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
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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
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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.
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Tissue-based map of the human proteome
Mathias Uhlén,Mathias Uhlén,Linn Fagerberg,Björn M. Hallström,Cecilia Lindskog,Per Oksvold,Adil Mardinoglu,Åsa Sivertsson,Caroline Kampf,Evelina Sjöstedt,Evelina Sjöstedt,Anna Asplund,IngMarie Olsson,Karolina Edlund,Emma Lundberg,Sanjay Navani,Cristina Al-Khalili Szigyarto,Jacob Odeberg,Dijana Djureinovic,Jenny Ottosson Takanen,Sophia Hober,Tove Alm,Per-Henrik Edqvist,Holger Berling,Hanna Tegel,Jan Mulder,Johan Rockberg,Peter Nilsson,Jochen M. Schwenk,Marica Hamsten,Kalle von Feilitzen,Mattias Forsberg,Lukas Persson,Fredric Johansson,Martin Zwahlen,Gunnar von Heijne,Jens Nielsen,Jens Nielsen,Fredrik Pontén +38 more
TL;DR: In this paper, a map of the human tissue proteome based on an integrated omics approach that involves quantitative transcriptomics at the tissue and organ level, combined with tissue microarray-based immunohistochemistry, to achieve spatial localization of proteins down to the single-cell level.
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Insights into the regulation of protein abundance from proteomic and transcriptomic analyses
TL;DR: Current understanding of the major factors regulating protein expression is summarized to demonstrate a substantial role for regulatory processes occurring after mRNA is made in controlling steady-state protein abundances.
Journal ArticleDOI
On the Dependency of Cellular Protein Levels on mRNA Abundance.
TL;DR: It is concluded that transcript levels by themselves are not sufficient to predict protein levels in many scenarios and to thus explain genotype-phenotype relationships and that high-quality data quantifying different levels of gene expression are indispensable for the complete understanding of biological processes.
References
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Visualization of Single RNA Transcripts in Situ
Andrea M. Femino,Fredric S. Fay,Fredric S. Fay,Kevin E. Fogarty,Kevin E. Fogarty,Robert H. Singer,Robert H. Singer +6 more
TL;DR: This approach extends the power of FISH to yield quantitative molecular information on a single cell by positioning probes along the transcription unit to determine the rates of transcription initiation and termination and messenger RNA processing.
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Stochastic protein expression in individual cells at the single molecule level
TL;DR: A microfluidic-based assay is demonstrated that allows real-time observation of the expression of β-galactosidase in living Escherichia coli cells with single molecule sensitivity and shows that protein production occurs in bursts, with the number of molecules per burst following an exponential distribution.
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Interaction network containing conserved and essential protein complexes in Escherichia coli
Gareth Butland,José M. Peregrín-Alvarez,Joyce Li,Wehong Yang,Xiaochun Yang,Veronica Canadien,Andrei Starostine,Dawn Richards,Bryan Beattie,Nevan J. Krogan,Michael Davey,John Parkinson,John Parkinson,Jack Greenblatt,Andrew Emili +14 more
TL;DR: Insight is provided into the function of previously uncharacterized bacterial proteins and the overall topology of a microbial interaction network, the core components of which are broadly conserved across Prokaryota.
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Gene Regulation at the Single-Cell Level
TL;DR: It is found that protein production rates fluctuate over a time scale of about one cell cycle, while intrinsic noise decays rapidly, which can form a basis for quantitative modeling of natural gene circuits and for design of synthetic ones.
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Control, exploitation and tolerance of intracellular noise
TL;DR: An exploration of the sources and consequences of noise calls for the use of stochastic models to explain the use, rejection and sensitivity to noise found in biological systems.