Impact of growth phase on the Escherichia coli meltome and proteome

Slides:

Advertisements

Similar presentations

SUPPLEMENTAL FIGURE S1. Growth in BHI after 12 days at 4°C of L

Advertisements

Microtubule perturbations cause Ste5 patches to form less reliably, delay patch formation, and cause patches to persist for less time Microtubule perturbations.

Microtubule perturbations affect pathway variability η2(P) and transmitted signal P at or upstream of the Ste5 recruitment step Microtubule perturbations.

GFP‐Sed5p localization defect in sgt2Δ.

Tuning the response of the DPI

Abundance of proteins matching selected subcellular locations and functions in CaCo‐2 cells. Abundance of proteins matching selected subcellular locations.

Global comparison of MinSpan pathways with databases of human‐defined pathways The pairwise connection specificity index (CSI) was calculated for all pathway.

Melting behavior of proteins identified in the Escherichia coli meltome and their properties Melting behavior of proteins identified in the Escherichia.

Thermal proteome profiling in Escherichia coli

Melting behavior of protein complexes

NSAF and GeneChip data have similar distribution properties.

Quantitative proteomics reveals daf‐16‐mediated reduction in protein metabolism in long‐lived daf‐2(e1370) mutants. Quantitative proteomics reveals daf‐16‐mediated.

Effects of ΔtolC on protein thermostability and abundance

Analysis of in silico flux changes along the exponential growth phase: (A) In silico flux changes from 24 to 36 h, from 36 to 48 h, and from 48 to 60 h.

Motif detectability corresponds to the phylogenetic profile of the cognate transcription factor. Motif detectability corresponds to the phylogenetic profile.

Characterization of the inferred factor associated with the differentiation state of the cell of origin Characterization of the inferred factor associated.

Data analysis of thermal proteome profiling

Distribution of summed MS1 intensities

Exo‐metabolomics profiling of major metabolites elucidated the metabolic capabilities of monospecies Exo‐metabolomics profiling of major metabolites elucidated.

Validation of the CCE associations by mass spectrometry.

Volume 138, Issue 4, Pages (August 2009)

Comparative analysis of RNA and protein profiles.

Model training of generalized Lotka–Volterra (gLV) to time‐resolved measurements of monospecies and pairwise assemblages Model training of generalized.

The human STRIPAK complex associates with RASF3 and MST1/2

Projecting cellular immunophenotypes onto Drop‐seq data

Correlating protein to mRNA and proteins per mRNA ratios

Validation cell‐type‐enriched culturing methods, metabolome dynamics, and mitochondria abundance and bioenergetics in differentiating organoids Validation.

Characterization of promoters relative to pAGA1

Differences in cellular organization emerge from quantitative proteomic experiments Differences in cellular organization emerge from quantitative proteomic.

Dermal architecture is defined by an inverse correlation between fibroblast proliferation and ECM deposition Dermal architecture is defined by an inverse.

Feature‐based COG enrichment analysis

Sensor optimization for thiosulfate and tetrathionate detection in the gut Sensor optimization for thiosulfate and tetrathionate detection in the gut A–F(A.

Changes to the growth conditions break the circuit by changing host gene expression Changes to the growth conditions break the circuit by changing host.

H-NS2-FLAG expression is upregulated in DMEM and M9 minimal medium and when cells enter the stationary growth phase. H-NS2-FLAG expression is upregulated.

Target identification of ampicillin and ciprofloxacin

Patient organoids respond more diverse to drugs and with lower therapeutic potential than 2D cultured patient cells Patient organoids respond more diverse.

Small‐molecule‐driven cell‐type enrichment as a model for intestinal differentiation Small‐molecule‐driven cell‐type enrichment as a model for intestinal.

Growth of L. monocytogenes strains AL4E, AT3E, and 10403S, derivative cured strain AT3Epc, and conjugation strains 10403SpclpL and 10403SpPL2 displayed.

Examples of protein that display profiles corresponding to GO/GROW and STOP signals.A, example of STOP profile: normalized spot volume profile of apoA-I.

Analysis of the phosphomimetic ProP‐PD selection results

The cell cycle influences circadian phase progression Circadian intervals with divisions (p1,d1,p2) last 21.95 ± 3.8 h (n = 1,926) and are significantly.

Francis Crick's central dogma of biology revolves around the transcription of mRNA from DNA, the translation of proteins from mRNA, and the degradation.

Notch activation in Notch1 positive feedback knock‐out intestine organoids Notch activation in Notch1 positive feedback knock‐out intestine organoids Intestine.

Comparison of proteomics and RNA‐Seq data.

Categorizing cell type‐specific auxin responses.

Comparison of nuclear surface area of HeLa and RKO cells

Dynamics of induction of mating promoters after pheromone stimulation

Simulation showing that the cell length variability of the entire population can mask abnormal cell length variability at a specific cell cycle period.

Subnetworks enriched for the hallmarks of cancer.

Proliferative advantage depends on environmental dynamics

Stage‐dependent diurnal transcript changes.

Distinct collagen structures in the upper and lower neonatal dermis (related to Fig 1)‏ Distinct collagen structures in the upper and lower neonatal dermis.

Reproducibility of DeathPro drug screens

A multitiered approach to characterize transcriptome structure.

Protein interactions at the nuclear pore.

Melting behavior of protein complexes

Antisense expression associates with larger gene expression variability. Antisense expression associates with larger gene expression variability. (A–D)

Experimental validation of predicted endocytosis functions in human.

Functional metabolic rearrangements in chloramphenicol‐resistant populations Functional metabolic rearrangements in chloramphenicol‐resistant populations.

Time‐course analysis of NICD degradation.

Competence initiation during the progression to spore formation.

Integration of proteomic data into the model

Characterization results of the lysis device in the final system using 3OC12HSL. Characterization results of the lysis device in the final system using.

Glucose pulses incorporate directly into the de novo biomass in non‐dividing cells Glucose pulses incorporate directly into the de novo biomass in non‐dividing.

Pou5f1 is required for proper developmental timing of gene expression.

(A) Observed significant protein fold‐changes during the fed–fasting transition in C57BL/6J (B6) and 129Sv (S9) mice fed with a normal diet (T0). (A) Observed.

Inhibitory effect of perhexiline on the proliferation of the HepG2 cell line A, BPerhexiline was used to mimic the effect of the l‐carnitine analog on.

Fraction of flux entering the PEP‐glyoxylate cycle as a function of hexose uptake rate in batch (A) and chemostat (B) cultures. Fraction of flux entering.

CRISPR‐Cas9 gene perturbation profiling in HeLa cells

BRI1 signaling at the dividing cells restores overall root growth

Presentation transcript:

Impact of growth phase on the Escherichia coli meltome and proteome Impact of growth phase on the Escherichia coli meltome and proteome Melting temperatures (Tm) of proteins in exponential and transition to stationary growth phases. Proteins highlighted in orange indicate significantly different melting behavior.Protein abundance in exponential and transition to stationary growth phases, as measured by the top3 intensity corresponding to the lowest temperature (see “Materials and Methods”). Proteins highlighted in orange indicate significantly different levels. Proteins were considered not detectable (n.d.) in one condition, if absent in three replicates in that condition, but detectable by at least three unique peptides in at least two replicates in the other condition.Respiratory activity in exponential and stationary cells determined as the conversion of triphenyltetrazolium chloride to triphenylformazan during the same time and normalized by OD (˜number of cells). n = 3; error bars represent standard deviation; **P < 0.01, Student's t‐test. André Mateus et al. Mol Syst Biol 2018;14:e8242 © as stated in the article, figure or figure legend