The bZIP intron RNA motif is an RNA structure guiding splicing of a non-canonical

intron An intron is any nucleotide sequence within a gene that is not expressed or operative in the final RNA product. The word ''intron'' is derived from the term ''intragenic region'', i.e. a region inside a gene."The notion of the cistron .e., gene. ...

from bZIP-containing genes called HAC1 in

yeast Yeasts are eukaryotic, single-celled microorganisms classified as members of the fungus kingdom. The first yeast originated hundreds of millions of years ago, and at least 1,500 species are currently recognized. They are estimated to constitut ...

XBP1 X-box binding protein 1, also known as XBP1, is a protein which in humans is encoded by the ''XBP1'' gene. The ''XBP1'' gene is located on chromosome 22 while a closely related pseudogene has been identified and localized to chromosome 5. The XBP ...

Metazoa Animals are multicellular, eukaryotic organisms in the biological kingdom Animalia. With few exceptions, animals consume organic material, breathe oxygen, are able to move, can reproduce sexually, and go through an ontogenetic stage in ...

, Hxl1 or Cib1 in

Basidiomycota Basidiomycota () is one of two large divisions that, together with the Ascomycota, constitute the subkingdom Dikarya (often referred to as the "higher fungi") within the kingdom Fungi. Members are known as basidiomycetes. More specifically, Basi ...

and bZIP60 in plants. Splicing is performed independently of the

spliceosome A spliceosome is a large ribonucleoprotein (RNP) complex found primarily within the nucleus of eukaryotic cells. The spliceosome is assembled from small nuclear RNAs (snRNA) and numerous proteins. Small nuclear RNA (snRNA) molecules bind to specifi ...

Ire1 The serine/threonine-protein kinase/endoribonuclease inositol-requiring enzyme 1 α (IRE1α) is an enzyme that in humans is encoded by the ''ERN1'' gene. Function The protein encoded by this gene is the ER to nucleus signalling 1 protein, a hu ...

, a

kinase In biochemistry, a kinase () is an enzyme that catalyzes the transfer of phosphate groups from high-energy, phosphate-donating molecules to specific substrates. This process is known as phosphorylation, where the high-energy ATP molecule don ...

with endoribonuclease activity. Exons are joined by a tRNA ligase. Recognition of the

splice sites is mediated by a base-paired

secondary structure Protein secondary structure is the three dimensional conformational isomerism, form of ''local segments'' of proteins. The two most common Protein structure#Secondary structure, secondary structural elements are alpha helix, alpha helices and beta ...

of the

mRNA In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of Protein biosynthesis, synthesizing a protein. mRNA is ...

that forms at the exon/intron boundaries. Splicing of the bZIP intron is a key regulatory step in the unfolded protein response (UPR). The Ire-mediated unconventional splicing was first described for HAC1 in ''

S. cerevisiae ''Saccharomyces cerevisiae'' () (brewer's yeast or baker's yeast) is a species of yeast (single-celled fungus microorganisms). The species has been instrumental in winemaking, baking, and brewing since ancient times. It is believed to have bee ...

''.

Consensus structure

The secondary structure of the bZIP intron is very well conserved, and consists of two hairpins (H2 and H3) around the splice sites, and an extended hairpin (H1) that brings the splice sites together (see figure). The sequence of the intron is well conserved only around the splice sites. Non-canonical splicing motifs CNG'CNG in the loop region of H2 and H3 hairpins are conserved. The consensus intron is very short in Metazoa (20, 23 or 26 nt). However, yeast species have a long (>100 nt) intron in HAC1. In ''

Saccharomyces cerevisiae ''Saccharomyces cerevisiae'' () (brewer's yeast or baker's yeast) is a species of yeast (single-celled fungus microorganisms). The species has been instrumental in winemaking, baking, and brewing since ancient times. It is believed to have been o ...

'' the long

pairs with the

5′ UTR The 5′ untranslated region (also known as 5′ UTR, leader sequence, transcript leader, or leader RNA) is the region of a messenger RNA (mRNA) that is directly upstream from the initiation codon. This region is important for the regulation of ...

and stalls the

ribosomes Ribosomes ( ) are macromolecular machines, found within all cells, that perform biological protein synthesis (mRNA translation). Ribosomes link amino acids together in the order specified by the codons of messenger RNA (mRNA) molecules to f ...

on the mRNA.

Mechanism of splicing

Environmental stress can cause proteins to misfold and aggregate. To protect from these undesirable processes, a cell can activate the unfolded protein response (UPR) pathway. Splicing of the bZIP mRNA by Ire1 is one of the highly regulated ways of activating the UPR in response to presence of unfolded proteins in the

endoplasmic reticulum The endoplasmic reticulum (ER) is, in essence, the transportation system of the eukaryotic cell, and has many other important functions such as protein folding. It is a type of organelle made up of two subunits – rough endoplasmic reticulum ( ...

(ER). ER stress activates the endoribonucleolytic activity of

IRE1 The serine/threonine-protein kinase/endoribonuclease inositol-requiring enzyme 1 α (IRE1α) is an enzyme that in humans is encoded by the ''ERN1'' gene. Function The protein encoded by this gene is the ER to nucleus signalling 1 protein, a hu ...

proteins.

recognizes splice-site motifs in bZIP transcript and cleaves it. Stem-loop structures around the splice sites and

-specific sequence motifs are both necessary and sufficient for splicing to occur. The joining of exons is performed by tRNA ligase (TRL1 in ''

'').

