RegulonDB is a database of the regulatory network of gene expression in ''Escherichia coli'' K-12.{{Cite journal, last=Gama-Castro, first=Socorro, last2=Salgado, first2=Heladia, last3=Santos-Zavaleta, first3=Alberto, last4=Ledezma-Tejeida, first4=Daniela, last5=Muñiz-Rascado, first5=Luis, last6=García-Sotelo, first6=Jair Santiago, last7=Alquicira-Hernández, first7=Kevin, last8=Martínez-Flores, first8=Irma, last9=Pannier, first9=Lucia, date=2016-01-04, title=RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond, journal=Nucleic Acids Research, volume=44, issue=D1, pages=D133–143, doi=10.1093/nar/gkv1156, issn=1362-4962, pmc=4702833, pmid=26527724 RegulonDB also models the organization of the genes in

transcription Transcription refers to the process of converting sounds (voice, music etc.) into letters or musical notes, or producing a copy of something in another medium, including: Genetics * Transcription (biology), the copying of DNA into RNA, the fir ...

units,

operon In genetics, an operon is a functioning unit of DNA containing a cluster of genes under the control of a single promoter. The genes are transcribed together into an mRNA strand and either translated together in the cytoplasm, or undergo splic ...

s and regulons. A total of 120 sRNAs with 231 total interactions which all together regulate 192 genes are also included. RegulonDB was founded in 1998 and also contributes data to the

EcoCyc In bioinformatics EcoCyc is a biological database for the bacterium ''Escherichia coli'' K-12. The EcoCyc project performs literature-based curation of the ''E. coli'' genome, and of ''E. coli'' transcriptional regulation, transporters, and metab ...

database.

Transcription factors and sensory-response units

bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of prokaryotic microorganisms. Typically a few micrometr ...

, such as ''E. coli'', genes, are regulated by

sequence In mathematics, a sequence is an enumerated collection of objects in which repetitions are allowed and order matters. Like a set, it contains members (also called ''elements'', or ''terms''). The number of elements (possibly infinite) is calle ...

elements in promoters and related binding sites). RegulonDB provides a database of such regulatory elements, their binding sites and the transcription factors that bind to these sites in ''E. coli''. RegulonDB 9.0 includes 184 experimentally determined

transcription factor In molecular biology, a transcription factor (TF) (or sequence-specific DNA-binding factor) is a protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence. The f ...

s (TFs) as well as 120 computationally predicted TFs, that is, a total of 304. The complete repertoire of 189 genetic sensory-response units (GENSOR units) are reported, integrating their signal, regulatory interactions, and metabolic pathways. A total of 78 GENSOR units have their four components highlighted; 119 include the genetic switch and the response, and 2 contain only the genetic switch. A total of 103 TFs have a known effector in RegulonDB, including 25 two-component systems. There were enough sites to build a motif for 93 TFs to infer 16,207 predicted TF binding sites. This set of predicted binding sites corresponds to 12,574 TF → gene regulatory interactions; this represents a recovery of 52% of the 1592 annotated regulatory interactions in the database for the 93 TFs for which RegulonDB has a position-weight matrix (PWM). If only TFs with a good-quality PWM are taken into account, the total number of predicted TF → gene interactions is 8,714, recovering 672 (57%) of annotated interactions for this TF subset. Semi-automatic curation produced a total of 3,195 regulatory interactions for 199 TFs.

Definitions

Check the glossary for all definitions

Transcription unit (TU)

A transcription unit is a set of one or more genes transcribed from a single promoter. A TU may also include regulatory protein binding sites affecting this promoter and a terminator. A complex operon with several promoters contains, therefore, several transcription units. A transcription unit must include all the genes in an operon.

Promoters and terminators

A promoter is defined in RegulonDB as the nucleotide sequence 60 bases upstream and 20 downstream from the precise initiation of transcription or +1. Terminators are regions where transcription ends, and RNA Polymerase unbinds from DNA.

Binding site

The TFs binding sites are physical DNA sites recognized by transcription factors within a genome, including enhancer, upstream activator (UAS) and operator sites that may bind repressors or activators.

Graphic display in RegulonDB

The graphic display of an

contains all the genes of its different transcription units, as well as all the regulatory elements involved in the transcription and regulation of those TUs. An operon is here conceived as a structural unit encompassing all genes and regulatory elements. An operon with several promoters located near each other may also have dual binding sites, indicating that such a site can activate one particular promoter, but repress a second one. In the same page, the collection of the different TUs is displayed below the operon. The graphic display of an operon contains all the genes of its different transcription units, as well as all the regulatory elements involved in the transcription and regulation of those TUs. The graphic display of a TU will always contain only one promoter -when known- with the binding sites that regulate its activity, followed by the transcribed genes. Note that dual sites are frequently displayed at a TU as repressors or activators. This is because the site will have a particular effect on the promoter of that TU.

References

External links

* http://regulondb.ccg.unam.mx/ Biological databases Gene expression