Evidence map›Paper›PMID 41648635›Full record

ArticlebioRxiv : the preprint server for biology2026

Spatiotemporal 4D Whole-cell Modeling of a Minimal Autotroph Reveals Central Carbon Metabolism Regulated Locally by Protein Megacomplexes via Post-translational ModiBications under Light Disturbance.

Connah G M Johnson, Aaron Chan, Jordan Rozum, August George, Amar D Parvate, Doo Nam Kim, Song Feng, Pavlo Bohutskyi, Zachary Johnson, Natalie Sadler and 11 more

Abstract readPreprint
In one paragraph

Article in bioRxiv : the preprint server for biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
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

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

21 authors.

Connah G M JohnsonPhysical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, 99352, United States of America.ORCID 0000-0002-4672-9628
Aaron ChanBeckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801-3028, United States of America.
Jordan RozumBiological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99352, United States of America.
August GeorgeBiological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99352, United States of America.
Amar D ParvateEnvironmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, 99354, United States of America.ORCID 0000-0001-9282-5015
Doo Nam KimBiological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99352, United States of America.
Song FengBiological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99352, United States of America.
Pavlo BohutskyiBiological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99352, United States of America.ORCID 0000-0002-0462-8132
Zachary JohnsonBiological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99352, United States of America.
Natalie SadlerBiological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99352, United States of America.
Marci GarciaBiological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99352, United States of America.
Xiaolu LiBiological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99352, United States of America.
Jesse TrejoBiological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99352, United States of America.
Ruonan WuBiological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99352, United States of America.
William SineathBiological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99352, United States of America.
Lindsey N AndersonResearch Computing, Pacific Northwest National Laboratory, Richland, Washington, 99352, United States of America.
James E EvansBiological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99352, United States of America.
Angad P MehtaDepartment of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
Wei-Jun QianBiological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99352, United States of America.
Zaida Luthey-SchultenBeckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801-3028, United States of America.
Margaret S CheungBiological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99352, United States of America.ORCID 0000-0001-9235-7661

Funding

ChimeraX -- Next Generation Visualization and Analysis Software for Multiscale ModelingR01GM129325 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI FERRIN, THOMAS E · 2018 to 2025
$5.2M
NIGMS NIH HHS R01 GM129325
6 · The paper itself

Abstract

Photosynthetic microorganisms rely on multiple pathways in central carbon metabolism to adapt to fluctuating light and energy availability across diel cycles. Mechanistic insight into the regulatory dynamics of this adaptation requires integrating processes spanning disparate timescales, from rapid redox-dependent post-translational modifications (PTMs) to slower changes in protein expression and metabolic pathway usage. To address this complexity beyond genome-based inference and traditional modeling, we develop a whole-cell four-dimensional (3D + time) model of the marine cyanobacterium

Indexed as

cryo-ETcyanobacteriaflux balance analysisgenome-scale metabolic modelingPhysical Sciences/Biophysics and Computational Biology: Biological Sciences/Systems Biologyproteomicssystems modelingtranscriptomes

Identifiers

PMID41648635
PMCPMC12871685

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.