Linear ubiquitination signals in adaptive immune responses

Abstract

Ubiquitin can form eight different linkage types of chains using the intrinsic Met 1 residue or one of the seven intrinsic Lys residues. Each linkage type of ubiquitin chain has a distinct three-dimensional topology, functioning as a tag to attract specific signaling molecules, which are so-called ubiquitin readers, and regulates various biological functions. Ubiquitin chains linked via Met 1 in a head-to-tail manner are called linear ubiquitin chains. Linear ubiquitination plays an important role in the regulation of cellular signaling, including the best-characterized tumor necrosis factor (TNF)-induced canonical nuclear factor-κB (NF-κB) pathway. Linear ubiquitin chains are specifically generated by an E3 ligase complex called the linear ubiquitin chain assembly complex (LUBAC) and hydrolyzed by a deubiquitinase (DUB) called ovarian tumor (OTU) DUB with linear linkage specificity (OTULIN). LUBAC linearly ubiquitinates critical molecules in the TNF pathway, such as NEMO and RIPK1. The linear ubiquitin chains are then recognized by the ubiquitin readers, including NEMO, which control the TNF pathway. Accumulating evidence indicates an importance of the LUBAC complex in the regulation of apoptosis, development, and inflammation in mice. In this article, I focus on the role of linear ubiquitin chains in adaptive immune responses with an emphasis on the TNF-induced signaling pathways.

Keywords: LUBAC; NEMO; NF-κB; TNF; apoptosis; linear ubiquitin chain.

Figure 1. Ubiquitination in the TNF-induced NF-κB signaling cascade

Different linkage types of ubiquitin chains including Met 1-, Lys 11-, Lys 48-, and Lys 63-linked ubiquitin chains participate in the TNF-induced NF-κB signaling pathway and have roles in fine-tuning the regulation of the downstream cascade. Ubiquitin chains are generated by E3 ligases (shown in orange), such as cIAP, HOIP containing LUBAC complex, and SCF-βTrCP. These ubiquitin chains are hydrolyzed by DUBs (in yellow) such as OTULIN and CYLD. A20 has a dual role as an E3 ligase as well as a DUB. Ubiquitination of the substrates including cIAPs, RIPK1, NEMO, and IκB-α have shown to be critical for the signaling pathway.

Figure 2. Linear ubiquitin interaction domains in different proteins

Schematic domain structures of the linear ubiquitin chain interacting proteins are shown. Linear ubiquitin interacting domains, such as the UBAN domains in NEMO, ABIN proteins and Optineurin, A20-ZF7, OTULIN-OTU and HOIL-1L-NZF-tail, are indicated in blue. Helix; HLX, Coiled-coil; CC, ABIN homology domain; AHD, NEMO-binding domain; NBD, leucine zipper; LZ, LC3-interacting region; LIR, ubiquitin-like; UBL, really interesting new gene; RING, in between ring; IBR.

Figure 3. Schematic domain structures of the LUBAC components and OTULIN

The LUBAC complex consists of HOIP, Sharpin, and HOIL-1L. Schematic domain structures, interactions with other components and interactions with ubiquitin molecules are indicated. The PH fold in Sharpin is used for homo-oligomerization. The UBL domains of Sharpin and HOIL-1L interact with HOIP-NZF2 and HOIP-UBA, respectively. OTULIN interacts with HOIP via the PUB domain. Sharpin-NZF, HOIP-NZF1 and HOIP-LDD interact with monoubiquitin (Protein Data Bank (pdb) code 1UBQ). OTULIN-OTU and HOIL-1L-NZF-C terminal tail bind to linear diubiquitin chain (pdb code 2W9N).

Figure 4. TNFR complex II-mediated apoptosis signaling cascades

The LUBAC complex participates not only in the TNFR complex I-mediated NF-κB signaling pathway, but also in the TNFR complex II-dependent apoptosis pathway. Sharpin inhibits TNFR complex II directly. HOIP and HOIL-1L play a role in the apoptosis regulation. An involvement of linear ubiquitinated substrates, DUBs such as OTULIN and CYLD is elusive.