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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
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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.
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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.
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Contributor(s) |
Mäkelä J, Papagiannakis A, Lin WH, Glenn S, Lanz MC, Swaffer M, Marinov GK, Skotheim JM, Jacobs-Wagner C |
Citation missing |
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Submission date |
Mar 13, 2024 |
Last update date |
Sep 01, 2024 |
Contact name |
Georgi Kolev Marinov |
Organization name |
STANFORD UNIVERSITY
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Department |
Genetics
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Street address |
279 Campus Drive West, Beckman Center, B-257A/259
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City |
Stanford |
State/province |
California |
ZIP/Postal code |
94305-5101 |
Country |
USA |
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Platforms (1) |
GPL34296 |
Illumina NovaSeq 6000 (Caulobacter vibrioides; Escherichia coli K-12) |
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Samples (8)
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Relations |
BioProject |
PRJNA1087324 |
Supplementary file |
Size |
Download |
File type/resource |
GSE261497_RAW.tar |
99.4 Mb |
(http)(custom) |
TAR (of BIGWIG) |
SRA Run Selector |
Raw data are available in SRA |
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