Evidence map›Paper›PMID 38597224›Full record

ArticleProteins2024

Insight into the autoproteolysis mechanism of the RsgI9 anti-σ factor from Clostridium thermocellum.

Allen Takayesu, Brendan J Mahoney, Andrew K Goring, Tobie Jessup, Rachel R Ogorzalek Loo, Joseph A Loo, Robert T Clubb

Open access · bronzeAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Proteins, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
1.1field-weighted citation impact, top 21% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

4 citing papers in PubMed, 2 citations in OpenAlex.

  1. Article
  2. Visual exoproteomics ofbioRxiv : the preprint server for biology · 2026
    Article
  3. Article
  4. Unique Fn3-like biosensor in σProtein science : a publication of the Protein Society · 2024
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors at 1 institution in 1 country.

Allen TakayesuDepartment of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, USA.
Brendan J MahoneyUCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, Los Angeles, California, USA.
Andrew K GoringDepartment of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, USA.
Tobie JessupDepartment of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, USA.
Rachel R Ogorzalek LooDepartment of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, USA.
Joseph A LooDepartment of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, USA.
Robert T ClubbDepartment of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, USA.ORCID 0000-0001-5718-3985
University of California, Los Angeles · US

Funding

Cell Surface Protein Anchoring in Gram-Positive BacteriaR01AI052217 · NIAID · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Robert Thompson Clubb · 2002 to 2026
$8.5M
UCLA Dentist-Scientist and Oral Health-Researcher Training ProgramT90DE030860 · NIDCR · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI TON-THAT, HUNG, WONG, DAVID T · 2021 to 2025
$2.1M
800 MHz NMR Console and Cryoprobe ReplacementS10OD025073 · OD · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI FEIGON, JULI · 2018 to 2018
$1.1M
Bruker Avance III Console and QCI Cryoprobe for a 600 MHz NMR SpectrometerS10OD016336 · OD · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI CLUBB, ROBERT THOMPSON · 2014 to 2014
$600k
BRUKER 800 MHZ TCI CRYOPROBE: STRUCTURES AND DYNAMICS OF PROTEINSS10RR022471 · NCRR · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI CLUBB, ROBERT THOMPSON · 2006 to 2006
$301k
NCRR NIH HHS S10 RR022471NIAID NIH HHS R01 AI052217NIDCR NIH HHS T90 DE030860NIDCR NIH HHS T90-DE030860NIH HHS R01-AI052217NIH HHS S10 OD016336NIH HHS S10OD016336NIH HHS S10 OD025073NIH HHS S10OD025073U.S. Department of Energy Office of Science DE-FC02-02ER63421Whitcome Pre-doctoral Fellowship in Molecular Biology
6 · The paper itself

Abstract

Clostridium thermocellum is a potential microbial platform to convert abundant plant biomass to biofuels and other renewable chemicals. It efficiently degrades lignocellulosic biomass using a surface displayed cellulosome, a megadalton sized multienzyme containing complex. The enzymatic composition and architecture of the cellulosome is controlled by several transmembrane biomass-sensing RsgI-type anti-σ factors. Recent studies suggest that these factors transduce signals from the cell surface via a conserved RsgI extracellular (CRE) domain (also called a periplasmic domain) that undergoes autoproteolysis through an incompletely understood mechanism. Here we report the structure of the autoproteolyzed CRE domain from the C. thermocellum RsgI9 anti-σ factor, revealing that the cleaved fragments forming this domain associate to form a stable α/β/α sandwich fold. Based on AlphaFold2 modeling, molecular dynamics simulations, and tandem mass spectrometry, we propose that a conserved Asn-Pro bond in RsgI9 autoproteolyzes via a succinimide intermediate whose formation is promoted by a conserved hydrogen bond network holding the scissile peptide bond in a strained conformation. As other RsgI anti-σ factors share sequence homology to RsgI9, they likely autoproteolyze through a similar mechanism.

Indexed as

Acetivibrio thermocellusBacterial ProteinsMolecular Dynamics SimulationProteolysisAmino Acid SequenceCellulosomesCrystallography, X-RayProtein BindingProtein Conformation, alpha-HelicalProtein Conformation, beta-StrandProtein DomainsRecombinant ProteinsSigma FactorTandem Mass SpectrometryBacterial ProteinsRecombinant ProteinsSigma Factoranti‐sigma factorautoproteolysiscellulosomeClostridium thermocellumconserved RsgI extracellular domainperiplasmic domainRsgI

Identifiers

PMID38597224
PMCPMC11222046
OpenAlexW4394683913

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.