GenoBase: comprehensive resource database of Escherichia coli K-12

Otsuka, Yuichi; Muto, Ai; Takeuchi, Rikiya; Okada, Chihiro; Ishikawa, Motokazu; Nakamura, Koichiro; Yamamoto, Nobuto; Dose, Hitomi; Nakahigashi, Kenji; Tanishima, Shigeki; Suharnan, Sivasundaram; Nomura, Wataru; Nakayashiki, Toru; Aref, Walid G.; Bochner, Barry R.; Conway, Tyrrell; Gribskov, Michael; Rudd, Kenneth E.; Tohsato, Yukako; Wanner, Barry L.; Mori, Hirotada

doi:10.1093/nar/gku1164

Cited by 35 publications

(47 citation statements)

References 51 publications

(60 reference statements)

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“…Notably, it provides a phenotype for 283 genes of uncharacterized function (out of 1,306 y‐genes). The Keio collection, as any genomewide deletion collection (Teng et al , ), is no stranger to gene duplications and compensatory mutations (Yamamoto et al , ; Otsuka et al , ). Although their occurrence can impact interpretation at the gene level, “suppressor” mutants tend to display more WT‐like behavior.…”

Section: Discussionmentioning

confidence: 99%

Genomewide phenotypic analysis of growth, cell morphogenesis, and cell cycle events in Escherichia coli

Campos

Govers

Irnov

et al. 2018

Molecular Systems Biology

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Cell size, cell growth, and cell cycle events are necessarily intertwined to achieve robust bacterial replication. Yet, a comprehensive and integrated view of these fundamental processes is lacking. Here, we describe an image‐based quantitative screen of the single‐gene knockout collection of Escherichia coli and identify many new genes involved in cell morphogenesis, population growth, nucleoid (bulk chromosome) dynamics, and cell division. Functional analyses, together with high‐dimensional classification, unveil new associations of morphological and cell cycle phenotypes with specific functions and pathways. Additionally, correlation analysis across ~4,000 genetic perturbations shows that growth rate is surprisingly not predictive of cell size. Growth rate was also uncorrelated with the relative timings of nucleoid separation and cell constriction. Rather, our analysis identifies scaling relationships between cell size and nucleoid size and between nucleoid size and the relative timings of nucleoid separation and cell division. These connections suggest that the nucleoid links cell morphogenesis to the cell cycle.

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Section: Discussionmentioning

confidence: 99%

Genomewide phenotypic analysis of growth, cell morphogenesis, and cell cycle events in Escherichia coli

Campos

Govers

Irnov

et al. 2018

Molecular Systems Biology

View full text Add to dashboard Cite

show abstract

“…Notably, it provides a phenotype for 283 genes of uncharacterized function (out of 1306 y-genes). The Keio collection, as any genome-wide deletion collection (Teng et al, 2013), is no stranger to gene duplications and compensatory mutations (Otsuka et al, 2015;Yamamoto et al, 2009). Although their occurrence can impact interpretation at the gene level, "suppressor" mutants tend to display more WT-like behavior.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide phenotypic analysis of growth, cell morphogenesis and cell cycle events in Escherichia coli.

Campos

Dobihal

Jacobs‐Wagner

2017

Preprint

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Cell size, cell growth and the cell cycle are necessarily intertwined to achieve robust bacterial replication. However, a comprehensive and integrated view of these fundamental processes is lacking. Here, we describe an image-based quantitative screen over the single-gene knockout collection of Escherichia coli, which led to the identification of many new genes involved in cell morphogenesis, population growth, nucleoid (bulk chromosome) dynamics and cell division. Functional analyses, together with high-dimensional classification, unveil new associations of morphological and cell cycle phenotypes with specific functions and pathways. Additionally, correlation analyses across ∼4,000 genetic perturbations demonstrate that growth rate is not a determinant of cell size. Cell width and length are also uncorrelated, suggesting that cells do not control their size by monitoring surface area or volume; instead cells appear to regulate width and length independently. Furthermore, our analysis identifies scaling relationships between cell size and nucleoid size and between nucleoid size and the relative timings of nucleoid separation and cell division, linking cell morphogenesis to the cell cycle via the global architecture of the chromosome.

