Specification of Standard Amino Acids by Stop Codons

Abstract

Translation termination is usually a very efficient process. When a stop codon enters the ribosomal A-site it is recognized by the termination complex which promotes release of the polypeptide and dissociation of the ribosome. However, the efficiency of termination depends of the local context of the stop codon. In a number of cases, programmed stop codon readthrough occurs allowing the synthesis of two polypeptides from the same mRNA. These events have been identified both in viral and in cellular genes. In cells, either standard or specialized amino acids (selenocystein, pyrrolysine) can be incorporated at the stop codon by near cognate or cognate tRNAs, respectively. In this chapter, we focus on readthrough events involving incorporation of standard amino acids. In addition to their biological relevance, stop codon readthrough sites are useful tools to study translation termination mechanisms, especially in eukaryotes where they are less understood. We present an overview of this field discussing the mechanisms involved and how new readthrough sites can be identified in databases. Finally we propose further directions to better understand termination and readthrough mechanisms.