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[[File:HAC_mRNA.jpg|thumb|right|Consensus structure of HAC1/XBP1 mRNA]]
[[File:HAC_mRNA.jpg|thumb|right|Consensus structure of HAC1/XBP1 mRNA]]


'''Hac1 Xbp1 intron''' is a non-canonical [[intron]] processed without use of [[spliceosome]]. A [[secondary structure]] of the [[mRNA]] is crucial in recognition of the [[intron]] splice sites. This non-canonical intron can be found in [[bZIP]]-containing genes called HAC1 in [[Fungi]] and [[XBP1]] in [[Metazoa]]. Splicing is performed by [[ERN1|IRE1]], a [[kinase]] with endoribinuclease activity<ref>{{cite journal |doi=10.1016/S0092-8674(00)80369-4 |author=Sidrauski C, Walter P |title=The transmembrane kinase Ire1p is a site-specific endonuclease that initiates mRNA splicing in the unfolded protein response |journal=Cell |volume=90 |issue=6 |pages=1031-9 |year=1997 |pmid=9323131 }}</ref>. Exons are joined by a tRNA ligase. The unconventional [[splicing]] was first described for HAC1 in ''[[S. cerevisiae]]''<ref>{{cite journal |doi= |author= |title= |journal= |volume= |issue= |pages= |year= |pmid= }}</ref>.
'''Hac1 Xbp1 intron''' is a non-canonical [[intron]] processed without use of [[spliceosome]]. A [[secondary structure]] of the [[mRNA]] is crucial in recognition of the [[intron]] splice sites. This non-canonical intron can be found in [[bZIP]]-containing genes called HAC1 in [[Fungi]] and [[XBP1]] in [[Metazoa]]. Splicing is performed by [[ERN1|IRE1]], a [[kinase]] with endoribinuclease activity<ref name=Sidrauski>{{cite journal |doi=10.1016/S0092-8674(00)80369-4 |author=Sidrauski C, Walter P |title=The transmembrane kinase Ire1p is a site-specific endonuclease that initiates mRNA splicing in the unfolded protein response |journal=Cell |volume=90 |issue=6 |pages=1031-9 |year=1997 |pmid=9323131 }}</ref>. Exons are joined by a tRNA ligase. The unconventional [[splicing]] was first described for HAC1 in ''[[S. cerevisiae]]''<ref name=Sidrauski/>.


==Intron conservation==
==Intron conservation==
The unconventional [[splicing]] was confirmed experimentally for following species:
The unconventional [[splicing]] was confirmed experimentally for following species:
* ''[[S. cerevisiae]]''
* ''[[S. cerevisiae]]''<ref name=Sidrauski/>
* [[human]]<ref>{{cite journal |doi=10.1016/S0092-8674(01)00611-0 |author=Yoshida H, Matsui T, Yamamoto A, Okada T, Mori K. |title=XBP1 mRNA is induced by ATF6 and spliced by IRE1 in response to ER stress to produce a highly active transcription factor |journal=Cell |volume=107 |issue=7 |pages=881-91 |year=2001 |pmid=11779464 }}</ref>
* [[mouse]] and ''[[Caenorhabditis elegans]]''
* [[mouse]] and ''[[Caenorhabditis elegans]]''<ref>{{cite journal |doi=10.1038/415092a |author=Calfon M, Zeng H, Urano F, Till JH, Hubbard SR, Harding HP, Clark SG, Ron D |title=IRE1 couples endoplasmic reticulum load to secretory capacity by processing the XBP-1 mRNA |journal=Nature |volume=415 |issue=6867 |pages=92-6 |year=2002 |pmid=11780124 }}</ref>
* [[human]]
* ''[[Trichoderma reesei]] and [[Aspergillus nidulans]]''<ref>{{cite journal |doi=10.1046/j.1365-2958.2003.03363.x |author=Saloheimo M, Valkonen M, Penttila M. |title=Activation mechanisms of the HAC1-mediated unfolded protein response in filamentous fungi |journal=Mol Microbiol |volume=47 |issue=4 |pages=1149-61 |year=2003 |pmid=12581366 }}</ref>
* ''[[Trichoderma reesei]]''
* ''[[Drosophila melanogaster]]''<ref>{{cite journal |doi=10.1038/sj.emboj.7601477 |author=Ryoo HD, Domingos PM, Kang MJ, Steller H. |title=Unfolded protein response in a Drosophila model for retinal degeneration |journal=EMBO J |volume=26 |issue=1 |pages=242-52 |year=2007 |pmid=17170705 }}</ref>
* ''[[Candida albicans]]''
* ''[[Candida albicans]]''<ref>{{cite journal |doi=10.1016/j.fgb.2008.06.001 |author=Wimalasena TT, Enjalbert B, Guillemette T, Plumridge A, Budge S, Yin Z, Brown AJ, Archer DB |title=Impact of the unfolded protein response upon genome-wide expression patterns, and the role of Hac1 in the polarized growth, of Candida albicans |journal=Fungal Genet Biol |volume=45 |issue=9 |pages=1235-47 |year=2008 |pmid=18602013 }}</ref>
* ''[[Yarrowia lipolytica]]''
* ''[[Yarrowia lipolytica]]''<ref>{{cite journal |doi=10.1002/yea.1762 |author=Oh MH, Cheon SA, Kang HA, Kim JY |title=Functional characterization of the unconventional splicing of Yarrowia lipolytica HAC1 mRNA induced by unfolded protein response |journal=Yeast |volume=27 |issue=7 |pages=443-52 |year=2010 |pmid=20162530 }}</ref>
* ''[[Drosophila melanogaster]]''
* ''[[Pichia pastoris]]''<ref>{{cite journal |doi=10.1186/1475-2859-9-49 |author=Guerfal M, Ryckaert S, Jacobs PP, Ameloot P, Van Craenenbroeck K, Derycke R, Callewaert N. |title=The HAC1 gene from Pichia pastoris: characterization and effect of its overexpression on the production of secreted, surface displayed and membrane proteins |journal=Microb Cell Fact |volume=9 |issue= |pages=49 |year=2010 |pmid=20591165 }}</ref>.
* ''[[Pichia pastoris]]''.
Computational methods predict HAC-like [[intron]] with its characteristic [[RNA structure]] in many other species of [[Fungi]], [[Vertebrates]], [[Arthropoda]], [[Nematoda]], [[Annelida]] and [[Mollusca]](ref.).
Computational methods predict HAC-like [[intron]] with its characteristic [[RNA structure]] in many other species of [[Fungi]], [[Vertebrates]], [[Arthropoda]], [[Nematoda]], [[Annelida]] and [[Mollusca]](ref.).


