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Exosome complex

The exosome complex (or PM/Scl complex, often just called the exosome) is a multi-protein complex, capable of degrading various types of RNAs. Exosome complexes can be found in both eukaryotic cells and archaea, while in bacteria a simpler complex called the degradosome carries out similar functions.

The core of the complex has a six-membered ring structure, to which other proteins are attached. In eukaryotic cells, it is present in the cytoplasm, nucleus and especially the nucleolus, although different proteins interact with the complex in these compartments, in order to regulate the RNA degradation activity of the complex to substrates specific for these cell compartments. Substrates of the exosome include messenger RNA, ribosomal RNA, and many species of small RNAs. The exosome has an exoribonucleolytic function, meaning it degrades RNA starting at one side (the so-called 3' end in this case), rather than cleaving the RNA at specific sites.

Although no causative relation between the complex and any disease is known, several proteins in the complex are the target of autoantibodies in patients with specific autoimmune diseases (especially the PM/Scl overlap syndrome) and some antimetabolitic chemotherapies for cancer function by blocking the activity of the complex.

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1 Discovery
2 Structure
3 Function
- 3.1 Enzymatic function
- 3.2 Substrates
4 Disease
- 4.1 Autoimmunity
- 4.2 Cancer
5 List of subunits
6 See also
7 References
8 Further reading

Discovery

The exosome was first discovered as an RNase in 1997 in the budding yeast Saccharomyces cerevisiae, an often used model organism.^[1] Not long after, in 1999, it was realized that the exosome was in fact the yeast equivalent of an already described complex in human cells, the so-called PM/Scl complex, which had been identified as an autoantigen in patients with certain autoimmune diseases years earlier (see below).^[2] Purification of this "PM/Scl complex" allowed the identification of more human exosome proteins and eventually the characterization of all components in the complex.^[3]^[4] In 2001, the increasing amount of genome data that had become available allowed the prediction of exosome proteins in archaea, although it would take another 2 years before the first exosome complex from an archaeal organism was first purified.^[5]^[6]

Structure

Core proteins

The core of the complex has a ring structure consisting of six proteins that all belong to the same class of RNases, the RNase PH-like proteins.^[7] In archaea there are two different PH-like proteins (called Rrp41 and Rrp42), each present three times in an alternating order. Eukaryotic exosome complexes have six different proteins that form the ring structure.^[8]^[9] Of these six eukaryotic proteins, three resemble the archaeal Rrp41 protein and the other three proteins are more similar to the archaeal Rrp42 protein.^[10]

Located on top of this ring are three proteins that have an S1 RNA binding domain (RBD). Two proteins in addition have a K-homology (KH) domain.^[7] In eukaryotes, three different "S1" proteins are bound to the ring, whereas in archaea either one or two different "S1" proteins can be part of the exosome (although there are always three S1 subunits attached to the complex).^[11]

This ring structure is very similar to that of the proteins RNase PH and PNPase. In bacteria, the protein RNase PH, which is involved in tRNA processing, forms a hexameric ring consisting of six identical RNase PH proteins.^[12] In the case of PNPase, which is a phosphorolytic RNA degrading protein found in bacteria and the chloroplasts and mitochondria of some eukaryotic organisms, two RNase PH domains and both an S1 and KH RNA binding domain are part of a single protein, which forms a trimeric complex that adopts a structure almost identical to that of the exosome.^[13] Because of this high similarity in both protein domains and structure, these complexes are thought to be evolutionary related and have a common ancestor.^[14] In bacteria, a separate RNase PH protein exists that is involved in transfer RNA processing, which has been shown to adopt a similar six-membered ring structure, but in this case consisting of 6 identical protein subunits.^[15] The RNase PH-like exosome proteins, PNPase and RNase PH all belong to the RNase PH family of RNases and are phosphorolytic exoribonucleases, meaning they use inorganic phosphate to remove nucleotides from the 3' end of RNA molecules.^[7]

Associated proteins

Besides these nine core exosome proteins, two other proteins often associate with the complex in eukaryotic organisms. One of these is Rrp44, a hydrolytic RNase, which belongs to the RNase R family of hydrolytic exoribonucleases (nucleases that use water to cleave the nucleotide bonds). In yeast, Rrp44 is associated with all exosome complexes and has a crucial role in the activity of the yeast exosome complex.^[16] Remarkably, while a human homologue of the protein exists, no evidence has been found to date that its human homologue is even associated with the human exosome complex.^[7] The second common associated protein is called Rrp6 (in yeast) or PM/Scl-100 (in human). Like Rrp44, this protein is a hydrolytic exoribonuclease, but in this case of the RNase D protein family.^[17] The protein PM/Scl-100 is most commonly part of exosome complexes in the nucleus of cells, but can form part of the cytoplasmic exosome complex as well.^[18]

