Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells.
Yuichi Taniguchi,Paul J. Choi,Gene-Wei Li,Huiyi Chen,Mohan Babu,Jeremy Hearn,Andrew Emili,X. Sunney Xie +7 more
Reads0
Chats0
TLDR
System-wide analyses of protein and mRNA expression in individual cells with single-molecule sensitivity using a newly constructed yellow fluorescent protein fusion library for Escherichia coli found that almost all protein number distributions can be described by the gamma distribution with two fitting parameters which, at low expression levels, have clear physical interpretations as the transcription rate and protein burst size.Abstract:
Protein and messenger RNA (mRNA) copy numbers vary from cell to cell in isogenic bacterial populations. However, these molecules often exist in low copy numbers and are difficult to detect in single cells. We carried out quantitative system-wide analyses of protein and mRNA expression in individual cells with single-molecule sensitivity using a newly constructed yellow fluorescent protein fusion library for Escherichia coli. We found that almost all protein number distributions can be described by the gamma distribution with two fitting parameters which, at low expression levels, have clear physical interpretations as the transcription rate and protein burst size. At high expression levels, the distributions are dominated by extrinsic noise. We found that a single cell's protein and mRNA copy numbers for any given gene are uncorrelated.read more
Citations
More filters
Journal ArticleDOI
Cell–cell contacts confine public goods diffusion inside Pseudomonas aeruginosa clonal microcolonies
Thomas Julou,Thierry Mora,Laurent Guillon,Vincent Croquette,Isabelle J. Schalk,David Bensimon,David Bensimon,Nicolas Desprat,Nicolas Desprat +8 more
TL;DR: In Pseudomonas aeruginosa microcolonies growing on solid substrate, it is found that the concentration of pyoverdine, a secreted iron chelator, is heterogeneous, with a maximum at the center of the colony, and quantitatively explain the formation of this gradient by local exchange between contacting cells rather than by global diffusion of py overdine.
Journal ArticleDOI
Biological mechanisms, one molecule at a time
Ignacio Tinoco,Ruben L. Gonzalez +1 more
TL;DR: The mechanistic information available from single-molecule experiments with the information typically obtained from ensemble studies is compared and how these two experimental approaches interface with each other is shown.
Journal ArticleDOI
Proteobacteria explain significant functional variability in the human gut microbiome
TL;DR: These results establish limits on functional redundancy and predict specific genes and taxa that may explain physiological differences between gut microbiomes that are applicable to shotgun metagenomes from any environment and can integrate data from multiple studies.
Journal ArticleDOI
A chemostat array enables the spatio-temporal analysis of the yeast proteome
Nicolas Dénervaud,Johannes Becker,Ricard Delgado-Gonzalo,Pascal Damay,Arun S. Rajkumar,Michael Unser,David Shore,Felix Naef,Sebastian J. Maerkl +8 more
TL;DR: A massively parallel microchemostat array capable of growing and observing 1,152 yeast-GFP strains on the single-cell level with 20 min time resolution is developed and identified four gene disruptions leading to abnormal ribonucleotide-diphosphate reductase localization.
Journal ArticleDOI
Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli.
TL;DR: This work develops semi-supervised normalization pipelines and performs experimental characterization to create Ecomics, a consistent, quality-controlled multi-omics compendium for Escherichia coli with cohesive meta-data information, and trains a multi-scale model that integrates four omics layers to predict genome-wide concentrations and growth dynamics.
References
More filters
疟原虫var基因转换速率变化导致抗原变异[英]/Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A
TL;DR: PfPMP1)与感染红细胞、树突状组胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作�ly.
Journal ArticleDOI
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection.
Tomoya Baba,Takeshi Ara,Miki Hasegawa,Yuki Takai,Yoshiko Okumura,Miki Baba,Kirill A. Datsenko,Masaru Tomita,Barry L. Wanner,Hirotada Mori,Hirotada Mori +10 more
TL;DR: These mutants—the ‘Keio collection’—provide a new resource not only for systematic analyses of unknown gene functions and gene regulatory networks but also for genome‐wide testing of mutational effects in a common strain background, E. coli K‐12 BW25113.
Journal ArticleDOI
Stochastic Gene Expression in a Single Cell
TL;DR: This work constructed strains of Escherichia coli that enable detection of noise and discrimination between the two mechanisms by which it is generated and reveals how low intracellular copy numbers of molecules can fundamentally limit the precision of gene regulation.
Journal ArticleDOI
Global analysis of protein localization in budding yeast
Won-Ki Huh,James V. Falvo,Luke C. Gerke,Adam S. Carroll,Russell W. Howson,Jonathan S. Weissman,Erin K. O'Shea +6 more
TL;DR: The construction and analysis of a collection of yeast strains expressing full-length, chromosomally tagged green fluorescent protein fusion proteins helps reveal the logic of transcriptional co-regulation, and provides a comprehensive view of interactions within and between organelles in eukaryotic cells.
Journal ArticleDOI
Fabrication of microfluidic systems in poly(dimethylsiloxane)
J.C. McDonald,David C. Duffy,Janelle R. Anderson,Daniel T. Chiu,Hongkai Wu,Olivier Schueller,George M. Whitesides +6 more
TL;DR: Fabrication of microfluidic devices in poly(dimethylsiloxane) (PDMS) by soft lithography provides faster, less expensive routes to devices that handle aqueous solutions.