Alternative splicing of arabidopsis IBR5 pre-mRNA generates two IBR5 isoforms with distinct and overlapping functions

PLoS ONE

Volumn 9, Issue 8, 2014, Pages

  Jayaweera, Thilanka ^a   Siriwardana, Chamindika ^a,b   Dharmasiri, Sunethra ^a   Quint, Marcel ^c,d   Gray, William M ^c   Dharmasiri, Nihal ^a  

^a Texas State University   (United States)

^b UNIVERSITY OF OKLAHOMA   (United States)

^c UNIVERSITY OF MINNESOTA   (United States)

^d LEIBNIZ INSTITUTE OF PLANT BIOCHEMISTRY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AUXIN; AUXIN BINDING PROTEIN 1; BINDING PROTEIN; DUAL SPECIFICITY PHOSPHATASE; ISOENZYME; MESSENGER RNA PRECURSOR; STEM CELL FACTOR; UNCLASSIFIED DRUG; ARABIDOPSIS PROTEIN; IBR5 PROTEIN, ARABIDOPSIS; ISOPROTEIN;

ALLELE; ALTERNATIVE RNA SPLICING; ARABIDOPSIS; ARTICLE; CATALYSIS; CONTROLLED STUDY; ENZYME ACTIVE SITE; ENZYME ACTIVITY; GENE EXPRESSION; GENE FUNCTION; IBR5 GENE; INDOLE 3 BUTYRIC ACID RESPONSE5 GENE; MUTANT; NONHUMAN; PHENOTYPE; PLANT GENE; PLANT HEIGHT; PLANT RESPONSE; PROTEIN DEGRADATION; PROTEIN FUNCTION; RNA SPLICING; ROOT DEVELOPMENT; ROOT GROWTH; SIGNAL TRANSDUCTION; VASCULAR BUNDLE (PLANT); GENETICS; METABOLISM; PHYSIOLOGY;

ALLELES; ALTERNATIVE SPLICING; ARABIDOPSIS PROTEINS; DUAL-SPECIFICITY PHOSPHATASES; PROTEIN ISOFORMS; SIGNAL TRANSDUCTION;

EID: 84929046351     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0102301     Document Type: Article

References (45)

