NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE261497 Query DataSets for GSE261497
Status Public on Sep 01, 2024
Title Genome concentration limits cell growth and modulates proteome composition in Escherichia coli
Organisms Escherichia coli K-12; Caulobacter vibrioides
Experiment type Expression profiling by high throughput sequencing
Summary Defining the cellular factors that drive growth rate and proteome composition is essential for understanding and manipulating cellular systems. In bacteria, ribosome concentration is known to be a constraining factor of cell growth rate, while gene concentration is usually assumed not to be limiting. Here, using single-molecule tracking, quantitative single-cell microscopy, and modeling, we show that genome dilution in Escherichia coli cells arrested for DNA replication results in a decrease in the concentration of active RNA polymerases and ribosomes. The resulting sub-linear scaling of total active RNA polymerases and ribosomes with cell size leads to sub-exponential growth, even within physiological cell sizes. Cell growth rate scales proportionally with the total number of active ribosomes in a DNA concentration-dependent manner. Tandem-mass-tag mass spectrometry experiments further revealed that a decrease in DNA-to-cell-volume ratio also incrementally remodels proteome composition with cell size. Altogether, our findings indicate that genome concentration is an important driver of exponential cell growth and a global modulator of proteome composition in E. coli. Comparison with studies on eukaryotic cells suggests DNA concentration-dependent scaling principles of gene expression across domains of life.
 
Overall design RNA-seq libraries associated with the project; CRISPRi oriC strain (SJ_XTL676) was grown in M9glyCAAT at 37°C and cells were collected 60, 120, 200, and 240 min after addition of 0.2% L-arabinose. For each timepoint, the aliquot was spun down, the supernatant was removed, and the pellet was flash-frozen. E. coli pellets were resuspended in ice cold phosphate buffer saline solution (PBS) and mixed with C. crescentus cells in approximately a 1-to-1 ratio based on OD600, with the intent of using the latter as a spike-in reference.
 
Contributor(s) Mäkelä J, Papagiannakis A, Lin WH, Glenn S, Lanz MC, Swaffer M, Marinov GK, Skotheim JM, Jacobs-Wagner C
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Mar 13, 2024
Last update date Sep 01, 2024
Contact name Georgi Kolev Marinov
Organization name STANFORD UNIVERSITY
Department Genetics
Street address 279 Campus Drive West, Beckman Center, B-257A/259
City Stanford
State/province California
ZIP/Postal code 94305-5101
Country USA
 
Platforms (1)
GPL34296 Illumina NovaSeq 6000 (Caulobacter vibrioides; Escherichia coli K-12)
Samples (8)
GSM8145371 A1_060min-arrest_RNA-rRNAdep
GSM8145372 A2_120min-arrest_RNA-rRNAdep
GSM8145373 A3_200min-arrest_RNA-rRNAdep
Relations
BioProject PRJNA1087324

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE261497_RAW.tar 99.4 Mb (http)(custom) TAR (of BIGWIG)
SRA Run SelectorHelp
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.