Protein cofactor competition regulates the action of a multifunctional RNA helicase in different pathways

Abstract

A rapidly increasing number of RNA helicases are implicated in several distinct cellular processes, however, the modes of regulation of multifunctional RNA helicases and their recruitment to different target complexes have remained unknown. Here, we show that the distribution of the multifunctional DEAH-box RNA helicase Prp43 between its diverse cellular functions can be regulated by the interplay of its G-patch protein cofactors. We identify the orphan G-patch protein Cmg1 (YLR271W) as a novel cofactor of Prp43 and show that it stimulates the RNA binding and ATPase activity of the helicase. Interestingly, Cmg1 localizes to the cytoplasm and to the intermembrane space of mitochondria and its overexpression promotes apoptosis. Furthermore, our data reveal that different G-patch protein cofactors compete for interaction with Prp43. Changes in the expression levels of Prp43-interacting G-patch proteins modulate the cellular localization of Prp43 and G-patch protein overexpression causes accumulation of the helicase in the cytoplasm or nucleoplasm. Overexpression of several G-patch proteins also leads to defects in ribosome biogenesis that are consistent with withdrawal of the helicase from this pathway. Together, these findings suggest that the availability of cofactors and the sequestering of the helicase are means to regulate the activity of multifunctional RNA helicases and their distribution between different cellular processes.

DHX15 regulates CMTR1-dependent gene expression and cell proliferation

“…The competition of cofactors for DHX15 was previously observed to regulate its distribution between different pathways (Heininger et al, 2016). DHX15 interacts with splicing factors, including TFIP11, and localises to nuclear splicing speckles (Tannukit et al, 2009).…”

“…Since we had observed that CMTR1 stimulates DHX15 helicase activity in vitro, we investigated whether it also influences DHX15 localisation in cells. Prp43, the yeast homologue of DHX15, occupies several cellular locations to execute different biological functions (Heininger et al, 2016). The different Prp43 locations are achieved by the competition of G-patch proteins, which recruit the helicase to different parts of the cell.…”

Structural insights into the mechanism of the DEAH-box RNA helicase Prp43

“…Here, it is involved in the maturation of 18S and 25S rRNAs with several reported binding sites on intermediates which vary in sequence and thus make a sequenced-based binding mechanism unlikely for Prp43 (Lebaron et al, 2005; Bohnsack et al, 2009). Lately, the involvement of Prp43 in a third distinct cellular function was illuminated and it was unraveled that Prp43 is also involved in the promotion of apoptosis (Heininger et al, 2016). …”

“…During rRNA maturation, Prp43 is associated with Pfa1 (Prp forty-three associated 1) or Gno1 (G-patch nucleolar protein 1) (Lebaron et al, 2005, 2009; Bohnsack et al, 2009). Moreover, its apoptotic function is implemented by the interaction with Cmg1 (Cytoplasmic and mitochondrial G-patch protein 1) (Heininger et al, 2016). The remaining G-patch protein from yeast is Spp2 (Suppressor of PRP protein 2) which interacts with another spliceosomal DEAH-box helicase, Prp2 (Warkocki et al, 2015).…”

Termination of pre-mRNA splicing requires that the ATPase and RNA unwindase Prp43 acts on the catalytic snRNA U6

“…Prp43p requires a co-factor of the G-patch protein family (Aravind and Koonin 1999;Robert-Paganin et al 2015) for efficient ATPase and RNA unwinding activity. Indeed, distinct Gpatch proteins serve to activate Prp43p in different processes, such as splicing and ribosome biogenesis (Tanaka et al 2007;Lebaron et al 2009;Chen et al 2014b;Heininger et al 2016;Boon et al 2006;Pandit et al 2006;Tsai et al 2005). In splicing, the conserved G-patch protein Ntr1p/Spp382p activates Prp43p and forms the NTR (NTC-Related) complex with Prp43p, Cwc23p, and Ntr2p, a factor that is found primarily in fungi and plants.…”