The Exosome A Proteasome for RNA?

is presumably because defects in one exosome subunit The eukaryotic cell contains a wide variety of RNA specause a failure to assemble the exosome properly, and cies that are either processed from 39-extended precurthe exosome per se is required for viability. This conclusors or degraded in a 39-to-59 direction. How 39-to-59 sion is supported by the observations that inactivation processing is controlled for different transcripts and disof any core component generally gives similar defects tinguished from complete 39-to-59 degradation of an in exosome-dependent events (Mitchell et al., 1997; JaRNA molecule is unknown. Surprisingly, a single comcobs Anderson and Parker, 1998; Allmang et al., 1999a, plex of multiple 39-to-59 exonucleases identified by the 1999b; van Hoof et al., 2000). In addition, there does not Tollervey lab, termed the exosome, catalyzes many of appear to be a substantial free pool of exosome subunits these reactions. For example, the exosome trims 5.8S (Mitchell et al., 1997; Allmang et al., 1999a). This hypothrRNA from a 39-extended precursor and functions in the esis would be similar to what has been observed for the 39-to-59 degradation of mRNA. In this review, we discuss proteasome. Here catalytic subunits are essential for the organization and functions of the exosome. structural reasons, but individual active sites are not The presence of multiple exonucleases in the exoessential (reviewed in Baumeister et al., 1998). However, some complex is analogous to a number of proteases two observations raise the formal possibility that exoboth in prokaryotes and eukaryotes, such as the proteasome subunits may have distinct essential functions some, that assemble in large complexes. In addition, both independent of the entire complex. First, in contrast to the exosome, and the proteasome, require ATPases subunits of the proteasome, which require assembly for for their functions (see below, and reviewed in Gottesactivity, isolated exosome subunits show exonucleoman et al., 1997; Baumeister et al., 1998; DeMartino and lytic activity (see above). Second, homologous human Slaughter, 1999). These similarities suggest that there cDNAs can complement at least some of the phenotypes may be a fundamental advantage to the compartmentalof yeast strains carrying mutations in the RRP4, RRP44, ization of degradative enzymes by their assembly into or CSL4 genes. This suggests that either the exosome larger complexes. subunits are sufficiently conserved to allow assembly What Is the Exosome? between different species, or that exosome subunits Based on copurification, the yeast exosome is a protein may be able to function individually. To resolve these complex that consists of a core of at least ten proteins issues, the analysis of mutant alleles of exosome sub(Rrp4p, Rrp40p to Rrp46p, Mtr3p, and Csl4p; Table 1; units that separate exonucleolytic activity from assemAllmang et al., 1999a). The stoichiometry of the different bly will be needed. subunits is unknown, but the sedimentation of the exoSimilar to the proteasome, the exosome is present in some in glycerol gradients (300–400 kDa; Mitchell et al., both the nucleus and the cytoplasm. This conclusion is 1997) is consistent with a single copy of each subunit. based on immunolocalization of core exosome subunits Strikingly, all ten subunits have been proposed to be and biochemical fractionation (Kinoshita et al., 1991; active 39-to-59 exoribonucleases (Allmang et al., 1999a). Mitchell et al., 1997; Allmang et al., 1999a; Zanchin and Six of the exosome subunits (Rrp41p, Rrp42p, Rrp43p, Goldfarb, 1999). However, the nuclear exosome has an Rrp45p, Rrp46p, and Mtr3p) appear to be 39-to-59 phosadditional subunit, Rrp6p, which is yet another active phorolytic enzymes, since they are related to the 39-to-59 39-to-59 exoribonuclease (Allmang et al., 1999a; Burkard exoribonucleases RNase PH and PNPase from Escheand Butler, 2000). Rrp6p is the only exosome subunit richia coli (Mian, 1997). These E. coli enzymes function that is not essential for viability, although rrp6D strains in the decay of mRNA and the processing of other RNAs. have strong defects in all the known nuclear exosome Unlike hydrolases they utilize phosphate as an attacking functions (see below). group during RNA digestion and produce nucleotide Several lines of evidence indicate that the exosome 59 diphosphates (NDPs). In support of these proposed is conserved in eukaryotes. For example, the majority activities, recombinant Rrp41p is a phosphate-stimuof the exosome subunits identified in yeast have strong lated exonuclease that produces NDPs (Mitchell et al., homologs in other eukaryotes. Moreover, two observa1997). In contrast, Rrp44p is related to the 39 hydrolases tions indicate that these homologs do form an exosome RNase II and RNase R from E. coli (Mian, 1997) and complex in other eukaryotes. First, the human homologs recombinant Rrp44p has 39-to-59 exonuclease activity of Rrp6p (PM-Scl100), Rrp4p, and Rrp45p (PM-Scl75) that releases nucleotide 59 monophosphates (NMPs; are found in the PM-Scl particle, which appears to be Mitchell et al., 1997). Recombinant Rrp4p, purified from the human exosome (Allmang et al., 1999a). Second, E. coli also has 39 exoribonuclease activity that releases the Schizosaccharomyces pombe homolog of Rrp44p,