Alternative splicing and protein diversity: plants versus animals

Journal article


Chaudhry, S., Khokhar, W., Jabre, I., Reddy, A., Byrne, L., Wilson, C. and Syed, N. 2019. Alternative splicing and protein diversity: plants versus animals. Frontiers in Plant Science. 10 (708). https://doi.org/10.3389/fpls.2019.00708
AuthorsChaudhry, S., Khokhar, W., Jabre, I., Reddy, A., Byrne, L., Wilson, C. and Syed, N.
Abstract

Plants, unlike animals, exhibit a very high degree of plasticity in their growth and development and employ diverse strategies to cope with the variations during diurnal cycles and stressful conditions. Plants and animals, despite their remarkable morphological and physiological differences, share many basic cellular processes and regulatory mechanisms.

Alternative splicing (AS) is one such gene regulatory mechanism that modulates gene expression in multiple ways. It is now well established that AS is prevalent in all multicellular eukaryotes including plants and humans. Emerging evidence indicates that in plants, as in animals, transcription and splicing are coupled. Here, we reviewed recent evidence in support of co-transcriptional splicing in plants and highlighted similarities and differences between plants and humans. An unsettled question in the field of AS is the extent to which splice isoforms contribute to protein diversity. To take a critical look at this question, we presented a comprehensive summary of the current status of research in this area in both plants and humans, discussed limitations with the currently used approaches and suggested improvements to current methods and alternative approaches.

We end with a discussion on the potential role of epigenetic modifications and chromatin state in splicing memory in plants primed with stresses.

KeywordsAlternative splicing; co-transcriptional splicing; protein diversity; intron retention; NMD; splicing memory; epigenetic modifications
Year2019
JournalFrontiers in Plant Science
Journal citation10 (708)
Digital Object Identifier (DOI)https://doi.org/10.3389/fpls.2019.00708
Publication dates
Print12 Jun 2019
Publication process dates
Deposited02 Jul 2019
Accepted13 May 2019
Accepted author manuscript
Output statusPublished
Additional information

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY).

Permalink -

https://repository.canterbury.ac.uk/item/88zy4/alternative-splicing-and-protein-diversity-plants-versus-animals

Download files

Accepted author manuscript
  • 3
    total views
  • 0
    total downloads
  • 0
    views this month
  • 0
    downloads this month

