SECIS element

Last updated
Selenocysteine insertion sequence 1
RF00031.jpg
Predicted secondary structure and sequence conservation of SECIS_1. Letters correspond to the IUPAC notation system for nucleotides.
Identifiers
SymbolSECIS_1
Alt. SymbolsSECIS
Rfam RF00031
Other data
RNA type Cis-reg
Domain(s) Eukaryota
GO GO:0001514
SO SO:1001274
PDB structures PDBe

In biology, the SECIS element (SECIS: selenocysteine insertion sequence) is an RNA element around 60 nucleotides in length that adopts a stem-loop structure. [1] 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.

Contents

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. [2] [3]

The SECIS element appears defined by sequence characteristics, i.e. particular nucleotides tend to be at particular positions in it, and a characteristic secondary structure. The secondary structure is the result of base-pairing of complementary RNA nucleotides, and causes a hairpin-like structure. The eukaryotic SECIS element includes non-canonical A-G base pairs, which are uncommon in nature, but are critically important for correct SECIS element function. 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. However, in Lokiarcheota, SECIS elements are more similar to eukaryotic elements. [4]

In bioinformatics, several computer programs have been created that search for SECIS elements within a genome sequence, based on the sequence and secondary structure characteristics of SECIS elements. These programs have been used in searches for novel selenoproteins. [5]

Species distribution

The SECIS element is found in a wide variety of organisms from all three domains of life (including their viruses). [5] [6] [7] [8] [9] [10] [11]

Related Research Articles

Selenocysteine Chemical compound

Selenocysteine is the 21st proteinogenic amino acid. Selenoproteins contain selenocysteine residues. Selenocysteine is an analogue of the more common cysteine with selenium in place of the sulfur.

Stop codon Codon that marks the end of a protein-coding sequence

In molecular biology, a stop codon is a codon that signals the termination of the translation process of the current protein. Most codons in messenger RNA correspond to the addition of an amino acid to a growing polypeptide chain, which may ultimately become a protein; stop codons signal the termination of this process by binding release factors, which cause the ribosomal subunits to disassociate, releasing the amino acid chain.

Pyrrolysine Chemical compound

Pyrrolysine is an α-amino acid that is used in the biosynthesis of proteins in some methanogenic archaea and bacteria; it is not present in humans. It contains an α-amino group, a carboxylic acid group. Its pyrroline side-chain is similar to that of lysine in being basic and positively charged at neutral pH.

Translation (biology) Cellular process of protein synthesis

In molecular biology and genetics, translation is the process in which ribosomes in the cytoplasm or endoplasmic reticulum synthesize proteins after the process of transcription of DNA to RNA in the cell's nucleus. The entire process is called gene expression.

Three prime untranslated region

In molecular genetics, the three prime untranslated region (3′-UTR) is the section of messenger RNA (mRNA) that immediately follows the translation termination codon. The 3′-UTR often contains regulatory regions that post-transcriptionally influence gene expression.

In molecular biology a selenoprotein is any protein that includes a selenocysteine amino acid residue. Among functionally characterized selenoproteins are five glutathione peroxidases (GPX) and three thioredoxin reductases, (TrxR/TXNRD) which both contain only one Sec. Selenoprotein P is the most common selenoprotein found in the plasma. It is unusual because in humans it contains 10 Sec residues, which are split into two domains, a longer N-terminal domain that contains 1 Sec, and a shorter C-terminal domain that contains 9 Sec. The longer N-terminal domain is likely an enzymatic domain, and the shorter C-terminal domain is likely a means of safely transporting the very reactive selenium atom throughout the body.

Proteinogenic amino acid Amino acid that is incorporated biosynthetically into proteins during translation

Proteinogenic amino acids are amino acids that are incorporated biosynthetically into proteins during translation. The word "proteinogenic" means "protein creating". Throughout known life, there are 22 genetically encoded (proteinogenic) amino acids, 20 in the standard genetic code and an additional 2 that can be incorporated by special translation mechanisms.

Signal recognition particle RNA

The signal recognition particle RNA, is part of the signal recognition particle (SRP) ribonucleoprotein complex. SRP recognizes the signal peptide and binds to the ribosome, halting protein synthesis. SRP-receptor is a protein that is embedded in a membrane, and which contains a transmembrane pore. When the SRP-ribosome complex binds to SRP-receptor, SRP releases the ribosome and drifts away. The ribosome resumes protein synthesis, but now the protein is moving through the SRP-receptor transmembrane pore.

GPX1

Glutathione peroxidase 1, also known as GPx1, is an enzyme that in humans is encoded by the GPX1 gene on chromosome 3. This gene encodes a member of the glutathione peroxidase family. Glutathione peroxidase functions in the detoxification of hydrogen peroxide, and is one of the most important antioxidant enzymes in humans.

SEPP1

Selenoprotein P is a protein that in humans is encoded by the SEPP1 gene.

SELS (gene)

Selenoprotein S, also known as SELS, is a human gene.

SECISBP2

SECIS-binding protein 2 is a protein that in humans is encoded by the SECISBP2 gene.

