SlmiR393 controls the auxin receptor homologous genes expression, and regulates sensitivity to auxin in tomato root growth

Scientia Horticulturae

Volumn 162, Issue , 2013, Pages 90-99

  Lin, Dongbo ^a   Yang, Yingwu ^a   Khalil, Rasha ^a   Xian, Zhiqiang ^a   Hu, Guojian ^a   Li, Zhengguo ^a  

^a CHONGQING UNIVERSITY   (China)

Author keywords

Auxin receptor homologue; Auxin sensitivity; SlmiR393; Tomato

Indexed keywords

BIOLOGICAL DEVELOPMENT; ENVIRONMENTAL RESPONSE; GENE EXPRESSION; GROWTH RATE; HORMONE; PLANT COMMUNITY; RNA; ROOT SYSTEM; SIGNALING; VEGETABLE;

EID: 84883272367     PISSN: 03044238     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.scienta.2013.07.028     Document Type: Article

References (48)

1. Addo-Quaye C., Eshoo T.W., Bartel D.P., Axtell M.J. Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Current Biology 2008, 18:758-762.
2. Alvarez J.P., Pekker I., Goldshmidt A., Blum E., Amsellem Z., Eshed Y. Endogenous and synthetic microRNAs stimulate simultaneous, efficient, and localized regulation of multiple targets in diverse species. Plant Cell 2006, 18:1134-1151.
3. Audran-Delalande C., Bassa C., Mila I., Regad F., Zouine M., Bouzayen M. Genome-wide identification, functional analysis and expression profiling of the Aux/IAA gene family in tomato. Plant and Cell Physiology 2012, 53:659-672.
4. Bartel D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004, 116:281-297.
5. Ben-Gera H., Shwartz I., Shao M.R., Shani E., Estelle M., Ori N. ENTIRE and GOBLET promote leaflet development in tomato by modulating auxin response. Plant Journal 2012, 70:903-915.
6. Bian H., Xie Y., Guo F., Han N., Ma S., Zeng Z., Wang J., Yang Y., Zhu M. Distinctive expression patterns and roles of the miRNA393/TIR1 homolog module in regulating flag leaf inclination and primary and crown root growth in rice (Oryza sativa). New Phytologist 2012, 196:149-161.
7. Chaabouni S., Jones B., Delalande C., Wang H., Li Z., Mila I., Frasse P., Latche A., Pech J.C., Bouzayen M. Sl-IAA3, a tomato Aux/IAA at the crossroads of auxin and ethylene signalling involved in differential growth. Journal of Experimental Botany 2009, 60:1349-1362.
8. Chapman E.J., Estelle M. Mechanism of auxin-regulated gene expression in plants. Annual Review of Genetics 2009, 43:265-285.
9. Chen C., Ridzon D.A., Broomer A.J., Zhou Z., Lee D.H., Nguyen J.T., Barbisin M., Xu N.L., Mahuvakar V.R., Andersen M.R., Lao K.Q., Livak K.J., Guegler K.J. Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Research 2005, 33:e179.
10. Chen H., Li Z., Xiong L. A plant microRNA regulates the adaptation of roots to drought stress. FEBS Letters 2012, 586:1742-1747.
11. Chen Z.H., Bao M.L., Sun Y.Z., Yang Y.J., Xu X.H., Wang J.H., Han N., Bian H.W., Zhu M.Y. Regulation of auxin response by miR393-targeted transport inhibitor response protein 1 is involved in normal development in Arabidopsis. Plant Molecular Biology 2011, 77:619-629.
12. Dharmasiri N., Dharmasiri S., Estelle M. The F-box protein TIR1 is an auxin receptor. Nature 2005, 435:441-445.
13. Dharmasiri N., Dharmasiri S., Weijers D., Lechner E., Yamada M., Hobbie L., Ehrismann J.S., Jurgens G., Estelle M. Plant development is regulated by a family of auxin receptor F box proteins. Developmental Cell 2005, 9:109-119.
14. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985, 39:783-791.
15. Feng J., Lai L., Lin R., Jin C., Chen J. Differential effects of Cucumber mosaic virus satellite RNAs in the perturbation of microRNA-regulated gene expression in tomato. Molecular Biology Reports 2012, 39:775-784.
16. Greenham K., Santner A., Castillejo C., Mooney S., Sairanen I., Ljung K., Estelle M. The AFB4 auxin receptor is a negative regulator of auxin signaling in seedlings. Current Biology 2011, 21:520-525.
17. Guo H.S., Xie Q., Fei J.F., Chua N.H. MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for arabidopsis lateral root development. Plant Cell 2005, 17:1376-1386.
18. Hagen G., Guilfoyle T. Auxin-responsive gene expression: genes, promoters and regulatory factors. Plant Molecular Biology 2002, 49:373-385.
19. Hayashi K. The interaction and integration of auxin signaling components. Plant and Cell Physiology 2012, 53:965-975.
20. Itaya A., Bundschuh R., Archual A.J., Joung J.-G., Fei Z., Dai X., Zhao P.X., Tang Y., Nelson R.S., Ding B. Small RNAs in tomato fruit and leaf development. Biochimica et Biophysica Acta 2008, 1779:99-107.
21. Jones B., Frasse P., Olmos E., Zegzouti H., Li Z.G., Latché A., Pech J.C., Bouzayen M. Down-regulation of DR12, an auxin-response-factor homolog, in the tomato results in a pleiotropic phenotype including dark green and blotchy ripening fruit. Plant Journal 2002, 32:603-613.
22. Jones-Rhoades M.W., Bartel D.P., Bartel B. MicroRNAs and their regulatory roles in plants. Annual Review of Plant Biology 2006, 57:19-53.
