Abstract
Main conclusion
This study systematically identifies 112 U2A genes from 80 plant species by combinatory bioinformatics analysis, which is important for understanding their phylogenetic history, expression profiles and for predicting specific functions.
Abstract
In eukaryotes, a pre-mRNA can generate multiple transcripts by removing certain introns and joining corresponding exons, thus greatly expanding the transcriptome and proteome diversity. The spliceosome is a mega-Dalton ribonucleoprotein (RNP) complex that is essential for the process of splicing. In spliceosome components, the U2 small nuclear ribonucleoprotein (U2 snRNP) forms the pre-spliceosome by association with the branch site. An essential component that promotes U2 snRNP assembly, named U2A, has been extensively identified in humans, yeast and nematodes. However, studies examining U2A genes in plants are scarce. In this study, we performed a comprehensive analysis and identified a total of 112 U2A genes from 80 plant species representing dicots, monocots, mosses and algae. Comparisons of the gene structures, protein domains, and expression patterns of 112 U2A genes indicated that the conserved functions were likely retained by plant U2A genes and important for responses to internal and external stimuli. In addition, analysis of alternative transcripts and splice sites of U2A genes indicated that the fifth intron contained a conserved alternative splicing event that might be important for its molecular function. Our work provides a general understanding of this splicing factor family in terms of genes and proteins, and it will serve as a fundamental resource that will contribute to further mechanistic characterization in plants.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Explore related subjects
Discover the latest articles and news from researchers in related subjects, suggested using machine learning.Availability of data and materials
The datasets supporting the conclusions of this article are included within the article and its additional files.
References
Ashkenazy H, Abadi S, Martz E, Chay O, Mayrose I, Pupko T, Ben-Tal N (2016) ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules. Nucleic Acids Res 44(W1):W344–W350. https://doi.org/10.1093/nar/gkw408
Bai R, Wan R, Yan C, Lei J, Shi Y (2018) Structures of the fully assembled Saccharomyces cerevisiae spliceosome before activation. Science (new York, NY) 360(6396):1423–1429. https://doi.org/10.1126/science.aau0325
Behrens SE, Galisson F, Legrain P, Lührmann R (1993) Evidence that the 60-kDa protein of 17S U2 small nuclear ribonucleoprotein is immunologically and functionally related to the yeast PRP9 splicing factor and is required for the efficient formation of prespliceosomes. Proc Natl Acad Sci USA 90(17):8229–8233. https://doi.org/10.1073/pnas.90.17.8229
Black DL, Chabot B, Steitz JA (1985) U2 as well as U1 small nuclear ribonucleoproteins are involved in premessenger RNA splicing. Cell 42(3):737–750. https://doi.org/10.1016/0092-8674(85)90270-3
Bringmann P, Lührmann R (1986) Purification of the individual snRNPs U1, U2, U5 and U4/U6 from HeLa cells and characterization of their protein constituents. EMBO J 5(13):3509–3516
Caspary F, Séraphin B (1998) The yeast U2A’/U2B complex is required for pre-spliceosome formation. EMBO J 17(21):6348–6358. https://doi.org/10.1093/emboj/17.21.6348
