Analysis of the interplay of protein biogenesis factors at the ribosome exit site reveals new role for NAC

Nyathi, Yvonne; Pool, Martin

doi:10.1083/jcb.201410086

Cited by 34 publications

(37 citation statements)

References 58 publications

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“…The ribosomal surface around the tunnel exit, which serves as a binding platform for RAC and Ssb, has been described as an universal adaptor site for cotranslational factors including chaperones, enzymes and targeting factors25253. It provides two main binding sites: Rpl25/Rpl35 (L23/L29 in E. coli ) for SRP, trigger factor, the translocon, YidC/Oxa1 and Map and Rpl31/Rpl17 (L17/L22 in eubacteria) for RAC, the nascent chain associated complex (NAC), the SRP receptor and peptide deformylase.…”

Section: Discussionmentioning

confidence: 99%

Interaction of the cotranslational Hsp70 Ssb with ribosomal proteins and rRNA depends on its lid domain

et al. 2016

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Cotranslational chaperones assist in de novo folding of nascent polypeptides in all organisms. In yeast, the heterodimeric ribosome-associated complex (RAC) forms a unique chaperone triad with the Hsp70 homologue Ssb. We report the X-ray structure of full length Ssb in the ATP-bound open conformation at 2.6 Å resolution and identify a positively charged region in the α-helical lid domain (SBDα), which is present in all members of the Ssb-subfamily of Hsp70s. Mutational analysis demonstrates that this region is strictly required for ribosome binding. Crosslinking shows that Ssb binds close to the tunnel exit via contacts with both, ribosomal proteins and rRNA, and that specific contacts can be correlated with switching between the open (ATP-bound) and closed (ADP-bound) conformation. Taken together, our data reveal how Ssb dynamics on the ribosome allows for the efficient interaction with nascent chains upon RAC-mediated activation of ATP hydrolysis.

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Section: Discussionmentioning

confidence: 99%

Interaction of the cotranslational Hsp70 Ssb with ribosomal proteins and rRNA depends on its lid domain

et al. 2016

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“…During translation, the ribosome acts as a platform for the binding of different factors that interact with the nascent chain (Nyathi and Pool 2015). Those factors that participate in peptide folding, processing, and subcellular targeting include, among others, the chaperones Trigger factor, Hsp70, and NAC (nascent-polypeptide associated complex), and the enzyme MetAP that removes the initial methionine of some proteins or enzymes involved in further modifications as Nmyristoyl or N-acetyl transferases.…”

Section: Ribosomal Protein Synthesis and Co-translational Folding In mentioning

confidence: 99%

“…In eukaryotes, secretory proteins posses a hydrophobic signal sequence that is recognized co-translationally by SRP (signal recognition particle), a ribonucleoprotein composed of six proteins and RNA. SRP bound to the ribosome at the exit site binds the emerging signal sequence and then targets the complex (ribosome-nascent chain-SRP) to the endoplasmic reticulum membrane via the interaction with an SRP receptor (Nyathi and Pool 2015).…”

Section: Ribosomal Protein Synthesis and Co-translational Folding In mentioning

confidence: 99%

Protein folding and tRNA biology

2017

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Polypeptides can fold into tertiary structures while they are synthesized by the ribosome. In addition to the amino acid sequence, protein folding is determined by several factors within the cell. Among others, the folding pathway of a nascent polypeptide can be affected by transient interactions with other proteins, ligands, or the ribosome, as well as by the translocation through membrane pores. Particularly, the translation machinery and the population of tRNA under different physiological or adaptive responses can dramatically affect protein folding. This review summarizes the scientific evidence describing the role of translation kinetics and tRNA populations on protein folding and addresses current efforts to better understand tRNA biology. It is organized into three main parts, which are focused on: (i) protein folding in the cellular context; (ii) tRNA biology and the complexity of the tRNA population; and (iii) available methods and technical challenges in the characterization of tRNA pools. In this manner, this work illustrates the ways by which functional properties of proteins may be modulated by cellular tRNA populations.

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“…It is unclear how the low complexity information exposed by the nascent chain suffices for accurate recognition by the many factors competing for the limited surface near the ribosomal exit site 2,3 . Questions remain even for the well-studied cotranslational targeting cycle to the endoplasmic reticulum (ER), involving recognition of linear hydrophobic Signal Sequences (SS) or Transmembrane Domains (TMD) by the Signal Recognition Particle (SRP) 4,5 .…”

mentioning

confidence: 99%

Cotranslational signal-independent SRP preloading during membrane targeting

Chartron

Hunt

Frydman

2016

Nature

160

228

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Ribosome-associated factors must faithfully decode the limited information available in nascent polypeptides to direct them to their correct cellular fate1. It is unclear how the low complexity information exposed by the nascent chain suffices for accurate recognition by the many factors competing for the limited surface near the ribosomal exit site2,3. Questions remain even for the well-studied cotranslational targeting cycle to the endoplasmic reticulum (ER), involving recognition of linear hydrophobic Signal Sequences (SS) or Transmembrane Domains (TMD) by the Signal Recognition Particle (SRP)4,5. Intriguingly, SRP is in low abundance relative to the large number of ribosome nascent chain complexes (RNCs), yet it accurately selects those destined to the ER6. Despite their overlapping specificities, SRP and the cotranslational Hsp70 SSB display exquisite mutually exclusive selectivity in vivo for their cognate RNCs7,8. To understand cotranslational nascent chain recognition in vivo, we interrogated the cotranslational membrane targeting cycle using ribosome profiling (herein Ribo-seq)9 coupled with biochemical fractionation of ribosome populations. Unexpectedly, SRP preferentially binds secretory RNCs before targeting signals are translated. We show non-coding mRNA elements can promote this signal-independent SRP pre-recruitment. Our study defines the complex kinetic interplay between elongation and determinants in the polypeptide and mRNA modulating SRP-substrate selection and membrane targeting.

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Analysis of the interplay of protein biogenesis factors at the ribosome exit site reveals new role for NAC

Abstract: The protein biogenesis factor NAC regulates the access of the enzyme MetAP and the signal recognition particle (SRP) to the ribosome, functions in SRP-dependent targeting, and can act to protect substrates from aggregation before translocation

Cited by 34 publications

References 58 publications

Interaction of the cotranslational Hsp70 Ssb with ribosomal proteins and rRNA depends on its lid domain

Interaction of the cotranslational Hsp70 Ssb with ribosomal proteins and rRNA depends on its lid domain

Protein folding and tRNA biology

Cotranslational signal-independent SRP preloading during membrane targeting

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