23. Kidner C.A., Martienssen R.A. The developmental role of microRNA in plants. Current Opinion in Plant Biology 2005, 8:38-44.
24. Letunic I., Doerks T., Bork P. SMART 6: recent updates and new developments. Nucleic Acids Research 2009, 37:D229-D232.
25. -δδCTmethod. Methods 2001, 25:402-408.
26. Mockaitis K., Estelle M. Auxin receptors and plant development: a new signaling paradigm. Annual Review of Cell and Developmental Biology 2008, 24:55-80.
27. Moxon S., Jing R., Szittya G., Schwach F., Pilcher R.L.R., Moulton V., Dalmay T. Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening. Genome Research 2008, 18:1602-1609.
28. Nagpal P., Walker L.M., Young J.C., Sonawala A., Timpte C., Estelle M., Reed J.W. AXR2 encodes a member of the Aux/IAA protein family. Plant Physiology 2000, 123:563-574.
29. Navarro L., Dunoyer P., Jay F., Arnold B., Dharmasiri N., Estelle M., Voinnet O., Jones J.D. A plant miRNA contributes to antibacterial resistance by repressing auxin signaling. Science 2006, 312:436.
30. Ouellet F., Overvoorde P.J., Theologis A. IAA17/AXR3: biochemical insight into an auxin mutant phenotype. Plant Cell 2001, 13:829-841.
31. Parry G., Calderon-Villalobos L.I., Prigge M., Peret B., Dharmasiri S., Itoh H., Lechner E., Gray W.M., Bennett M., Estelle M. Complex regulation of the TIR1/AFB family of auxin receptors. Proceedings of the National Academy of Sciences of the United States of America 2009, 106:22540-22545.
32. Pilcher R.L.R., Moxon S., Pakseresht N., Moulton V., Manning K., Seymour G., Dalmay T. Identification of novel small RNAs in tomato (Solanum lycopersicum). Planta 2007, 226:709-717.
33. Ren Z., Li Z., Miao Q., Yang Y., Deng W., Hao Y. The auxin receptor homologue in Solanum lycopersicum stimulates tomato fruit set and leaf morphogenesis. Journal of Experimental Botany 2011, 62:2815-2826.
34. Rubio-Somoza I., Cuperus J.T., Weigel D., Carrington J.C. Regulation and functional specialization of small RNA-target nodes during plant development. Current Opinion in Plant Biology 2009, 12:622-627.
35. Santner A., Estelle M. Recent advances and emerging trends in plant hormone signalling. Nature 2009, 459:1071-1078.
36. Si-Ammour A., Windels D., Arn-Bouldoires E., Kutter C., Ailhas J., Meins F., Vazquez F. miR393 and secondary siRNAs regulate expression of the TIR1/AFB2 auxin receptor clade and auxin-related development of Arabidopsis leaves. Plant Physiology 2011, 157:683-691.
37. Sunkar R., Kapoor A., Zhu J.K. Posttranscriptional induction of two Cu/Zn superoxide dismutase genes in Arabidopsis is mediated by downregulation of miR398 and important for oxidative stress tolerance. Plant Cell 2006, 18:2051-2065.
38. Sunkar R., Zhu J.K. Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 2004, 16:2001-2019.
39. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 2011, 28:2731-2739.
40. Tan X., Calderon-Villalobos L.I.A., Sharon M., Zheng C., Robinson C.V., Estelle M., Zheng N. Mechanism of auxin perception by the TIR1 ubiquitin ligase. Nature 2007, 446:640-645.
41. Vanneste S., De Rybel B., Beemster G.T., Ljung K., De Smet I., Van Isterdael G., Naudts M., Iida R., Gruissem W., Tasaka M. Cell cycle progression in the pericycle is not sufficient for SOLITARY ROOT/IAA14-mediated lateral root initiation in Arabidopsis thaliana. Plant Cell 2005, 17:3035-3050.
42. Vidal E.A., Araus V., Lu C., Parry G., Green P.J., Coruzzi G.M., Gutierrez R.A. Nitrate-responsive miR393/AFB3 regulatory module controls root system architecture in Arabidopsis thaliana. Proceedings of the National Academy of Sciences of the United States of America 2010, 107:4477-4482.
43. Wang H., Jones B., Li Z., Frasse P., Delalande C., Regad F., Chaabouni S., Latche A., Pech J.C., Bouzayen M. The tomato Aux/IAA transcription factor IAA9 is involved in fruit development and leaf morphogenesis. Plant Cell 2005, 17:2676-2692.
44. 2+-ATPase and triggers the formation of phased small interfering RNAs in tomato reproductive growth. Plant Cell 2011, 23:3185-3203.
45. Xia K., Wang R., Ou X., Fang Z., Tian C., Duan J., Wang Y., Zhang M. OsTIR1 and OsAFB2 downregulation via OsmiR393 overexpression leads to more tillers, early flowering and less tolerance to salt and drought in rice. PLoS ONE 2012, 7:e30039.
46. Xing S., Salinas M., Höhmann S., Berndtgen R., Huijser P. miR156-targeted and nontargeted SBP-box transcription factors act in concert to secure male fertility in Arabidopsis. Plant Cell 2010, 22:3935-3950.
47. Zhang B., Pan X., Cobb G.P., Anderson T.A. Plant microRNA: a small regulatory molecule with big impact. Developmental Biology 2006, 289:3-16.
48. Zhang X., Zou Z., Zhang J., Zhang Y., Han Q., Hu T., Xu X., Liu H., Li H., Ye Z. Over-expression of sly-miR156a in tomato results in multiple vegetative and reproductive trait alterations and partial phenocopy of the sft mutant. FEBS Letters 2011, 585:435-439.