Revision as of 15:15, 7 January 2011

File:HAC mRNA.jpg
Consensus structure of HAC1/XBP1 mRNA

Hac1 Xbp1 intron is a non-canonical intron processed without use of spliceosome. A secondary structure of the mRNA is crucial in recognition of the intron splice sites. This non-canonical intron can be found in bZIP-containing genes called HAC1 in Fungi and XBP1 in Metazoa. Splicing is performed by IRE1, a kinase with endoribinuclease activity[1]. Exons are joined by a tRNA ligase. The unconventional splicing was first described for HAC1 in S. cerevisiae[1].

Intron conservation

The unconventional splicing was confirmed experimentally for following species:

Computational methods predict HAC-like intron with its characteristic RNA structure in many other species of Fungi, Vertebrates, Arthropoda, Nematoda, Annelida and Mollusca(ref.).


Mechanism of splicing

Splicing of HAC1 and XBP1 transcripts is highly regulated. It occurs in response to presence of unfolded proteins in the endoplasmic reticulum (ER). ER stress activates the endoribonucleolytic activity of IRE1 proteins. IRE1 recognizes splice-site motifs in HAC1 or XBP1 transcripts and cleaves them. Stem-loop structures around splice sites and IRE1-specific sequence motifs (maybe figure here?) are required and sufficient for the process. Joining of exons is performed by tRNA ligase (TRL1 in Saccharomyces cerevisiae)[9].

Consensus structure

Consensus structure of the HAC1/XBP1 intron consists of H2 and H3 hairpins marking the splice sites and H1A and H1B hairpins that bring splice sites together. The usual intron is very short (20, 23 or 26 nt). However, 14 yeast species have a long (>100 nt) intron in HAC1. In Saccharomyces cerevisiae long intron pairs with the 5' UTR and stalls the ribosomes on mRNA.


References

  1. ^ a b c Sidrauski C, Walter P (1997). "The transmembrane kinase Ire1p is a site-specific endonuclease that initiates mRNA splicing in the unfolded protein response". Cell. 90 (6): 1031–9. doi:10.1016/S0092-8674(00)80369-4. PMID 9323131.
  2. ^ Yoshida H, Matsui T, Yamamoto A, Okada T, Mori K. (2001). "XBP1 mRNA is induced by ATF6 and spliced by IRE1 in response to ER stress to produce a highly active transcription factor". Cell. 107 (7): 881–91. doi:10.1016/S0092-8674(01)00611-0. PMID 11779464.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  3. ^ Calfon M, Zeng H, Urano F, Till JH, Hubbard SR, Harding HP, Clark SG, Ron D (2002). "IRE1 couples endoplasmic reticulum load to secretory capacity by processing the XBP-1 mRNA". Nature. 415 (6867): 92–6. doi:10.1038/415092a. PMID 11780124.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  4. ^ Saloheimo M, Valkonen M, Penttila M. (2003). "Activation mechanisms of the HAC1-mediated unfolded protein response in filamentous fungi". Mol Microbiol. 47 (4): 1149–61. doi:10.1046/j.1365-2958.2003.03363.x. PMID 12581366.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  5. ^ Ryoo HD, Domingos PM, Kang MJ, Steller H. (2007). "Unfolded protein response in a Drosophila model for retinal degeneration". EMBO J. 26 (1): 242–52. doi:10.1038/sj.emboj.7601477. PMID 17170705.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  6. ^ Wimalasena TT, Enjalbert B, Guillemette T, Plumridge A, Budge S, Yin Z, Brown AJ, Archer DB (2008). "Impact of the unfolded protein response upon genome-wide expression patterns, and the role of Hac1 in the polarized growth, of Candida albicans". Fungal Genet Biol. 45 (9): 1235–47. doi:10.1016/j.fgb.2008.06.001. PMID 18602013.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  7. ^ Oh MH, Cheon SA, Kang HA, Kim JY (2010). "Functional characterization of the unconventional splicing of Yarrowia lipolytica HAC1 mRNA induced by unfolded protein response". Yeast. 27 (7): 443–52. doi:10.1002/yea.1762. PMID 20162530.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  8. ^ Guerfal M, Ryckaert S, Jacobs PP, Ameloot P, Van Craenenbroeck K, Derycke R, Callewaert N. (2010). "The HAC1 gene from Pichia pastoris: characterization and effect of its overexpression on the production of secreted, surface displayed and membrane proteins". Microb Cell Fact. 9: 49. doi:10.1186/1475-2859-9-49. PMID 20591165.{{cite journal}}: CS1 maint: multiple names: authors list (link) CS1 maint: unflagged free DOI (link)
  9. ^ {{cite journal}}: Empty citation (help)
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