Ceulemans H, De Maeyer M, Stalmans W, Bollen M (1999) A capping domain for LRR protein interaction modules. FEBS Lett 456(3):349–351. https://doi.org/10.1016/s0014-5793(99)00965-5
Chen MX, Lu CC, Sun PC, Nie YX, Tian Y, Hu QJ, Das D, Hou XX, Gao B, Chen X, Liu SX, Zheng CC, Zhao XY, Dai L, Zhang J, Liu YG (2021a) Comprehensive transcriptome and proteome analyses reveal a novel sodium chloride responsive gene network in maize seed tissues during germination. Plant, Cell Environ 44(1):88–101. https://doi.org/10.1111/pce.13849
Chen MX, Mei LC, Wang F, Boyagane Dewayalage IKW, Yang JF, Dai L, Yang GF, Gao B, Cheng CL, Liu YG, Zhang J, Hao GF (2021b) PlantSPEAD: a web resource towards comparatively analysing stress-responsive expression of splicing-related proteins in plant. Plant Biotechnol J 19(2):227–229. https://doi.org/10.1111/pbi.13486
Chen MX, Zhang KL, Gao B, Yang JF, Tian Y, Das D, Fan T, Dai L, Hao GF, Yang GF, Zhang J, Zhu FY, Fang YM (2020a) Phylogenetic comparison of 5’ splice site determination in central spliceosomal proteins of the U1–70K gene family, in response to developmental cues and stress conditions. The Plant J 103(1):357–378. https://doi.org/10.1111/tpj.14735
Chen MX, Zhang KL, Zhang M, Das D, Fang YM, Dai L, Zhang J, Zhu FY (2020b) Alternative splicing and its regulatory role in woody plants. Tree Physiol 40(11):1475–1486. https://doi.org/10.1093/treephys/tpaa076
Chen MX, Zhang Y, Fernie AR, Liu YG, Zhu FY (2021c) SWATH-MS-based proteomics: strategies and applications in plants. Trends Biotechnol 39(5):433–437. https://doi.org/10.1016/j.tibtech.2020.09.002
Chen MX, Zhu FY, Gao B, Ma KL, Zhang Y, Fernie AR, Chen X, Dai L, Ye NH, Zhang X, Tian Y, Zhang D, Xiao S, Zhang J, Liu YG (2020c) Full-length transcript-based proteogenomics of rice improves its genome and proteome annotation. Plant Physiol 182(3):1510–1526. https://doi.org/10.1104/pp.19.00430
Chen MX, Zhu FY, Wang FZ, Ye NH, Gao B, Chen X, Zhao SS, Fan T, Cao YY, Liu TY, Su ZZ, Xie LJ, Hu QJ, Wu HJ, Xiao S, Zhang J, Liu YG (2019) Alternative splicing and translation play important roles in hypoxic germination in rice. J Exp Bot 70(3):817–833. https://doi.org/10.1093/jxb/ery393
Dziembowski A, Ventura AP, Rutz B, Caspary F, Faux C, Halgand F, Laprévote O, Séraphin B (2004) Proteomic analysis identifies a new complex required for nuclear pre-mRNA retention and splicing. EMBO J 23(24):4847–4856. https://doi.org/10.1038/sj.emboj.7600482
Fresco LD, Harper DS, Keene JD (1991) Leucine periodicity of U2 small nuclear ribonucleoprotein particle (snRNP) A’ protein is implicated in snRNP assembly via protein-protein interactions. Mol Cell Biol 11(3):1578–1589. https://doi.org/10.1128/mcb.11.3.1578-1589.1991
Gao K, Masuda A, Matsuura T, Ohno K (2008) Human branch point consensus sequence is yUnAy. Nucleic Acids Res 36(7):2257–2267. https://doi.org/10.1093/nar/gkn073
Keller EB, Noon WA (1984) Intron splicing: a conserved internal signal in introns of animal pre-mRNAs. Proc Natl Acad Sci USA 81(23):7417–7420. https://doi.org/10.1073/pnas.81.23.7417
Konarska MM, Sharp PA (1987) Interactions between small nuclear ribonucleoprotein particles in formation of spliceosomes. Cell 49(6):763–774. https://doi.org/10.1016/0092-8674(87)90614-3
Lerner MR, Boyle JA, Mount SM, Wolin SL, Steitz JA (1980) Are snRNPs involved in splicing? Nature 283(5743):220–224. https://doi.org/10.1038/283220a0
