Genetic interactions suggest multiple distinct roles of the arch and core helicase domains of Mtr4 in Rrp6 and exosome function

Klauer, A. Alejandra; Hoof, Ambro van

doi:10.1093/nar/gks1013

Cited by 22 publications

(23 citation statements)

References 31 publications

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“…They were also less recovered with Mtr4Δarch relative to Mtr4, consistent with pre-rRNA maturation defects reported for strains carrying arch mutations (Fig. S1C) 13, 14, 38, 39 . In contrast, the major ncRNA classes, CUTs, SUTs and XUTs, were strongly recovered with Air2 and Trf4, relative to Air1 plus Trf5.…”

Section: Resultssupporting

confidence: 88%

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Substrate Specificity of the TRAMP Nuclear Surveillance Complexes

Delan-Forino

Spanos

Rappsilber

et al. 2020

Preprint

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During nuclear surveillance in yeast, the RNA exosome functions together with the TRAMP complexes. These include the DEAH-box RNA helicase Mtr4 together with an RNA-binding protein (Air1 or Air2) and a poly(A) polymerase (Trf4 or Trf5). To better determine how RNA substrates are targeted, we analyzed protein and RNA interactions for TRAMP components. Mass spectrometry identified three distinct TRAMP complexes formed in vivo. These complexes preferentially assemble on different classes of transcripts. Unexpectedly, on many substrates, including pre-rRNAs and pre-mRNAs, binding specificity was apparently conferred by Trf4 and Trf5. Clustering of mRNAs by TRAMP association showed co-enrichment for mRNAs with functionally related products, supporting the significance of surveillance in regulating gene expression. We compared binding sites of TRAMP components with multiple nuclear RNA binding proteins, revealing preferential colocalization of subsets of factors. TRF5 deletion reduced Mtr4 recruitment and increased RNA abundance for mRNAs specifically showing high Trf5 binding.

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Section: Resultssupporting

confidence: 88%

“…We compared strains in which the endogenous gene was HTP tagged for Air1, Air2, Trf4, Trf5, and Mtr4, as well as the exosome exonucleases Rrp44 and Rrp6. The Mtr4 arch domain is implicated in substrate recruitment 13, 14, 38, 39 , so we also constructed and analyzed a tagged Mtr4 mutant lacking this region (Mtr4Δarch) (Fig. S1A).…”

Section: Resultsmentioning

confidence: 99%

Substrate Specificity of the TRAMP Nuclear Surveillance Complexes

Delan-Forino

Spanos

Rappsilber

et al. 2020

Preprint

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“…In contrast, depletion of Mtr4 or deletion of the arch domain induced accumulation of several rRNA substrates, which included not only 5.8S rRNA precursors but also the 5 0 ETS fragment (cleaved from the 35S rRNA precursor during rRNA processing), which was no longer degraded by the exosome (de la Cruz et al, 1998;Jackson et al, 2010;Klauer and van Hoof, 2013). When the N terminus of Nop53, required for interaction with Mtr4, was truncated ( Figure 1D), an accumulation of 5.8S precursors (7S and 5.8S+30) was observed, whereas the 5 0 ETS remained unaffected ( Figure 1F).…”

Section: Nop53 Interacts Directly With the Exosome-associated Helicasmentioning

confidence: 99%

“…This domain emanates from the helicase core and is composed of two anti-parallel coiled coils, followed by the globular b-barrel structure, termed the KOW (Kyrpides-Ouzounis-Woese), a domain that is found in a number of ribosomal proteins. In vivo analysis has linked the Mtr4 arch domain to a subset of exosome-mediated processes that include the maturation of the 5.8S rRNA and degradation of the 5 0 ETS (external transcribed spacer) rRNA spacer fragment (Klauer and van Hoof, 2013). Additionally, it has been suggested that the arch is involved in RNA binding, since the KOW domain of Mtr4 and the equivalent domain in Ski2 can bind RNA in vitro (Halbach et al, 2012;Weir et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

The Exosome Is Recruited to RNA Substrates through Specific Adaptor Proteins

Thoms

Thomson

Baßler

et al. 2015

Cell

186

218

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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.

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“…The helicase regions contain the DExH core typical of processive 3 ′ -5 ′ RNA-dependent ATPases as well as a specialized insertion generally known as the "arch" domain for its characteristic curved structure (Jackson et al 2010;Weir et al 2010;Halbach et al 2012;Johnson and Jackson 2013). In vivo, the arch of Mtr4 is required for 5.8S rRNA maturation and 5 ′ ETS degradation (Jackson et al 2010;Klauer and van Hoof 2012) while the arch of Ski2 promotes the cytoplasmic functions of the exosome (Klauer and van Hoof 2012).…”

Section: Introductionmentioning

confidence: 99%

Structural insights into the interaction of the nuclear exosome helicase Mtr4 with the preribosomal protein Nop53

Falk

Tants

Basquin

et al. 2017

RNA

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The nuclear exosome and the associated RNA helicase Mtr4 participate in the processing of several ribonucleoprotein particles (RNP), including the maturation of the large ribosomal subunit (60S). S. cerevisiae Mtr4 interacts directly with Nop53, a ribosomal biogenesis factor present in late pre-60S particles containing precursors of the 5.8S rRNA. The Mtr4-Nop53 interaction plays a pivotal role in the maturation of the 5.8S rRNA, providing a physical link between the nuclear exosome and the pre-60S RNP. An analogous interaction between Mtr4 and another ribosome biogenesis factor, Utp18, directs the exosome to an earlier preribosomal particle. Nop53 and Utp18 contain a similar Mtr4-binding motif known as the arch-interacting motif (AIM). Here, we report the 3.2 Å resolution crystal structure of S. cerevisiae Mtr4 bound to the interacting region of Nop53, revealing how the KOW domain of the helicase recognizes the AIM sequence of Nop53 with a network of hydrophobic and electrostatic interactions. The AIM-interacting residues are conserved in Mtr4 and are not present in the related cytoplasmic helicase Ski2, rationalizing the specificity and versatility of Mtr4 in the recognition of different AIM-containing proteins. Using nuclear magnetic resonance (NMR), we show that the KOW domain of Mtr4 can simultaneously bind an AIM-containing protein and a structured RNA at adjacent surfaces, suggesting how it can dock onto RNPs. The KOW domains of exosomeassociated helicases thus appear to have evolved from the KOW domains of ribosomal proteins and to function as RNPbinding modules in the context of the nuclear exosome.

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Genetic interactions suggest multiple distinct roles of the arch and core helicase domains of Mtr4 in Rrp6 and exosome function

Cited by 22 publications

References 31 publications

Substrate Specificity of the TRAMP Nuclear Surveillance Complexes

Substrate Specificity of the TRAMP Nuclear Surveillance Complexes

The Exosome Is Recruited to RNA Substrates through Specific Adaptor Proteins

Structural insights into the interaction of the nuclear exosome helicase Mtr4 with the preribosomal protein Nop53

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