In eukaryotic organisms, there exist at least three distinct multi-protein assemblies that are jointly referred to as 'PCI complexes' [1
] and have a similar subunit architecture despite their fundamentally different function: i) the proteasome lid, a subcomplex of the 19S proteasome regulator and the 26S proteasome, ii) the COP9 signalosome or CSN complex, and iii) the eukaryotic translation initiation factor eIF3. As a common feature, these complexes are composed of multiple subunits harbouring the PCI domain, named after the three participating complexes [2
], sometimes also referred to as the PINT domain [3
]. Other subunits of these complexes are characterized by a second shared homology domain called MPN (M
Among these complexes, the proteasome lid and the CSN share a particular degree of analogy. Both complexes consist of eight core subunits, six of them of the PCI class and two of the MPN class. As described previously [1
] and summarized in table , there is a clear 1:1 correspondence between the paralogous sets of PCI and MPN subunits. In addition, a similar ring-shaped structure was observed for the two complexes [4
] and there is evidence that in those rings paralogous subunits occupy equivalent positions [5
]. By contrast, the eIF3 complex has a smaller number of PCI subunits (table ) and its two MPN subunits are absent in several unicellular eukaryotes. Unlike the proteasome lid and the CSN, the eIF3 complex contains a number of non-PCI/non-MPN subunits, which are required for its function in translation.
PCI complexes and their subunit correspondence
Despite the common homology domains and a similar structure, the functions of the three PCI complexes are very different. The proteasome lid, in combination with the 'base' complex containing a hexameric ring of AAA-ATPases, forms the 19S regulatory particle, which in turn constitutes an essential subcomplex of the 26S proteasome [6
]. The lid complex contains an intrinsic deubiquitinating activity, which is encoded by the MPN subunit Rpn11 that has the hallmarks of a metalloprotease [7
]. No specific function has been described for the PCI subunits of the lid. The CSN complex has been first described as a regulator of photomorphogenesis in plants, but seems to regulate diverse cellular processes like signal transduction, regulation of transcription or cell proliferation [10
]. Csn5, an MPN-bearing subunit of the signalosome, which is analogous to Rpn11, also encodes a metalloprotease that is essential for the removal of the ubiquitin-like protein Nedd8 from cullins [12
] The third PCI complex, the translation initiation factor eIF3, promotes the formation of preinitiation complexes and works as a scaffold by binding to other initiation factors, to ribosomes and to mRNA [13
]. Both MPN subunits of eIF3 lack the residues necessary for metal binding [8
] and are most likely catalytically inactive.
So far, the metal-containing MPN subunits and the non-PCI/non-MPN portion of the complex constitute the only known carriers of functionality. The PCI proteins themselves seem to be the main building blocks of the complexes, a fact already suggested by their high abundance. There are several hints that the PCI subunits are crucial for proper complex assembly [16
]. The MPN subunits of the three complexes are rather well conserved and the detection of MPN domains and their boundaries is relatively straightforward. By contrast, the degree of conservation between PCI subunits is highly variable. Sequence similarity between the corresponding subunits of proteasome lid and CSN is generally easy to spot, while the detection of similarity between other paralogous PCI subunits typically requires sophisticated sequence comparison approaches, such as the generalized profile method [2
]. A particular challenge is the detection of the highly divergent PCI domains in the budding yeast CSN-like complex [21
] and those of the eIF3 complex, where only three PCI subunits could be detected in the initial survey [2
]. Due to this difficulties, it is to be expected that there are still a number of highly divergent PCI domain proteins in eukaryotic genomes, which have eluded detection so far. A second issue in the bioinformatical definition of the PCI domain concerns the position of its N-terminal boundary. In general, homology domains are thought to correspond to structural domains in the sense of autonomous folding units; they are typically characterized by a pronounced loss of sequence similarity at the domain boundaries. While this is true for the PCI domain C-terminus, the N-terminal domain boundary is blurred through a gradual decay in sequence similarity instead of a sharp drop. As a consequence, different PCI domain boundaries have been used in the literature [2
] and in various domain databases like PROSITE [22
], Pfam [23
] and SMART [24
]. The corresponding accession numbers are PS50250, PF01399 and SM00088, respectively.
During an exhaustive bioinformatical analysis of proteasome subunits and other components of the ubiquitin/proteasome system, we obtained two independent results jointly suggesting that a structure-based redefinition of the PCI domain is appropriate: on one hand, we detected multiple instances of TPR-like repeats in the N-terminus of many PCI proteins, which suggests that the homology between the proteasome and CSN components is not restricted to the PCI domain itself. On the other hand, we detected a previously overlooked PCI domain in the novel eIF3 subunit eIF3k [25
]. Most interestingly, an X-ray structure of eIF3k has been published recently [26
]. Based on this structure and on our alignment data, we suggest a bipartite consensus model for the canonical PCI proteins, consisting of a C-terminal 'winged helix' domain preceded by an extended helical repeat region. We use this model to re-evaluate some bioinformatical and experimental findings that have been enigmatic so far.