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
Duplex-specific nuclease efficiently removes rRNA for prokaryotic RNA-seq
Hana Yi,Yong-Joon Cho,Sungho Won,Jong Eun Lee,Hyung Jin Yu,Su Jin Kim,Gary P. Schroth,Shujun Luo,Jongsik Chun +8 more
TL;DR: The results clearly showed that the DSN treatment was more efficient at removing rRNA than the Hyb method was, while preserving the original relative abundance of mRNA species in bacterial cells, and it is proposed that, for bacterial mRNA-seq experiments, D SN treatment should be preferred to Hyb-based methods.
Journal ArticleDOI
A Stress Response that Monitors and Regulates mRNA Structure Is Central to Cold Shock Adaptation
TL;DR: A two-member mRNA surveillance system that enables recovery of translation during acclimation is identified and an autoregulatory switch in which Csps tune their own expression to cellular demand enables dynamic control of global translation.
Journal ArticleDOI
What shapes eukaryotic transcriptional bursting
TL;DR: The impact on transcriptional bursting of different molecular aspects of transcription such as the chromatin environment, nucleosome occupancy, histone modifications, the number and affinity of regulatory elements, DNA looping and transcription factor availability is recapitulate.
Journal ArticleDOI
Indirect and suboptimal control of gene expression is widespread in bacteria
Morgan N. Price,Adam M. Deutschbauer,Jeffrey M. Skerker,Kelly M. Wetmore,Kelly M. Wetmore,Troy Ruths,Jordan Mar,Jennifer V. Kuehl,Wenjun Shao,Adam P. Arkin,Adam P. Arkin +10 more
TL;DR: It is proposed that most genes are under indirect control: their expression responds to signal(s) that are not directly related to the genes’ function, and it is shown that gene regulation is often maladaptive in the laboratory.
Journal ArticleDOI
Diverse Spatial Expression Patterns Emerge from Unified Kinetics of Transcriptional Bursting.
TL;DR: Both the rate of polymerase initiation and the switching rates are tightly constrained across all expression levels, predicting synchronous patterning outcomes at all positions in the embryo and indicate a path to general rules in transcriptional regulation.
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.