Intron conservation

Ire-mediated unconventional splicing of the bZIP intron has been confirmed experimentally in the following species: * Yeast: ''

'', '' Candida albicans'', ''

Yarrowia lipolytica ''Yarrowia'' is a fungal genus in the family Dipodascaceae. For a while the genus was monotypic, containing the single species ''Yarrowia lipolytica'', a yeast that can use unusual carbon sources, such as hydrocarbons. This has made it of interes ...

'', ''

Pichia pastoris ''Pichia pastoris'' is a species of methylotrophic yeast. It was found in the 1960s, with its feature of using methanol as a source of carbon and energy. After years of study, ''P. pastoris'' was widely used in biochemical research and biotech i ...

'', ''

Candida parapsilosis ''Candida parapsilosis'' is a fungal species of yeast that has become a significant cause of sepsis and of wound and tissue infections in immunocompromised people. Unlike ''Candida albicans'' and ''Candida tropicalis'', ''C. parapsilosis'' is not ...

'' * Animals:

human Humans (''Homo sapiens'') are the most abundant and widespread species of primate, characterized by bipedalism and exceptional cognitive skills due to a large and complex brain. This has enabled the development of advanced tools, culture, ...

mouse A mouse ( : mice) is a small rodent. Characteristically, mice are known to have a pointed snout, small rounded ears, a body-length scaly tail, and a high breeding rate. The best known mouse species is the common house mouse (''Mus musculus' ...

and ''

Caenorhabditis elegans ''Caenorhabditis elegans'' () is a free-living transparent nematode about 1 mm in length that lives in temperate soil environments. It is the type species of its genus. The name is a blend of the Greek ''caeno-'' (recent), ''rhabditis'' (ro ...

'', fruit fly, honey bee,

carp Carp are various species of oily freshwater fish from the family Cyprinidae, a very large group of fish native to Europe and Asia. While carp is consumed in many parts of the world, they are generally considered an invasive species in parts of ...

whiteleg shrimp Whiteleg shrimp (''Litopenaeus vannamei'', synonym ''Penaeus vannamei''), also known as Pacific white shrimp or King prawn, is a species of prawn of the eastern Pacific Ocean commonly caught or farmed for food. Description ''L. vannamei'' grows ...

*Other Fungi: ''

Trichoderma reesei ''Trichoderma reesei'' is a mesophilic and filamentous fungus. It is an anamorph of the fungus ''Hypocrea jecorina''. ''T. reesei'' can secrete large amounts of cellulolytic enzymes (cellulases and hemicellulases). Microbial cellulases have ...

'' and ''

Aspergillus nidulans ''Aspergillus nidulans'' (also called ''Emericella nidulans'' when referring to its sexual form, or teleomorph) is one of many species of filamentous fungi in the phylum Ascomycota. It has been an important research organism for studying eukaryot ...

'', '' Neurospora crassa'', ''

Cryptococcus neoformans ''Cryptococcus neoformans'' is an encapsulated yeast belonging to the class Tremellomycetes and an obligate aerobe that can live in both plants and animals. Its teleomorph is a filamentous fungus, formerly referred to ''Filobasidiella neoformans' ...

'', ''

Ustilago maydis Corn smut is a plant disease caused by the pathogenic fungus ''Ustilago maydis'' that causes smut on maize and teosinte. The fungus forms galls on all above-ground parts of corn species. It is edible, and is known in Mexico as the delicacy ''h ...

'' * Plants:

Arabidopsis thaliana ''Arabidopsis thaliana'', the thale cress, mouse-ear cress or arabidopsis, is a small flowering plant native to Eurasia and Africa. ''A. thaliana'' is considered a weed; it is found along the shoulders of roads and in disturbed land. A winter a ...

maize Maize ( ; ''Zea mays'' subsp. ''mays'', from es, maíz after tnq, mahiz), also known as corn (North American and Australian English), is a cereal grain first domesticated by indigenous peoples in southern Mexico about 10,000 years ago. Th ...

. Computational methods predict a bZIP

with its characteristic RNA structure in 128 out of 156 species studied. In

Fungi A fungus ( : fungi or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as a kingdom, separately from ...

a bZIP intron was initially found only in

Ascomycota Ascomycota is a phylum of the kingdom Fungi that, together with the Basidiomycota, forms the subkingdom Dikarya. Its members are commonly known as the sac fungi or ascomycetes. It is the largest phylum of Fungi, with over 64,000 species. The def ...

(in 52 out of 63 species analysed) but experimental studies showed it is also present in

and other Candida species. All 45 vertebrate genomes analysed, 19 of Arthropoda, 7 of Nematoda, 2 of Annelida and 2 of

Mollusca Mollusca is the second-largest phylum of invertebrate animals after the Arthropoda, the members of which are known as molluscs or mollusks (). Around 85,000 extant species of molluscs are recognized. The number of fossil species is esti ...

contain a characteristic HAC1-like structure in an open reading frame.

References

{{reflist, 2 RNA splicing Non-coding RNA