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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Strong expression of cyclin B2 mRNA correlates with a poor prognosis in patients with non-small cell lung cancer
Shinogu Takashima,Hajime Saito,Naoko Takahashi,Kazuhiro Imai,Satoshi Kudo,Maiko Atari,Yoshitaro Saito,Satoru Motoyama,Yoshihiro Minamiya +8 more
TL;DR: Stronger expression of cyclin B2 mRNA in tumor cells is an independent predictor of a poor prognosis in patients with adenocarcinoma of lung, and there was no significance in the 5-year overall survival rates among the patients with squamous cell carcinoma between expressing lower and higher level of Cyclin B 2 mRNA.
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Single molecule experimentation in biological physics: exploring the living component of soft condensed matter one molecule at a time
Oliver Harriman,Mark C. Leake +1 more
TL;DR: Recent experimental approaches in biological physics which can be applied to investigate the living component of soft condensed matter to a precision of a single molecule are discussed.
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The Ongoing Quest to Crack the Genetic Code for Protein Production.
TL;DR: How advances supported by high-throughput analysis of synthetic gene libraries as well as by state-of-the-art biomolecular techniques further strengthen understanding of the gene expression process and how they can be harnessed to optimize protein production is discussed.
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Avoidance of stochastic RNA interactions can be harnessed to control protein expression levels in bacteria and archaea.
TL;DR: A new global factor is presented, called mRNA:ncRNA avoidance, and evidence that avoidance increases translational efficiency is provided, and it is demonstrated that GFP levels correlate well with interaction avoidance, enabling precise modulation of protein abundance.
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Sequence features of E. coli mRNAs affect their degradation.
TL;DR: In this paper, the authors calculated three properties for each mRNA in the E. coli transcriptome: G+C content, tRNA adaptation index (tAI), and folding energy, and correlated these properties with the experimental transcript half life measured for each transcript and detected significant correlations.
References
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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.
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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.
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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.
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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.