1. Dharmasiri N, Dharmasiri S, Weijers D, Lechner E, Yamada M, et al. (2005b) Plant development is regulated by a family of auxin receptor F-box proteins. Development Cell 9: 109-119. (Pubitemid 40903664)
2. Gray WM, Kepinski S, Rouse D, Leyser O, Estelle M (2001) Auxin regulatesSCFTIR1-Dependent degradation of Aux/IAA proteins. Nature 414: 271-276.
3. Dharmasiri N, Dharmasiri S, Estelle M (2005a) The F-box protein TIR1 is anauxin receptor. Nature 435(7041): 441-445. (Pubitemid 40734235)
4. Caderon-Villalobos A, Lee S, De Oliveira C, Ivetac A, Brandt W, et al. (2012) Acombinatorial TIR1/AFB-Aux/IAA co-receptor system for differential sensingof auxin. Nat Chem Biol 8: 477-485.
5. Quint M, Ito H, Zhang W, Gray WM (2005) Characterization of a noveltemperature-sensitive allele of the CUL1/AXR6 subunit of SCF ubiquitinligases. Plant Journal 43: 371-383. (Pubitemid 41577005)
6. Monroe-Augustus M, Zolman B, Bartel B (2003) A dual-specificity phosphataselikeprotein modulating auxin and abscisic acid responsiveness in Arabidopsis. Plant Cell 15: 2979-2991. (Pubitemid 37546265)
7. Strader LC, Monroe-Augustus M, Bartel B (2008a) The IBR5 phosphatasepromotes Arabidopsis auxin responses through a novel mechanism distinct fromTIR1-mediated repressor degradation. BMC Plant Biology 8: 41.
8. Tromas A, Paque S, Stierlé V, Quettier AL, Muller P, et al. (2013) Auxin-Binding Protein 1 is a negative regulator of the SCFTIR1/AFB pathway. Naturecommunications 4: doi:10.1038/ncomms3496.
9. Lee JS, Wang S, Sritubtim S, Chen J, Ellis B (2009) Arabidopsis mitogenactivatedprotein kinase MPK12 interacts with the MAPK phosphatase IBR5and regulates auxin signaling. The Plant Journal 57(6): 975-985.
10. Ichimura K, Shinozaki K, Tena G, Sheen J, Henry Y, et al. (2002) Mitogen-activatedprotein kinase cascades in plants: a new nomenclature. Trends in plantscience 7(7): 301-308. (Pubitemid 36726514)
11. Staiger D, Brown JW (2013) Alternative splicing at the intersection of biologicaltiming, development, and stress responses. The Plant Cell Online 25(10): 3640-3656.
12. Qin F, Shinozaki K, Yamaguchi-Shinozaki K (2011) Achievements andChallenges in Understanding Plant Abiotic Stress Responses and Tolerance. Plant and Cell Physiology 52: 1569-1582.
13. Jammes F, Song C, Shin D, Munemasa S, Takeda K, et al. (2009) MAP kinasesMPK9 and MPK12 are preferentially expressed in guard cells and positivelyregulate ROS-mediated ABA signaling. Proc Natl Acad Sci USA 106(48):20520-20525.
14. Jammes F, Yang X, Xiao S, Kwak J (2011) Two Arabidopsis guard cell-preferentialMAPK genes, MPK9 and MPK12, function in biotic stressresponse. Plant Signal Behav 6(11): 1875-1877.
15. Li Y, Feng D, Zhang D, Su J, Zhang Y, et al. (2012) Rice MAPK phosphataseIBR5 negatively regulates drought stress tolerance in transgenic Nicotianatabacum. Plant Science 188: 10-16.
16. Gray WM, Muskett PR, Chuang HW, Parker JE (2003) Arabidopsis SGT1b isrequired for SCFTIR1-mediated auxin response. The Plant Cell Online 15(6):1310-1319.
17. Chuang HW, Zhang W, Gray WM (2004) Arabidopsis ETA2, an apparentortholog of the human cullin-interacting protein CAND1, is required for auxinresponses mediated by the SCFTIR1 ubiquitin ligase. The Plant Cell Online16(7): 1883-1897. (Pubitemid 38908782)
18. Brunoud G, Wells DM, Oliva M, Larrieu A, Mirabet V, et al. (2012) A novelsensor to map auxin response and distribution at high spatio- temporalresolution. Nature 482(7383): 103-106.
19. Xu T, Wen M, Nagawa S, Fu Y, Chen JG, et al. (2010) Cell Surface-and RhoGTPase-Based Auxin Signaling Controls Cellular Interdigitation in Arabidopsis. Cell 143(1): 99-110.
20. Huang GT, Ma SL, Bai LP, Zhang L, Ma H, et al. (2012) Signal transductionduring cold, salt, and drought stresses in plants. Molecular biology reports 39(2):969-987.
21. Camps M, Nichols A, Arkinstall S (2000) Dual specificity phosphatases: A genefamily for control of MAP kinase function. FASEB J 14: 6-16. (Pubitemid 30051518)
22. Filichkin SA, Priest HD, Givan SA, Shen R, Bryant DW, et al. (2010) Genomewidemapping of alternative splicing in Arabidopsis thaliana. Genome research20(1): 45-58.
