REVIEW PAPER
Alternative splicing in plant stress response
1
Institute of Bioorganic Chemistry, PAS, Poznań, Poland
Submission date: 2015-07-31
Acceptance date: 2016-03-07
Publication date: 2016-04-20
BioTechnologia 2016;97(1):9-17
KEYWORDS
TOPICS
ABSTRACT
Alternative splicing is a cellular process in which multiple mRNA transcripts are created from a single gene. Comparative studies of splicing on plant and animal systems have revealed differences between those two kingdoms in splice-site recognition, distribution of various splice types, and overall frequency of splicing events. Moreover, global analysis of plant genomes showed an impact of alternative splicing on crop domestication and trait selection. In recent years, new functions of this process in plant development and stress responses were described. From known examples of spliced transcripts emerges a complicated picture of mutual relationship of splicing process with various molecular machineries taking part in regulation of gene expression. For now, we know that splicing is coupled with nonsense-mediated mRNA decay and dependent on chromatin modification. It also influences miRNA pathway. This review summarizes the role of alternative spliced transcripts in expression of plant genetic information especially in response to biotic and abiotic stress conditions.
REFERENCES (49)
1.
Anderson P.A., Lawrence G.J., Morrish B.C., Ayliffe M.A., Finnegan E.J., Ellis J.G. (1997) Inactivation of the flax rust resistance gene M associated with loss of a repeated unit within the leucine-rich repeat coding region. Plant Cell 9: 641-651.
2.
Ayliffe M.A., Frost D.V., Finnegan E.J., Lawrence G.J., Anderson P.A., Ellis J.G. (1999) Analysis of alternative transcripts of the flax L6 rust resistance gene. Plant J. 17: 287-292.
3.
Barbazuk W.B., Yan F., McGinnis K.M. (2008) Genome-wide analyses of alternative splicing in plants: Opportunities and challenges. Genome Res. 18: 1381-1392.
4.
Bentem de la Fuente van S., Anrather D., Roitinger E., Djamei A., Hufnagl T., Barta A. et al. (2006) Phosphoproteomics reveals extensive in vivo phosphorylation of Arabidopsis proteins involved in RNA metabolism. Nucleic Acids Res. 34: 3267-3278.
5.
Boothby T.C., Ziper R., van der Weele C.M., Wolniak S.M. (2013) Removal of retained introns regulates translation in the rapidly developing gametophyte of Mersilea vestia. Dev. Cell 5: 517-529.
6.
Braunschweig U., Gueroussov S., Plocik A.M., Graveley B.R., Blencowe B.J. (2013) Dynamic integration of splicing within gene regulatory pathways. Cell 152: 1252-1269.
7.
Drechsel G., Kahles A., Keserwani A.K., Stauffer E., Behr J., Derewe P. et al. (2013) Nonsense-mediated decay of alternative precursor mRNA splicing variants is a major determinant of the Arabidopsis steady state transcriptome. Plant Cell 25: 3726-3742.
8.
Ellis J.D., Barrios-Rodiles M., Colak R., Irimia M., Kim T., Calarco J.A. et al. (2012) Tissue-specific alternative splicing remodels protein-protein interaction networks. Mol Cell. 6: 884-892.
9.
Fung R.W., Wang C.Y., Smith D.L., Gross K.C., Tao Y., Tian M. (2006) Characterization of alternative oxidase (AOX) gene expression in response to methyl salicylate and methyl jasmonate pre-treatment and low temperature in tomatoes. J. Plant Physiol. 163: 1049-1060.
10.
Gupta S., Wang B., Stryker G.A., Zanetti M.E., Lal S.K. (2005) Two novel arginine/serine (SR) proteins in maize are differentially spliced and utilize non – canonical splice sites. Biochim. Biophys. Acta 1728: 105-114.
11.
Iida K., Seki M., Sakurai T., Satou M., Akiyama K., Toyoda T., Konagaya A., Shinozaki K. (2004) Genome-wide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences. Nucleic Acids Res. 32: 5096-5103.
12.
