Since accurate translation from mRNA to protein is critical to survival, cells have developed translational quality control systems. Bacterial ribosomes stalled on truncated mRNA are rescued by a system involving tmRNA and SmpB referred to as trans-translation. Here, we review current understanding of the mechanism of trans-translation. Based on results obtained by using directed hydroxyl radical probing, we propose a new type of molecular mimicry during trans-translation. Besides such chemical approaches, biochemical and cryo-EM studies have revealed the structural and functional aspects of multiple stages of trans-translation. These intensive works provide a basis for studying the dynamics of tmRNA/SmpB in the ribosome. 1. Introduction Translation from the genetic information contained in mRNA to the amino acid sequence of a protein is performed on the ribosome, a large ribonucleoprotein complex composed of three RNA molecules and over 50 proteins. The ribosome is a molecular machine that catalyzes the synthesis of a polypeptide from its substrate, aminoacyl-tRNA. Ribosomes that translate a problematic mRNA, such as that lacking a stop codon, can stall at its 3′ end and produce an incomplete, potentially deleterious protein. Trans-translation is known as the highly sophisticated system in bacteria to recycle ribosomes stalled on defective mRNAs and add a short tag-peptide to the C-terminus of the nascent polypeptide as the degradation signal [1–4] (Figure 1). Thus, the tagged polypeptide from truncated mRNA is preferentially degraded by cellular proteases including ClpXP, ClpAP, Lon, FtsH, and Tsp [1, 5–7], and truncated mRNA is released from the stalled ribosomes to be degraded by RNases [8]. The process of trans-translation is facilitated by transfer-messenger RNA (tmRNA, also known as 10Sa RNA or SsrA RNA), which is a unique hybrid molecule that functions as both tRNA and mRNA (Figure 2). It comprises two functional domains, the tRNA domain partially mimicking tRNA [9] and the mRNA domain, which includes the coding region for the tag-peptide, surrounded by four pseudoknot structures [10–14]. As predicted from the tRNA-like secondary structure, the 3′ end of tmRNA is aminoacylated by alanyl-tRNA synthetase (AlaRS) like that of canonical tRNA [15, 16]. The function as tRNA is a prerequisite for the function as mRNA, indicating the importance of the elaborate interplay of the two functions [2]. Thus, “trans-translation” has been proposed: Ala-tmRNA somehow enters the stalled ribosome, allowing translation to resume by switching the original mRNA to
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