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Record W2983451369 · doi:10.7554/elife.04872.021

Author response: Actin dynamics tune the integrated stress response by regulating eukaryotic initiation factor 2α dephosphorylation

2014· peer-review· en· W2983451369 on OpenAlexaff
Joseph E. Chambers, Lucy E. Dalton, Hanna J. Clarke, Elke Malzer, Caia Dominicus, Vruti Patel, Greg B. G. Moorhead, David Ron, Stefan J. Marciniak

Bibliographic record

Venuenot available
Typepeer-review
Languageen
FieldBiochemistry, Genetics and Molecular Biology
TopicViral Infectious Diseases and Gene Expression in Insects
Canadian institutionsUniversity of Calgary
Fundersnot available
KeywordsEukaryotic translationPhosphataseeIF2ActinProtein subunitInitiation factorBiologyPhosphorylationCell biologyIntegrated stress responseTranslation (biology)Eukaryotic initiation factorBiochemistryGeneMessenger RNA

Abstract

fetched live from OpenAlex

For a cell to build a protein, it must first copy the instructions contained within a gene. A complex molecular machine called a ribosome then reads these instructions and translates them into a protein. This translation process involves a number of steps. Proteins called eukaryotic translation initiation factors (or eIFs for short) coordinate the first step in the process, which is known as ‘initiation’. The eIFs also provide the cell with ways to control how quickly it makes proteins. For example, when a cell is stressed, either by starvation or toxins, it adds a phosphate group onto part of an eIF protein, called eIF2α. This modification makes this eIF protein less able to initiate translation, and so the cell builds fewer proteins and conserves more of its resources during times of stress. Once the stressful conditions are over, the phosphate group is removed from eIF2α by an enzyme called a phosphatase. This phosphatase contains two subunits: one that recognizes eIF2α and another that removes the phosphate group. However, experiments that attempted to recreate this phosphatase activity using just these two subunits in a test tube failed to generate a working enzyme that specifically targeted the phosphate group of eIF2α. This suggests that in cells this enzyme contains an additional unknown subunit. Now, Chambers, Dalton et al. (and Chen et al.) report the identity of a ‘missing’ third subunit as a protein known as globular-actin or G-actin. Chambers, Dalton et al. engineered human and fruit fly cells to add ‘molecular handles’ on the two known subunits of the phosphatase enzyme. These handles could then be used to essentially pull these proteins out of the mixture of molecules within a cell and see what other proteins came along too. Both of the known subunits ‘pulled’ G-actin along with them; this suggested that it could be the missing part of the phosphatase enzyme. Further experiments confirmed that G-actin works together with the other two subunits to specifically remove the phosphate group from eIF2α in mouse cells that had been stressed using a harmful chemical. Individual G-actin proteins can bind together to form long filaments, and signals that encourage a cell to divide or move also trigger the formation of actin filaments. This reduces the activity of the phosphatase enzyme by depriving it of a crucial component, i.e., free G-actin proteins. As such, the new mechanism described by Chambers, Dalton et al. suggests how growth and movement signals might also change a cell's sensitivity to stress. These findings may hopefully enable stressed cells to be targeted by drugs to treat disease; but future work is needed to clarify under what circumstances the integration of such signals into the stress response is beneficial to the cell.

Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.

How this classification was reachedexpand

Full frame machine prediction

Teacher imitation

Not calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.

metaresearch head score (Codex)0.000
metaresearch head score (Gemma)0.001
Version: metacan-v3-hybrid-931329e0061cValidation status: machine_predicted_unvalidated
Candidate categoriesnone
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Not applicable · Consensus signal: none
GenreCandidate signal: Commentary · Consensus signal: none
Teacher disagreement score0.083
Threshold uncertainty score0.277

Distilled classifier scores by category (both heads)

CategoryCodexGemma
Metaresearch0.0000.001
Meta-epidemiology (narrow)0.0010.000
Meta-epidemiology (broad)0.0010.000
Bibliometrics0.0000.000
Science and technology studies0.0010.001
Scholarly communication0.0020.001
Open science0.0010.001
Research integrity0.0020.002
Insufficient payload (model declined to judge)0.0830.034

Machine scores (provisional)

The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.

Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.

Opus teacher head0.019
GPT teacher head0.310
Teacher spread0.291 · how far apart the two teachers sit on this one work
Validation statusscore_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it

Classification

machine, unvalidated

Machine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.

The models applied no category: nothing in the taxonomy fit this work.
Study designNot applicable
Domainnot available
GenreCommentary

How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".

Quick stats

Citations0
Published2014
Admission routes1
Has abstractyes

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