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Methylation of rRNA nucleotides is an effective means of conferring resistance to antibiotics that target the bacterial ribosome. This type of resistance seems to have evolved as self-defence mechanisms in bacteria such as Streptomyces species that synthesize ribosome-targeting drugs. The self-defence mechanisms were subsequently recruited by pathogenic bacteria including streptococcal and staphylococcal species, where resistance to macrolides and related drugs is now a prevalent clinical problem. In this article, we review the methylation events in bacterial rRNA that confer resistance, and discuss how the molecular mechanisms of resistance can be explained from the recent crystal structures of antibiotics bound to the ribosome.

During protein synthesis, codons in mRNA are translated sequentially in frame on the ribosome following strict decoding rules. This process is usually very accurate. However, in some cases, recoding events occur at selected codons, leading to a high frequency of frameshifting or stop codon readthrough. The factors influencing these noncanonical decoding events are very diverse; among them are the codon usage and context, the presence of a stable mRNA secondary structure downstream of the decoding sites and the type and relative abundance of normally modified tRNA. Here, we discuss the role of certain modified nucleotides of tRNAs in a few cases of frameshifting and readthrough that occur in Bacteria and Eukarya. While in some cases the effect of a given modified nucleotide in a tRNA is to increase accuracy of the recoding process, in a few other cases the reverse has been observed. This review illustrates the power of using well characterized recoding systems, coupled with specific defects of RNA modification enzymes to assay for translational fidelity under conditions.

Major advances in the understanding of adenosine deaminases acting on RNA (ADARs) have come from the generation of ADAR mutant animals. In mice, is a widely expressed essential gene and loss of function in embryos leads to apoptosis through unknown mechanisms in many different cell types. Mammalian is required primarily to edit glutamate receptor transcripts in the nervous system. The genome contains one gene; mutant flies are normal in morphology and lifespan, but severely compromised neurologically and behaviourally. In , double mutants in and genes are viable with chemosensory defects that appear to arise from interactions between RNA editing and RNA interference. ADARs also extensively deaminate long double-stranded (ds) RNA in a process that has been proposed to have anti-viral effects. Genome sequences have facilitated progress in identifying edited RNAs. The majority of the twenty-three edited transcripts identified in encode proteins involved in rapid chemical and electrical neurotransmission and extensive editing of embedded RNAs has been found.

The sequencing of genomes from higher organisms demonstrated that the number and complexity of expressed mRNA sequences and proteins exceeds the quantity of predicted genes. This disparity has been attributed to a variety of cellular mechanisms including the use of alternative promoters, mRNA splice sites and/or polyadenylation sites. Additionally, single nucleotide modifications within RNA, and more recently DNA, can generate diversity in protein expression. C to U or dC to dU modification at specific sites within RNA or DNA can arise from targeted editing activities rather than spontaneous mutation and is catalyzed by APOBEC-1 or related zinc-dependent, cytidine deaminases. The function and substrate specificity are known for only five of the ten deaminases in the APOBEC-1 Related Protein family. Hence, exciting discoveries are predicted regarding the role of editing enzymes as modifiers of protein expression in normal physiology, in conferring resistance to invading pathogens, and possibly activities underlying human disease.

Reverse transcription is a central step in HIV-1 replication that represents a typical case of interplay between viral and cellular factors. HIV-1 diverts a cellular tRNA, tRNA, to prime reverse transcription. The post-transcriptional modifications of tRNA are crucial for completion of reverse transcription. In some HIV-1 isolates, they are required for efficient initiation of (–) strand DNA synthesis, and in all strains, methylation of A58 is required to allow productive strand transfer during (+) strand DNA synthesis. On the other hand, some human cell types have evolved an innate antiretroviral mechanism by promoting extensive deamination of the (–) strand DNA during reverse transcription. In the absence of viral defence, this hyper-editing induces DNA degradation and lethal mutagenesis of the viral DNA. However, Vif, one of the HIV-1 “accessory” proteins, is able to inhibit DNA deamination by preventing incorporation of the editing enzymes APOBEC3G and APOBEC3F into the viral particles.

Selenium is an essential micronutrient in the diet of mammals and has many health benefits. Selenium-containing proteins are responsible for most, if not all, of these benefits. This element is incorporated into protein as selenocysteine (Sec), the 21st amino acid in the genetic code. There are two species of Sec tRNA in mammalian cells that differ by a single 2’-O-hydroxymethyl group on the ribosyl moiety at position 34 (Um34). The relationship between this modification and selenoprotein synthesis was examined in mice in which the wild type Sec tRNA gene was replaced with a mutant Sec tRNA transgene incapable of forming Um34. This mouse line did not express several stress-related selenoproteins, whereas the levels of several selenoproteins thought to serve housekeeping functions were normal. This novel form of protein regulation occurred at the translational level. The Um34 modification in Sec tRNA, therefore, plays a crucial role in regulating the expression of a subset of mammalian selenoproteins and is a requisite for the synthesis of several stress-related selenoproteins.