UGA codon

The stem-loop structure in the noncoding 3 region of selenoprotein mRNAs has also been termed a SECTS element in mammals although it has a different overall structure. ° In silica analysis of the human genome sequence, using this consensus SECTS element along with the presence of the characteristic UGA codon within an exon, has led to the discovery of several new selenoproteins, including a selenium-dependent methionine sulfoxide reductase. It has been shown that a specific complex exists for selenoprotein synthesis that shuttles between the nucleus and the cytosol. This possibly protects the preformed complex for nonsense-mediated decay to allow for more efficient selenoprotein synthesis. The specific tRNA needed for selenocysteine... 

Selenocysteine (Sec) Selenocysteine is incorporated into a small number of proteins in species from all three kingdoms of life by a suppressor tRNASec that reads certain UGA codons, which are marked as representing selenocysteine.449 450 The selenocysteinyl-tRNA is made from a seryl-tRNA (Eq. 29-7) as described further in Chapters 16 and 24. In E. coli selenocysteine is present in three proteins, all formate dehydrogenases. The archaeon Methanococcus jannaschii contains genes for seven selenocysteine-containing proteins. Only one Sec-containing protein has been found in the nematode Caenorhabditis elegans and none in the yeast... 

Incorporation of selenocysteyl-tRNASer into protein in response to the UGA codon requires SELB (the protein product of the selB gene in E. coli). SELB is homologous in sequence to EF-Tu and probably replaces it in translation by specifically recognizing selenocysteyl-tRNA and UGA in the appropriate sequence context. Selenocysteyl-tRNASer, in combination with SELB, must be capable of competing with termination factors for the translation of the termination codon when it occurs in the right context of bases. This process is known as site-specific variation in translation elongation. 

Another peculiarity of the mitochondrial code emerged from a study of yeast codon usage. By comparing tables 29.3 and 29.1, you will see that the mitochondrial code has several differences in code word meaning. The codons beginning with CU represent Thr instead of Leu, the AUA codon represents Met instead of He, and the UGA codon represents Trp rather than a stop signal. 

Klug et al. (1999) selected RNA sequences that bind the Sel B protein of E. coli, an elongation factor which recognizes a stem-loop structure and drives the incorpor-ation of selenocysteine in response to an opal (UGA) codon immediately upstream of the structure. The wild-type hairpin recognized by Sel B in the dehydrogenase G mRNA was used as a competitor for the selection allowing the RNA pool to evolve very quickly. In four cycles high affinity aptamers (Kd 1 nM) were selected. Several aptamers bound 50-fold... 

The genetic code is not universal but is the same in most organisms. Exceptions are found in mitochondrial genomes where some codons specify different amino acids to that normally encoded by nuclear genes. In mitochondria, the UGA codon does not specify termination of translation but instead encodes for tryptophan. Similarly, in certain protozoa UAA and UAG encode glutamic acid instead of acting as termination codons. 

The question of the biosynthesis of GSHPx has been the subject of much research and it is now known with certainty that the formation of the seleno-cysteinyl residue depends on the existence of a gene that specifies a unique UGA codon that codes specifically for selenocysteine the complimentary tRNA binds serine to which is then added the selenyl moiety to form selenocysteine which is added to the nascent protein by the normal translational process [13], This mechanism has also been demonstrated for the biosynthesis of other seleno-enzymes in several bacterial species [14-16]. 

A result emerging from the genetic analysis of selenoproteins was the discovery that selenocysteine is the 21st amino acid encoded in DNA. Its insertion is directed by an in-frame UGA codon in the selenoprotein mRNA. UGA is used for this purpose in all three lines of descent (bacteria, archaea, and eukarya) The consistent use of UGA as a signal points to a common evolutionary origin of the selenocysteine coding system. 

On the basis of a dual function of UGA as a codon for selenocysteine insertion and for translation termination within a single cell, it has to be assured (1) that this UGA codon is not used as a termination signal and (2) that selenocysteyl-tRNA is directed only to this position. The results of a biochemical analysis indeed revealed that this is achieved by the formation of a complex between SelB, selenocysteyl-tRNA, and the stem-loop structure downstream of the UGA. The binding to the SECIS element was shown to involve an ultimate 17-kDa C-terminal domain of SelB. 

Sec) (9). In bacteria, Sec is inserted cotranslationaUy at an in-frame UGA codon that is upstream of an RNA stem-loop. In E. coli, SerRS produces the mischarged Ser-tRNA , which is then converted to Sec-tRNA by Sec synthase (SelA). A GTP-dependent elongation factor SelB binds to Sec-tRNA and forms a complex that recognizes specific mRNA sequences called selenocysteine insertion elements (SECIS), that are located 3 to a UGA codon on a stalled ribosome-bound mRNA. It is also responsible for delivering Sec-tRNA to the A site of the ribosome (9). 

Hence, we conclude that the higher molecular weight form of NT-3 was caused by reading through of the UGA stop codon by tryptophan incorporation. The UGA codon has been well documented to be leaky in early study on microbial molecular biology (9). Its use should be minimized in bacterial expression system. 

Selenium is incorporated into Se-requiring enzymes by the modification of serine. This serine is not modified when it is in the free state or when it occurs in a polypeptide chain. The serine residue in question is modified when it occurs boimd to transfer RNA, that is, eis the aminoacyl-tRNA derivative. Seryl-tRNA is converted to selenocysteinyl-tRNAby the action of selenocysteine synthase (Stur-chler et al, 1993). The codon for selenocysteine is UGA (TGA in DNA UGA in mRNA). The fact that this particular triplet of bases codes for an amino acid is very imusual, as UGA normally is a stop codon. Stop codons occur in mRNA and signal the termination of synthesis of the protein however, in the case of the UGA codons that code for selenocysteine residues, regions of the mRNA that lie beyond the coding sequence somehow convert the UGA from a codon that halts translation to one that codes for selenocysteine (Figure 10.55). The structure of selenocysteine is shown in Figure 10.56. 

Gladyshev, VN University of Nebraska Identity of terminator and selenocysteine UGA codons CRISP 2001... 

The genetic code (also called "the code") is almost, but not quite, universal. That is, it is almost, but not quite, the same in prokaryotes, eukaryotes and viruses. The rare exceptions are known of only in mitochondria and a few protozoans. One alternate coding sequence is the UGA codon, which in the universal genetic code is a STOP codon (i.e., it stops translation, see below), but in many organisms can occasionally specify the rare amino acid, selenocysteine (Table 27.1). 

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