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
Microspatial gene expression patterns in the Amazon River Plume.
Brandon M. Satinsky,Byron C. Crump,Christa B. Smith,Shalabh Sharma,Brian L. Zielinski,Mary Doherty,Jun Meng,Shulei Sun,Patricia M. Medeiros,John H. Paul,Victoria J. Coles,Patricia L. Yager,Mary Ann Moran +12 more
TL;DR: Investigation of expression of genes mediating elemental cycling at the microspatial scale in the ocean’s largest river plume using, to the authors' knowledge, the first fully quantitative inventory of genes and transcripts finds gene regulation differences were more important than genome abundance differences in explaining why microenvironment transcriptomes differed.
Journal ArticleDOI
Direct detection and drug-resistance profiling of bacteremias using inertial microfluidics
Han Wei Hou,Roby P. Bhattacharyya,Roby P. Bhattacharyya,Deborah T. Hung,Deborah T. Hung,Jongyoon Han +5 more
TL;DR: A method to rapidly isolate bacteria from whole blood using inertial microfluidics and directly determine pathogen identity and antibiotic susceptibility with hybridization-based RNA detection is described.
Journal ArticleDOI
Method of conditional moments (MCM) for the Chemical Master Equation
TL;DR: It is proved that the MCM provides a generalization of previous approximations of the CME based on hybrid modeling and moment-based methods and improves upon these existing methods, as illustrated using a model for the dynamics of stochastic single-gene expression.
Journal ArticleDOI
Soluble oligomerization provides a beneficial fitness effect on destabilizing mutations
TL;DR: It is found that mutational destabilization of DHFR proteins in E. coli is counterbalanced at 42 °C by their soluble oligomerization, thereby restoring structural stability and protecting against aggregation, and suggesting that protein homeostatic machinery plays an active role in maintaining intracellular concentrations of proteins.
Journal ArticleDOI
A high resolution map of a cyanobacterial transcriptome
TL;DR: A comprehensive study of a cyanobacterial transcriptome, that of Synechococcus elongatus PCC 7942, generated by combining three high-resolution data sets: RNA sequencing, tiling expression microarrays, and RNA polymerase chromatin immunoprecipitation sequencing is performed.
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.