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The diageotropica gene of tomato encodes a cyclophilin: a novel player in auxin signaling

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Abstract

The single gene, auxin-resistant diageotropica (dgt) mutant of tomato displays a pleiotropic auxin-related phenotype that includes a slow gravitropic response, lack of lateral roots, reduced apical dominance, altered vascular development, and reduced fruit growth. Some auxin responses are unaltered in dgt plants, however, and the levels, metabolism, and transport of auxin appear normal, indicating that the Dgt gene encodes a component of a specific auxin signaling pathway. By combining map-based cloning with comparative microsynteny, we determined that the Dgt gene encodes a cyclophilin (CYP) (LeCYP1; gi:170439) that has not previously been identified as a component of auxin signaling and plant development. Each of the three known dgt alleles contains a unique mutation in the coding sequence of LeCyp1. Alleles dgt 1-1and dgt 1-2 contain single nucleotide point mutations that generate an amino acid change (G137R) and a stop codon (W128stop), respectively, while dgt dp has an amino acid change (W128CΔ129–133) preceding a 15 bp deletion. Complementation of dgt plants with the wild-type LeCyp1 gene restored the wild-type phenotype. Each dgt mutation reduced or nullified the peptidyl–prolyl isomerase activity of the GST–LeCYP1 fusion proteins in vitro. RT-PCR and immunoblot analyses indicated that the dgt mutations do not affect the expression of LeCyp1 mRNA, but the accumulation of LeCYP1 protein is greatly reduced for all three mutant alleles. The CYP inhibitor, cyclosporin A, partially mimics the effects of the dgt mutation in inhibiting auxin-induced adventitious root initiation in tomato hypocotyl sections and reducing the auxin-induced expression of the early auxin response genes, LeIAA10 and 11. These observations confirm that the PPIase activity of the tomato CYP, LeCYP1, encoded by the Dgt gene is important for specific aspects of auxin regulation of plant growth, development, and environmental responses.

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Abbreviations

dgt :

diageotropica

CYP:

Cyclophilin

CsA:

Cyclosporin A

1-NAA:

α-Napthaleneacetic acid

PPIase:

Peptidyl–prolyl isomerase

References

  • Ausubel FM, Brent RR, Kingston ER, Moore DD, Seidman GJ, Smith AJ, Struhl K (1997) Short protocols in molecular biology. Wiley, New York

    Google Scholar 

  • Balbi V, Lomax TL (2003) Regulation of early tomato fruit development by the diageotropica gene. Plant Physiol 131:186–197

    Article  PubMed  CAS  Google Scholar 

  • Berardini TZ, Bollman K, Sun H, Poethig RS (2001) Regulation of vegetative phase change in Arabidopsis thaliana by cyclophilin 40. Science 291:2405–2407

    Article  PubMed  CAS  Google Scholar 

  • Buchholz WG, Harris-Haller L, DeRose RT, Hall TC (1994) Cyclophilins are encoded by a small gene family in rice. Plant Mol Biol 25:837–843

    Article  PubMed  CAS  Google Scholar 

  • Chou IT, Gasser CS (1997) Characterization of the cyclophilin gene family of Arabidopsis thaliana and phylogenetic analysis of known cyclophilin proteins. Plant Mol Biol 35:873–892

    Article  PubMed  CAS  Google Scholar 

  • Coenen C, Lomax TL (1998) The diageotropica gene differentially affects auxin and cytokinin responses throughout development in tomato. Plant Physiol 117:63–72

    Article  PubMed  CAS  Google Scholar 

  • Cyert MS, Kunisawa R, Kaim D, Thorner J (1991) Yeast has homologs (CNA1 and CNA2 gene products) of mammalian calcineurin, a calmodulin-regulated phosphoprotein phosphatase. Proc Natl Acad Sci USA 88:7376–7380

    Article  PubMed  CAS  Google Scholar 

  • Dellarporta SL, Wood J, Hicks JB (1983) A plant DNA minipreparation, Version II. Plant Mol Biol Rep 1:19–21

