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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Riboregulation of the bacterial actin-homolog MreB by DsrA small noncoding RNA
Bastien Cayrol,Emilie Fortas,Claire Martret,Grzegorz M. Cech,Anna Kloska,Stephane Caulet,Stephane Caulet,Marion Barbet,Sylvain Trépout,Sylvain Trépout,Sergio Marco,Sergio Marco,Aziz Taghbalout,Florent Busi,Florent Busi,Grzegorz Węgrzyn,Véronique Arluison,Véronique Arluison +17 more
TL;DR: It is proposed that the sRNA pathway helps to adapt to changes in temperature, but also indirectly mediates long-term regulation of MreB concentration.
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Optimization of sample preparation and green color imaging using the mNeonGreen fluorescent protein in bacterial cells for photoactivated localization microscopy
Iris Stockmar,Helge Feddersen,Kimberly Cramer,Kimberly Cramer,Stephan Gruber,Kirsten Jung,Marc Bramkamp,Jae Yen Shin,Jae Yen Shin +8 more
TL;DR: A simple data post-processing step that uses temporal and spatial information of molecule localizations to further reduce artifacts arising from simultaneous emission of nearby emitters is introduced and is expected to allow a broad use of mNeonGreen for super-resolution microscopy, which is so far difficult to achieve.
Journal ArticleDOI
Analysis of Translation Elongation Dynamics in the Context of an Escherichia coli Cell
TL;DR: A stochastic framework is used to simulate the process of translation in the context of an Escherichia coli cell by gathering the available biochemical data into a ribosome kinetics description and derives an equation that can accurately predict codon elongation rates based on the abundances of free tRNA in the cell, and can be used to assist transcript design.
Journal ArticleDOI
Methods and applications of absolute protein quantification in microbial systems.
Sandra Maaß,Dörte Becher +1 more
TL;DR: This review aims for discussion of different small-scale and large-scale approaches for absolute protein quantification in bacterial cells to picture biological processes and explore life in deeper detail.
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MYMIV-AC2, a geminiviral RNAi suppressor protein, has potential to increase the transgene expression.
TL;DR: The Mungbean Yellow Mosaic India Virus (MYMIV) belonging to the genus Begomovirus within the family of Geminiviridae encodes an RSS called the AC2 protein, which is used to elevate the expression of the transgenes in GFP transgenic tobacco lines.
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.
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.