The importance of the SR linker reflects the expansion of intrinsically disordered protein regions (IDRs) in the proteome during the evolution from bacteria to higher eukaryotes ( Ward et al., 2004 Oldfield et al., 2005). 1 A), and suggested that RBR is responsible for ribosome binding. (2015) examined two charged segments in the SR linker, channel binding region (CBR residues 129–176) and ribosome binding region (RBR residues 205–250 Fig. Eukaryotic SR cosediments with empty 80S ribosomes, and the SR linker is important in mediating ribosome binding ( Mandon et al., 2003). SRα binds tightly to SRβ via its N-terminal X-domain, which is connected to the NG-domain through an ∼200-residue intrinsically disordered linker. SRβ is a single-pass transmembrane protein anchored at the ER. While bacterial SR is a single protein in which the NG-domain is preceded by two amphiphilic lipid-binding helices, eukaryotic SR is a heterodimer of SRα and SRβ subunits. On the other hand, multiple studies have implicated the eukaryotic SR in interaction with and sensing the ribosome ( Bacher et al., 1999 Fulga et al., 2001 Legate and Andrews, 2003 Mandon et al., 2003 Jadhav et al., 2015). Single-molecule measurements showed that the ribosome unlocks SRP from an autoinhibited state and allows SRP to sample an active conformation that is conducive to SR binding ( Lee et al., 2018). The ribosome-induced stimulation is eukaryote-specific, and its underlying molecular mechanism remains incompletely understood. Recent work showed that the interaction between mammalian SRP and SR is accelerated ∼100-fold by the 80S ribosome and 20-fold by the signal sequence ( Bacher et al., 1996 Mandon et al., 2003 Lee et al., 2018). The eukaryotic SRP contains a larger 7SL RNA on which five additional protein subunits (SRP19, SRP68/72, and SRP9/14) are assembled. SRP has undergone an extensive expansion in size and complexity during evolution. Specifically, RNCs bearing a functional signal sequence preorganize SRP into a conformation in which the conserved GNRA (N is A, C, G, or U R is A or G) tetraloop of the 4.5S RNA is positioned to contact a basic surface on the NG-domain of FtsY this contributes a key interaction that enables the rapid recruitment of FtsY in response to recognition of the correct cargo ( Zhang et al., 2008 Shen and Shan, 2010 Shen et al., 2011). The GTP-dependent interaction of SRP with FtsY is extensively regulated by the signal sequence and 4.5S RNA in the bacterial SRP pathway to enable efficient and selective cotranslational protein targeting ( Zhang and Shan, 2014 Shan, 2016). SRP54 contains a methionine-rich M-domain that binds signal sequences on the nascent polypeptide and a special GTPase domain, termed NG, that dimerizes with a homologous NG-domain in SR (named FtsY in bacteria). The most conserved components of SRP and SR can be found in bacteria, where SRP is composed of a 4.5S RNA tightly bound to the SRP54 protein (named Ffh in bacteria). The interaction of SRP with the SRP receptor (SR) recruits the ribosome-nascent chain complex (RNC) to the target membrane, where the RNC is unloaded onto the Sec61p (or SecYEG in bacteria) translocation machinery, and the nascent protein is integrated into or translocated across the membrane. Targeting initiates when SRP recognizes an N-terminal signal sequence or the first transmembrane domain of a nascent polypeptide emerging from the ribosome exit tunnel. Signal recognition particle (SRP) is a universally conserved targeting machine that cotranslationally delivers the majority of membrane and secretory proteins, which compose nearly 30% of the proteome, to the eukaryotic ER or the bacterial plasma membrane ( Akopian et al., 2013 Zhang and Shan, 2014). Kinetic analyses and comparison with the bacterial SRP further suggest that the SR MoRF functionally replaces the essential GNRA tetraloop in the bacterial SRP RNA, providing an example for the replacement of RNA function by proteins during the evolution of ancient ribonucleoprotein particles. These results demonstrate a novel role for MoRF elements and provide a mechanism for the ribosome-induced activation of the mammalian SRP pathway. Loss of the MoRF in the SRP receptor (SR) largely abolishes the ability of the ribosome to activate SRP-SR assembly and impairs cotranslational protein targeting. Here we report that a MoRF element, located in the disordered linker domain of the mammalian signal recognition particle (SRP) receptor and conserved among eukaryotes, plays an essential role in sensing the ribosome during cotranslational protein targeting to the endoplasmic reticulum. Molecular recognition features (MoRFs) provide interaction motifs in intrinsically disordered protein regions to mediate diverse cellular functions.
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