Evolution and function of the epithelial cell-specific ER stress sensor IRE1β

Abstract

Barrier epithelial cells lining the mucosal surfaces of the gastrointestinal and respiratory tracts interface directly with the environment. As such, these tissues are continuously challenged to maintain a healthy equilibrium between immunity and tolerance against environmental toxins, food components, and microbes. An extracellular mucus barrier, produced and secreted by the underlying epithelium plays a central role in this host defense response. Several dedicated molecules with a unique tissue-specific expression in mucosal epithelia govern mucosal homeostasis. Here, we review the biology of Inositol-requiring enzyme 1β (IRE1β), an ER-resident endonuclease and paralogue of the most evolutionarily conserved ER stress sensor IRE1α. IRE1β arose through gene duplication in early vertebrates and adopted functions unique from IRE1α which appear to underlie the basic development and physiology of mucosal tissues.

Fig. 1. Schematic representation of yeast IRE1 and human IRE1α and IRE1β.

All three IRE1 proteins share a similar overall structure, containing a luminal sensor domain, a transmembrane (TM) and juxtamembrane (JM) domain and the cytoplasmic enzymatic kinase and endonuclease domains. Numbers indicate % identity to the corresponding domain of human IRE1β.

Fig. 2. IRE1β is enriched in mucus-secreting cells in the gastrointestinal tract and airways.

Representation of ERN2 expression levels based on available single cell datasets. Red indicates detection of high expression levels, blue indicates absence of expression. Top panel (airways). ERN2 transcript is readily detected in goblet cells and club cells of the large and small airways, and weakly detected in ciliated cells. Bottom panel (intestinal tract). ERN2 transcript is mostly detected in goblet cells, with additional (lower) expression reported in Paneth, and enteroendocrine cells.

Fig. 3. Phylogenetic tree of IRE1 and IRE1-like sequences from selected organisms.

A multiple sequence alignment of 96 IRE1 and IRE1-like coding sequences was made using MAFFT. A maximum-likelihood phylogenetic tree was constructed with IQ-TREE and visualized with FigTree (http://tree.bio.ed.ac.uk/software/figtree/). Numbers indicate bootstrap values. The scale bar for the branch lengths represents genetic distances in the number of estimated nucleotide substitutions per site.

Fig. 4. Impact of sequence variation on IRE1β structure and function.

a, b Sequence conservation was mapped onto the surface of human IRE1α luminal domain (a, pdb 2hz6) and cytosolic domains (b, pdb 4z7h.) Conservation and coloring was calculated using ConSurf server^, with multiple sequence alignment from Fig. 3. c Close-up view of putative interactions in (left panel) nucleotide binding pocket and (right panel) back-to-back dimer interface for IRE1β model (generated from 4z7h template using MODELER.^,). In the dimer representation individual protomers are colored in darker and lighter (IRE1α) blue or (IRE1β) green. Residues are labeled with BOLD’ (e.g., R627′) and REGULAR (e.g., R627) font for the different protomers. The surface rendering shows the electrostatic potential (Negative–Neutral–Positive, Red–White–Blue) mapped onto the solvent excluded surface of one protomer with key interacting residues shown in cartoon and stick representation for the other protomer at the interface. Residues in cartoon view are labeled with regular type face black lettering (e.g., D592), and the position of residues on the surface rendering are labeled with bold type face black lettering (e.g., R617′).

Fig. 5. Schematic summarizing the function of IRE1β in mucosal homeostasis.

IRE1β contributes to XBP1 splicing and/or RIDD activity to maintain mucosal homeostasis in goblet cells (via regulation of Muc2 and Agr2) and enterocytes (via regulation of Mttp). In cells where both isoforms are present, IRE1β interacts with IRE1α oligomers in a manner to suppress stress-induced XBP1 splicing. In comparison with IRE1α, IRE1β displays reduced phosphorylation, impaired oligomerization, and a weaker endonuclease activity.