A cautionary tale on targeting prediction algorithms: limits and opportunities DOI Creative Commons
Sven B. Gould,

Jonas Magiera,

Carolina García García

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Dec. 18, 2023

Abstract Mitochondria and plastids import thousands of proteins. Their experimental localisation remains a frequent task, but can be resource-intensive sometimes impossible. Hence, hundreds studies make use algorithms that predict based on protein’s sequence. reliability across evolutionary diverse species is unknown. Here, we evaluate the performance common (TargetP, Localizer WoLFPSORT) for four photosynthetic eukaryotes which plastid mitochondrial proteome data available, 171 using orthology inferences. The match between predictions ranges from 75% to as low 2%. Results worsen distance training query increases, especially plant mitochondria borders random sampling. Specificity, sensitivity precision analyses highlight cross-organelle errors uncover divergence organelles main driver current issues. results encourage train next generation neural networks an more set organelle proteins optimizing reliability.

Language: Английский

Interplay of Proteostasis Capacity and Protein Aggregation: Implications for Cellular Function and Disease DOI Creative Commons
Mark S. Hipp, F. Ulrich Hartl

Journal of Molecular Biology, Journal Year: 2024, Volume and Issue: 436(14), P. 168615 - 168615

Published: May 16, 2024

Eukaryotic cells are equipped with an intricate proteostasis network (PN), comprising nearly 3,000 components dedicated to preserving proteome integrity and sustaining protein homeostasis. This protective system is particularly important under conditions of external intrinsic cell stress, where inherently dynamic proteins may unfold lose functionality. A decline in capacity associated the aging process, resulting a reduced folding efficiency newly synthesized deficit cellular degrade misfolded proteins. critical consequence PN insufficiency accumulation cytotoxic aggregates that underlie various age-related neurodegenerative other pathologies. By interfering specific components, toxic place excessive burden on PN's ability maintain integrity. initiates feed-forward loop, wherein generation aggregated ultimately leads collapse demise.

Language: Английский

Citations

17
Mechanism of chaperone recruitment and retention on mitochondrial precursors DOI
Szymon Juszkiewicz,

Sew-Yeu Peak-Chew,

Ramanujan S. Hegde

et al.

Molecular Biology of the Cell, Journal Year: 2025, Volume and Issue: 36(4)

Published: Jan. 29, 2025

Nearly all mitochondrial proteins are imported into mitochondria from the cytosol. How nascent precursors acquire and sustain import competence in cytosol under normal stress conditions is incompletely understood. Here, we show that conditions, Hsc70 Hsp90 systems interact with redundantly minimize precursor degradation. During acute stress, buffers degradation, preserving an import-competent state until resolution. Unexpectedly, buffering by relies critically on a targeting signal (MTS), absence of which greatly decreases precursor–Hsp90 interaction. Site-specific photo-cross-linking biochemical reconstitution showed how MTS directly engages co-chaperones (St13 Stip1) (p23 Cdc37) to facilitate chaperone retention mature domain. Thus, has previously unappreciated role regulating dynamics buffer their degradation maintain competence, functions may restoration homeostasis after stress.

Language: Английский

Citations

1
ER Stress as a Sentinel Mechanism for ER Ca2+ Homeostasis DOI Creative Commons

Tadashi Makio,

Junsheng Chen, Thomas Simmen

et al.

Cell Calcium, Journal Year: 2024, Volume and Issue: 124, P. 102961 - 102961

Published: Oct. 18, 2024

Language: Английский

Citations

7
Mechanism of chaperone coordination during cotranslational protein folding in bacteria DOI Creative Commons

Alžběta Roeselová,

Sarah Maslen, Santosh Shivakumaraswamy

et al.

Molecular Cell, Journal Year: 2024, Volume and Issue: 84(13), P. 2455 - 2471.e8

Published: July 1, 2024

Protein folding is assisted by molecular chaperones that bind nascent polypeptides during mRNA translation. Several structurally distinct classes of promote de novo folding, suggesting their activities are coordinated at the ribosome. We used biochemical reconstitution and structural proteomics to explore basis for cotranslational chaperone action in bacteria. found binding disfavored close ribosome, allowing precede recruitment. Trigger factor recognizes compact intermediates expose an extensive unfolded surface, dictates DnaJ access chains. uses a large surface diverse recruits DnaK sequence-diverse solvent-accessible sites. Neither factor, DnaJ, nor destabilize intermediates. Instead, collaborate protect incipient structure polypeptide well beyond ribosome exit tunnel. Our findings show how network selects modulates