Export as

Related outputs

Genome-wide identification of splicing quantitative trait loci (sQTLs) in diverse ecotypes of Arabidopsis thaliana
Khokhar, W., Hassan, M., Reddy, A., Chaudhary, S., Jabre, I., Byrne, L. and Syed, N. 2019. Genome-wide identification of splicing quantitative trait loci (sQTLs) in diverse ecotypes of Arabidopsis thaliana. Frontiers in Plant Science. 10 (1160). https://doi.org/10.3389/fpls.2019.01160
Perspective on alternative splicing and proteome complexity in plants
Chaudhary, S., Jabre, I., Reddy, A., Staiger, D. and Syed, N. 2019. Perspective on alternative splicing and proteome complexity in plants. Trends in Plant Science. 24 (6), pp. 496-506. https://doi.org/10.1016/j.tplants.2019.02.006
Genetic diversity and structure of northern populations of the declining coastal plant Eryngium maritimum
Ievina, B., Rostoks, N., Syed, N., Flavell, A. and Ievinsh, G. 2019. Genetic diversity and structure of northern populations of the declining coastal plant Eryngium maritimum. Proceedings of the Latvian Academy of Sciences. Section B. Natural, Exact, and Applied Sciences.. 0 (0). https://doi.org/10.2478/prolas-2019-0008
Does co-transcriptional regulation of alternative splicing mediate plant stress responses?
Jabre, I., Reddy, A., Kalyna, M., Chaudhary, S., Khokhar, W., Byrne, L., Wilson, C. and Syed, N. 2019. Does co-transcriptional regulation of alternative splicing mediate plant stress responses? Nucleic Acids Research. 47 (6), pp. 2716-2726. https://doi.org/10.1093/nar/gkz121
Integrating research and knowledge exchange in the Science Undergraduate Curriculum: embedding employability through research-involved teaching
Harvey, C., Bertolo-Pardo, E. and Byrne, L. 2017. Integrating research and knowledge exchange in the Science Undergraduate Curriculum: embedding employability through research-involved teaching. in: Renes, S. (ed.) Global Voices in Higher Education In-Tech. pp. 111-128
Alternative splicing and protein diversity: plants versus animals
Chaudhary, S., Khokhar, W., Jabre, I., Reddy A.S.N., Byrne, L., Wilson, C.M. and Syed, N. 2019. Alternative splicing and protein diversity: plants versus animals. Frontiers in Plant Science. 10 (708). https://doi.org/10.3389/fpls.2019.00708
‘Something in the way she moves’: The functional significance of flexibility in the multiple roles of protein disulfide isomerase (PDI)
Freedman, R., Desmond, J., Byrne, L., Heal, J., Howard, M., Sanghera, N., Walker, K., Wallis, A., Wells, S., Williamson, R. and Romer, R. 2017. ‘Something in the way she moves’: The functional significance of flexibility in the multiple roles of protein disulfide isomerase (PDI). Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics. 1865 (11 (A)), pp. 1383-1394. https://doi.org/10.1016/j.bbapap.2017.08.014
A comparative study between molecular and agro-morphological methods for describing genetic relationships in Tunisian faba bean populations
Syed, N. 2016. A comparative study between molecular and agro-morphological methods for describing genetic relationships in Tunisian faba bean populations. Journal of New Sciences: Agri & Biotech. 27 (8), pp. 1513-1518.
Comparative analysis of the drought-responsive transcriptome in soybean lines contrasting for canopy wilting
Prince, S., Joshi, T., Mutava, R., Syed, N., Joao Vitor, M., Patil, G., Song, L., Wang, J., Lin, L., Chen, W., Shannon, J., Valliyodan, B., Xu, D. and Nguyen, H. 2015. Comparative analysis of the drought-responsive transcriptome in soybean lines contrasting for canopy wilting. Plant Science. 240, pp. 65-78. https://doi.org/10.1016/j.plantsci.2015.08.017
Winter Aconite (Eranthis hyemalis) Lectin as a cytotoxic effector in the lifecycle of Caenorhabditis elegans
McConnell, M., Lisgarten, D., Byrne, L., Harvey, S. and Bertolo-Pardo, E. 2015. Winter Aconite (Eranthis hyemalis) Lectin as a cytotoxic effector in the lifecycle of Caenorhabditis elegans. PeerJ. https://doi.org/10.7717/peerj.1206
Cell division is essential for elimination of the yeast [PSI+] prion by guanidine hydrochloride
Byrne, L., Cox, B., Coleman, D., Ridout, M., Morgan, B. and Tuiteq, M. 2007. Cell division is essential for elimination of the yeast [PSI+] prion by guanidine hydrochloride. Proceedings of the National Academy of Sciences of the United States of America (PNAS). 104 (28), pp. 11688-11693. https://doi.org/10.1073/pnas.0701392104
Genome-Tagged Amplification (GTA): a PCR-based method to prepare sample-tagged amplicons from hundreds of individuals for next generation sequencing
Ho, T., Cardle, L., Xu, X., Bayer, M., Prince, K., Mutava, R., Marshall, D. and Syed, N. 2014. Genome-Tagged Amplification (GTA): a PCR-based method to prepare sample-tagged amplicons from hundreds of individuals for next generation sequencing. Molecular Breeding. 34 (3), pp. 977-988. https://doi.org/10.1007/s11032-014-0090-7
