ArticleBMC systems biology2013
Lessons from the modular organization of the transcriptional regulatory network of Bacillus subtilis.
Article in BMC systems biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed, 29 citations in OpenAlex.
- Understanding energy fluctuation during the transition state: The role of AbrB in Bacillus licheniformis.Microbial cell factories · 2024Article
- Comparative Genomic Analysis Reveals Potential Pathogenicity and Slow-Growth Characteristics of GenusMicrobiology spectrum · 2022Article
- Distribution and preservation of the components of the engulfment. What is beyond representative genomes?PloS one · 2021Article
- Machine learning uncovers independently regulated modules in the Bacillus subtilis transcriptome.Nature communications · 2020Article
- Abasy Atlas v2.2: The most comprehensive and up-to-date inventory of meta-curated, historical, bacterial regulatory networks, their completeness and system-level characterization.Computational and structural biotechnology journal · 2020Article
- Adaptation to Adversity: the Intermingling of Stress Tolerance and Pathogenesis in Enterococci.Microbiology and molecular biology reviews : MMBR · 2019Review
- Microbial life cycles link global modularity in regulation to mosaic evolution.Nature ecology & evolution · 2019Article
- Diversity, versatility and complexity of bacterial gene regulation mechanisms: opportunities and drawbacks for applications in synthetic biology.FEMS microbiology reviews · 2019Review
- Evolutionary constraints on the complexity of genetic regulatory networks allow predictions of the total number of genetic interactions.Scientific reports · 2019Article
- Impact of nanoparticles on the Bacillus subtilis (3610) competence.Scientific reports · 2018Article
- Dynamic sporulation gene co-expression networks for Bacillus subtilis 168 and the food-borne isolate Bacillus amyloliquefaciens: a transcriptomic model.Microbial genomics · 2018Article
- Feedbacks from the metabolic network to the genetic network reveal regulatory modules in E. coli and B. subtilis.PloS one · 2018Article
- The Genome-Scale Integrated Networks in Microorganisms.Frontiers in microbiology · 2018Review
- Reconstruction and topological characterization of the sigma factor regulatory network of Mycobacterium tuberculosis.Nature communications · 2016Article
- Abasy Atlas: a comprehensive inventory of systems, global network properties and systems-level elements across bacteria.Database : the journal of biological databases and curation · 2016Article
- An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network.Molecular systems biology · 2015Article
- Bacillus subtilis subsp. subtilis CBMDC3f with antimicrobial activity against Gram-positive foodborne pathogenic bacteria: UV-MALDI-TOF MS analysis of its bioactive compounds.World journal of microbiology & biotechnology · 2015Article
- Global analysis of photosynthesis transcriptional regulatory networks.PLoS genetics · 2014Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe regulation of gene expression at the transcriptional level is a fundamental process in prokaryotes. Among the different kind of mechanisms modulating gene transcription, the one based on DNA binding transcription factors, is the most extensively studied and the results, for a great number of model organisms, have been compiled making it possible the in silico construction of their corresponding transcriptional regulatory networks and the analysis of the biological relationships of the components of these intricate networks, that allows to elucidate the significant aspects of their organization and evolution.
resultsWe present a thorough review of each regulatory element that constitutes the transcriptional regulatory network of Bacillus subtilis. For facilitating the discussion, we organized the network in topological modules. Our study highlight the importance of σ factors, some of them acting as master regulators which characterize modules by inter- or intra-connecting them and play a key role in the cascades that define relevant cellular processes in this organism. We discussed that some particular functions were distributed in more than one module and that some modules contained more than one related function. We confirm that the presence of paralogous proteins confers advantages to B. subtilis to adapt and select strategies to successfully face the extreme and changing environmental conditions in which it lives.
conclusionsThe intricate organization is the product of a non-random network evolution that primarily follows a hierarchical organization based on the presence of transcription and σ factor, which is reflected in the connections that exist within and between modules.
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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.