Genome-wide identification and analysis of the SBP-box family genes in apple (Malus×domestica Borkh.)

Plant Physiology and Biochemistry

Volumn 70, Issue , 2013, Pages 100-114

  Li, Jun ^a   Hou, Hongmin ^a   Li, Xiaoqin ^a   Xiang, Jiang ^a   Yin, Xiangjing ^a   Gao, Hua ^a   Zheng, Yi ^b   Bassett, Carole L ^c   Wang, Xiping ^a  

^a NORTHWEST A F UNIVERSITY   (China)

^b Boyce Thompson Institute for Plant Research   (United States)

^c AGRICULTURAL RESEARCH SERVICE   (United States)

Author keywords

Apple; Gene expression; Hormone response; MdmiR156; Phylogeny; SBP box gene; Synteny

Indexed keywords

ABSCISIC ACID; ETHYLENE; GIBBERELLIN; JASMONIC ACID METHYL ESTER; MICRORNA; PHYTOHORMONE; SALICYLIC ACID; TRANSCRIPTION FACTOR; VEGETABLE PROTEIN;

AA; ABA; AMINO ACID(S); APPLE; ARABIDOPSIS; ARTICLE; ETH; GA; GENE DUPLICATION; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; HORMONE RESPONSE; MALUS; MDMIR156; MEJA; METABOLISM; MOLECULAR EVOLUTION; MULTIGENE FAMILY; NLS; NUCLEAR LOCALIZATION SIGNAL; PHYLOGENY; PHYSIOLOGICAL STRESS; PLANT CHROMOSOME; PLANT DEVELOPMENT; PLANT GENE; PLANT GENOME; PLANT STRUCTURES; SA; SBP; SBP-BOX GENE; SIGNAL TRANSDUCTION; SPL; SQUAMOSA PROMOTER BINDING PROTEIN; SQUAMOSA PROMOTER BINDING PROTEIN-LIKE; SYNTENY;

AA; ABA; ABSCISIC ACID; AMINO ACID(S); APPLE; ETH; ETHYLENE; GA; GENE EXPRESSION; GIBBERELLIN; HORMONE RESPONSE; MDMIR156; MEJA; METHYL JASMONATE; MICRORNA; MIRNA; NLS; NUCLEAR LOCALIZATION SIGNAL; PHYLOGENY; SA; SALICYLIC ACID; SBP; SBP-BOX GENE; SPL; SQUAMOSA PROMOTER BINDING PROTEIN; SQUAMOSA PROMOTER BINDING PROTEIN-LIKE; SYNTENY;

ARABIDOPSIS; CHROMOSOMES, PLANT; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; GENOME, PLANT; MALUS; MULTIGENE FAMILY; PHYLOGENY; PLANT DEVELOPMENT; PLANT GROWTH REGULATORS; PLANT PROTEINS; PLANT STRUCTURES; SIGNAL TRANSDUCTION; STRESS, PHYSIOLOGICAL; SYNTENY; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

ARABIDOPSIS; MALUS X DOMESTICA;

EID: 84879437970     PISSN: 09819428     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.plaphy.2013.05.021     Document Type: Article

References (46)