SEP15

15 kDa selenoprotein is a protein that in humans is encoded by the SEP15 gene. Two alternatively spliced transcript variants encoding distinct isoforms have been found for this gene.

SEPW1

Selenoprotein W is a protein that in humans is encoded by the SEPW1 gene.

SEPX1

Methionine-R-sulfoxide reductase B1 is an enzyme that in humans is encoded by the SEPX1 gene.

SELT

Selenoprotein T, also known as SELT, is a protein that in humans is encoded by the SELT gene.

PYLIS downstream sequence Structure on some mRNA sequences

In biology, the PYLIS downstream sequence is a stem-loop structure that appears on some mRNA sequences. This structural motif was previously thought to cause the UAG (amber) stop codon to be translated to the amino acid pyrrolysine instead of ending the protein translation. However, it has been shown that PYLIS has no effect upon the efficiency of the UAG suppression, hence even its name is, in fact, incorrect.

GPX6

Glutathione peroxidase 6 (GPx-6) is an enzyme that in humans is encoded by the GPX6 gene.

Although it is toxic in large doses, selenium is an essential micronutrient for animals. In plants, it sometimes occurs in toxic amounts as forage, e.g. locoweed. Selenium is a component of the amino acids selenocysteine and selenomethionine. In humans, selenium is a trace element nutrient that functions as cofactor for glutathione peroxidases and certain forms of thioredoxin reductase. Selenium-containing proteins are produced from inorganic selenium via the intermediacy of selenophosphate (PSeO33−).

Selenoprotein o

Selenoprotein O is a protein that in humans is encoded by the SELENOO gene.

References

  1. ↑ Walczak R, Westhof E, Carbon P, Krol A (April 1996). "A novel RNA structural motif in the selenocysteine insertion element of eukaryotic selenoprotein mRNAs". RNA. 2 (4): 367–379. PMC   1369379 . PMID   8634917.
  2. ↑ Wilting R, Schorling S, Persson BC, Böck A (March 1997). "Selenoprotein synthesis in archaea: identification of an mRNA element of Methanococcus jannaschii probably directing selenocysteine insertion". Journal of Molecular Biology. 266 (4): 637–641. doi:10.1006/jmbi.1996.0812. PMID   9102456.
  3. ↑ Rother M, Resch A, Wilting R, Böck A (2001). "Selenoprotein synthesis in archaea". BioFactors. 14 (1–4): 75–83. doi:10.1002/biof.5520140111. PMID   11568443.
  4. ↑ Mariotti, Marco; Lobanov, Alexei V.; Manta, Bruno; Santesmasses, Didac; Bofill, Andreu; Guigó, Roderic; Gabaldón, Toni; Gladyshev, Vadim N. (2016). "LokiarchaeotaMarks the Transition between the Archaeal and Eukaryotic Selenocysteine Encoding Systems". Molecular Biology and Evolution. 33 (9): 2441–2453. doi: 10.1093/molbev/msw122 . ISSN   0737-4038. PMC   4989117 . PMID   27413050.
  5. 1 2 Lambert A, Lescure A, Gautheret D (September 2002). "A survey of metazoan selenocysteine insertion sequences". Biochimie. 84 (9): 953–959. doi:10.1016/S0300-9084(02)01441-4. PMID   12458087.
  6. ↑ Mix H, Lobanov AV, Gladyshev VN (2007). "SECIS elements in the coding regions of selenoprotein transcripts are functional in higher eukaryotes". Nucleic Acids Research. 35 (2): 414–423. doi:10.1093/nar/gkl1060. PMC   1802603 . PMID   17169995.
  7. ↑ Cassago A, Rodrigues EM, Prieto EL, Gaston KW, Alfonzo JD, Iribar MP, Berry MJ, Cruz AK, Thiemann OH (October 2006). "Identification of Leishmania selenoproteins and SECIS element". Molecular and Biochemical Parasitology. 149 (2): 128–134. doi:10.1016/j.molbiopara.2006.05.002. PMID   16766053.
  8. ↑ Mourier T, Pain A, Barrell B, Griffiths-Jones S (February 2005). "A selenocysteine tRNA and SECIS element in Plasmodium falciparum". RNA. 11 (2): 119–122. doi:10.1261/rna.7185605. PMC   1370700 . PMID   15659354.
  9. ↑ Kryukov GV, Castellano S, Novoselov SV, Lobanov AV, Zehtab O, Guigó R, Gladyshev VN (May 2003). "Characterization of mammalian selenoproteomes". Science. 300 (5624): 1439–1443. Bibcode:2003Sci...300.1439K. doi:10.1126/science.1083516. PMID   12775843. S2CID   10363908.
  10. ↑ Kryukov GV, Gladyshev VN (May 2004). "The prokaryotic selenoproteome". EMBO Reports. 5 (5): 538–543. doi:10.1038/sj.embor.7400126. PMC   1299047 . PMID   15105824.
  11. ↑ Krol A (August 2002). "Evolutionarily different RNA motifs and RNA-protein complexes to achieve selenoprotein synthesis". Biochimie. 84 (8): 765–774. doi:10.1016/S0300-9084(02)01405-0. PMID   12457564.
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