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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Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale
Joanne K. Liu,Edward J. O’Brien,Joshua A. Lerman,Karsten Zengler,Karsten Zengler,Bernhard O. Palsson,Adam M. Feist,Adam M. Feist +7 more
TL;DR: The i JL1678-ME model as mentioned in this paper was proposed to capture the functional content of membranes, cellular compartment-specific composition, and that it can be utilized to examine the effect of perturbing an expanded set of network components.
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In vivo translation rates can substantially delay the cotranslational folding of the Escherichia coli cytosolic proteome.
Prajwal Ciryam,Prajwal Ciryam,Richard I. Morimoto,Michele Vendruscolo,Christopher M. Dobson,Edward P. O'Brien +5 more
TL;DR: A chemical kinetic equation with genomic and proteomic data is combined to predict domain folding probabilities as a function of nascent chain length for Escherichia coli cytosolic proteins synthesized on both arrested and continuously translating ribosomes.
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New RNA-seq approaches for the study of bacterial pathogens
TL;DR: Dual RNA-seq analyzing pathogen and host simultaneously has revealed roles of noncoding RNAs during infection and enabled the correlation of bacterial gene activity with specific host responses.
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Simultaneous cross-evaluation of heterogeneous E. coli datasets via mechanistic simulation
Derek N. Macklin,Travis A. Ahn-Horst,Heejo Choi,Nicholas A. Ruggero,Javier Carrera,John C. Mason,Gwanggyu Sun,Eran Agmon,Mialy M. DeFelice,Inbal Maayan,Keara Michelle Lane,Ryan K. Spangler,Taryn E. Gillies,Morgan L. Paull,Sajia Akhter,Samuel R. Bray,Daniel Weaver,Ingrid M. Keseler,Peter D. Karp,Jerry H. Morrison,Markus W. Covert +20 more
TL;DR: A large-scale, integrated modeling approach to simultaneously cross-evaluate millions of heterogeneous data against themselves, based on an extensive computer model of Escherichia coli that accounts for the function of 1214 genes, providing the most natural, intuitive interpretation of an integrated dataset.
Journal ArticleDOI
Protein Homeostasis Imposes a Barrier on Functional Integration of Horizontally Transferred Genes in Bacteria.
Shimon Bershtein,Adrian W.R. Serohijos,Sanchari Bhattacharyya,Michael Manhart,Jeong-Mo Choi,Wanmeng Mu,Jingwen Zhou,Eugene I. Shakhnovich +7 more
TL;DR: By apparently distinguishing between self and non-self proteins, protein homeostasis imposes an immediate and global barrier to the functional integration of foreign genes by decreasing the intracellular abundance of their products.
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.