Kalyna M., Simpson C.G., Syed N.H., Lewandowska D., Maraquez Y. et al. (2012) Alternative splicing and nonsensemediated decay modulate expression of important regulatory genes in Arabidopsis. Nucleic Acids Res. 6: 2454-2469.
13.
Kazan K. (2003) Alternative splicing and proteome diversity in plants: the tip of the iceberg has just emerged. Trends Plant Sci. 8: 468-471.
14.
Keren H., Lev-Maor G., Ast G. (2010) Alternative splicing and evolution: diversification, exon definition and function. Nat. Rev. Gen. 5: 345-355.
15.
Kervestin S., Jacobson A. (2012) NMD: A multifaceted response to premature translation termination. Nat. Rev. Mol. Cell Biol. 13: 700-712.
16.
Kim E., Goren A., Ast G. (2008) Alternative splicing: current perspectives. Bioessays 30: 38-47.
17.
Ko C.H., Brendel V., Taylor R.D., Walbot V. (1998) U-richness is a defining feature of plant introns and may function as an intron recognition signal in maize. Plant Mol. Biol. 36: 573-583.
18.
Kong J., Gong J.M., Zhang Z.G., Zhang J.S., Chen S.Y. (2003) A new AOX homologous gene OsIM1 from rice (Oryza sativa L.) with an alternative splicing mechanism under salt stress. Theor. Appl. Genet. 107: 326-331.
19.
Latijnhouwers M.J., Pairoba C.F., Brendel V., Walbot V., Carle-Urioste J.C. (1999) Test of the combinatorial model of intron recognition in a native maize gene. Plant Mol. Biol. 41: 637-644.
20.
Lazar G., Goodmann H.M. (2000) The Arabidopsis splicing factor SR1 is regulated by alternative splicing. Plant Mol. Biol. 42: 571-581.
21.
Lorkovic Z.J., Wieczorek Kirk D.A., Lambermon M.H.L., Filipowicz W. (2000) Pre-mRNA splicing in higher plants. Trends Plant Sci. 5: 160-167.
22.
Lund A.A., Rhoads D.M., Lund A.L., Cerny R.L., Elthon T.E. (2001) In vivo modifications of the maize mitochondrial small heat stress protein, HSP22. J. Biol. Chem. 276: 29924-29929.
23.
Marquez Y., Brown J.W.S., Simpson C., Barta A., Kalyna M. (2012) Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis. Genome Res. 22: 1184-1195.
24.
Marrs K.A., Wlabot V. (1997) Expression and RNA splicing of the maize glutathione S-transferase Bronze2 gene is regulated by Cadmium and other stresses. Plant Physiol. 113: 93-102.
25.
Merkin J., Russell C., Chen P., Burge C.B. (2012) Evolutionary dynamics of gene isoform regulation in Mammalian tissues. Science 338: 1593-1599.
26.
Morere-Le Paven M., Anzala F., Recton A., Limami A.M. (2007) Differential transcription initiation and alternative RNA splicing of Knox7 a class 2 homeobox gene of maize. Gene 401: 71-79.
27.
Palusa S.G., Ali G.S., Reddy A.S.N. (2007) Alternative splicing of pre-mRNA of Arabidopsis serine/arginine-rich proteins: regulation by hormones and stresses. Plant J. 49: 1091-1107.
28.
Palusa S.G., Reddy A.S.N. (2010) Extensive coupling of alternative splicing of pre-mRNA of serine/arginine (SR) genes with nonsense-mediated decay. New Phytol. 185: 83-89.
29.
Pan Q., Shai Q., Lee L.J., Frey B.J., Blencowe B.J. (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat. Genet. 40: 1413-1415.
30.
Parker J.E., Coleman M.J., Szabò V., Frost L.N., Schmidt R., van der Biezen E.A., Moores T., Dean C., Daniels M.J., Jones J.D. (1997) The Arabidopsis downy mildew resistance gene RPP5 shares similarity to the toll and interleukin- 1 receptors with N and L6. Plant Cell. 9: 876-894.
31.
