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
Posted Content
Hi-throughput gene expression analysis at the level of single proteins using a microfluidic turbidostat and automated cell tracking
TL;DR: In this article, a method combining microfluidics, time-lapsed single-molecule microscopy and automated image analysis was developed for the observation of an excess of 3000 complete cell cycles of exponentially growing Escherichia coli cells per experiment.
Journal ArticleDOI
Delayed Protein Synthesis Reduces the Correlation between mRNA and Protein Fluctuations
Tomáš Gedeon,Pavol Bokes +1 more
TL;DR: This work reports that its introduction into the two-stage model reduces the cross correlation between instantaneous mRNA and protein levels and indicates that the experimentally observed sample correlation coefficient may increase if the protein measurements are shifted back in time by the value of the delay.
Journal ArticleDOI
Escherichia coli can survive stress by noisy growth modulation.
Om Patange,Christian Schwall,Matt Jones,Casandra Villava,Douglas A. Griffith,Andrew Phillips,James C. W. Locke,James C. W. Locke +7 more
TL;DR: This work shows how noisy expression of a key stress-response regulator, RpoS, allows E. coli to modulate its growth dynamics to survive future adverse environments, and reveals a dynamic positive feedback loop between R PoS and growth rate that produces multi-generation RPoS pulses.
Journal ArticleDOI
Translational Cross Talk in Gene Networks
TL;DR: A stochastic model is investigated for this phenomenon, in which gene transcripts of different types compete for a finite pool of ribosomes, and when mRNA fluctuations dominate ribosomal fluctuations, a strong anticorrelation extremum reliably occurs near the transition from the underloaded to the overloaded regime.
Journal ArticleDOI
The proteome and phosphoproteome of Neurospora crassa in response to cellulose, sucrose and carbon starvation
Yi Xiong,Samuel T. Coradetti,Xin Li,Marina A. Gritsenko,Therese R. W. Clauss,Vlad Petyuk,David G. Camp,Richard D. Smith,Jamie H. D. Cate,Feng Yang,N. Louise Glass +10 more
TL;DR: Global proteomic and phosphoproteomic profiles of the plant biomass degrading filamentous fungus Neurospora crassa are obtained and a comparison between proteomes and transcriptomes under identical carbon conditions suggests that extensive post-transcriptional regulation occurs in N. crASSa in response to exposure to cellulosic material.
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.