Lundin M, Mikkelsen B, Gudim M, Syed M (2000) Gene structure of the U2 snRNP-Specific A’ protein gene from Salmo salar: alternative transcripts observed. Mar Biotechnol (NY) 2(2):204–211. https://doi.org/10.1007/s101269900015
Matera AG, Wang Z (2014) A day in the life of the spliceosome. Nat Rev Mol Cell Biol 15(2):108–121. https://doi.org/10.1038/nrm3742
Moore MJ, Query CC, Sharp PA (1993) Splicing of precursors to mRNA by the spliceosome. In: Gesteland RF, Atkins TR (eds) The RNA world, 1st edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbour, pp 303–357
Nagengast AA, Salz HK (2001) The Drosophila U2 snRNP protein U2A’ has an essential function that is SNF/U2B" independent. Nucleic Acids Res 29(18):3841–3847. https://doi.org/10.1093/nar/29.18.3841
Padgett RA (2012) New connections between splicing and human disease. Trends Genetics 28(4):147–154. https://doi.org/10.1016/j.tig.2012.01.001
Patel AA, Steitz JA (2003) Splicing double: insights from the second spliceosome. Nat Rev Mol Cell Biol 4(12):960–970. https://doi.org/10.1038/nrm1259
Pikielny CW, Teem JL, Rosbash M (1983) Evidence for the biochemical role of an internal sequence in yeast nuclear mRNA introns: implications for U1 RNA and metazoan mRNA splicing. Cell 34(2):395–403. https://doi.org/10.1016/0092-8674(83)90373-2
Plaschka C, Lin PC, Charenton C, Nagai K (2018) Prespliceosome structure provides insights into spliceosome assembly and regulation. Nature 559(7714):419–422. https://doi.org/10.1038/s41586-018-0323-8
Polycarpou-Schwarz M, Gunderson SI, Kandels-Lewis S, Seraphin B, Mattaj IW (1996) Drosophila SNF/D25 combines the functions of the two snRNP proteins U1A and U2B’ that are encoded separately in human, potato, and yeast. RNA (new York, NY) 2(1):11–23
Price SR, Evans PR, Nagai K (1998) Crystal structure of the spliceosomal U2B"-U2A’ protein complex bound to a fragment of U2 small nuclear RNA. Nature 394(6694):645–650. https://doi.org/10.1038/29234
Rimmele ME, Belasco JG (1998) Target discrimination by RNA-binding proteins: role of the ancillary protein U2A’ and a critical leucine residue in differentiating the RNA-binding specificity of spliceosomal proteins U1A and U2B". RNA (new York, NY) 4(11):1386–1396. https://doi.org/10.1017/s1355838298981171
Saldi T, Wilusz C, MacMorris M, Blumenthal T (2007) Functional redundancy of worm spliceosomal proteins U1A and U2B’’. Proc Natl Acad Sci USA 104(23):9753–9757. https://doi.org/10.1073/pnas.0701720104
Scherly D, Dathan NA, Boelens W, van Venrooij WJ, Mattaj IW (1990) The U2B’’ RNP motif as a site of protein-protein interaction. EMBO J 9(11):3675–3681
Simpson GG, Clark GP, Rothnie HM, Boelens W, van Venrooij W, Brown JW (1995) Molecular characterization of the spliceosomal proteins U1A and U2B" from higher plants. EMBO J 14(18):4540–4550
Singh RK, Cooper TA (2012) Pre-mRNA splicing in disease and therapeutics. Trends Mol Med 18(8):472–482. https://doi.org/10.1016/j.molmed.2012.06.006
van der Feltz C, Hoskins AA (2019) Structural and functional modularity of the U2 snRNP in pre-mRNA splicing. Crit Rev Biochem Mol Biol 54(5):443–465. https://doi.org/10.1080/10409238.2019.1691497
Wahl MC, Will CL, Lührmann R (2009) The spliceosome: design principles of a dynamic RNP machine. Cell 136(4):701–718. https://doi.org/10.1016/j.cell.2009.02.009