Core clock, SUB1, and ABAR genes mediate flooding and drought responses via alternative splicing in soybean
Syed, N., Prince, S., Mutava, R., Patil, G., Li, S., Chen, W., Babu, V., Joshi, T., Khan, S. and Nguyen, H. 2015. Core clock, SUB1, and ABAR genes mediate flooding and drought responses via alternative splicing in soybean. Journal of Experimental Botany. https://doi.org/10.1093/jxb/erv407
Understanding abiotic stress tolerance mechanisms in soybean: a comparative evaluation of soybean response to drought and flooding stress
Mutava, R., Prince, S., Syed, N., Song, L., Valliyodan, B., Chen, W. and Nguyen, H. 2015. Understanding abiotic stress tolerance mechanisms in soybean: a comparative evaluation of soybean response to drought and flooding stress. Plant physiology and biochemistry : PPB / Société française de physiologie végétale. 86, pp. 109-20. https://doi.org/10.1016/j.plaphy.2014.11.010
Sequence-specific amplification polymorphisms (SSAPs): a multi-locus approach for analyzing transposon insertions
Syed, N. and Flavell, A. 2007. Sequence-specific amplification polymorphisms (SSAPs): a multi-locus approach for analyzing transposon insertions. Nature Protocols. 1 (6), pp. 2746-2752. https://doi.org/10.1038/nprot.2006.407
Genetic diversity analysis in Vicia species using retrotransposon-based SSAP markers
Sanz, A., Gonzalez, S., Syed, N., Suso, M., Saldaña, C. and Flavell, A. 2007. Genetic diversity analysis in Vicia species using retrotransposon-based SSAP markers. Molecular Genetics and Genomics. 278 (4), pp. 433-441. https://doi.org/10.1007/s00438-007-0261-x
Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis
Kalyna, M., Simpson, C., Syed, N., Lewandowska, D., Marquez, Y., Kusenda, B., Marshall, J., Fuller, J., Cardle, L., McNicol, J., Dinh, H., Barta, A. and Brown, J. 2012. Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis. Nucleic Acids Research. 40 (6), pp. 2454-2469. https://doi.org/10.1093/nar/gkr932
Alternative splicing mediates responses of the Arabidopsis circadian clock to temperature changes
James, A., Syed, N., Bordage, S., Marshall, J., Nimmo, G., Jenkins, G., Herzyk, P., Brown, J. and Nimmo, H. 2012. Alternative splicing mediates responses of the Arabidopsis circadian clock to temperature changes. The Plant Cell. 24 (3), pp. 961-981. https://doi.org/10.1105/tpc.111.093948
Alternative splicing in plants – coming of age
Syed, N., Kalyna, M., Marquez, Y., Barta, A. and Brown, J. 2012. Alternative splicing in plants – coming of age. Trends in Plant Science. 17 (10), pp. 616-623. https://doi.org/10.1016/j.tplants.2012.06.001
Thermoplasticity in the plant circadian clock: how plants tell the time-perature
James, A., Syed, N., Brown, J. and Nimmo, H. 2012. Thermoplasticity in the plant circadian clock: how plants tell the time-perature. Plant Signaling & Behavior. 7 (10), pp. 1219-1223. https://doi.org/10.4161/psb.21491
Inbred lines as testers for combining ability in cotton
Syed, W., Mehdi, S. and Syed, N. 1994. Inbred lines as testers for combining ability in cotton. Pakistan Journal of Scientific Research. 46, pp. 93-95.
Genetic study of lint percentage and staple length in cotton
Syed, W., Mehdi, S. and Syed, N. 1994. Genetic study of lint percentage and staple length in cotton. Pakistan Journal of Science. 46 (3-4), pp. 123-124.
Phenotypic recurrent selection for earliness in a random mated population of sunflower (Helianthus annuus L.)
Syed, N., Mehdi, S. and Syed, N. 1995. Phenotypic recurrent selection for earliness in a random mated population of sunflower (Helianthus annuus L.). Pakistan Journal of Scientific Research. 47 (3-4), pp. 62-65.
Two cycles of phenotypic recurrent selection for earliness in a random mated population of sunflower (Helianthus annuus L.)
Syed, N., Mehdi, S., Khan, I. and Syed, N. 1995. Two cycles of phenotypic recurrent selection for earliness in a random mated population of sunflower (Helianthus annuus L.). Science International (Lahore). 7, pp. 201-202.
Association of agronomic and economic characters of cotton
Syed, W., Mehdi, S. and Syed, N. 1995. Association of agronomic and economic characters of cotton. Pakistan Journal of Scientific Research. 47, pp. 46-49.
Fast and reliable genotype validation using microsatellite markers in Arabidopsis thaliana
Virk, P., Pooni, H., Syed, N. and Kearsey, M. 1999. Fast and reliable genotype validation using microsatellite markers in Arabidopsis thaliana. Theoretical and Applied Genetics. 98 (3-4), pp. 462-464. https://doi.org/10.1007/s001220051092
Genetic mapping of Sorghum bicolor (L.) Moench QTLs that control variation in tillering and other morphological characters
Hart, G., Schertz, K., Peng, Y. and Syed, N. 2001. Genetic mapping of Sorghum bicolor (L.) Moench QTLs that control variation in tillering and other morphological characters. Theoretical and Applied Genetics. 103 (8), pp. 1232-1242. https://doi.org/10.1007/s001220100582
