Genome-wide identification and functional analysis of the splicing component SYF2/NTC31/p29 across different plant species
This study systematically identifies plant SYF2/NTC31/p29 genes from 62 plant species by a combinatory bioinformatics approach, revealing the importance of this gene family in phylogenetics, duplication, transcriptional, and post-transcriptional regulation.
Alternative splicing is a post-transcriptional regulatory mechanism, which is critical for plant development and stress responses. The entire process is strictly attenuated by a complex of splicing-related proteins, designated splicing factors. Human p29, also referred to as synthetic lethal with cdc forty 2 (SYF2) or the NineTeen complex 31 (NTC31), is a core protein found in the NTC complex of humans and yeast. This splicing factor participates in a variety of biological processes, including DNA damage repair, control of the cell cycle, splicing, and tumorigenesis. However, its function in plants has been seldom reported. Thus, we have systematically identified 89 putative plant SYF2s from 62 plant species among the deposited entries in the Phytozome database. The phylogenetic relationships and evolutionary history among these plant SYF2s were carefully examined. The results revealed that plant SYF2s exhibited distinct patterns regarding their gene structure, promoter sequences, and expression levels, suggesting their functional diversity in response to developmental cues or stress treatments. Although local duplication events, such as tandem duplication and retrotransposition, were found among several plant species, most of the plant species contained only one copy of SYF2, suggesting the existence of additional mechanisms to confer duplication resistance. Further investigation using the model dicot and monocot representatives Arabidopsis and rice SYF2s indicated that the splicing pattern and resulting protein isoforms might play an alternative role in the functional diversity.
KeywordsAlternative splicing Gene expression Gene family Phylogenetics Plants Promoter
This work was supported by the Natural Science Foundation of Guangdong Province (2018A030313030), Natural Science Foundation of Shandong Province (BS2015NY002), Funds of Shandong “Double Top” Program, the China Postdoctoral Science Foundation (2017M622801), Shenzhen Overseas Talents Innovation and Entrepreneurship Funding Scheme (The Peacock Scheme, KQTD201101) and Hong Kong Research Grant Council (AoE/M-05/12, AoE/M-403/16, GRF CUHK14160516, 14177617, 12100318).
Compliance with ethical standards
Conflict of interest
The authors declare no conflicts of interest.
- Benyehuda S, Dix I, Russell CS, Mcgarvey M, Beggs JD, Kupiec M (2000) Genetic and physical interactions between factors involved in both cell cycle progression and pre-mRNA splicing in Saccharomyces cerevisiae. Genetics 156:1503–1517Google Scholar
- Csaba K, Femke D, Nicolas V, Dóra S, Zsuzsa K (2012) The spliceosome-activating complex: molecular mechanisms underlying the function of a pleiotropic regulator. Front Plant Sci 3:9Google Scholar
- Liu Y, Ni T, Xue Q, Lv L, Chen B, Cui X, Cui Y, Wang Y, Mao G, Ji L (2014b) Involvement of p29/SYF2/fSAP29/NTC31 in the progression of NSCLC via modulating cell proliferation. Pathology 211:36–42Google Scholar
- Vlad IM, Balaji VS, Vikas CR, Ramani D, Larry S D (2008) Automatic online tuning for fast Gaussian summation. Adv Neural Inf Process SystGoogle Scholar
- Zhu FY, Chen MX, Ye NH, Shi L, Ma KL, Yang JF, Cao YY, Zhang YJ, Yoshida T, Fernie AR, Fan GY, Wen B, Zhou R, Liu TY, Fan T, Gao B, Zhang D, Hao GF, Xiao S, Liu YG, Zhang JH (2017b) Proteogenomic analysis reveals alternative splicing and translation as part of the abscisic acid response in Arabidopsis seedlings. Plant J 91:518–533CrossRefGoogle Scholar