Regulon

Thank you for visiting nature. You are using a browser version with limited support for CSS. Regulon obtain the best experience, we recommend you use a more up to date browser or turn off compatibility mode in Internet Explorer, regulon. In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript, regulon.

In molecular genetics , a regulon is a group of genes that are regulated as a unit, generally controlled by the same regulatory gene that expresses a protein acting as a repressor or activator. This terminology is generally, although not exclusively, used in reference to prokaryotes , whose genomes are often organized into operons ; the genes contained within a regulon are usually organized into more than one operon at disparate locations on the chromosome. A modulon is a set of regulons or operons that are collectively regulated in response to changes in overall conditions or stresses, but may be under the control of different or overlapping regulatory molecules. The term stimulon is sometimes used to refer to the set of genes whose expression responds to specific environmental stimuli. Commonly studied regulons in bacteria are those involved in response to stress such as heat shock. The heat shock response in E.

Regulon

Federal government websites often end in. The site is secure. Ma ; ude. Regulons, which serve as co-regulated gene groups contributing to the transcriptional regulation of microbial genomes, have the potential to aid in understanding of underlying regulatory mechanisms. In this study, we designed a novel computational pipeline, regulon identification based on comparative genomics and transcriptomics analysis RECTA , for regulon prediction related to the gene regulatory network under certain conditions. A total of 51 regulons were identified, 14 of which have computational-verified significance. Among these 14 regulons, five of them were computationally predicted to be connected with acid stress response. Validated by literature, 33 genes in Lactococcus lactis MG were found to have orthologous genes which were associated with six regulons. An acid response related regulatory network was constructed, involving two trans-membrane proteins, eight regulons llrA , llrC , hllA , ccpA , NHP6A, rcfB , regulons 8 and 39 , nine functional modules, and 33 genes with orthologous genes known to be associated with acid stress. The predicted response pathways could serve as promising candidates for better acid tolerance engineering in Lactococcus lactis. Our RECTA pipeline provides an effective way to construct a reliable gene regulatory network through regulon elucidation, and has strong application power and can be effectively applied to other bacterial genomes where the elucidation of the transcriptional regulation network is needed. Genomic and transcriptomic analyses have been widely used for elucidating gene regulatory network GRN hierarchies and offering insight into the coordination of response capabilities in microorganisms [ 1 , 2 , 3 , 4 ]. One way to study the mechanism of transcriptional regulation in microbe genomics is regulon prediction. A regulon is a group of co-regulated operons, which contains single or multiple consecutive genes along the genome [ 5 , 6 , 7 ].

As shown in Fig. While numerous regulons have been experimentally identified in a few model organisms including E, regulon.

Women are particularly important patients for us. We are perfectly aware of their needs. For many decades, we have been performing very in-depth analyses of their health and illnesses that may affect women of different ages. This section contains information intended solely for doctors, pharmacists and other persons authorised to receive specialty medical information. If you are a doctor, pharmacist or are otherwise authorised to receive specialty medical information continue to the next page. We are all looking forward to new, excellent medicines and even more effective therapies.

Thank you for visiting nature. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser or turn off compatibility mode in Internet Explorer. In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript. This protocol explains how to perform a fast SCENIC analysis alongside standard best practices steps on single-cell RNA-sequencing data using software containers and Nextflow pipelines.

Regulon

In molecular genetics , a regulon is a group of genes that are regulated as a unit, generally controlled by the same regulatory gene that expresses a protein acting as a repressor or activator. This terminology is generally, although not exclusively, used in reference to prokaryotes , whose genomes are often organized into operons ; the genes contained within a regulon are usually organized into more than one operon at disparate locations on the chromosome. A modulon is a set of regulons or operons that are collectively regulated in response to changes in overall conditions or stresses, but may be under the control of different or overlapping regulatory molecules. The term stimulon is sometimes used to refer to the set of genes whose expression responds to specific environmental stimuli. Commonly studied regulons in bacteria are those involved in response to stress such as heat shock. The heat shock response in E. Regulons involving virulence factors in pathogenic bacteria are of particular research interest; an often-studied example is the phosphate regulon in E. The Ada regulon in E.

Douma manga

Publication types Research Support, Non-U. Zhou C. Hence, these 51 motif clusters correspond to 51 regulons dataset S3. RegPredict: An integrated system for regulon inference in prokaryotes by comparative genomics approach. Product category Rx. This tool integrates differential gene expression, co-expression analysis, cis-regulatory motif identification, and comparative genomics to predict and validate regulons associated with acid response. Among the nine functional modules, llrA was found connected to five of them, and NHP6A related to three. Finally, we extracted the upstream sequence set P A , according to the operon group O A , as the orthologous promoters. Intuitively, the smaller an EASE score is, the more significant matching between a predicted operon cluster and a known regulon has. Bioenergy Research 7, — Hoskins J.

.

Inferring regulatory networks from experimental morphological phenotypes: a computational method reverse-engineers planarian regeneration. Firstly, the efficiency of a score is defined as the numbers of operon pairs, being in known regulons, in top n operon pairs n is from 0 to 25, by intervals out of totally 3,, operon pairs ranked according to this score. Finally, we identified heavy sub-graphs in the new graph to infer regulons. Regulon elucidation is the basis for studying the bacterial global transcriptional regulation network. Ethics declarations Competing interests The authors declare no competing financial interests. Also for some regulons, their motifs tend to be less conserved 41 and are hard to be identified, which makes the motif prediction suffers the high false positive rate in their prediction. Authority control databases : National Germany. Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata. If the corresponding EASE score of a predicted regulon is under a certain cutoff 1e-3 , its member genes tend to be co-expressed under specific conditions and it is determined as a supported one by the transcriptomic data. If you are a doctor, pharmacist or are otherwise authorised to receive specialty medical information continue to the next page. Therefore, we can claim that such a phylogenetic footprinting strategy can provide more informative promoters in motif finding for those operons involved in local regulons, without or with low number of co-regulated operons in their host genome. Cumley N. Gupta S. Introduction Reconstruction of global transcriptional regulatory networks is a key to understand gene function and evolution, thus it is one of the critical aspects of microbial genomics, especially in the era of high throughput genome sequencing 1 , 2 , 3 , 4.