Regulatory proteins

Apart from these two tightly-bound protein subunits, many proteins interact with the exosome complex in both the cytoplasm and nucleus of cells. These loosely-associated proteins may regulate the activity and specificity of the exosome complex. In the cytoplasm, the exosome interacts with AU rich element (ARE) binding proteins (e.g. KRSP and TTP), which can promote or prevent degradation of mRNAs. The nuclear exosome associates with RNA binding proteins (e.g. MPP6 in humans and Rrp47/C1D in humans and yeast) that control ribosomal RNA processing.^[7]

In addition to single proteins, other protein complexes interact with the exosome. One of those is the cytoplasmic Ski complex, which includes an RNA helicase (Ski2) and is involved in mRNA degradation.^[19] In the nucleus, the processing of rRNA and snoRNA by the exosome is mediated by the TRAMP complex, which contains both RNA helicase (Mtr4) and polyadenylation (Trf4) activity.^[20]

Function

Enzymatic function

As stated above, the exosome complex contains many proteins that contain ribonuclease domains. These are all 3'-5' exoribonuclease domains, meaning the enzymes degrade RNA molecules from their 3' end. The complex contains both phosphorolytic exoribonucleases (the RNase PH-like proteins) and, in eukaryotes, also hydrolytic exoribonucleases (the RNase R and RNase D domain proteins). The phosphorolytic enzymes use inorganic phosphate to cleave the phosphodiester bonds - releasing nucleotide disphosphates. The hydrolytic enzymes use water to hydrolyse these bonds - releasing nucleotide monosphosphates).

In archaea, the Rrp41 subunit of the complex is a phosphorolytic exoribonuclease. Three copies of this protein are present in the ring and this enzyme is responsible for the activity of the complex.^[9] In eukaryotes, none of the human RNase PH subunits have retained this catalytic activity, meaning the core ring structure of the human exosome has no enzymatically-active protein.^[21] In yeast this is compensated by one of the associated hydrolytic enzymes, Rrp44, which is responsible for most of the exosome ribonuclease activity^[22], but this particular hydrolytic subunit may be restricted to yeast, as no protein homologous to Rrp44 is present in the human (and archaeal) exosome complex.^[23]^[24]

Still, in both human and yeast, another hydrolytic enzyme can be associated with the complex (Rrp6), which contributes to the activity of the yeast exosome and is solely resonsible for the activity of the human complex. Although originally the S1 domain proteins were thought to have 3'-5' hydrolytic exoribonuclease activity as well, this existence of this activity has recently been questioned and these proteins might have just a role in binding substrates prior to their degradation by the complex.^[22]

Substrates

The exosome is involved in the degradation an processing of a wide variety of RNA species. In the cytoplasm of cells, it is involved in the turn-over of messenger RNA (mRNA) molecules. The complex can degrade mRNA molecules that have been tagged for degradation because they contain errors, through interactions with proteins from the nonsense mediated decay or non-stop decay pathways. Alternatively, mRNAs are degraded as part of their normal turnover. Several proteins that stabilize or destabilize mRNA molecules through binding to AU-rich elements in the 3' UTR of mRNAs interact with the exosome complex.^[25]^[26]^[27] In the nucleus, the exosome is required for the correct processing of several small nuclear RNA molecules.^[28] Finally, the nucleolus is the compartment where the majority of the exosome complexes are found. There it plays a role in the processing of the 5.8S ribosomal RNA (the first identified function of the exosome) and of several small nucleolar RNA.^[1]^[29]^[28]

Although most cells have other enzymes that can degrade RNA, either from the 3' or 5' end of the RNA, the exosome complex is essential for cell survival. When the expression of exosome proteins is artificially reduced or stopped, for example by RNA interference, growth stops and the cells eventually die. Both the core proteins of the exosome complex, as well as the two main associated proteins, are essential proteins.^[30] Bacteria do not have an exosome complex, however, similar functions are performed by a simpler complex that includes the protein PNPase, called the degradosome.^[31]

