Nutrient-rich growth

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Single-Cell Extraction: For enzymatic digestion, pronase (Septomyces argeus, 1 mg/mL) was applied for 25 minutes at room temperature for P0 to P8 datasets. Cells were dissociated and triturated into a single-cell suspension in ACSF supplemented with 1% fetal calf serum (FCS) and DNase (1 µL/10 mL). Trituration was performed using three glass Pasteur pipettes of decreasing diameters. For P30 datasets, enzymatic digestion and cell dissociation were carried out using the Worthington Papain Dissociation System, following the manufacturer’s instructions. Single-Nuclei Extraction: For nuclei isolation, the Hibernate™-E Medium was removed, and 500 µL of chilled 0.1X NP40 Lysis Buffer was added. Tissue was homogenized using a Pellet Pestle (15 strokes) and incubated on ice for 5 minutes. The suspension was pipette-mixed 10 times using a wide-bore pipette tip and incubated for an additional 10 minutes on ice. Following lysis, 500 µL of chilled wash buffer was added, and the mixture was pipette-mixed 5 times using a regular-bore pipette tip. The suspension was filtered through a 30 µm cell strainer into a 50 mL tube to remove debris. The filtered suspension was transferred to a 1.5 mL tube and centrifuged at 950 × g for 10 minutes at 4°C. The supernatant was carefully removed, and the nuclei pellet was retained for downstream analysis. (2)
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NA (2)
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CHEBI ID

CHEBI:28044 (6)
CHEBI:15741 (6)
CHEBI:17822 (5)
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CHEBI:32816 (4)
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CHEBI:33508 (4)
CHEBI:18012 (4)
CHEBI:22653 (4)

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Ribitol (3)
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Cysteinylglycine disulfide* (2)

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False (1)

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Classification

bacteria (22)
fungi (3)
protozoa (2)

Modelling Approach

Constraint-based model (1)

Study type

Transcription profiling by array (139)
RNA-seq of coding RNA (63)
RNA-seq of coding RNA from single cells (31)
ChIP-seq (24)
RNA-seq of total RNA (8)
Methylation profiling by high throughput sequencing (6)
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Lab affiliation

Basic Immune System of Plants / Protein Mass Spectrometry Max Planck Institute for Plant Breeding Research Carl-von-Linne-Weg 10, 50829 Cologne, Germany (2)
Institute for Systems Biology, Seattle, WA, USA (2)
1The Shraga Segal Department of Microbiology, Immunology, and Genetics, Ben-Gurion University of the Negev, Israel (1)
Applied Proteomics Lab, Department of Biology, Maynooth University, Co. Kildare, Ireland (1)
Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS) Technical University of Munich (TUM) Gregor-Mendel-Strasse 4 85354 Freising Germany (1)
CNRS, UMR7242, ESBS, Bld Sébastien Brant, F-67412 Illkirch, France. Université de Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, F-67412 Illkirch, France. (1)
Dep. Microbiology University of Osnabrueck Faculty Biology / Chemistry Division Microbiology Barbarastrasse 11 49076 Osnabrueck (1)
Department of Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Biochemistry and Molecular Biology, University of Córdoba, Campus de Rabanales, Building C6, Crta. Madrid, Km 396, 14071 Córdoba, Spain (1)
Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Kolkata, Mohanpur, District: Nadia, West Bengal, Pin Code: 741246, India (1)
Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, D-17489 Greifswald, Germany (1)
Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen (1)
Equipe ProbiHôte Unité MICALIS Centre INRAE Domaine de Vilvert 78350 Jouy en Josas Tél: 01 34 65 24 69 (1)
Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium (1)
HMI, IMB, UiT The Arctic University of Norway, Norway (1)
Helmholtz-Centre for Environmental Research - UFZ GmbH Department of Molecular Systems Biology Permoserstrasse 15 04318 Leipzig, Germany (1)
Institute of Cell Biology, University of Bern, Bern, Switzerland (1)
Institute of Microbiology, Department of Microbial Proteomics, Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany (1)
Institute of Physiology, University of Zurich, 8057 Zurich, Switzerland (1)
LIST_Environmental and industrial biotechnologies Bioprocessing and formulation L-4940, BASCHARAGE LUXEMBOURG (1)
MRC London Institute of Medical Sciences Proteomics & Metabolomics Facility Hammersmith Hospital Campus Du Cane Road London, W12 0NN United Kingdom (1)
MSAP USR 3290 CNRS Cité scientifique Villeneuve d'Ascq France (1)
Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, China (1)
Singapore Professor of Biological Engineering Professor of Biological Engineering Massachusetts Institute of Technology Department of Biological Engineering, 56-731 77 Massachusetts Ave. Cambridge, MA 02139 (1)
Universitat Autònoma de Barcelona (1)
University of Guelph (1)
head of R&D in Center of Food and Fermentation Technologies (1)