23. Marquez Y, Brown JW, Simpson C, Barta A, Kalyna M (2012) Transcriptomesurvey reveals increased complexity of the alternative splicing landscape inArabidopsis. Genome research 22(6): 1184-1195.
24. Filichkin SA, Mockler TC (2012) Unproductive alternative splicing andnonsense mRNAs: a widespread phenomenon among plant circadian clockgenes. Biology direct 7(1): 20.
25. Li W, Lin WD, Ray P, Lan P, Schmidt W (2013) Genome-Wide Detection ofCondition-Sensitive Alternative Splicing in Arabidopsis Roots. Plant physiology:doi:10.1104/pp. 113.217778.
26. Streitner C, Simpson C, Shaw P, Danisman S, Brown J, et al. (2013) Smallchanges in ambient temperature affects alternative splicing in Arabidopsisthaliana. Plant signaling & behavior 8(7): e24638.
27. Yan K, Liu P, Wu CA, Yang GD, Xu R, et al. (2012) Stress-Induced AlternativeSplicing Provides a Mechanism for the Regulation of MicroRNA Processing inArabidopsis thaliana . Molecular cell 48(4): 521-531.
28. Tang F, Yang S, Gao M, Zhu H (2013) Alternative splicing is required forRCT1-mediated disease resistance in Medicago truncatula. Plant molecularbiology 1: 8.
29. Kriechbaumer V, Wang P, Hawes C, Abell BM (2012) Alternative splicing of theauxin biosynthesis gene YUCCA4 determines its subcellular compartmentation. The Plant Journal 70(2): 292-302.
30. Remy E, Cabrito TR, Baster P, Batista RA, Teixeira MC, et al. (2013) A majorfacilitator superfamily transporter plays a dual role in polar auxin transport anddrought stress tolerance in Arabidopsis. The Plant Cell Online 25(3): 901-926.
31. Freeman J, Li A, Wei G, Li H, Kertesz N, Lesche R, et al. (2003) PTEN tumorsuppressor regulates p53 protein levels and activity through phosphatase-dependentand -independent mechanisms. Cancer cell 02: 03.
32. Cho H, Kim T, Mancebo H, Lane W, Flores O, et al. (1999) A proteinphosphatase functions to recycle RNA polymerase II. Genes & Development 13:1540-1552. (Pubitemid 29297922)
33. Strader LC, Monroe-Augustus M, Rogers K, Lin G, Bartel B (2008b)Arabidopsis IBA responce5 (ibr5) suppressors separate responses to varioushormones. Genetics 180(4): 2019-2032.
34. Parry G, Villalobos AC, Prigge M, Peret B, Dharmasiri S, et al. (2009) Complexregulation of the TIR1/AFB family of auxin receptors. Proc Natl Acad Sci USA706: 22540-22545.
35. Ulm R, Ichimura K, Mizoguchi T, Peck SC, Zhu T, et al. (2002) Distinctregulation of salinity and genotoxic stress responses by Arabidopsis MAP kinasephosphatase 1. EMBO J 21: 6483-6493. (Pubitemid 35448426)
36. Lee JS, Ellis BE (2007) Arabidopsis MAPK phosphatase 2 (MKP2) positivelyregulates oxidativestress tolerance and inactivates the MPK3 and MPK6MAPKs, J Biol Chem 282: 25020-25029.
37. Lee SC, Luan S (2012) ABA signal transduction at the crossroad of biotic andabiotic stress responses. Plant, Cell & Environment 35(1): 53-60.
38. Vanderauwera S, Zimmermann P, Rombauts S, Vandenabeele S, LangerbartelsC, et al. (2005) Genome-Wide Analysis of Hydrogen Peroxide-Regulated geneExpression in Arabidopsis Reveals a High Light-Induced TranscriptionalCluster Involved in Anthocyanin Biosynthesis. Plant Physiology 139: 806-821. (Pubitemid 43907108)
39. Tromas A, Braun N, Muller P, Khodus T, Paponov IA, et al. (2009) TheAUXIN BINDING PROTEIN 1 is required for differential auxin responsesmediating root growth. PLoS One 4(9): e6648.
40. Dharmasiri N, Dharmasiri S, Jones AM, Estelle M (2003) Auxin action in a cell-freesystem. Current Biology 13: 1418-1422.
41. Oono Y, Chen QG, Overvoorde PJ, Köhler C, Theologis A (1998) age mutants of Arabidopsis exhibit altered auxin-regulated gene expression. The Plant CellOnline 10(10): 1649-1662. (Pubitemid 28542136)
42. Bendahmane A, Querci M, Kanyuka K, Baulcombe DC (2000) Agrobacteriumtransient expression system as a tool for the isolation of disease resistance genes:application to the Rx2 locus in potato. The Plant Journal 21(1): 73-81. (Pubitemid 30115699)
43. Lincoln C, Britton J, Estelle M (1990) Growth and Development of the axrlMutants of Arabidopsis. The Plant Cell 2: 1071-1080.
44. Rasband WS (1997) ImageJ, US National Institutes of Health, Bethesda, Maryland, USA.
45. Jefferson A (1987) Assaying chimeric genes in plants: The GUS gene fusionsystem. Plant Molecular Biology Reporter 5(4): 387-405.