Disease

Autoimmunity

The exosome complex is the target of autoantibodies in patients that suffer from various autoimmune diseases. These autoantibodies are mainly found in people that suffer from the PM/Scl overlap syndrome, an autoimmune disease in which patients have symptoms from both scleroderma and either polymyositis or dermatomyositis.^[32] Autoantibodies can be detected in the serum of patients by a variety of assays. In the past, the most commonly used methods were double immunodiffusion using calf thymus extracts, immunofluorescence on HEp-2 cells or immunoprecipitation from human cell extracts. In immunoprecipitation assays with sera from anti-exosome positive sera, a distinctive set of proteins is precipitated. Already years before the exosome complex was identified, this pattern was termed the PM/Scl complex.^[33] Immunofluorescence using sera from these patients usually shows a typical staining of the nucleolus of cells, which sparked the suggestion that the antigen recognized by autoantibodies might be important in ribosome synthesis.^[34] More recently, recombinant exosome proteins have become available and these have been used to develop line immunoassays (LIAs) and enzyme linked immunosorbent assays (ELISAs) for detecting these antibodies.^[7]

In these diseases, antibodies are mainly directed against two of the proteins of the complex, called PM/Scl-100 (the RNase D like protein) and PM/Scl-75 (one of the RNase PH like proteins from the ring) and antibodies recognizing these proteins are found in approximately 30% of patients with the PM/Scl overlap syndrome.^[35] Although these two proteins are the main target of the autoantibodies, other exosome subunits and associated proteins (like C1D) can be targeted in these patients.^[36]^[37] Currently, the most sensitive way to detect these antibodies is by using a peptide, derived from the PM/Scl-100 protein, as the antigen in an ELISA, instead of complete proteins. By this method, autoantibodies are found in up to 55% of patients with the PM/Scl overlap syndrome, but they can also be detected in patients suffering from either scleroderma, polymyositis or dermatomyositis alone.^[38]

As the autobodies are mainly found in patients that have characteristics of several different autoimmune diseases, the clinical symptoms of these patients can vary widely. The symptoms that are seen most often are the typical symptoms of the individual autoimmune diseases and include Raynaud's phenomenon, arthritis, myositis and scleroderma.^[39] Treatment of these patients is symptomatic and is similar to treatment for the individual autoimmune disease, often involving either immunosuppressive or immunomodulating drugs.^[40]

Cancer

The exosome has been shown to be inhibited by the antimetabolite drug fluorouracil, which is a drug used in chemotherapy treatment of cancer. It is one of the most successful drugs for treating solid tumors. In yeast cells treated with fluorouracil, defects were seen in the processing of ribosomal RNA, identical to those seen when the activity of the exosome was blocked by molecular biological strategies. Lack of correct ribosomal RNA processing is lethal to cells, explaining the antimetabolic effect of the drug.^[41]

List of subunits

Legend	General name	Domains	Human	Yeast (S. cerevisiae)	Archaea	MW (kD)	Human gene	Yeast gene
1	Csl4	S1 RBD	hCsl4	Csl4p/Ski4p	Csl4	21-32	EXOSC1	YNL232W
2	Rrp4	S1/KH RBD	hRrp4	Rrp4p	Rrp4	28-39	EXOSC2	YHR069C
3	Rrp40	S1/KH RBD	hRrp40	Rrp40p	(Rrp4)^[42]	27-32	EXOSC3	YOL142W
4	Rrp41	RNase PH	hRrp41	Rrp41p/Ski6p	Rrp41	26-28	EXOSC4	YGR195W
5	Rrp46	RNase PH	hRrp46	Rrp46p	(Rrp41)^[42]	25-28	EXOSC5	YGR095C
6	Mtr3	RNase PH	hMtr3	Mtr3p	(Rrp41)^[42]	24-37	EXOSC6	YGR158C
7	Rrp42	RNase PH	hRrp42	Rrp42p	Rrp42	29-32	EXOSC7	YDL111C
8	Rrp43	RNase PH	OIP2	Rrp43p	(Rrp42)^[42]	30-44	EXOSC8	YCR035C
9	Rrp45	RNase PH	PM/Scl-75	Rrp45p	(Rrp42)^[42]	34-49	EXOSC9	YDR280W
10	Rrp6	RNase D	PM/Scl-100	Rrp6p	n/a	84-100	EXOSC10	YOR001W
11	Rrp44	RNase R	(hDis3)^[43]	Rrp44p/Dis3p	n/a	105-113	KIAA1008	YOL021C

