Ribosome exit tunnel electrostatics

Tubulins play crucial roles in cell division, intracellular traffic, and cell shape. Tubulin concentration is autoregulated by feedback control of messenger RNA (mRNA) degradation via an unknown mechanism. We identified tetratricopeptide protein 5 (TTC5) as a tubulin-specific ribosome-associating factor that triggers cotranslational degradation of tubulin mRNAs in response to excess soluble tubulin. Structural analysis revealed that TTC5 binds near the ribosome exit tunnel and engages the amino terminus of nascent tubulins. TTC5 mutants incapable of ribosome or nascent tubulin interaction abolished tubulin autoregulation and showed chromosome segregation defects during mitosis. Our findings show how a subset of mRNAs can be targeted for coordinated degradation by a specificity factor that recognizes the nascent polypeptides they encode.

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Ribosome exit tunnel can entropically stabilize -helices

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.0508234102 ◽

2005 ◽

Vol 102 (52) ◽

pp. 18956-18961 ◽

Cited By ~ 106

Author(s):

G. Ziv ◽

G. Haran ◽

D. Thirumalai

Keyword(s):

Exit Tunnel ◽

Ribosome Exit Tunnel

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Quantitative Analysis and Modeling of Translation using Ribosome Profiling Data: How Biophysical Properties of the Ribosome Exit Tunnel and the Nascent Polypeptide Modulate the Elongation Rate

Biophysical Journal ◽

10.1016/j.bpj.2016.11.200 ◽

2017 ◽

Vol 112 (3) ◽

pp. 30a-31a

Author(s):

Khanh Dao Duc ◽

Zain H. Saleem ◽

Yun S. Song

Keyword(s):

Quantitative Analysis ◽

Elongation Rate ◽

Ribosome Profiling ◽

Biophysical Properties ◽

Nascent Polypeptide ◽

Exit Tunnel ◽

Ribosome Exit Tunnel

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Cotranslational Protein Folding inside the Ribosome Exit Tunnel

Cell Reports ◽

10.1016/j.celrep.2015.07.065 ◽

2015 ◽

Vol 12 (10) ◽

pp. 1533-1540 ◽

Cited By ~ 145

Author(s):

Ola B. Nilsson ◽

Rickard Hedman ◽

Jacopo Marino ◽

Stephan Wickles ◽

Lukas Bischoff ◽

...

Keyword(s):

Protein Folding ◽

Exit Tunnel ◽

Ribosome Exit Tunnel

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An ER translocon for multi-pass membrane protein biogenesis

eLife ◽

10.7554/elife.56889 ◽

2020 ◽

Vol 9 ◽

Cited By ~ 7

Author(s):

Philip T McGilvray ◽

S Andrei Anghel ◽

Arunkumar Sundaram ◽

Frank Zhong ◽

Michael J Trnka ◽

...

Keyword(s):

Membrane Proteins ◽

Membrane Protein ◽

Glutamate Transporter ◽

Cell Physiology ◽

Transmembrane Segments ◽

Cryo Electron Microscopy ◽

Protein Biogenesis ◽

Exit Tunnel ◽

Ribosome Exit Tunnel ◽

Molecular Framework

Membrane proteins with multiple transmembrane domains play critical roles in cell physiology, but little is known about the machinery coordinating their biogenesis at the endoplasmic reticulum. Here we describe a ~ 360 kDa ribosome-associated complex comprising the core Sec61 channel and five accessory factors: TMCO1, CCDC47 and the Nicalin-TMEM147-NOMO complex. Cryo-electron microscopy reveals a large assembly at the ribosome exit tunnel organized around a central membrane cavity. Similar to protein-conducting channels that facilitate movement of transmembrane segments, cytosolic and luminal funnels in TMCO1 and TMEM147, respectively, suggest routes into the central membrane cavity. High-throughput mRNA sequencing shows selective translocon engagement with hundreds of different multi-pass membrane proteins. Consistent with a role in multi-pass membrane protein biogenesis, cells lacking different accessory components show reduced levels of one such client, the glutamate transporter EAAT1. These results identify a new human translocon and provide a molecular framework for understanding its role in multi-pass membrane protein biogenesis.

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Nascent SecM chain interacts with outer ribosomal surface to stabilize translation arrest

Biochemical Journal ◽

10.1042/bcj20190723 ◽

2020 ◽

Vol 477 (2) ◽

pp. 557-566

Author(s):

Mikihisa Muta ◽

Ryo Iizuka ◽

Tatsuya Niwa ◽

Yuanfang Guo ◽

Hideki Taguchi ◽

...