Language: Английский

Citations

6
Multi-protein assemblies orchestrate co-translational enzymatic processing on the human ribosome DOI Creative Commons
Marius A. Klein, Klemens Wild, Irmgard Sinning

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Sept. 3, 2024

Abstract Nascent chains undergo co-translational enzymatic processing as soon their N-terminus becomes accessible at the ribosomal polypeptide tunnel exit (PTE). In eukaryotes, N-terminal methionine excision (NME) by Methionine Aminopeptidases (MAP1 and MAP2), acetylation (NTA) N-Acetyl-Transferase A (NatA), is most common combination of subsequent modifications carried out on 80S ribosome. How these processes are coordinated in context a rapidly translating ribosome has remained elusive. Here, we report two cryo-EM structures multi-enzyme complexes assembled vacant human ribosomes, indicating routes for NME-NTA. Both assemblies form independent nascent chain substrates. Irrespective route, NatA occupies non-intrusive ‘distal’ binding site which does not interfere with MAP1 or MAP2 nor other ribosome-associated factors (RAFs). can partake coordinated, dynamic assembly through hydra-like chaperoning function abundant Polypeptide-Associated Complex (NAC). contrast to MAP1, completely covers PTE thus incompatible NAC recruitment. Together, our data provide structural framework orchestration NME NTA protein biogenesis.

Language: Английский

Citations

5
NAC regulates metabolism and cell fate in intestinal stem cells DOI Creative Commons
Sofia Ramalho, Ferhat Alkan, Stefan Prekovic

et al.

Science Advances, Journal Year: 2025, Volume and Issue: 11(2)

Published: Jan. 8, 2025

Intestinal stem cells (ISCs) face the challenge of integrating metabolic demands with unique regenerative functions. Studies have shown an intricate interplay between metabolism and cell capacity; however, it is still not understood how this process regulated. Combining ribosome profiling CRISPR screening in intestinal organoids, we identify nascent polypeptide–associated complex (NAC) as a key mediator process. Our findings suggest that NAC responsible for relocalizing ribosomes to mitochondria regulating ISC metabolism. Upon inhibition, show decreased import mitochondrial proteins, which are needed oxidative phosphorylation, and, consequently, enable maintain identity. Furthermore, overexpression NACα sufficient drive respiration promote Ultimately, our results reveal pivotal role localization, metabolism, function, providing insights into potential mechanism behind it.

Language: Английский

Citations

0
Mechanistic insights into protein biogenesis and maturation on the ribosome DOI

Alfred Lentzsch,

Jae Ho Lee, Shu‐ou Shan

et al.

Journal of Molecular Biology, Journal Year: 2025, Volume and Issue: unknown, P. 169056 - 169056

Published: Feb. 1, 2025

Language: Английский

Citations

0
Mechanism and engineering of endoplasmic reticulum-localized membrane protein folding in Saccharomyces cerevisiae DOI

Yuhuan Luo,

Jian‐Jiang Zhong, Han Xiao

et al.

Metabolic Engineering, Journal Year: 2025, Volume and Issue: unknown

Published: March 1, 2025

Language: Английский

Citations

0
Mechanisms of COPII coat assembly and cargo recognition in the secretory pathway DOI

Katie W Downes,

Giulia Zanetti

Nature Reviews Molecular Cell Biology, Journal Year: 2025, Volume and Issue: unknown

Published: March 25, 2025

Language: Английский

Citations

0
The nascent polypeptide-associated complex (NAC) as regulatory hub on ribosomes DOI
Laurenz Rabl, Elke Deuerling

Biological Chemistry, Journal Year: 2025, Volume and Issue: unknown

Published: April 1, 2025

Abstract The correct synthesis of new proteins is essential for maintaining a functional proteome and cell viability. This process tightly regulated, with ribosomes associated protein biogenesis factors ensuring proper production, modification, targeting. In eukaryotes, the conserved nascent polypeptide-associated complex (NAC) plays central role in coordinating early processing by regulating ribosome access multiple factors. NAC recruits modifying enzymes to ribosomal exit site N-terminus directs secretory into SRP-mediated targeting pathway. this review we will focus on these pathways, which are critical summarize recent advances understanding cotranslational functions mechanisms higher eukaryotes.

Language: Английский

Citations

0