title: Conserved RNA structures in the non-canonical Hac1/Xbp1 intron.
abstract: The unconventional splicing of Hac1 by the ribonuclease Ire1 is a key event in the activation of the unfolded protein response (UPR) in Saccharomyces cerevisiae. This splicing is independent of the spliceosome and is mediated by a secondary structure at the intron-exon boundaries of the mRNA. Similar unconventional splicing was also described for the gene Xbp1 in human, mouse, C. elegans and D. melanogaster, and for Hac1 in five other fungi. We used reported RNA structures to build a multiple sequence alignment and the Infernal package to search for homologous structures. We identified homologous non-canonical intron structures in 128 out of 156 searched eukaryotic genomes. Our results show that the sequence of the Hac1/Xbp1 intron is highly conserved only around the splice sites recognized by Ire1. The consensus structure of the Hac1/Xbp1 mRNA is well conserved in Fungi and Metazoa and resembles structures previously described. We show that a typical Hac1/Xbp1 intron is very short, only 20-26 bases, whereas yeast species have a long intron (> 100 bases). We identified six species with unambiguous Hac1/Xbp1 homologs that have lost the non-canonical intron structure. We propose that these species use a different mechanism to regulate the UPR.
authors: Faculty of Life Sciences, University of Manchester, Manchester UK.
authors: Katarzyna B
authors: KB
authors: Hooks
authors: Sam
authors: S
authors: Griffiths-Jones
references: EMBO J. 1999 Jun 1;18(11):3119-32
references: 10357823
references: Mol Biol Cell. 1997 Oct;8(10):1845-62
references: 9348528
references: Cell. 2010 Mar 19;140(6):900-17
references: 20303879
references: BMC Evol Biol. 2006 Nov 22;6:99
references: 17121679
references: Yeast. 2010 Jul;27(7):443-52
references: 20162530
references: Genome Res. 2004 Apr;14(4):708-15
references: 15060014
references: In Silico Biol. 2007;7(2):151-4
references: 17688440
references: Nucleic Acids Res. 2009 Jan;37(Database issue):D555-9
references: 18948289
references: Proc Natl Acad Sci U S A. 2006 Jun 20;103(25):9566-71
references: 16760254
references: Microb Cell Fact. 2010 Jun 30;9:49
references: 20591165
references: Bioinformatics. 2005 Jan 15;21(2):257-9
references: 15377506
references: Fungal Genet Biol. 2008 Sep;45(9):1235-47
references: 18602013
references: Cell. 2001 Oct 5;107(1):103-14
references: 11595189
references: Cell. 1996 Nov 1;87(3):391-404
references: 8898193
references: Cell. 2001 Dec 28;107(7):881-91
references: 11779464
references: Nucleic Acids Res. 2010 Jan;38(Database issue):D613-9
references: 19906737
references: J Mol Biol. 1999 May 21;288(5):911-40
references: 10329189
references: Mol Microbiol. 2003 Feb;47(4):1149-61
references: 12581366
references: Cell. 1997 Sep 19;90(6):1031-9
references: 9323131
references: Bioinformatics. 2009 Aug 1;25(15):1974-5
references: 19398448
references: J Cell Sci. 2009 Aug 15;122(Pt 16):2877-86
references: 19622636
references: Bioinformatics. 2009 May 15;25(10):1335-7
references: 19307242
references: Nucleic Acids Res. 2009 Jan;37(Database issue):D136-40
references: 18953034
references: Nature. 2002 Jan 3;415(6867):92-6
references: 11780124
references: Cell. 2001 Dec 28;107(7):893-903
references: 11779465
references: EMBO J. 2007 Jan 10;26(1):242-52
references: 17170705
references: Genes Dev. 1998 Jun 15;12(12):1812-24
references: 9637683