Keyword(s):

Gene Expression ◽

Translation Elongation ◽

Translation Arrest ◽

C Terminus ◽

Exit Tunnel ◽

Ribosome Exit Tunnel ◽

Α Helix ◽

Key Residues ◽

Bacterial Secretion ◽

Downstream Gene Expression

SecM, a bacterial secretion monitor protein, posttranscriptionally regulates downstream gene expression via translation elongation arrest. SecM contains a characteristic amino acid sequence called the arrest sequence at its C-terminus, and this sequence acts within the ribosomal exit tunnel to stop translation. It has been widely assumed that the arrest sequence within the ribosome tunnel is sufficient for translation arrest. We have previously shown that the nascent SecM chain outside the ribosomal exit tunnel stabilizes translation arrest, but the molecular mechanism is unknown. In this study, we found that residues 57–98 of the nascent SecM chain are responsible for stabilizing translation arrest. We performed alanine/serine-scanning mutagenesis of residues 57–98 to identify D79, Y80, W81, H84, R87, I90, R91, and F95 as the key residues responsible for stabilization. The residues were predicted to be located on and near an α-helix-forming segment. A striking feature of the α-helix is the presence of an arginine patch, which interacts with the negatively charged ribosomal surface. A photocross-linking experiment showed that Y80 is adjacent to the ribosomal protein L23, which is located next to the ribosomal exit tunnel when translation is arrested. Thus, the folded nascent SecM chain that emerges from the ribosome exit tunnel interacts with the outer surface of the ribosome to stabilize translation arrest.

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Residue-by-residue analysis of cotranslational membrane protein integration in vivo

10.1101/2020.09.27.315283 ◽

2020 ◽

Author(s):

Felix Nicolaus ◽

Ane Metola ◽

Daphne Mermans ◽

Amanda Liljenström ◽

Ajda Krč ◽

...

Keyword(s):

Profile Analysis ◽

Residue Analysis ◽

Transmembrane Helix ◽

Point Mutations ◽

Dependent Manner ◽

Integration Process ◽

Pulling Forces ◽

Exit Tunnel ◽

Ribosome Exit Tunnel

AbstractWe follow the cotranslational biosynthesis of three multi-spanning E. coli inner membrane proteins in vivo using high-resolution Force Profile Analysis. The force profiles show that the nascent chain is subjected to rapidly varying pulling forces during translation, and reveal unexpected complexities in the membrane integration process. We find that an N-terminal cytoplasmic domains can fold in the ribosome exit tunnel before membrane integration starts, that charged residues and membrane-interacting segments such as re-entrant loops and surface helices flanking a transmembrane helix (TMH) can advance or delay membrane integration, and that point mutations in an upstream TMH can affect the pulling forces generated by downstream TMHs in a highly position-dependent manner, suggestive of residue-specific interactions between TMHs during the integration process.

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The shape of the bacterial ribosome exit tunnel affects cotranslational protein folding

eLife ◽

10.7554/elife.36326 ◽

2018 ◽

Vol 7 ◽

Cited By ~ 25

Author(s):

Renuka Kudva ◽

Pengfei Tian ◽

Fátima Pardo-Avila ◽

Marta Carroni ◽

Robert B Best ◽

...

Keyword(s):

Protein Folding ◽

Protein Domain ◽

Coarse Grained ◽

E Coli ◽

Folded Structure ◽

Bacterial Ribosome ◽

Folded Proteins ◽

Exit Tunnel ◽

Ribosome Exit Tunnel ◽

Dynamics Simulations

The E. coli ribosome exit tunnel can accommodate small folded proteins, while larger ones fold outside. It remains unclear, however, to what extent the geometry of the tunnel influences protein folding. Here, using E. coli ribosomes with deletions in loops in proteins uL23 and uL24 that protrude into the tunnel, we investigate how tunnel geometry determines where proteins of different sizes fold. We find that a 29-residue zinc-finger domain normally folding close to the uL23 loop folds deeper in the tunnel in uL23 Δloop ribosomes, while two ~ 100 residue proteins normally folding close to the uL24 loop near the tunnel exit port fold at deeper locations in uL24 Δloop ribosomes, in good agreement with results obtained by coarse-grained molecular dynamics simulations. This supports the idea that cotranslational folding commences once a protein domain reaches a location in the exit tunnel where there is sufficient space to house the folded structure.

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