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Landscape and dynamics of TadA-dependent RNA editing in Escherichia coli reveal a role in nutrient-rich growth

Adenosine-to-inosine A-to-I mRNA editing alters genetic information post-transcriptionally and can impact protein sequence and function, yet its regulation in bacteria remains unclear. Here, we profiled A-to-I editing in Escherichia coli across nutrient-rich LB and minimal M9 media and different gro...

ORGANISM(S): Bacteria Escherichia coli (strain K12)

2026-03-24 | PXD075028 | Pride

Tada-dependent rna editing Nutrient-rich growth

Energy-translation coupling limits yeast anaerobic growth

This study employs yeast as a model system to thoroughly investigate the differences in regulatory mechanisms under various nutrient limitation conditions, utilizing a systems biology approach integrated with techniques such as multi-omics analysis.To obtain a comprehensive quantitative landscap...

2026-05-24 | MTBLS14573 | MetaboLights

Cancer-cell-secreted exosomal miR-105 promotes tumour growth through the Myc-dependent metabolic reprogramming of stromal cells

Cancer and other cells residing in the same niche engage various modes of interactions to synchronize and to buffer the negative effects of environmental changes. Extracellular miRNAs have been recently implicated in the intercellular crosstalk. Here we show a mechanistic model involving breast-canc...

2018-07-10 | MTBLS626 | MetaboLights

E. coli BW25113 proteomics in nutrient-rich and minimal medium

E. coli BW25113 growth in a nutrient-rich medium supplemented with 20 proteinogenic amino acid medium was studied and compared to growth in minimal medium. Proteome data from these experiments revealed significant differences in amino acid synthesis and transport proteins that were reduced in the nu...

ORGANISM(S): Escherichia coli

2020-02-18 | PXD011726 | Pride

E. coli rich medium

The Vibrio vulnificus stressosome is dispensable in nutrient-rich media

Not available

S-EPMC10436020 | biostudies-literature

Nematodes enhance plant growth and nutrient uptake under C and N-rich conditions.

Not available

S-EPMC5015107 | biostudies-literature

Mycobacterium smegmatis: CarD depletion (mgm1703) vs Control (mgm1701)

Transcriptional profiling of Mycobacterium smegmatis comparing the effects of wild type levels of CarD expression with CarD depletion. Transcriptional profile of the mgm1701 control strain was compared with that of mgm1703, a strain where CarD transcription is regulated by a Tet-On system. Both stra...

ORGANISM(S): Mycobacterium smegmatis

2010-05-16 | E-GEOD-15437 | biostudies-arrayexpress

Proteome constraints reveal targets for improving microbial fitness in nutrient-rich environments.

Not available

S-EPMC8022198 | biostudies-literature

Effects of Nutrient Limitation on the Synthesis of N-Rich Phytoplankton Toxins: A Meta-Analysis.

Not available

S-EPMC7232484 | biostudies-literature

Proteomic analysis of the wheat pathogenic fungus Zymoseptoria tritici

Z. tritici is a fungal pathogen causing the disease septoria tritici blotch, one of the most economically devastating foliar diseases in wheat. The molecular basis underlying Z. tritici growth, development and pathogenicity is not fully understood yet. Compared to the genomic investigations in this ...

ORGANISM(S): Zymoseptoria tritici (strain CBS 115943 / IPO323) (Speckled leaf blotch fungus) (Septoria tritici)

2018-07-05 | PXD002147 | Pride

Zymoseptoria tritici Scx In planta Fungal proteomics

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