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
- 4 March 2020
- journal article
- research article
- Published by Wiley in The Plant Journal
- Vol. 103 (1), 357-378
- https://doi.org/10.1111/tpj.14735
Abstract
Intron‐containing genes have the ability to generate multiple transcript isoforms by splicing, thereby greatly expanding eukaryotic transcriptome and proteome. In eukaryotic cells, precursor mRNA (pre‐mRNA) splicing is performed by a mega‐macromolecular complex defined as a spliceosome. Among its splicing components, U1 small nuclear ribonucleoprotein (U1 snRNP) is the smallest subcomplex involved in early spliceosome assembly and 5’‐splice site recognition. Its central component, named as U1‐70K, has been extensively characterized in animals and yeast. However, very few investigations on U1‐70K genes have been conducted in plants. To this end, we performed a comprehensive study to systematically identify 115 U1‐70K genes from 67 plant species, ranging from algae to angiosperms. Phylogenetic analysis suggested that expansion of plant U1‐70K gene family was likely driven by whole genome duplications. Subsequent comparisons of gene structures, protein domains, promoter regions and conserved splicing patterns indicated that plant U1‐70Ks are likely to preserve their conserved molecular function across plant lineage, and play an important functional role in response to environmental stresses. Furthermore, genetic analysis by using T‐DNA insertion mutants suggested that Arabidopsis U1‐70K may be involved in response to osmotic stress. Our results provide a general overview of this gene family in Viridiplantae and will act as a reference source to carry out future mechanistic studies on this U1 snRNP‐specific splicing factor.Keywords
Funding Information
- National Natural Science Foundation of China (NSFC31701341)
- Natural Science Foundation of Guangdong Province (2018A030313030)
- Glaucoma Research Foundation (CUHK14160516, 14177617, 12100318)
This publication has 86 references indexed in Scilit:
- U1 snRNP Determines mRNA Length and Regulates Isoform ExpressionCell, 2012
- Ancient whole genome duplications, novelty and diversification: the WGD Radiation Lag-Time ModelCurrent Opinion in Plant Biology, 2012
- Interaction between the RNA binding domains of Ser-Arg splicing factor 1 and U1-70K snRNP protein determines early spliceosome assemblyProceedings of the National Academy of Sciences of the United States of America, 2011
- HMGA1a Trapping of U1 snRNP at an Authentic 5′ Splice Site Induces Aberrant Exon Skipping in Sporadic Alzheimer's DiseaseMolecular and Cellular Biology, 2010
- New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0Systematic Biology, 2010
- Angiosperm genome comparisons reveal early polyploidy in the monocot lineageProceedings of the National Academy of Sciences of the United States of America, 2009
- MEME SUITE: tools for motif discovery and searchingNucleic Acids Research, 2009
- Spatial mapping of splicing factor complexes involved in exon and intron definitionThe Journal of cell biology, 2008
- Requirements for gene silencing mediated by U1 snRNA binding to a target sequenceNucleic Acids Research, 2008
- MUSCLE: multiple sequence alignment with high accuracy and high throughputNucleic Acids Research, 2004