References

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^ Allmang et al. (1999). "The yeast exosome and human PM-Scl are related complexes of 3' --> 5' exonucleases". Genes and Development 13 (16): 2148-58. PMID 10465791.
^ Brouwer et al. (2001). "Three novel components of the human exosome". Journal of Biological Chemistry 276: 6177-84. PMID 11110791.
^ Chen et al. (2001). "AU binding proteins recruit the exosome to degrade ARE-containing mRNAs". Cell 107: 451-64. PMID 11719186.
^ Koonin et al. (2001). "Prediction of the archaeal exosome and its connections with the proteasome and the translation and transcription machineries by a comparative-genomic approach". Genome Research 11 (2): 240-52. PMID 11157787.
^ Evguenieva-Hackenberg et al. (2003). "An exosome-like complex in Sulfolobus solfataricus". EMBO Reports 4 (9): 889-93. PMID 12947419.
^ ^a ^b ^c ^d ^e ^f Schilders et al. (2006). "Cell and molecular biology of the exosome: how to make or break an RNA". International review of cytology 251: 159-208. PMID 16939780.
^ Lorentzen et al. (2005). "The archaeal exosome core is a hexameric ring structure with three catalytic subunits". Nature Structural & Molecular Biology 12: 575-81. PMID 15951817.
^ ^a ^b Shen et al. (2006). "A view to a kill: structure of the RNA exosome". Cell 127: 1093-5. PMID 17174886.
^ Raijmakers et al. (2002). "Protein-protein interactions between human exosome components support the assembly of RNase PH-type subunits into a six-membered PNPase-like ring". Journal of Molecular Biology 323: 653-63. PMID 12419256.
^ Walter et al. (2006). "Characterization of native and reconstituted exosome complexes from the hyperthermophilic archaeon Sulfolobus solfataricus". Molecular Microbiology 62: 1076-89. PMID 17078816.
^ Ishii et al. (2003). "Crystal structure of the tRNA processing enzyme RNase PH from Aquifex aeolicus". Journal of Biological Chemistry 278: 32397-404. PMID 12746447.
^ Symmons et al. (2000). "A duplicated fold is the structural basis for polynucleotide phosphorylase catalytic activity, processivity, and regulation". Structure 8: 1215-26. PMID 11080643.
^ Lin-Chao et al. (2007). "The PNPase, exosome and RNA helicases as the building components of evolutionarily-conserved RNA degradation machines". Journal of Biomedical Science 14: 523-32.
^ Harlow et al. (2004). "Crystal structure of the phosphorolytic exoribonuclease RNase PH from Bacillus subtilis and implications for its quaternary structure and tRNA binding". Protein Science 13: 668-77. PMID 14767080.
^ Schneider et al. (2007). "The exosome subunit Rrp44 plays a direct role in RNA substrate recognition". Molecular Cell 27: 324-31. PMID 17643380.
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^ Wang et al. (2005). "Domain interactions within the Ski2/3/8 complex and between the Ski complex and Ski7p". RNA 11: 1291-302. PMID 16043509.
^ LaCava et al. (2005). "RNA degradation by the exosome is promoted by a nuclear polyadenylation complex". Cell 121: 713-24. PMID 15935758.
^ Liu et al. (2007). "Erratum: Reconstitution, activities, and structure of the eukaryotic RNA exosome". Cell 131: 188-189. PMID 17174896.
^ ^a ^b Dziembowski et al. (2007). "A single subunit, Dis3, is essentially responsible for yeast exosome core activity". Nature Structural & Molecular Biology 14: 15-22. PMID 17173052.
^ Liu et al. (2006). "Reconstitution, activities, and structure of the eukaryotic RNA exosome". Cell 127: 1223-37. PMID 17174896.
^ Lorentzen et al. (2005). "Structural basis of 3' end RNA recognition and exoribonucleolytic cleavage by an exosome RNase PH core". Molecular Cell 20: 473-81. PMID 16285928.
^ LeJeune et al. (2003). "Nonsense-mediated mRNA decay in mammalian cells involves decapping, deadenylating, and exonucleolytic activities". Molecular Cell 12: 675-87. PMID 14527413.
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^ ^a ^b Allmang et al. (1999). "Functions of the exosome in rRNA, snoRNA and snRNA synthesis". EMBO Journal 18: 5399-410. PMID 10508172.
^ Schilders et al. (2005). "MPP6 is an exosome-associated RNA-binding protein involved in 5.8S rRNA maturation". Nucleic Acids Research 33: 6795-804. PMID 16396833.
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^ Schilders et al. (2007). "C1D is a major autoantibody target in patients with the polymyositis-scleroderma overlap syndrome". Arthritis & Rheumatism 56: 2449-54. PMID 17599775.
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^ ^a ^b ^c ^d ^e In archaea several exosome proteins are present in multiple copies, to form the full core of the exosome complex.
^ Although the yeast protein Rrp44 is part of the yeast complex, its human homologue hDis3 has never been found to be associated with the human complex.