As the name says, ubiquitin is a small protein expressed ubiquitously. Ubiquitination occurs on the Lys residues of the target proteins through enzymatic actions of E1 (activating enzyme), E2 (conjugating enzyme) and E3 (ligase) (Figure 1A). Interestingly, ubiquitin itself has 7 Lys that can be used for ubiquitination, leading 7 different homotypic-linkages of chain formation (Ikeda, EMBO Rep, 2008, Figure 1B).
It is probably possible that the substrates are modified by ubiquitin chains with a mixture of different linkage types or by branched chains in vivo (Figure 1C). Each of the chain types possesses a very distinct structure (Figure 1D), which contributes to their own unique protein networks (Ikeda, Cell, 2010). To our surprise, ubiquitin recently was found to form linearly-linked (Met1-linked/ head-to-tail/ tandem repeated) chains under a specific condition (Rahighi, Cell, 2009, Ikeda, Nature, 2011, Figure 1B).

These chains are produced by a ligase complex called LUBAC (linear-ubiquitin assembly complex). LUBAC was originally found to contain 2 proteins, HOIP with catalytic centre and HOIL-1L. We recently discovered SHARPIN as the 3rd component of LUBAC (Ikeda, Nature, 2011, Figure 2A). HOIP is the E3 ligase with a catalytic centre in its RBR (Ring-Between-Ring fingers) domain. Interestingly, HOIP requires one of the adaptor molecules, SHARPIN or HOIL-1L for the E3 ligase activity (Figure 2B). Even though ubiquitin has been studied intensively in the last decade, it is not yet well understood how RBR type E3 ligase functions enzymatically.
One of our focuses is to clarify how the enzymatic action of LUBAC is controlled. By clarifying the regulatory mechanism, we aim to identify novel RBR-type E3 ligases, which generate linear ubiquitin chains.

A concept of linear ubiquitin chains is just about to be spread in the ubiquitin filed. Our SILAC-based mass spectrometry analysis showed that a concentration of linear ubiquitin chains in cells is relatively low in comparison to other linkage types (Ikeda, Nature, 2011). This suggests that linear ubiquitination is tightly regulated to function in specific conditions. So far, the only known condition where linear ubiquitin chains play a role is inflammatory responses (Figure 3A, B, and C).
We aim to deepen our knowledge in inflammatory and cell death signalling that are controlled by linear ubiquitin networks. Our major goal is to discover such specific conditions and understand ‘what linear-ubiquitin chains do in regulation of physiology’. To this end, we use combined techniques of biochemistry and genetically modified animal models (Figure 3C).