biology

RegulonDB

RegulonDB is a biology topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand RegulonDB rather than just read about it. In short: RegulonDB is a database of the regulatory network of gene expression in Escherichia coli K-12. RegulonDB also models the organization of the genes in transcription units, operons and regulons.

Key takeaways

RegulonDB belongs to biology; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect RegulonDB to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of RegulonDB from memory before moving on to harder problems.

Reference excerpt

RegulonDB is a database of the regulatory network of gene expression in Escherichia coli K-12. RegulonDB also models the organization of the genes in transcription units, operons 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 database.

Transcription factors and sensory-response units In bacteria, such as E. coli, genes, are regulated by sequence 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 factors (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 Archived 2017-06-18 at the Wayback Machine.

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 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. 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/ Archived 2017-05-07 at the Wayback Machine

Worked examples

Example 1 — a first encounter with RegulonDB

Start with the simplest possible case. Write down what RegulonDB claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In biology, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to RegulonDB before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about RegulonDB ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of RegulonDB

In research: RegulonDB appears in biology research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses RegulonDB in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: RegulonDB is common in secondary-school and first-year university syllabi. It links to neighbouring topics Biological databases, Gene expression, so understanding it makes those chapters shorter.
In everyday life: Look for RegulonDB outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

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How to study RegulonDB in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what RegulonDB means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain RegulonDB out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is RegulonDB in simple terms?

RegulonDB is a database of the regulatory network of gene expression in Escherichia coli K-12. RegulonDB also models the organization of the genes in transcription units, operons and regulons.

Why does RegulonDB matter?

Because it connects several biology ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study RegulonDB?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on RegulonDB.