Human MFAP1 is a cryptic ortholog of the Saccharomyces cerevisiae Spp381 splicing factor

Abstract

BackgroundPre-mRNA splicing involves the stepwise assembly of a pre-catalytic spliceosome, followed by its catalytic activation, splicing catalysis and disassembly. Formation of the pre-catalytic spliceosomal B complex involves the incorporation of the U4/U6.U5 tri-snRNP and of a group of non-snRNP B-specific proteins. While in Saccharomyces cerevisiae the Prp38 and Snu23 proteins are recruited as components of the tri-snRNP, metazoan orthologs of Prp38 and Snu23 associate independently of the tri-snRNP as members of the B-specific proteins. The human spliceosome contains about 80 proteins that lack obvious orthologs in yeast, including most of the B-specific proteins apart from Prp38 and Snu23. Conversely, the tri-snRNP protein Spp381 is one of only five S. cerevisiae splicing factors without a known human ortholog.ResultsUsing InParanoid, a state-of-the-art method for ortholog inference between pairs of species, and systematic BLAST searches we identified the human B-specific protein MFAP1 as a putative ortholog of the S. cerevisiae tri-snRNP protein Spp381. Bioinformatics revealed that MFAP1 and Spp381 share characteristic structural features, including intrinsic disorder, an elongated shape, solvent exposure of most residues and a trend to adopt α-helical structures. In vitro binding studies showed that human MFAP1 and yeast Spp381 bind their respective Prp38 proteins via equivalent interfaces and that they cross-interact with the Prp38 proteins of the respective other species. Furthermore, MFAP1 and Spp381 both form higher-order complexes that additionally include Snu23, suggesting that they are parts of equivalent spliceosomal sub-complexes. Finally, similar to yeast Spp381, human MFAP1 partially rescued a growth defect of the temperature-sensitive mutant yeast strain prp38-1.ConclusionsHuman B-specific protein MFAP1 structurally and functionally resembles the yeast tri-snRNP-specific protein Spp381 and thus qualifies as its so far missing ortholog. Our study indicates that the yeast Snu23-Prp38-Spp381 triple complex was evolutionarily reprogrammed from a tri-snRNP-specific module in yeast to the B-specific Snu23-Prp38-MFAP1 module in metazoa, affording higher flexibility in spliceosome assembly and thus, presumably, in splicing regulation.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-017-0923-1) contains supplementary material, which is available to authorized users.

Splicing and epigenetic factors jointly regulate epidermal differentiation

“…Both Gene Ontology and protein interaction database analysis of the interacting proteins revealed that ZMAT2 interacts with components of the (pre-) spliceosome (Figures 3C,D). These findings are in line with crystal structures of the budding yeast pre-spliceosome, showing that the putative ZMAT2 ortholog snu23 associates with the B* (pre-catalytic) complex (Plaschka, Lin and Nagai, 2017;Ulrich and Wahl, 2017). Our biochemical experiments identifying ZMAT2 as an interactor of the pre-spliceosome in human keratinocytes, together with our screen and validation analysis implicate RNA splicing as a potential key regulatory process in epidermal renewal and differentiation.…”

“…It is possible that ZMAT2 transiently interacts with the human spliceosome to facilitate and fine-tune these transitions. If this is the case, the timing of its association with the spliceosome might influence the efficiencies of competing splicing mechanisms, spliceosome composition or conformation (Ulrich and Wahl, 2017). Although we can only speculate about the molecular mechanisms behind our observations at this point, the combined evidence from our proteomic data and literature identified ZMAT2 as regulator of (alternative) splicing in epidermal stem cells.…”

“…In contrast, in humans these two proteins are recruited independently from the tri-snRNP and are therefore considered non-snRNP proteins. There are seven more of these non-snRNP proteins in humans (Ulrich and Wahl, 2017) which are referred to as B-specific proteins. Although some of these proteins can influence splice-site selection (e.g.…”

The SWI/SNF subunits BRG1 affects alternative splicing by changing RNA binding factor interactions with RNA

“…Instead, splicing can be achieved by several different mechanisms using the concurrent actions of a vast number of proteins and RNAs. Large-scale network analysis suggests that enhancer proteins interact by promoting the assembly of spliceosome sub complexes, whereas silencing occurs through RNA interactions (Ulrich and 2017;Guimarães et al, 2018). The combinatorial effect of different RNA splicing regulators is shown by the results of the knock-down of the factors on inclusion of MYL6 exon.…”

Non-coding parts of genomes as the basis of epigenetic heredity

“…Основная часть первичных транскриптов многоклеточных содержит более одного интрона и способна к альтернативному сплайсингу, в результате которого образуются различные мРНК из одного гена, что используется в дифференцировке клеток (Ulrich, Wahl, 2017). Поэтому количество генов, способных к альтернативному сплайсингу, возрастает при эволюционной диверсификации типов клеток в связи с усложнением программ развития (Bush et al, 2017).…”