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
Patterns of Bacterial and Archaeal Gene Expression through the Lower Amazon River
Brandon M. Satinsky,Christa B. Smith,Shalabh Sharma,Nicholas D. Ward,Alex V. Krusche,Jeffrey E. Richey,Patricia L. Yager,Byron C. Crump,Mary Ann Moran +8 more
TL;DR: Analysis of metatranscriptomic and metagenomic datasets from the lower reaches of the Amazon River between Obidos and the river mouth revealed microbial transcript and gene pools dominated by Actinob bacteria, Thaumarchaeota, Bacteroidetes, Acidobacteria, Betaproteobacteria and Planctomycetes.
Journal ArticleDOI
Dynamic competition between transcription initiation and repression: Role of nonequilibrium steps in cell-to-cell heterogeneity.
TL;DR: Overall, it is shown that nonequilibrium steps of transcription initiation systematically increase the cell-to-cell heterogeneity in bacterial populations and allows also weak promoters to give substantial transcriptional noise.
Journal ArticleDOI
Generalized Schemes for High-Throughput Manipulation of the Desulfovibrio vulgaris Genome
Swapnil R. Chhabra,Swapnil R. Chhabra,Gareth Butland,Dwayne A. Elias,John-Marc Chandonia,O.-Y. Fok,O.-Y. Fok,Thomas R. Juba,Amita Gorur,Simon Allen,C. M. Leung,Kimberly L. Keller,Sonia A. Reveco,Sonia A. Reveco,Grant M. Zane,Elizabeth S. Semkiw,R. Prathapam,Barbara Gold,Mary E. Singer,Mario Ouellet,Mario Ouellet,Evelin D. Szakal,Danielle M. Jorgens,Morgan N. Price,H. E. Witkowska,Harry R. Beller,Harry R. Beller,Adam P. Arkin,Adam P. Arkin,Adam P. Arkin,Terry C. Hazen,Terry C. Hazen,Mark D. Biggin,Manfred Auer,Judy D. Wall,Jay D. Keasling,Jay D. Keasling,Jay D. Keasling +37 more
TL;DR: This work highlights the use of synthetic biological tools to assemble custom suicide vectors with reusable and interchangeable DNA “parts” to facilitate chromosomal modification at designated loci to enable an array of downstream applications, including gene replacement and the creation of gene fusions with affinity purification or localization tags.
Journal ArticleDOI
Coupling between noise and plasticity in E. coli.
TL;DR: This work found significant positive correlation between noise and plasticity in E. coli and suggested that noise–plasticity coupling is an evolvable trait in yeast and may constrain evolution of gene expression and promoter usage.
Journal ArticleDOI
Quantitative Determination of Dark Chromophore Population Explains the Apparent Low Quantum Yield of Red Fluorescent Proteins
Jord C. Prangsma,Robert Molenaar,Laura van Weeren,Daphne S. Bindels,Lindsay Haarbosch,Jente Stouthamer,Theodorus W. J. Gadella,Vinod Subramaniam,Willem L. Vos,Christian Blum +9 more
TL;DR: It is determined that mCherry, mKate2, and mRuby2 have a considerable fraction of dark chromophores up to 45%, which explains both the low measured quantum yields of red emitting proteins reported in the literature and the difficulties in developing high quantum yield variants of such proteins.
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.