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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Quantifying the contribution of chromatin dynamics to stochastic gene expression reveals long, locus-dependent periods between transcriptional bursts.
José Viñuelas,Gaël Kaneko,Antoine Coulon,Elodie Vallin,Valérie Morin,Camila Mejia-Pous,Jean-Jacques Kupiec,Guillaume Beslon,Olivier Gandrillon +8 more
TL;DR: This work sheds a new light on the mechanisms of gene expression in higher eukaryotic cells, and argues in favor of relatively slow dynamics with long (hours to days) periods of quiet state.
Journal ArticleDOI
In search of principles for a Theory of Organisms
Giuseppe Longo,Maël Montévil,Maël Montévil,Carlos Sonnenschein,Carlos Sonnenschein,Ana M. Soto,Ana M. Soto +6 more
TL;DR: This theory would complement the theory of evolution that addresses phylogenesis, and would posit theoretical extensions to accepted physical principles and default states in order to grasp the living state of matter and define proper biological observables.
Journal ArticleDOI
Long-Distance Cooperative and Antagonistic RNA Polymerase Dynamics via DNA Supercoiling.
Sangjin Kim,Sangjin Kim,Bruno Beltran,Bruno Beltran,Irnov Irnov,Irnov Irnov,Christine Jacobs-Wagner +6 more
TL;DR: Evidence is provided for a built-in mechanism by which co-transcribing RNAPs display either collaborative or antagonistic dynamics over long distances through transcription-induced DNA supercoiling, given that transcription on topologically constrained DNA is the norm across organisms.
Journal ArticleDOI
Enhancing metaproteomics—The value of models and defined environmental microbial systems
Florian-Alexander Herbst,Vanessa Lünsmann,Henrik Kjeldal,Nico Jehmlich,Andreas Tholey,Martin von Bergen,Martin von Bergen,Jeppe Lund Nielsen,Robert L. Hettich,Jana Seifert,Per Halkjær Nielsen +10 more
TL;DR: Model systems are useful to evaluate the challenges encountered within metaproteomics, including species complexity and coverage, biomass availability, or reliable protein extraction, and can be considered as a step forward to better understand microbial community responses and ecological functions of single member organisms.
Journal ArticleDOI
Protein costs do not explain evolution of metabolic strategies and regulation of ribosomal content : Does protein investment explain an anaerobic bacterial Crabtree effect?
Anisha Goel,Anisha Goel,Thomas H. Eckhardt,Pranav Puri,Anne de Jong,Filipe Branco dos Santos,Martin Giera,Fabrizia Fusetti,Willem M. de Vos,Jan Kok,Bert Poolman,Douwe Molenaar,Oscar P. Kuipers,Bas Teusink +13 more
TL;DR: The authors showed that Lactococcus lactis is either poorly adapted to growth at low and constant glucose concentrations, or that protein costs play a less important role in fitness than hitherto assumed.
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.