Wan R, Bai R, Yan C, Lei J, Shi Y (2019) Structures of the catalytically activated yeast spliceosome reveal the mechanism of branching. Cell 177(2):339-351.e313. https://doi.org/10.1016/j.cell.2019.02.006
Waterhouse A, Bertoni M, Bienert S, Studer G, Tauriello G, Gumienny R, Heer FT, de Beer TAP, Rempfer C, Bordoli L, Lepore R, Schwede T (2018) SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res 46(W1):W296–W303. https://doi.org/10.1093/nar/gky427
Weber G, DeKoster GT, Holton N, Hall KB, Wahl MC (2018) Molecular principles underlying dual RNA specificity in the Drosophila SNF protein. Nat Commun 9(1):2220. https://doi.org/10.1038/s41467-018-04561-6
Will CL, Lührmann R (2011) Spliceosome structure and function. Cold Spring Harbor Perspec Biol. https://doi.org/10.1101/cshperspect.a003707
Williams SG, Hall KB (2011) Human U2B″ protein binding to snRNA stemloops. Biophys Chem 159(1):82–89. https://doi.org/10.1016/j.bpc.2011.05.010
Williams SG, Hall KB (2014) Binding affinity and cooperativity control U2B″/snRNA/U2A’ RNP formation. Biochemistry 53(23):3727–3737. https://doi.org/10.1021/bi500438e
Williams SG, Harms MJ, Hall KB (2013) Resurrection of an Urbilaterian U1A/U2B″/SNF protein. J Mol Biol 425(20):3846–3862. https://doi.org/10.1016/j.jmb.2013.05.031
Wu H, Sun L, Wen Y, Liu Y, Yu J, Mao F, Wang Y, Tong C, Guo X, Hu Z, Sha J, Liu M, Xia L (2016) Major spliceosome defects cause male infertility and are associated with nonobstructive azoospermia in humans. Proc Natl Acad Sci USA 113(15):4134–4139. https://doi.org/10.1073/pnas.1513682113
Yan C, Wan R, Shi Y (2019) Molecular mechanisms of pre-mRNA splicing through structural biology of the spliceosome. Cold Spring Harbor Perspec Biol. https://doi.org/10.1101/cshperspect.a032409
Yuan S, Chan HCS, Hu Z (2017) Using PyMOL as a platform for computational drug design. Wiley Interdisciplinary Rev-Comput Mol Sci. https://doi.org/10.1002/wcms.1298
Zhang KL, Feng Z, Yang JF, Yang F, Yuan T, Zhang D, Hao GF, Fang YM, Zhang J, Wu C, Chen MX, Zhu FY (2020) Systematic characterization of the branch point binding protein, splicing factor 1, gene family in plant development and stress responses. BMC Plant Biol 20(1):379. https://doi.org/10.1186/s12870-020-02570-6
Acknowledgements
This work was supported by the Natural Science Foundation of Jiangsu Province (SBK2020042924), National Natural Science Foundation of China (NSFC31701341), NJFU project funding (GXL2018005), the Technology Plan Program of Shenzhen (JSGG20170822153048662), The Science Technology and Innovation Committee of Shenzhen (GJHZ20190821160401654), Platform funding for Guangdong Provincial Key Laboratory of Seed and Seedling Health Management Technology (2021B1212050011) and Hong Kong Research Grant Council (AoE/M-403/16, GRF12100318, 12103220). We thank Dr. HHK Achala for language polishment on the manuscript.
Author information
Authors and Affiliations
Corresponding authors
Ethics declarations
Conflict of interest
The authors have no conflicts of interest to declare.
Additional information
Communicated by Anastasios Melis.
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Liu, Y., Tian, Y., Wang, LX. et al. Phylogeny and conservation of plant U2A/U2A’, a core splicing component in U2 spliceosomal complex. Planta 255, 25 (2022). https://doi.org/10.1007/s00425-021-03752-8
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s00425-021-03752-8