Dual Binding Mode of the Nascent Polypeptide-associated Complex Reveals a Novel Universal Adapter Site on the Ribosome

Abstract

Nascent polypeptide-associated complex (NAC) was identified in eukaryotes as the first cytosolic factor that contacts the nascent polypeptide chain emerging from the ribosome. NAC is present as a homodimer in archaea and as a highly conserved heterodimer in eukaryotes. Mutations in NAC cause severe embryonically lethal phenotypes in mice, Drosophila melanogaster, and Caenorhabditis elegans. In the yeast Saccharomyces cerevisiae NAC is quantitatively associated with ribosomes. Here we show that NAC contacts several ribosomal proteins. The N terminus of ␤NAC, however, specifically contacts near the tunnel exit ribosomal protein Rpl31, which is unique to eukaryotes and archaea. Moreover, the first 23 amino acids of ␤NAC are sufficient to direct an otherwise non-associated protein to the ribosome. In contrast, ␣NAC (Egd2p) contacts Rpl17, the direct neighbor of Rpl31 at the ribosomal tunnel exit site. Rpl31 was also recently identified as a contact site for the SRP receptor and the ribosome-associated complex. Furthermore, in Escherichia coli peptide deformylase (PDF) interacts with the corresponding surface area on the eubacterial ribosome. In addition to the previously identified universal adapter site represented by Rpl25/Rpl35, we therefore refer to Rpl31/Rpl17 as a novel universal docking site for ribosome-associated factors on the eukaryotic ribosome.

The biological functions of Naa10 — From amino-terminal acetylation to human disease

“…However, different models suggest that SRP function is influenced by NAC and that this dynamic interplay is important for protein targeting to the ER (Zhang et al, 2012). Also, NAC has been shown to bind uL23 (Wegrzyn et al, 2006), although other studies identified eL31 as the major ribosomal binding site of NAC (Pech et al, 2010; Zhang et al, 2012). Therefore, it would be interesting to see if and how NatA may be involved in this process and what the consequences are for the acetylation status of proteins.…”

The ribosome-associated complex antagonizes prion formation in yeast

“…The NAC is a heterodimeric complex that associates with ribosomes near the polypeptide exit tunnel. 31 Although the function of the NAC is poorly defined, it is thought to have roles in co-translational protein folding 32 and in protein targeting to mitochondria 33 and the endoplasmic reticulum. 34 The RAC consists of the Heat Shock Protein (Hsp) 70/40 pair Ssz1/ Zuo1, 35 which is anchored to the ribosome in close proximity to the polypeptide exit tunnel via a charged C-terminal region of Zuo1.…”

Finding nascent proteins the right home

“…NAC transiently associates with the large ribosomal subunit close to the peptide tunnel exit and binds a broad spectrum of ribosome-nascent chain complexes (RNCs) ( 3). In vitro NAC association sterically prevents indiscriminate binding of RNCs to the ER membrane, regardless of whether the nascent chain has a signal sequence or not ( 4,5). Addition of SRP, however, specifically rescues ER targeting of signal-containing RNCs ( 6).…”

“…Finally, Gamerdinger et ( 4), and that NAC binds translating ribosomes, unless an emerging signal sequence provides a selective binding advantage to SRP. Other in vitro data suggest that there is an alternative NAC ribosome binding site near eL31 ( 5,12), and that both NAC and SRP concomitantly bind the ribosome ( 12). SRP could quickly scan translating ribosomes irrespective of NAC presence, until an emerging signal sequence triggers strong SRP binding and NAC release.…”

“…For example, during the cell division cycle, a large multiprotein E3 ligase, the anaphase-promoting complex/cyclosome (APC/C), utilizes two E2 enzymes, UBE2C and UBE2S, to target proteins for destruction ( 3). On pages 199 and 200 of this issue, two Research Articles by Lu et al focus on these reactions and illuminate, at the single-molecule level, the process of ubiquitination by APC/C ( 4), as well as the recognition and subsequent destruction of APC/C substrates by proteasomes ( 5). Both studies substantially enrich our knowledge of ubiquitination and degradation, reveal new properties of APC/C and the proteasome, and challenge established concepts about the ubiquitin-proteasome system.…”