    Article  Google Scholar 

  • Dharmasiri N, Dharmasiri S, Jones AM, Estelle M (2003) Auxin action in a cell-free system. Curr Biol 13:1418–1422

    Article  PubMed  CAS  Google Scholar 

  • Fischer G, Wittmann-Liebold B, Lang K, Kiefhaber T, Schmid FX (1989) Cyclophilin and peptidyl–prolyl cis–trans isomerase are probably identical proteins. Nature 337:476–478

    Article  PubMed  CAS  Google Scholar 

  • Fleming AJ, Mandel T, Roth I, Kuhlemeier C (1993) The patterns of gene expression in the tomato shoot apical meristem. Plant Cell 5:297–309

    Article  PubMed  CAS  Google Scholar 

  • Friml J (2003) Auxin transport—shaping the plant. Curr Opin Plant Biol 6:7–12

    Article  PubMed  CAS  Google Scholar 

  • Fujino DW, Nissen SJ, Jones AD, Burger DW, Bradford KJ (1988) Quantification of indole-3-acetic acid in dark-grown seedlings of diageotropica and epinastic mutants of tomato (Lycopersicon esculentum Mill). Plant Physiol 88:780–784

    PubMed  CAS  Google Scholar 

  • Gamborg OL, Miller RA, Ojima K (1968) Nutrient requirements of suspension cultures of soybean root cells. Exp Cell Res 50:151–158

    Article  PubMed  CAS  Google Scholar 

  • Garbers C, DeLong A, Deruere J, Bernasconi P, Soll D (1996) A mutation in protein phosphatase 2A regulatory subunit A affects auxin transport in Arabidopsis. EMBO J 15:2115–2124

    PubMed  CAS  Google Scholar 

  • Gasser CS, Gunning DA, Budelier KA, Brown SM (1990) Structure and expression of cytosolic cyclophilin/peptidyl–prolyl cis–trans isomerase of higher plants and production of active tomato cyclophilin in Escherichia coli. Proc Natl Acad Sci USA 87:9519–9523

    Article  PubMed  CAS  Google Scholar 

  • Geisler M, Kolukisaoglu HU, Bouchard R, Billion K, Berger J, Saal B, Frangne N, Koncz-Kalman Z, Koncz C, Dudler R, Blakeslee JJ, Murphy AS, Martinoia E, Schulz B (2003) TWISTED DWARF1, a unique plasma membrane-anchored immunophilin-like protein, interacts with Arabidopsis multidrug resistance-like transporters AtPGP1 and AtPGP19. Mol Biol Cell 14:4238–4249

    Article  PubMed  CAS  Google Scholar 

  • Geldner N, Anders N, Wolters H, Keicher J, Kornberger W, Muller P, Delbarre A, Ueda T, Nakano A, Jurgens G (2003) The Arabidopsis GNOM ARF-GEF mediates endosomal recycling, auxin transport, and auxin-dependent plant growth. Cell 112:219–230

    Article  PubMed  CAS  Google Scholar 

  • Gothel SF, Marahiel MA (1999) Peptidyl–prolyl cis–trans isomerases, a superfamily of ubiquitous folding catalysts. Cell Mol Life Sci 55:423–436

    Article  PubMed  CAS  Google Scholar 

  • Grebe M, Gadea J, Steinmann T, Kientz M, Rahfeld JU, Salchert K, Koncz C, Jurgens G (2000) A conserved domain of the arabidopsis GNOM protein mediates subunit interaction and cyclophilin 5 binding. Plant Cell 12:343–356

    Article  PubMed  CAS  Google Scholar 

  • Hammarberg T, Provost P, Persson B, Radmark O (2000) The N-terminal domain of 5-lipoxygenase binds calcium and mediates calcium stimulation of enzyme activity. J Biol Chem 275:38787–38793

