PXD071222

PXD071222 is an original dataset announced via ProteomeXchange.

Title	Coordination Between Cytoplasmic and Envelope Densities Shapes Cellular Geometry in Escherichia coli
Description	Microbes exhibit precise control over their composition and geometry in order to adapt and grow in diverse environments. However, the mechanisms that orchestrate this simultaneous regulation, and how they are causally linked, remains poorly understood. In this work, we derive and experimentally test a biophysical model of cell size regulation in Escherichia coli which relates the cellular surface-to-volume ratio to the total macromolecular composition and partitioning of the proteome between cellular compartments. Central to this model is the observation that the macromolecular density of the cytoplasm and the protein density within the cell membranes are maintained at a constant ratio across growth conditions. Using quantitative mass spectrometry, single-cell microscopy, and biochemical assays, we show this model quantitatively predicts a non-linear relationship between the surface-to-volume ratio, proteome localization, and the total ribosome content of the cell. This model holds under perturbations of intracellular ppGpp concentrations–thereby changing the ribosomal content–demonstrating that cellular geometry is not strictly determined by the cellular growth rate. These findings provide a biophysical link between the coregulation of proteome organization and cellular geometry, offering a quantitative framework for understanding bacterial size regulation across conditions.
HostingRepository	PRIDE
AnnounceDate	2025-11-26
AnnouncementXML	Submission_2025-11-26_08:20:07.532.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Michael Lanz
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: NEWT:562;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2025-11-25 15:15:44	ID requested
⏵ 1	2025-11-26 08:20:08	announced

Dataset with its publication pending

submitter keyword: cell growth,Cell size, proteome allocations

Jonas Cremer
contact affiliation	Department of Biology, Stanford University
contact email	jonas.cremer@stanford.edu
lab head
Michael Lanz
contact affiliation	Stanford University
contact email	mikelanz@stanford.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/11/PXD071222

PRIDE project URI

• PRIDE
  1. PXD071222
     1. Label: PRIDE project
     2. Name: Coordination Between Cytoplasmic and Envelope Densities Shapes Cellular Geometry in Escherichia coli