SECIS element
Encyclopedia
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 selenocysteine
s. (UGA is normally a stop codon
.) SECIS elements are thus a fundamental aspect of messenger RNA
s encoding selenoprotein
s, proteins that include one or more selenocysteine residues.
In bacteria
the SECIS element appears soon after the UGA codon it affects. In archaea
and eukaryote
s, 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.
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.
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.
Biology
Biology is a natural science concerned with the study of life and living organisms, including their structure, function, growth, origin, evolution, distribution, and taxonomy. Biology is a vast subject containing many subdivisions, topics, and disciplines...
, the SECIS element (SECIS: selenocysteine insertion sequence) is an RNA element
Cis-regulatory element
A cis-regulatory element or cis-element is a region of DNA or RNA that regulates the expression of genes located on that same molecule of DNA . This term is constructed from the Latin word cis, which means "on the same side as". These cis-regulatory elements are often binding sites for one or...
around 60 nucleotides in length that adopts a stem-loop
Stem-loop
Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded DNA or, more commonly, in RNA. The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same strand, usually complementary in nucleotide sequence when read in opposite directions,...
structure. This structural motif
Structural motif
In a chain-like biological molecule, such as a protein or nucleic acid, a structural motif is a supersecondary structure, which appears also in a variety of other molecules...
(pattern of nucleotides) directs the cell
Cell (biology)
The cell is the basic structural and functional unit of all known living organisms. It is the smallest unit of life that is classified as a living thing, and is often called the building block of life. The Alberts text discusses how the "cellular building blocks" move to shape developing embryos....
to translate UGA codons as selenocysteine
Selenocysteine
Selenocysteine is an amino acid that is present in several enzymes .-Nomenclature:...
s. (UGA is normally a stop codon
Stop codon
In the genetic code, a stop codon is a nucleotide triplet within messenger RNA that signals a termination of translation. Proteins are based on polypeptides, which are unique sequences of amino acids. Most codons in messenger RNA correspond to the addition of an amino acid to a growing polypeptide...
.) SECIS elements are thus a fundamental aspect of messenger RNA
Messenger RNA
Messenger RNA is a molecule of RNA encoding a chemical "blueprint" for a protein product. mRNA is transcribed from a DNA template, and carries coding information to the sites of protein synthesis: the ribosomes. Here, the nucleic acid polymer is translated into a polymer of amino acids: a protein...
s encoding selenoprotein
Selenoprotein
In molecular biology a selenoprotein is any protein that includes a selenocysteine amino acid residue. Among functionally characterized selenoproteins are five glutathione peroxidases and three thioredoxin reductases, which both contain only one Se-Cys. Selenoprotein P is the most common...
s, proteins that include one or more selenocysteine residues.
In bacteria
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
the SECIS element appears soon after the UGA codon it affects. In archaea
Archaea
The Archaea are a group of single-celled microorganisms. A single individual or species from this domain is called an archaeon...
and eukaryote
Eukaryote
A eukaryote is an organism whose cells contain complex structures enclosed within membranes. Eukaryotes may more formally be referred to as the taxon Eukarya or Eukaryota. The defining membrane-bound structure that sets eukaryotic cells apart from prokaryotic cells is the nucleus, or nuclear...
s, 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
Methanococcus
In taxonomy, Methanococcus is a genus of the Methanococcaceae.Methanococcus is a genus of coccoid methanogens. They are all mesophiles, except the thermophilic M. thermolithotrophicus and the hyperthermophilic M. jannaschii...
, is located in the 5' UTR.
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
Secondary structure
In biochemistry and structural biology, secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids...
. The secondary structure is the result of base-pairing of complementary RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
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.
In bioinformatics
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
, several computer programs have been created that search for SECIS elements within a genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
sequence, based on the sequence and secondary structure characteristics of SECIS elements. These programs have been used in searches for novel selenoproteins.