    Article  PubMed  CAS  Google Scholar 

  • He Z, Li L, Luan S (2004) Immunophilins and parvulins. Superfamily of peptidyl prolyl isomerases in Arabidopsis. Plant Physiol 134:1248–1267

    Article  PubMed  CAS  Google Scholar 

  • Jackson K, Soll D (1999) Mutations in a new Arabidopsis cyclophilin disrupt its interaction with protein phosphatase 2A. Mol Gen Genet 262:830–838

    Article  PubMed  CAS  Google Scholar 

  • Jones DA, Jones JDG (1996) Allelism tests, in is alleleic to com, dp is allelic to dgt and pu-2 is alleleic to al. TGC report 46

  • Kelly MO, Bradford KJ (1986) Insensitivity of the diageotropica tomato mutant to auxin. Plant Physiol 82:713–717

    PubMed  CAS  Google Scholar 

  • Kepinski S, Leyser O (2005) The Arabidopsis F-box protein TIR1 is an auxin receptor. Nature 435:446–451

    Article  PubMed  CAS  Google Scholar 

  • Kinoshita T, Shimazaki K (1999) Characterization of cytosolic cyclophilin from guard cells of Vicia faba L. Plant Cell Physiol 40:53–59

    PubMed  CAS  Google Scholar 

  • Knapp S, Larondelle Y, Rossberg M, Furtek D, Theres K (1994) Transgenic tomato lines containing Ds elements at defined genomic positions as tools for targeted transposon tagging. Mol Gen Genet 243:666–673

    PubMed  CAS  Google Scholar 

  • Konieczny A, Ausubel FM (1993) A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers. Plant J 4:403–410

    Article  PubMed  CAS  Google Scholar 

  • Krummrei U, Bang R, Schmidtchen R, Brune K, Bang H (1995) Cyclophilin-A is a zinc-dependent DNA binding protein in macrophages. FEBS Lett 371:47–51

    Article  PubMed  CAS  Google Scholar 

  • Kudla J, Xu Q, Harter K, Gruissem W, Luan S (1999) Genes for calcineurin B-like proteins in Arabidopsis are differentially regulated by stress signals. Proc Natl Acad Sci USA 96:4718–4723

    Article  PubMed  CAS  Google Scholar 

  • Kullertz G, Liebau A, Rucknagel P, Schierhorn A, Diettrich B, Fischer G, Luckner M (1999) Stress-induced expression of cyclophilins in proembryonic masses of Digitalis lanata does not protect against freezing/thawing stress. Planta 208:599–605

    Article  PubMed  CAS  Google Scholar 

  • Laemmli UK (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227:680–685

    Article  PubMed  CAS  Google Scholar 

  • Lippuner V, Chou IT, Scott SV, Ettinger WF, Theg SM, Gasser CS (1994) Cloning and characterization of chloroplast and cytosolic forms of cyclophilin from Arabidopsis thaliana. J Biol Chem 269:7863–7868

    PubMed  CAS  Google Scholar 

  • Lippuner V, Cyert MS, Gasser CS (1996) Two classes of plant cDNA clones differentially complement yeast calcineurin mutants and increase salt tolerance of wild-type yeast. J Biol Chem 271:12859–12866

    Article  PubMed  CAS  Google Scholar 

  • Liscum E, Reed JW (2002) Genetics of Aux/IAA and ARF action in plant growth and development. Plant Mol Biol 49:387–400

    Article  PubMed  CAS  Google Scholar 

  • Liu J, Albers MW, Chen CM, Schreiber SL, Walsh CT (1990) Cloning, expression, and purification of human cyclophilin in Escherichia coli and assessment of the catalytic role of cysteines by site-directed mutagenesis. Proc Natl Acad Sci USA 87:2304–2308

    Article  PubMed  CAS  Google Scholar 

  • Liu J, Farmer JD, Jr., Lane WS, Friedman J, Weissman I, Schreiber SL (1991) Calcineurin is a common target of cyclophilin–cyclosporin A and FKBP–FK506 complexes. Cell 66:807–815

