ArticleCell systems2019
Determination of the Gene Regulatory Network of a Genome-Reduced Bacterium Highlights Alternative Regulation Independent of Transcription Factors.
Article in Cell systems, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed, 51 citations in OpenAlex.
- Opportunities for artificial intelligence and synthetic biology in designing living drug delivery systems.Advanced drug delivery reviews · 2026Review
- Living Microbial Drugs.Chemistry (Weinheim an der Bergstrasse, Germany) · 2026Review
- Predicting the protein interaction landscape of a free-living bacterium with pooled-AlphaFold3.Molecular systems biology · 2026Article
- Dual mode of delivery ofmBio · 2026Article
- When less is more: cell size reduction as a metabolic lifeline inFrontiers in microbiology · 2026Article
- A versatile plug and play bacterial chassis based on a fast-growing Mycoplasma species.Nucleic acids research · 2025Article
- Quantitative essentiality in a reduced genome: a functional, regulatory and structural fitness map.Molecular systems biology · 2025Article
- Emergence of supercoiling-mediated regulatory networks through the evolution of bacterial chromosome organization.PLoS computational biology · 2025Article
- Modeling combinatorial regulation from single-cell multi-omics provides regulatory units underpinning cell type landscape using cRegulon.Genome biology · 2025Article
- Heterologous protein exposure and secretion optimization in Mycoplasma pneumoniae.Microbial cell factories · 2024Article
- Functional surface expression of immunoglobulin cleavage systems in a candidate Mycoplasma vaccine chassis.Communications biology · 2024Article
- ProTInSeq: transposon insertion tracking by ultra-deep DNA sequencing to identify translated large and small ORFs.Nature communications · 2024Article
- WhiA transcription factor provides feedback loop between translation and energy production in a genome-reduced bacterium.Frontiers in microbiology · 2024Article
- Transcriptional profiling and genetic analysis of a cystic fibrosis airway-relevant model shows asymmetric responses to growth in a polymicrobial community.Microbiology spectrum · 2023Article
- Comprehensive quantitative modeling of translation efficiency in a genome-reduced bacterium.Molecular systems biology · 2023Article
- Evolution of a minimal cell.Nature · 2023Article
- Engineered live bacteria suppress Pseudomonas aeruginosa infection in mouse lung and dissolve endotracheal-tube biofilms.Nature biotechnology · 2023Article
- Performance evaluation of E-nose and E-tongue combined with machine learning for qualitative and quantitative assessment of bear bile powder.Analytical and bioanalytical chemistry · 2023Article
- Development of a Serum-Free Medium To Aid Large-Scale Production ofMicrobiology spectrum · 2023Article
- Transcriptional Profiling and Genetic Analysis of a Cystic Fibrosis Airway-Relevant Model Shows Asymmetric Responses to Growth in a Polymicrobial Community.bioRxiv : the preprint server for biology · 2023Article
Corrections and comments
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Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Here, we determined the relative importance of different transcriptional mechanisms in the genome-reduced bacterium Mycoplasma pneumoniae, by employing an array of experimental techniques under multiple genetic and environmental perturbations. Of the 143 genes tested (21% of the bacterium's annotated proteins), only 55% showed an altered phenotype, highlighting the robustness of biological systems. We identified nine transcription factors (TFs) and their targets, representing 43% of the genome, and 16 regulators that indirectly affect transcription. Only 20% of transcriptional regulation is mediated by canonical TFs when responding to perturbations. Using a Random Forest, we quantified the non-redundant contribution of different mechanisms such as supercoiling, metabolic control, RNA degradation, and chromosome topology to transcriptional changes. Model-predicted gene changes correlate well with experimental data in 95% of the tested perturbations, explaining up to 70% of the total variance when also considering noise. This analysis highlights the importance of considering non-TF-mediated regulation when engineering bacteria.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.