Spontaneous gene flow and population structure in wild and cultivated chicory, Cichorium intybus L.
Kiær, L., Felber, F., Flavell, A., Guadagnuolo, R., Guiatti, D., Hauser, T., Olivieri, A., Scotti, I., Syed, N., Vischi, M., Wiel, C. and Jørgensen, R. 2009. Spontaneous gene flow and population structure in wild and cultivated chicory, Cichorium intybus L. Genetic Resources and Crop Evolution. 56 (3), pp. 405-419. https://doi.org/10.1007/s10722-008-9375-1
Molecular markers for the identification of resistance genes and marker-assisted selection in breeding wheat for leaf rust resistance
Vida, G., Gál, M., Uhrin, A., Veisz, O., Syed, N., Flavell, A., Wang, Z. and Bedő, Z. 2009. Molecular markers for the identification of resistance genes and marker-assisted selection in breeding wheat for leaf rust resistance. Euphytica. 170 (1-2), pp. 67-76. https://doi.org/10.1007/s10681-009-9945-0
Development of retrotransposon-based SSAP molecular marker system for study of genetic diversity in sea holly (Eryngium maritimum L.)
Levina, B., Syed, N., Flavell, A., Ievinsh, G. and Rostoks, N. 2010. Development of retrotransposon-based SSAP molecular marker system for study of genetic diversity in sea holly (Eryngium maritimum L.). Plant Genetic Resources. 8 (3), pp. 258-266. https://doi.org/10.1017/S1479262110000316
A hAT superfamily transposase recruited by the cereal grass genome
Muehlbauer, G., Bhau, B., Syed, N., Heinen, S., Cho, S., Marshall, D., Pateyron, S., Buisine, N., Chalhoub, B. and Flavell, A. 2006. A hAT superfamily transposase recruited by the cereal grass genome. Molecular Genetics and Genomics. 275 (6), pp. 553-563. https://doi.org/10.1007/s00438-006-0098-8
Genetics of quantitative traits in Arabidopsis thaliana
Kearsey, M., Pooni, H. and Syed, N. 2003. Genetics of quantitative traits in Arabidopsis thaliana. Heredity. 91 (5), pp. 456-464. https://doi.org/10.1038/sj.hdy.6800306
Genetic mapping and QTL analysis of fiber-related traits in cotton (Gossypium)
Mei, M., Syed, N., Gao, W., Thaxton, P., Smith, C., Stelly, D. and Chen, Z. 2004. Genetic mapping and QTL analysis of fiber-related traits in cotton (Gossypium). Theoretical and Applied Genetics. 108 (2), pp. 280-291. https://doi.org/10.1007/s00122-003-1433-7
Optimising the construction of a substitution library in Arabidopsis thaliana using computer simulations
Syed, N., Pooni, H., Mei, M., Chen, Z. and Kearsey, M. 2004. Optimising the construction of a substitution library in Arabidopsis thaliana using computer simulations. Molecular Breeding. 13 (1), pp. 59-68. https://doi.org/10.1023/B:MOLB.0000012845.37366.b5
Molecular marker genotypes, heterozygosity and genetic interactions explain heterosis in Arabidopsis thaliana
Syed, N. and Chen, Z. 2005. Molecular marker genotypes, heterozygosity and genetic interactions explain heterosis in Arabidopsis thaliana. Heredity. 94 (3), pp. 295-304. https://doi.org/10.1038/sj.hdy.6800558
Ty1-copia retrotransposon-based SSAP marker development in cashew (Anacardium occidentale L.)
Syed, N., Sureshsundar, S., Wilkinson, M., Bhau, B., Cavalcanti, J. and Flavell, A. 2005. Ty1-copia retrotransposon-based SSAP marker development in cashew (Anacardium occidentale L.). Theoretical and Applied Genetics. 110 (7), pp. 1195-1202. https://doi.org/10.1007/s00122-005-1948-1
A detailed linkage map of lettuce based on SSAP, AFLP and NBS markers
Syed, N., Sørensen, A., Antonise, R., Wiel, C., Linden, C., van 't Westende, W., Hooftman, D., Nijs, H. and Flavell, A. 2006. A detailed linkage map of lettuce based on SSAP, AFLP and NBS markers. Theoretical and Applied Genetics. 112 (3), pp. 517-527. https://doi.org/10.1007/s00122-005-0155-4
The number and transmission of [PSI+] prion seeds (Propagons) in the yeast Saccharomyces cerevisiae
Byrne, L., Cole, D., Cox, B., Ridout, M., Morgan, B. and Tuite, M. 2009. The number and transmission of [PSI+] prion seeds (Propagons) in the yeast Saccharomyces cerevisiae. PLoS ONE. 4 (3), p. e4670. https://doi.org/10.1371/journal.pone.0004670
Mapping of the ligand-binding site on the b′ domain of human PDI: interaction with peptide ligands and the x-linker region
Byrne, L., Sidhu, A., Wallis, A., Ruddock, L., Freedman, R., Howard, M. and Williamson, R. 2009. Mapping of the ligand-binding site on the b′ domain of human PDI: interaction with peptide ligands and the x-linker region. Biochemical Journal. 423 (2), pp. 209-217. https://doi.org/10.1042/BJ20090565
The ligand-binding b' domain of human protein disulphide-isomerase mediates homodimerization
Wallis, A., Sidhu, A., Byrne, L., Howard, M., Ruddock, L., Williamson, R. and Freedman, R. 2009. The ligand-binding b' domain of human protein disulphide-isomerase mediates homodimerization. Protein Science. 18 (12), pp. 2569-2577. https://doi.org/10.1002/pro.270