1. Klein J., Saedler H., Huijser P. Anew family of DNA binding proteins includes putative transcriptional regulators of the Antirrhinum majus floral meristem identity gene SQUAMOSA. Mol. Gen. Genet. 1996, 250:7-16.
2. Cardon G., Höhmann S., Klein J., Nettesheim K., Saedler H., Huijser P. Molecular characterization of the Arabidopsis SBP-box genes. Gene 1999, 237:91-104.
3. Xie K., Wu C., Xiong L. Genomic organization, differential expression, and interaction of SQUAMOSA promoter-binding-like transcription factors and microRNA156 in rice. Plant Physiol. 2006, 142:280-293.
4. Birkenbihl R.P., Jach G., Saedler H., Huijser P. Functional dissection of the plant-specific SBP-domain: overlap of the DNA-binding and nuclear localization domains. J.Mol. Biol. 2005, 352:585-596.
5. Guo A.Y., Zhu Q.H., Gu X., Ge S., Yang J., Luo J. Genome-wide identification and evolutionary analysis of the plant specific SBP-box transcription factor family. Gene 2008, 418:1-8.
6. Lännenpää M., Jänönen I., Holtta-Vuori M., Gardemeister M., Porali I., Sopanen T. Anew SBP-box gene BpSPL1 in silver birch (Betula pendula). Physiol. Plant. 2004, 120:491-500.
7. Kropat J., Tottey S., Birkenbihl R.P., Depege N., Huijser P., Merchant S. Aregulator of nutritional copper signaling in Chlamydomonas is an SBP domain protein that recognizes the GTAC core of copper response element. Proc. Natl. Acad. Sci. U. S. A. 2005, 102:18730-18735.
8. Riese M., Höhmann S., Saedler H., Münster T., Huijser P. Comparative analysis of the SBP-box gene families in P.patens and seed plants. Gene 2007, 401:28-37.
9. Chuck G., Whipple C., Jackson D., Hake S. The maize SBP-box transcription factor encoded by tasselsheath4 regulates bract development and the establishment of meristem boundaries. Development 2010, 137:1243-1250.
10. Lu S., Yang C., Chiang V.L. Conservation and diversity of microRNA-associated copper-regulatory networks in Populus trichocarpa. J.Integr. Plant Biol. 2011, 53:879-891.
11. Salinas M., Xing S., Höhmann S., Berndtgen R., Huijser P. Genomic organization, phylogenetic comparison and differential expression of the SBP-box family of transcription factors in tomato. Planta 2011, 235:1171-1184.
12. Cardon G.H., Höhmann S., Nettesheim K., Saedler H., Huijser P. Functional analysis of the Arabidopsis thaliana SBP-box gene SPL3: a novel gene involved in the floral transition. Plant J. 1997, 12:367-377.
13. Unte U.S., Sorensen A.M., Pesaresi P., Gandikota M., Leister D., Saedler H., Huijser P. SPL8, an SBP-box gene that affects pollen sac development in Arabidopsis. Plant Cell 2003, 15:1009-1019.
14. Wu G., Poethig R.S. Temporal regulation of shoot development in Arabidopsis thaliana by miR156 and its target SPL3. Development 2006, 133:3539-3547.
15. Schwarz S., Grande A.V., Bujdoso N., Saedler H., Huijser P. The microRNA regulated SBP-box genes SPL9 and SPL15 control shoot maturation in Arabidopsis. Plant Mol. Biol. 2008, 67:183-195.
16. Gandikota M., Birkenbihl R.P., Höhmann S., Cardon G.H., Saedler H., Huijser P. The miRNA156/157 recognition element in the 3'UTR of the Arabidopsis SBP box gene SPL3 prevents early flowering by translational inhibition in seedlings. Plant J. 2007, 49:683-693.
17. Wang J.W., Schwab R., Czech B., Mica E., Weigel D. Dual effects of miR156-targeted SPL genes and CYP78A5/KLUH on plastochron length and organ size in Arabidopsis thaliana. Plant Cell 2008, 20:1231-1243.
18. Jung J.H., Seo P.J., Kang S.K., Park C.M. miR172 signals are incorporated into the miR156 signaling pathway at the SPL3/4/5 genes in Arabidopsis developmental transitions. Plant Mol. Biol. 2011, 76:35-45.
19. 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.
20. Zhang Y., Schwarz S., Saedler H., Huijser P. SPL8, a local regulator in a subset of gibberellin-mediated developmental processes in Arabidopsis. Plant Mol. Biol. 2007, 63:429-439.
21. Yamasaki H., Hayashi M., Fukazawa M., Kobayashi Y., Shikanai T. SQUAMOSA promoter binding protein-like7 is a central regulator for copper homeostasis in Arabidopsis. Plant Cell 2009, 21:347-361.
22. Miura K., Ikeda M., Matsubara A., Song X.J., Ito M., Asano K., Matsuoka M., Kitano H., Ashikari M. OsSPL14 promotes panicle branching and higher grain productivity in rice. Nat. Genet. 2010, 42:545-549.
23. Wang S., Wu K., Yuan Q., Liu X., Liu Z., Lin X., Zeng R., Zhu H., Dong G., Qian Q., Zhang G., Fu X. Control of grain size, shape and quality by OsSPL16 in rice. Nat. Genet. 2012, 44:950-954.
24. Manning K., Tör M., Poole M., Hong Y.G., Thompson A.J., King G.J., Giovannoni J.J., Seymour G.B. Anaturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nat. Genet. 2006, 38:948-952.
