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
Rfam RF00031
Other data
RNA type Cis-reg
Domain(s) Eukaryota
GO GO:0001514
SO SO:1001274
PDB structures PDBe
Selenocysteine insertion sequence 2
Identifiers
SymbolSECIS_2
Rfam RF01988
Other data
Domain(s) Bacteria (seed), Eukaryota (hits)
PDB structures PDBe
Selenocysteine insertion sequence 3
Identifiers
SymbolSECIS_3
Rfam RF01989
Other data
Domain(s) Bacteria (seed), Eukaryota (hits)
PDB structures PDBe
Selenocysteine insertion sequence 5
Identifiers
SymbolSECIS_4
Rfam RF01990
Other data
Domain(s) Bacteria
PDB structures PDBe
Selenocysteine insertion sequence 5
Identifiers
SymbolSECIS_5
Rfam RF01991
Other data
Domain(s) Eukaryota (only Plasmodium )
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

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. [2] [3]

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. [4] 60S ribosomal protein L30 also recognizes SECIS, though its role is less well-understood. [5]

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. [6] 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. [5]

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. [6]

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. [6]

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.

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.

Species distribution

The SECIS element is found in a wide variety of organisms from all three domains of life (including their viruses). [7] [11] [12] [13] [14] [15] [16]

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. 1 2 Novoselov, SV; Lobanov, AV; Hua, D; Kasaikina, MV; Hatfield, DL; Gladyshev, VN (8 May 2007). "A highly efficient form of the selenocysteine insertion sequence element in protozoan parasites and its use in mammalian cells". Proceedings of the National Academy of Sciences of the United States of America. 104 (19): 7857–62. Bibcode:2007PNAS..104.7857N. doi: 10.1073/pnas.0610683104 . PMC   1876537 . PMID   17470795.
  5. 1 2 Allmang, C.; Krol, A. (November 2006). "Selenoprotein synthesis: UGA does not end the story". Biochimie. 88 (11): 1561–1571. doi:10.1016/j.biochi.2006.04.015. PMID   16737768.
  6. 1 2 3 Mariotti, Marco; Lobanov, Alexei V.; Manta, Bruno; Santesmasses, Didac; Bofill, Andreu; Guigó, Roderic; Gabaldón, Toni; Gladyshev, Vadim N. (2016). "Lokiarchaeota Marks 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.
  7. 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.
  8. ↑ Mariotti, M; Lobanov, AV; Guigo, R; Gladyshev, VN (August 2013). "SECISearch3 and Seblastian: new tools for prediction of SECIS elements and selenoproteins". Nucleic Acids Research. 41 (15): e149. doi:10.1093/nar/gkt550. PMC   3753652 . PMID   23783574.
  9. 1 2 Santesmasses, D; Mariotti, M; Gladyshev, VN (1 September 2020). "Bioinformatics of Selenoproteins". Antioxidants & Redox Signaling. 33 (7): 525–536. doi:10.1089/ars.2020.8044. PMC   7409585 . PMID   32031018.
  10. ↑ Kryukov, GV; Gladyshev, VN (May 2004). "The prokaryotic selenoproteome". EMBO Reports. 5 (5): 538–43. doi:10.1038/sj.embor.7400126. PMC   1299047 . PMID   15105824.
  11. ↑ 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.
  12. ↑ 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.
  13. ↑ 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.
  14. ↑ 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.
  15. ↑ 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.
  16. ↑ 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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