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“…Cells expressing this protein showed a nonhomogeneous distribution of fluorescence throughout the cell volume, with visible puncta of more intense fluorescence (data not shown). Previous work has similarly shown that fusion of Dps with the green fluorescent protein (GFP) resulted in aggregation of this fusion protein in E. coli cells (44). This strain was therefore excluded from further experimentation.…”

Section: Construction Of a Reporter Strain For Dps Productionmentioning

confidence: 99%

Single-Cell Analysis of the Dps Response to Oxidative Stress

et al. 2016

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Microorganisms have developed an elaborate spectrum of mechanisms to respond and adapt to environmental stress conditions. Among these is the expression of dps, coding for the DNA-binding protein from starved cells. Dps becomes the dominant nucleoid-organizing protein in stationary-phase Escherichia coli cells and is required for robust survival under stress conditions, including carbon or nitrogen starvation, oxidative stress, metal exposure, and irradiation. To study the complex regulation of Dps in E. coli, we utilized time-lapse fluorescence microscopy imaging to examine the kinetics, input encoding, and variability of the Dps response in single cells. In the presence of an oxidative stressor, we observed a single pulse of activation of Dps production. Bacteria encounter many stresses during their development, and they need to be able to adapt quickly to the environment to survive. Bacterial response mechanisms frequently involve specific sets of genes that are activated to help the cell adapt to stress. Alternative sigma factors, of which Escherichia coli has seven, are a frequently used regulatory mechanism (1). While housekeeping genes expressed during exponential growth are controlled by the transcription factor 70 (2, 3), alternative sigma factors act as transcription initiation factors to control the activation of specialized regulons under specific growth or stress conditions (4). The general stress response sigma factor S activates the transcription of Ͼ70 genes, conferring resistance to carbon/phosphate/nitrogen starvation, heat shock, high/low pH, UV radiation, and oxidative stress, among others (5, 6).Microorganisms living in an aerobic environment unavoidably encounter oxidative stress as a by-product of their aerobic metabolism (7). The resultant formation of reactive oxygen species (ROS) can lead to damage to cellular components, including membranes, DNA, and proteins (8). As an adaptation to this condition, bacteria produce enzymes, such as superoxide dismutases and reductases, to scavenge these toxic components (9). Additionally, cells also face external sources of oxidative stress: macrophages produce superoxide and nitric oxide to kill invading bacteria (10), following perception of pathogens, plants also induce the synthesis of organic peroxides (11), certain communities of microorganisms excrete ROS to inhibit the growth of their competitors (12), and exposure to environmental redox cycling compounds can cause damaging intracellular redox reactions (13).In this challenging environment, bacteria have developed refined molecular mechanisms of defense. The DNA-binding protein from starved cells (Dps) plays a crucial role during stress exposure. Escherichia coli dps mutants experience a severe reduction in survival when exposed to any of several different stressors, including oxidative stress, heat shock, metal exposure, UV and gamma irradiation, or extreme pH (14-16). Additionally, Dps was shown to protect cells against DNA strand breakage (17). In E. coli, the protective effect of...

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GenoBase: comprehensive resource database of Escherichia coli K-12

Cited by 35 publications

References 51 publications

Genomewide phenotypic analysis of growth, cell morphogenesis, and cell cycle events in Escherichia coli

Genomewide phenotypic analysis of growth, cell morphogenesis, and cell cycle events in Escherichia coli

Genome-wide phenotypic analysis of growth, cell morphogenesis and cell cycle events in Escherichia coli.

Single-Cell Analysis of the Dps Response to Oxidative Stress

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