Regulation of NAB2 mRNA 3′-end formation requires the core exosome and the Trf4p component of the TRAMP complex

Abstract

The nuclear exosome functions in a variety of pathways catalyzing formation of mature RNA 39-ends or the destruction of aberrant RNA transcripts. The RNA 39-end formation activity of the exosome appeared restricted to small noncoding RNAs. However, the nuclear exosome controls the level of the mRNA encoding the poly(A)-binding protein Nab2p in a manner requiring an A 26 sequence in the mRNA 39 untranslated regions (UTR), and the activities of Nab2p and the exosome-associated exoribonuclease Rrp6p. Here we show that the A 26 sequence inhibits normal 39-end processing of NAB2 mRNA in vivo and in vitro, and makes formation of the mature 39-end dependent on trimming of the transcript by the core exosome and the Trf4p component of the TRAMP complex from a downstream site. The detection of mature, polyadenylated transcripts ending at, or within, the A 26 sequence indicates that exosome trimming sometimes gives way to polyadenylation of the mRNA. Alternatively, Rrp6p and the TRAMP-associated Mtr4p degrade these transcripts thereby limiting the amount of Nab2p in the cell. These findings suggest that NAB2 mRNA 39-end formation requires the exosome and TRAMP complex, and that competition between polyadenylation and Rrp6p-dependent degradation controls the level of this mRNA.

The Mitogen-Activated Protein Kinase Slt2 Regulates Nuclear Retention of Non-Heat Shock mRNAs during Heat Shock-Induced Stress

“…The role of the essential mRNA-binding protein Nab2 in hsp mRNA export has not been examined; yet, Nab2 is emerging as a key factor involved in coupling mRNA processing and export events (33,52,75). Our previous work defined Nab2 as essential for bulk mRNA export and a physiological target for release from mRNPs during NPC translocation (70).…”

Rrp6, Rrp47 and Cofactors of the Nuclear Exosome

“…Interestingly, NAB2 mRNA 3' end formation occurs by a non-canonical mechanism that requires Exo10 and the Trf4 component of the TRAMP complex. 37 A similar mechanism forms the mature end of the CTH2 mRNA and, possibly other mRNAs. 38 Rrp6 and the TRAMP complex regulate the levels of histone mRNAs by degrading the transcripts and contributing to their removal at the end of the S-phase of the cell cycle.…”

Air proteins control differential TRAMP substrate specificity for nuclear RNA surveillance

“…Despite the critical role the exosome plays in RNA surveillance, important questions remain about its activation and the mechanism used to distinguish between RNAs destined for processing or for degradation. The highly conserved TRAMP complex, composed of a noncanonical poly(A) polymerase (Trf4 or Trf5 in S. cerevisiae), a zincknuckle protein (Air1 or Air2), and an RNA helicase (Mtr4), enhances exosome degradation or processing through successive rounds of polyadenylation and subsequent recruitment of the degradation machinery (Vanacova et al 2005;Wyers et al 2005;Egecioglu et al 2006;Houseley et al 2007;Rougemaille et al 2007;Ciais et al 2008;Grzechnik and Kufel 2008;Roth et al 2009). Thus, TRAMP plays a critical role in determining nuclear RNA fate, but the molecular details that govern its specificity remain unknown.…”

“…Despite significant similarities between the complexes, recent experiments suggest differences in substrate specificities (Egecioglu et al 2006;Ciais et al 2008;Roth et al 2009). For example, TRAMP5 appears to preferentially enhance the degradation of aberrant rRNA precursors (Houseley et al 2007).…”