    Article  PubMed  CAS  Google Scholar 

  • Luan S, Lane WS, Schreiber SL (1994) pCyP B: a chloroplast-localized, heat shock-responsive cyclophilin from fava bean. Plant Cell 6: 885–892

    Article  PubMed  CAS  Google Scholar 

  • Marivet J, Margis-Pinheiro M, Frendo P, Burkard G (1994) Bean cyclophilin gene expression during plant development and stress conditions. Plant Mol Biol 26:1181–1189

    Article  PubMed  CAS  Google Scholar 

  • Marivet J, Frendo P, Burkard G (1995) DNA sequence analysis of a cyclophilin gene from maize: developmental expression and regulation by salicylic acid. Mol Gen Genet 247:222–228

    Article  PubMed  CAS  Google Scholar 

  • Mikol V, Kallen J, Walkinshaw MD (1994) X-ray structure of a cyclophilin B/cyclosporin complex: comparison with cyclophilin A and delineation of its calcineurin-binding domain. Proc Natl Acad Sci USA 91:5183–5186

    Article  PubMed  CAS  Google Scholar 

  • Mito N, Bennett AB (1995) The diageotropica mutation and synthetic auxins differentially affect the expression of auxin-regulated genes in tomato. Plant Physiol 109:293–297

    Article  PubMed  CAS  Google Scholar 

  • Nebenfuhr A, White TJ, Lomax TL (2000) The diageotropica mutation alters auxin induction of a subset of the Aux/IAA gene family in tomato. Plant Mol Biol 44:73–84

    Article  PubMed  CAS  Google Scholar 

  • Nozawa A, Koizumi N, Sano H (2001) An Arabidopsis SNF1-related protein kinase, AtSR1, interacts with a calcium-binding protein, AtCBL2, of which transcripts respond to light. Plant Cell Physiol 42:976–981

    Article  PubMed  CAS  Google Scholar 

  • Nuc K, Nuc P, Slomski R (2001) Yellow lupine cyclophilin transcripts are highly accumulated in the nodule meristem zone. Mol Plant Microbe Interact 14: 1384–1394

    Article  PubMed  CAS  Google Scholar 

  • Oh K, Hardeman K, Ivanchenko MG, Ellard-Ivey M, Nebenfuhr A, White TJ, Lomax TL (2002) Fine mapping in tomato using microsynteny with the Arabidopsis genome: the Diageotropica (Dgt) locus. Genome Biol 3: research0049

  • Perez-Perez JM, Ponce MR, Micol JL (2004) The ULTRACURVATA2 gene of Arabidopsis encodes an FK506-binding protein involved in auxin and brassinosteroid signaling. Plant Physiol 134:101–117

    Article  PubMed  CAS  Google Scholar 

  • Pratt WB, Krishna P, Olsen LJ (2001) Hsp90-binding immunophilins in plants: the protein movers. Trends Plant Sci 6:54–58

    Article  PubMed  CAS  Google Scholar 

  • Rashotte AM, DeLong A, Muday GK (2001) Genetic and chemical reductions in protein phosphatase activity alter auxin transport, gravity response, and lateral root growth. Plant Cell 13:1683–1697

    Article  PubMed  CAS  Google Scholar 

  • Reed JW (2001) Roles and activities of Aux/IAA proteins in Arabidopsis. Trends Plant Sci 6:420–425

    Article  PubMed  CAS  Google Scholar 

  • Reinhardt D, Wittwer F, Mandel T, Kuhlemeier C (1998) Localized upregulation of a new expansin gene predicts the site of leaf formation in the tomato meristem. Plant Cell 10:1427–1437

    Article  PubMed  CAS  Google Scholar 

  • Rice MS, Lomax TL (2000) The auxin-resistant diageotropica mutant of tomato responds to gravity via an auxin-mediated pathway. Planta 210:906–913

