This chapter focuses on the mechanisms by which the post-transcriptional modifications regulate the codon recognition of tRNAs, primarily from the viewpoint of conformational characteristics of modified nucleosides. Post-transcriptional modifications are heavily involved in the specificities of codon recognition and also of aminoacylation. Interestingly, the roles of the modifications in the anticodon are in many cases the altered conformational properties such as conformational "rigidity" and "flexibility," which directly result in the rigidity or flexibility in codon recognition, although the chemical structures of the modified nucleosides are so much different from each other. It is quite natural because the "wobble" of the base from the original location for the Watson-Crick base pair is essential for non-Watson-Crick base pairing. In the future, more direct structural studies should be done on the anticodon-codon recognition in the decoding center of the ribosome. In addition to such studies at the level of molecular structures, biological studies on the roles of posttranscriptional modifications are required. For example, Q is mostly conserved from bacteria to higher eukaryotes but is missing in tRNAs from Mycoplasma and mitochondria. If the Q modification is not indispensable for protein synthesis, it is a wonder that why many organisms have to have such a complicated hypermodification. The real biological role of Q may be to play an essential role in other unknown functions of tRNA. For answering this question, more biological approaches such as gene targeting of modification enzymes in mammalian systems appear to be important and are therefore in progress in laboratories.

Modified Nucleosides and Codon Recognition

N4-acetylcytidine (ac4C) is often considered to be a conservative, chemically modified nucleoside present on tRNA and rRNA. Recent studies have shown extensive ac4C modifications in human and yeast mRNAs. ac4C helps to correctly read codons during translation and improves translation efficiency and the stability of mRNA. At present, the research of ac4C involves a variety of detection methods. The formation of ac4C is closely related to N-acetyltransferase 10 (NAT10) and its helpers, such as putative tRNA acetyltransferase (TAN1) for tRNA ac4C and small nucleolar RNA (snoRNA) for rRNA ac4C. Also, ac4C is associated with the development, progression, and prognosis of a variety of human diseases. Here, we summarize the history of ac4C research and the detection technologies of ac4C. We then summarized the role and mechanism of ac4C in gene-expression regulation and demonstrated the relevance of ac4C to a variety of human diseases, especially cancer. Finally, we list the future challenges of the ac4C research and demonstrate a research strategy for the interactions among several abundant modified nucleosides on mRNA.

The Processing, Gene Regulation, Biological Functions, and Clinical Relevance of N4-Acetylcytidine on RNA: A Systematic Review.

N4-Acetylcytidine. A previously unidentified labile component of the small subunit of eukaryotic ribosomes.

The posttranscriptional modifications of tRNA's anticodon stem and loop (ASL) domain represent a third level, a third code, to the accuracy and efficiency of translating mRNA codons into the correct amino acid sequence of proteins. Modifications of tRNA's ASL domain are enzymatically synthesized and site specifically located at the anticodon wobble position-34 and 3'-adjacent to the anticodon at position-37. Degeneracy of the 64 Universal Genetic Codes and the limitation in the number of tRNA species require some tRNAs to decode more than one codon. The specific modification chemistries and their impact on the tRNA's ASL structure and dynamics enable one tRNA to decode cognate and "wobble codons" or to expand recognition to synonymous codons, all the while maintaining the translational reading frame. Some modified nucleosides' chemistries prestructure tRNA to read the two codons of a specific amino acid that shares a twofold degenerate codon box, and other chemistries allow a different tRNA to respond to all four codons of a fourfold degenerate codon box. Thus, tRNA ASL modifications are critical and mutations in genes for the modification enzymes and tRNA, the consequences of which is a lack of modification, lead to mistranslation and human disease. By optimizing tRNA anticodon chemistries, structure, and dynamics in all organisms, modifications ensure translational fidelity of mRNA transcripts.

T. Yahagi

Papers

Characterization of C + located in the first position of the anticodon of Escherichia coli tRNA Met as N 4 -acetylcytidine.