25. Preston J.C., Hileman L.C. SQUAMOSA-promoter binding PROTEIN 1 initiates flowering in Antirrhinum majus through the activation of meristem identity genes. Plant J. 2010, 62:704-712.
26. Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., Kalyanaraman A., Fontana P., Bhatnagar S.K., Troggio M., Pruss D., Salvi S., Pindo M., Baldi P., Castelletti S., Cavaiuolo M., Coppola G., Costa F., Cova V., DalRi A., Goremykin V., Komjanc M., Longhi S., Magnago P., Malacarne G., Malnoy M., Micheletti D., Moretto M., Perazzolli M., Si-Ammour A., Vezzulli S., Zini E., Eldredge G., Fitzgerald L.M., Gutin N., Lanchbury J., Macalma T., Mitchell J.T., Reid J., Wardell B., Kodira C., Chen Z., Desany B., Niazi F., Palmer M., Koepke T., Jiwan D., Schaeffer S., Krishnan V., Wu C., Chu V.T., King S.T., Vick J., Tao Q., Mraz A., Stormo A., Stormo K., Bogden R., Ederle D., Stella A., Vecchietti A., Kater M.M., Masiero S., Lasserre P., Lespinasse Y., Allan A.C., Bus V., Chagne D., Crowhurst R.N., Gleave A.P., Lavezzo E., Fawcett J.A., Proost S., Rouze P., Sterck L., Toppo S., Lazzari B., Hellens R.P., Durel C.E., Gutin A., Bumgarner R.E., Gardiner S.E., Skolnick M., Egholm M., VandePeer Y., Salamini F., Viola R. The genome of the domesticated apple (Malus×domestica Borkh.). Nat. Genet. 2010, 42:833-839.
27. Yang Z., Wang X., Gu S., Hu Z., Xu H., Xu C. Comparative study of SBP-box gene family in Arabidopsis and rice. Gene 2008, 407:1-11.
28. Yu H., Song C., Jia Q., Wang C., Li F., Nicholas K.K., Zhang X., Fang J. Computational identification of microRNAs in apple expressed sequence tags and validation of their precise sequences by miR-RACE. Physiol. Plant. 2011, 141:56-70.
29. Xu G., Guo C., Shan H., Kong H. Divergence of duplicate genes in exon-intron structure. Proc. Natl. Acad. Sci. U. S. A. 2012, 109:1187-1192.
30. Bowers J.E., Chapman B.A., Rong J., Paterson A.H. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 2003, 422:433-438.
31. Blanc G., Wolfe K.H. Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 2004, 16:1667-1678.
32. Paterson A., Bowers J., Chapman B. Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc. Natl. Acad. Sci. U. S. A. 2004, 101:9903-9908.
33. Wang X., Shi X., Hao B., Ge S., Luo J. Duplication and DNA segmental loss in the rice genome: implications for diploidization. New Phytol. 2005, 165:937-946.
34. Lyons E., Pedersen B., Kane J., Alam M., Ming R., Tang H., Wang X., Bowers J., Paterson A., Lisch D., Freeling M. Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids. Plant Physiol. 2008, 148:1772-1781.
35. Shikata M., Koyama T., Mitsuda N., Ohme-Takagi M. Arabidopsis SBP-box genes SPL10, SPL11 and SPL2 control morphological change in association with shoot maturation in the reproductive phase. Plant Cell Physiol. 2009, 50:2133-2145.
36. Wang J.W., Czech B., Weigel D. miR156-regulated SPL transcription factors define an endogenous flowering pathway in Arabidopsis thaliana. Cell 2009, 138:738-749.
37. Gou J.Y., Felippes F.F., Liu C.J., Weigel D., Wang J. Negative regulation of anthocyanin biosynthesis in Arabidopsis by a miR156-targeted SPL transcription factor. Plant Cell 2011, 23:1512-1522.
38. Martin R.C., Asahina M., Liu P.-P., Kristof J.R., Coppersmith J.L., Pluskota W.E., Bassel G.W., Goloviznina N.A., Nguyen T.T., Martínez-Andújar C., Arun Kumar M.B., Pupel P., Nonogaki H. The regulation of post-germinative transition from the cotyledon- to vegetative-leaf stages by microRNA-targeted SQUAMOSA promoter-binding protein LIKE13 in Arabidopsis. Seed Sci. Res. 2010, 20:89-96.
39. Stone J.M., Liang X., Nekl E.R., Stiers J.J. Arabidopsis AtSPL14, a plant-specific SBP-domain transcription factor, participates in plant development and sensitivity to fumonisin B1. Plant J. 2005, 41:744-754.
40. Wang H., Nussbaum-Wagler T., Li B., Zhao Q., Vigouroux Y., Faller M., Bomblies K., Lukens L., Doebley J.F. The origin of the naked grains of maize. Nature 2005, 436:714-719.
41. Zhang X., Zou Z., Zhang J., Zhang Y., Han Q., Hua 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 Lett. 2010, 585:435-439.
42. Wang Y., Hu Z., Yang Y., Chen X., Chen G. Function annotation of an SBP-box gene in Arabidopsis based on analysis of co-expression networks and promoters. Int. J. Mol. Sci. 2009, 10:116-132.
43. Glazebrook J. Contrasting mechanisms of defense against biotrophic and necrotrophic pathogens. Annu. Rev. Phytopathol. 2005, 43:205-227.
44. Mauch-Mani B., Mauch F. The role of abscisic acid in plant-pathogen interactions. Curr. Opin. Plant Biol. 2005, 8:409-414.
45. Davies W.J., Jones H.G. Abscisic Acid Physiology and Biochemistry 1991, BIOS Scientific Publishers.
46. Tamura K., Dudley J., Nei M., Kumar S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version4.0. Mol. Biol. Evol. 2007, 24:1596-1599.