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Exosome Journal Club July 7, 2006

Exosome Journal Club July 7, 2006. Eur. J. Cell Biol . 2004, 83, 175-183. Nature Struct. Mol. Biol . 2004, 11, 121-126. TRENDS Cell Biol . 2002, 12, 90-96. History.

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Exosome Journal Club July 7, 2006

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  1. Exosome Journal Club July 7, 2006 Eur. J. Cell Biol. 2004, 83, 175-183. Nature Struct. Mol. Biol. 2004, 11, 121-126. TRENDS Cell Biol. 2002, 12, 90-96.

  2. History • The human exosome, originally designated PM/Scl complex, was first identified as an autoantigen in 1977. Patients with this antigen have overlapped syndromes of Polymyositis (PM, 多發性肌炎) and scleroderma (Scl, 硬皮病). • The PM/Scl antigen was shown to be a nucleolar complex consisting of 11-16 proteins. The main autoantigenic proteins are PM/Scl-100 and PM/Scl-75. • Yeast exosome discovered in 1997. A screen for strains with defects in 5.8S rRNA processing identified a mutant (rrp4p) that produced a ladder of 3’-extended 5.8S molecule (1996). Five proteins in exosome, Rrp4p, Rrp41p, Rrp42p, Rrp43p and Rrp44p, are required for 3’ processing of the 5.8S rRNA (1997). • The PM/Scl complex was shown to be the human equivalent of yeast exosome (Rrp6p homologous to PM/Scl-100 in 1998, Rrp6p found in yeast exsome in 1999). • Be careful, small membrane vesicles secreted by cells are also termed “exosome”.

  3. red: in vitro 3’-5’exonuclease activity RNase PH RNase PH Exosome Core Proteins: 6 x RNase PH + 3 x S1/KH E. ColiArcheal Yeast Human Conserved domain PNPase Rrp41 Rrp41p/Ski6p hRrp41p RNase PH (x 3) (x 3) Rrp46p hRrp46p RNase PH (Crn-5) Mtr3p hMtr3p RNase PH Rrp42 Rrp42phRrp42p RNase PH (x 3) Rrp43pOIP2 RNase PH Rrp45p PM/Scl-75 RNase PH Csl4 Csl4p/Ski4p hCsl4p S1 RBD (the only one without RNase activity) Rrp4p Rrp4phRrp4p S1/KH Rrp40p hRrp40p S1/KH Other common proteins: (RNase R?) Rrp44p/Dis3p (hDis3p) RNase R (RNase D?) Rrp6p PM/Scl-100 RNase D (Crn-3) (nuclear only) E. Coli PNPase Polynucleotide phosphorylase

  4. Three dimensional model of the yeast exosome Aloy, P. et al. EMBO Reports, 2004, 3, 628-635. A complex prediction: three dimensional model of the yeast exosome.

  5. Other Exosome Associated Proteins E. ColiArcheal Yeast HumanConservedComments domain (RhlB?) Skip2p hMtr3p DEAD box Skip3p hRrp42p TRP repeat Ski8p OIP2 WD40 repeats Ski7p PM/Scl-75 GTPase MPP6 No yeast homologue Rrp47p (CID) CID nuclear exosome only (RhlB?) Mtr4p (KIAA0052) DEAD box nuclear exosome only Gsp1p (Ran) GTPase Interact with Dis3p Nip7p (CGI-37) Interact with Dis3pRpp14 Interact with OIP2

  6. Location of exosome cytoplasm, nucleoplasm and nucleolus The nucleolus is roughly spherical, and is surrounded by a layer of condensed chromatin. Nucleoli are made of protein and ribosomal DNA (rDNA) sequences of chromosomes. Most plant and animal cells have one or more nucleoli, but some cell types do not have any. Since nucleoli carry out the production and maturation of ribosomes, large numbers of ribosomes are found inside them. Functions: Biogenesis and degradation of many RNA species

  7. Pathways of eukaryotic mRNA turnover The 3’ to 5’ decay is mediated by exosome. Most mRNA is degraded by the 3’-5’ exosome in mammalian cells. Nature Struct. Mol. Biol. 2004, 11, 121-127.

  8. 1. Exosome in mRNA Turnover In yeast, exosome is recruited to mRNA by Ski2p/Ski3p/Ski8p complex and Ski7p. Skip2p is a ATP-dependent DEAD box helicase. In human, ARE-binding proteins TTP, KSRP and RHAU interact with exosome. PM/Scl-75 binds ARE. ARE: AU-rich elements Exosome is recruited to mRNA without translation termination codons by an interaction between ribosomes stalled at the 3’ end of the transcript and a G-protein domain in Ski7p, which closely resembles translation elongation and termination factors that interact with the A site of the ribosomes.

  9. 2. Exosome in RNA Processing • Processing of rRNA and tRNA Maturation of yeast 5.8S ribosomal RNA • Processing of small RNAs The nuclear exosome is involved in the maturation of the 3’ end of these RNA molecules like the U1, U4 and U5 snRNAs and a wide variety of small nucleolar RNAs.

  10. Exosome in ribosomal RNA processing in yeast Rrp6p mutants exhibits a unique accumulation of a (5.8S+30) rRNA precursor that is blocked by depletion of Rrp41 or Rrp45.

  11. 3. Exosome in quality control of (pre-)mRNA

  12. 4. Exosome in anti-viral protection Super killer phenotype: An enhanced replication of dsRNA viruses in infected ski- strains compared to infected wild-type strains (Ridley et al., 1984). Ski2p/Ski3p/Ski8p complex and Ski7p likely recruits the viral RNA to the exosome complex (Butler, et al., TRENDS Cell Biol., 2002, 12, 90-96).

  13. Questions remain unanswered • What are the differences in the composition of the nuclear and cytoplasmic exosome? • What is the detailed structure of exosome subunits? • What is the substrate specificity of exosome??? • What are the mechanisms determining substrate specificity? • What are the mechanisms by which the exosome is recruited to substrate RNA? • What are the mechanisms of up- and down-regulation of exosome activity?

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