PMID:26317469

Citation	Thoms, M, Thomson, E, Baßler, J, Gnädig, M, Griesel, S and Hurt, E (2015) The Exosome Is Recruited to RNA Substrates through Specific Adaptor Proteins. Cell 162:1029-38
Abstract	The exosome regulates the processing, degradation, and surveillance of a plethora of RNA species. However, little is known about how the exosome recognizes and is recruited to its diverse substrates. We report the identification of adaptor proteins that recruit the exosome-associated helicase, Mtr4, to unique RNA substrates. Nop53, the yeast homolog of the tumor suppressor PICT1, targets Mtr4 to pre-ribosomal particles for exosome-mediated processing, while a second adaptor Utp18 recruits Mtr4 to cleaved rRNA fragments destined for degradation by the exosome. Both Nop53 and Utp18 contain the same consensus motif, through which they dock to the "arch" domain of Mtr4 and target it to specific substrates. These findings show that the exosome employs a general mechanism of recruitment to defined substrates and that this process is regulated through adaptor proteins.
Links	PubMed Online version:10.1016/j.cell.2015.07.060
Keywords	Amino Acid Sequence; Animals; Ascomycota/chemistry; Ascomycota/classification; Ascomycota/genetics; DEAD-box RNA Helicases/chemistry; DEAD-box RNA Helicases/metabolism; Exosomes/metabolism; Humans; Models, Molecular; Molecular Sequence Data; Nuclear Proteins/chemistry; Nuclear Proteins/metabolism; Nucleic Acid Conformation; RNA, Fungal/chemistry; RNA, Fungal/metabolism; RNA, Ribosomal/chemistry; RNA, Ribosomal/metabolism; Ribosomal Proteins/chemistry; Ribosomal Proteins/metabolism; Ribosomes/metabolism; Saccharomyces cerevisiae/metabolism; Saccharomyces cerevisiae Proteins/chemistry; Saccharomyces cerevisiae Proteins/metabolism; Sequence Alignment
edit table

Annotations

Gene product	Qualifier	GO Term	Evidence Code	with/from	Aspect	Extension	Notes	Status
YEAST:MTR4		GO:0000292: RNA fragment catabolic process	ECO:0000315:		P		RNA polymerase I produces pre-rRNA that is processed into several fragments, including the 5’-ETS (external transcribed spacer) and 7S pre-rRNA. The RNA exosome is a 3’ to 5’ exonuclease involved in the processing of 7S pre-rRNA into mature 5.8S rRNA and in the degradation of the 5’-ETS. The exosome requires protein cofactors that interact with the Mtr4 helicase for substrate specificity. Figure 1 F is a northern blot that shows that S. cerevisiae strains with a deletion in Mtr4’s essential arch domain accumulate 5’-ETS (lane 2). A wilde type Mtr4 strain shows that 5’ETS is degraded as it is absent on the northern blot (lane 1). Therefore, lanes 1 and 2 show that Mtr4 is involved in the breakdown of a fragment of RNA, such as excised introns or sequences removed from ribosomal RNA during processing (Go termGO:0000292)	complete CACAO 12153
YEAST:MTR4		GO:0000460: maturation of 5.8S rRNA	ECO:0000315:		P		RNA polymerase I produces pre-rRNA that is processed into several fragments, including the 5’-ETS (external transcribed spacer) and 7S pre-rRNA. The RNA exosome is a 3’ to 5’ exonuclease involved in the processing of 7S pre-rRNA into mature 5.8S rRNA and in the degradation of the 5’-ETS. The exosome requires protein cofactors that interact with the Mtr4 helicase for substrate specificity. One of these cofactors is Nop53. The N-terminus of Nop53 is required for binding with the arch domain of Mtr4, and subsequently for presentation of the 7S pre-rRNA substrate to the RNA exosome. The northern blot in Figure 1 shows that S. cerevisiae strains with wild type Mtr4 and Nop53 accumulate no 7S-pre-rRNA. Conversely, mutants with a deletion in either the arch domain of Mtr4 or the N terminus of Nop53 show accumulation of 7S-pre-rRNA. Therefore these two proteins are involved in he maturation of a precursor 5.8S ribosomal RNA (rRNA) molecule into a mature 5.8S rRNA molecule (GO:0000460)	complete CACAO 12154
YEAST:NOP53		GO:0000460: maturation of 5.8S rRNA	ECO:0000315:		P		RNA polymerase I produces pre-rRNA that is processed into several fragments, including the 5’-ETS (external transcribed spacer) and 7S pre-rRNA. The RNA exosome is a 3’ to 5’ exonuclease involved in the processing of 7S pre-rRNA into mature 5.8S rRNA and in the degradation of the 5’-ETS. The exosome requires protein cofactors that interact with the Mtr4 helicase for substrate specificity. One of these cofactors is Nop53. The N-terminus of Nop53 is required for binding with the arch domain of Mtr4, and subsequently for presentation of the 7S pre-rRNA substrate to the RNA exosome. The northern blot in Figure 1 shows that S. cerevisiae strains with wild type Mtr4 and Nop53 accumulate no 7S-pre-rRNA. Conversely, mutants with a deletion in either the arch domain of Mtr4 or the N terminus of Nop53 show accumulation of 7S-pre-rRNA. Therefore these two proteins are involved in the maturation of a precursor 5.8S ribosomal RNA (rRNA) molecule into a mature 5.8S rRNA molecule (GO:0000460)	complete CACAO 12155
YEAST:UTP18		GO:0000292: RNA fragment catabolic process	ECO:0000315:		P		RNA polymerase I produces pre-rRNA that is processed into several fragments, including the 5’-ETS (external transcribed spacer) and 7S pre-rRNA. The RNA exosome is a 3’ to 5’ exonuclease involved in the processing of 7S pre-rRNA into mature 5.8S rRNA and in the degradation of the 5’-ETS. The exosome requires protein cofactors that interact with the Mtr4 helicase for substrate specificity. One of these cofactors is Utp18. The N-terminus of Utp18 is required for binding with the arch domain of Mtr4, and subsequently for presentation of the 5’-ETS substrate to the RNA exosome. Figure 4C shows a northern blot where in lane 5, the N-terminus Utp18 S. cerevisiae mutant accumulates 5’-ETS. The wild type Utp18 strain showed no band for 5’ETS, showing it was degraded. Therefore, Utp18 is involved in the breakdown of a fragment of RNA, such as excised introns or sequences removed from ribosomal RNA during processing (Go termGO:0000292).	complete CACAO 12161

References

See Help:References for how to manage references in GONUTS.