Puhakainen T., Hess M.W., Makela P., Svensson J., Heino P., Palva E.T. (2004) Overexpression of multiple dehydrin genes enhances tolerance to freezing stress in Arabidopsis. Plant Mol. Biol. 54: 743-753. Quesada V., Macknight R., Dean C., Simpson G.G. (2003) Autoregulation of FCA pre-mRNA processing controls Arabidopsis flowering time. EMBO J. 22: 3142-3152.
32.
Reddy A.S.N. (2004) Plant serine /arginine – rich proteins and their role in pre – mRNA splicing. Trends Plant Sci. 9: 541-547.
33.
Reddy A.S.N. (2007) Alternative Splicing of Pre-Messenger RNAs in Plants in the Genomic Era. Annu. Rev. Plant Biol. 58: 267-294.
34.
Seo P.J., Park M.J., Park C.M. (2013) Alternative splicing of transcription factors in plant responses to low temperature stress: mechanisms and functions. Planta 6: 1415-1424.
35.
Severing E.I., van Djik A.D.J., Stiekema W., van Ham R.C.H.J. (2009) Comparative analysis indicates that alternative splicing in plants has a limited role in functional expansion of the proteome. BMC Genomics 10: 154.
36.
Severing E.I., van Dijk A.D., Morabito G., Busscher-Lange J., Immink R.G., can Ham R.C. (2012) Predicting the impact of alternative splicing on plant MADS domain protein function, PLoS One 7: e30524.
38.
Shi H., Xiong L., Stevenson B., Lu T., Zhu J.K. (2002) The Arabidopsis salt overly sensitive 4 mutants uncover a critical role for vitamin B6 in plant salt tolerance. Plant Cell 14: 575-588.
39.
Steiger D., Zecca L., Wieczorek Kirk D.A., Apel K., Eckstein L. (2003) The circadian clock regulated RNA-binding protein AtGRP7 autoregulates its expression by influencing alternative splicing of its own pre-mRNA. Plant J. 33: 361-371.
40.
Tipathy B.C., Oelmuller R. (2012) Reactive oxygen species generation and signaling in plants. Plant Signal Behav. 7: 1621-1633.
41.
Turner P.C., McLennan A.G., Bates A.D., White M.R.H. (2004) Krótkie wykłady. Biologia molekularna. Wyd. Nauk. PWN, Warszawa.
42.
Xiao H., Nassuth A. (2006) Stress- and development-induced expression of splicied and unspliced transcripts from two highly similar dehydrin 1 genes in V. riparia and V. vinifera. Plant Cell Rep. 25: 968-977.
43.
Xiong L., Yang L. (2003) Disease resistance and abiotic stress tolerance in rice are inversely modulated by an abscisic acid-inducible mitogen-activated protein kinase. Plant Cell 15: 745-759.
44.
Yan K., Liu P., Wu C.A., Yang G.D., Xu R., Guo Q.H., Huang J.G., Zheng C.C. (2012) Stress-induced alternative splicing provides a mechanism for the regulation of micro-RNA processing in Arabidopsis thaliana. Mol. Cell 48: 521-531.
45.
Yang G.D., Yan K., Wu B.J., Wang Y.H., Gao Y.X., Zheng C.C. (2012) Genomewide analysis of intronic microRNAs in rice and Arabidopsis. J. Genet. 91: 313-324.
46.
Yang S., Tang F., Zhu H. (2014) Alternative splicing in plant immunity. Int. J. Mol. Sci. 15: 10424-10445.
47.
Yang X., Zhang H., Li L. (2012) Alternative mRNA processing increases the complexity of microRNA-based gene regulation in Arabidopsis. Plant J. 70: 421-431.
48.
Yap K., Lin Z.Q., Khandelia P., Friedman B., Makeyev E. (2012) Coordinated regulation of neuronal mRNA steadystate levels through developmentally controller intron retention. Genes Dev. 11: 1209-1223.
49.
Zhiguo E., Wang L., Zhou J. (2013) Splicing and alternative splicing in rice and humans. BMB Rep. 46: 439-447.
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