chemistry

SECIS element

SECIS element is a chemistry 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 SECIS element rather than just read about it. In short: In biology, the SECIS element (SECIS: selenocysteine insertion sequence) is an RNA element around 60 nucleotides in length that adopts a stem-loop structure. This structural motif (pattern of nucleotides) directs the cell to translate UGA codons as selenocysteines (UGA is normally a stop codon).

Key takeaways

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

Reference excerpt

In biology, the SECIS element (SECIS: selenocysteine insertion sequence) is an RNA element around 60 nucleotides in length that adopts a stem-loop structure. This structural motif (pattern of nucleotides) directs the cell to translate UGA codons as selenocysteines (UGA is normally a stop codon). SECIS elements are thus a fundamental aspect of messenger RNAs encoding selenoproteins, proteins that include one or more selenocysteine residues.

Location and function In bacteria the SECIS element appears soon after the UGA codon it affects. In archaea and eukaryotes, it occurs in the 3' UTR of an mRNA, and can cause multiple UGA codons within the mRNA to code for selenocysteine. One archaeal SECIS element, in Methanococcus, is located in the 5' UTR. In any case, it serves to recruit EEFSEC or SelB, the specialized homolog of EF-Tu/eEF1&alpha, with the ability to read tRNASec.

Characteristics The SECIS elements appear defined by sequence characteristics (particular nucleotides tend to be at particular positions in it), and a characteristic bent-hairpin secondary structure due to base-pairing of complementary RNA nucleotides. Although the eukaryotic, archaeal and bacterial SECIS elements each share a general hairpin structure, they are not alignable, e.g. an alignment-based scheme to recognize eukaryotic SECIS elements will not be able to recognize archaeal SECIS elements.

Bacterial SECIS Bacterial SECIS is recognized by SelB. Each element targets one UGA codon. Rfam provides three separate groups of bacterial SECIS.

Eukaryotic SECIS Eukaryotic SECIS elements are recognized by SBP2, which in turn binds EEFSEC to provide for elongation. In most cases the "kink-turn" part bound to SBP2 has a very conserved sequence "AUGA", but "GGGA" has also been found. 60S ribosomal protein L30 also recognizes SECIS, though its role is less well-understood. The eukaryotic SECIS element consists of a small stem, a "kink-turn" core with AUGA/GGGA, another stem, and a terminal loop of 5-30 nt. In "Group II" SECIS elements the terminal loop is interrupted by a stem. The eukaryotic SECIS element includes wobble A-G base pairs, which are uncommon in nature, but are critically important for correct SECIS element function. Rfam provides two groups of eukaryotic SECIS. SECIS_1 is built from animal sequences. SECIS_5 is built from Plasmodium sequences.

Archaeal SECIS It is unclear which piece of the archaeal translation machinery is responsible for recognizing SECIS. They have a version of SelB/EEFSEC, but it has neither the bacterial SECIS-recognizing expansion nor the eukaryotic RBP2-recognizing expansion. Archaeal SECIS consists of a "base" stem ending in GC-rich pairs, a conserved bulge region, a small (3bp) GC-rich stem, and a terminal AT-rich loop of 3-8 nt. Lokiarcheota, a group of archaea believed to be related to the archaeal ancestor of eukaryotes, use eukaryotic-like kink-turn "AUGA" SECIS elements with no conserved bulge on a few families of selenoproteins. This type is believed to have evolved from the SECIS element from archaeal VhuD proteins, which also has a "AUGA" part but is not predicted to form a kink-turn. Lokiarcheota have no identified version of SBP2, but they do have L30.

Detection in bioinformatics

From known SECIS elements SECIS elements can be found using the sequence and secondary structure characteristics of groups of known SECIS elements. Methods are open-source unless specifically noted.

The ERPIN program for RNA motif search was used to find new SECIS elements in animals, resulting in the identification of novel families of selenoproteins. Rfam provides five pre-built profiles for the Infernal RNA covariance search program as well as matches in GenBank sequences. SECISearch3 is broadly applicable to eukaryotes. It starts by finding candidates using three existing methods, Infernal, Covels, and SECISearch. It then merges the candidates, refines their structures, and filters the structures for hard-coded constraints. Both SECISearch3 and SECISearch are closed source and accessible through web services only. SECISearch3 is the best method for eukaryotes as of 2020. The identification of SECIS elements remains difficult in eukaryotes, especially non-animal ones. bSECISearch uses a RNAfold-based method similar to the original SECISearch to find bacterial SECIS. It is closed source and accessible through web services only. A version of SECISearch was adapted for the archaeal SCEIS consensus. This version is neither available as a download nor as an online service. New families of selenoproteins have been found by searching for SECIS elements and checking the associated protein-coding region for UGA.

From known selenoproteins New types of SECIS elements have been found by searching for protein-coding regions homologous to known selenoproteins, then checking the 3' UTR for secondary structure.

An unusual "GGGA" type of SECIS element was found in Toxoplasma and Neospora for their version of selenoprotein T.

Species distribution The SECIS element is found in a wide variety of organisms from all three domains of life (including their viruses).

References

External links

Page for SECIS element 1 at Rfam

Page for SECIS element 2 at Rfam

Page for SECIS element 3 at Rfam

Page for SECIS element 4 at Rfam

Page for SECIS element 5 at Rfam

Illustrations

Worked examples

Example 1 — a first encounter with SECIS element

Start with the simplest possible case. Write down what SECIS element claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In chemistry, 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 SECIS element 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 SECIS element 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 SECIS element

In research: SECIS element appears in chemistry 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 SECIS element 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: SECIS element is common in secondary-school and first-year university syllabi. It links to neighbouring topics Cis-regulatory RNA elements, Gene expression, Rfam pages needing a picture, so understanding it makes those chapters shorter.
In everyday life: Look for SECIS element 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 SECIS element in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what SECIS element 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 SECIS element out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is SECIS element in simple terms?

Why does SECIS element matter?

Because it connects several chemistry 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 SECIS element?

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 SECIS element.