    Article  PubMed  CAS  Google Scholar 

  • Saito T, Tadakuma K, Takahashi N, Ashida H, Tanaka K, Kawamukai M, Matsuda H, Nakagawa T (1999) Two cytosolic cyclophilin genes of Arabidopsis thaliana differently regulated in temporal- and organ-specific expression. Biosci Biotechnol Biochem 63:632–637

    Article  PubMed  CAS  Google Scholar 

  • Swarup R, Friml J, Marchant A, Ljung K, Sandberg G, Palme K, Bennett M (2001) Localization of the auxin permease AUX1 suggests two functionally distinct hormone transport pathways operate in the Arabidopsis root apex. Genes Dev 15:2648–2653

    Article  PubMed  CAS  Google Scholar 

  • Takahashi N, Hayano T, Suzuki M (1989) Peptidyl–prolyl cis–trans isomerase is the cyclosporin A-binding protein cyclophilin. Nature 337:473–475

    Article  PubMed  CAS  Google Scholar 

  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882

    Article  PubMed  CAS  Google Scholar 

  • Tiwari SB, Hagen G, Guilfoyle T (2003) The roles of auxin response factor domains in auxin-responsive transcription. Plant Cell 15:533–543

    Article  PubMed  CAS  Google Scholar 

  • Van der Hoeven R, Ronning C, Giovannoni J, Martin G, Tanksley S (2002) Deductions about the number, organization, and evolution of genes in the tomato genome based on analysis of a large expressed sequence tag collection and selective genomic sequencing. Plant Cell 14:1441–1456

    Article  PubMed  Google Scholar 

  • Xiang C, Han P, Lutziger I, Wang K, Oliver DJ (1999) A mini binary vector series for plant transformation. Plant Mol Biol 40:711–717

    Article  PubMed  CAS  Google Scholar 

  • Yang WM, Inouye CJ, Seto E (1995) Cyclophilin A and FKBP12 interact with YY1 and alter its transcriptional activity. J Biol Chem 270:15187–15193

    Article  PubMed  CAS  Google Scholar 

  • Zobel RW (1973) Some physiological characteristics of the ethyolene-requiring tomato mutant Diageotropica. Plant Physiol 52:385–389

    PubMed  CAS  Google Scholar 

  • Zobel RW (1974) Control of morphogenesis in the ethylene-requiring tomato mutant diageotropica. Can J Bot 52:735–741

    Google Scholar 

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Acknowldegements

We thank Drs. Charles Gasser, Valerian Dolja, and Nadine Anders for providing anti-AtCYP18-3/ROC1 antiserum, pCB302-3, and pGST::ROC1, respectively. Drs. Warren Coffeen and Victor Hsu are acknowledged for critical reading of the manuscript and advice for PPIase assay, respectively. The University of Washington Genome Center performed BAC clone sequencing. This work was supported by a NSF Integrative Plant Biology Program grant (IBN-0105357) to T.L.L.

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  1. KwangChul Oh

    Present address: Plant Gene Expression Center, Department of Plant and Microbial Biology, University of California Berkeley, 800 Buchanan St., Albany, CA, 94710, USA

  2. Terri L. Lomax

    Present address: Exploration Systems Mission Directorate, NASA Headquarters, Washington, DC, 20546-0001, USA

Authors and Affiliations

  1. Department of Botany and Plant Pathology and the Center for Gene Research and Biotechnology, Oregon State University, Corvallis, OR, 97331-2902, USA

    KwangChul Oh, Maria G. Ivanchenko, T. J. White & Terri L. Lomax

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  1. KwangChul Oh
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  2. Maria G. Ivanchenko
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Correspondence to KwangChul Oh.

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Oh, K., Ivanchenko, M.G., White, T.J. et al. The diageotropica gene of tomato encodes a cyclophilin: a novel player in auxin signaling. Planta 224, 133–144 (2006). https://doi.org/10.1007/s00425-005-0202-z

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