## 1 Introduction  
The evolutionary sequence diversity of tRNAs is constrained by the selective pressures to maintain key nucleotides recognized by a variety of cellular factors, such as aminoacyl-tRNA synthetases, translation factors and a variety of other factors that utilize tRNAs for functions beyond that of protein synthesis. These cellular processes include both ribosome-dependent and ribosome-independent peptide bond formation reactions in addition to other cellular processes [1]. Perhaps the only examples where the biological role of tRNAs do not present evolutionary constraints are the role of a host's tRNA acting as primers for reverse transcriptase in retroviruses and retrotransposons [2].  
It has become increasingly clear that the translational machinery is not the only cellular system that utilizes aminoacyl-tRNAs as substrates. Specific aminoacyl-tRNAs have been demonstrated to serve as a source of activated amino acids in tRNA-dependent ribosome-independent peptide bond formationsin processes such as peptidoglycan biosynthesis [3; 4], cellular membrane remodeling [5; 6; 7], antibiotic biosynthesis [8; 9], and targeted proteolysis [10]. The utilization of aminoacyl-tRNA as substrates by the enzymes central to these functions results in the potential for the competition for tRNA substrates between the translational machinery and ribosome-independent peptide bond formation reactions.  
A variety of mechanisms have been proposed for how these aminoacyl-tRNAs evade the translation machinery, for example, in some gram-positive eubacteria, aminoacyl-tRNAs are substrates for the synthesis of the interpeptide linkers of cell wall peptidoglycan biosynthesis [3; 4]. In _Staphylococcus aureus_, a specialized tRNAGly isoacceptor which appears to not be efficiently used by the translational machinery but is preferentially utilized for peptidoglycan biosynthesis [11]. The development of specialized tRNA isoacceptors may be a mechanism to prevent a detrimental competition for substrates between translation and cell wall biosynthesis, both highly active processes during cell growth. Other examples of evasion mechanisms include limiting access to the aminoacyl-tRNAs by channeling the substrates through enzyme complexes with aminoacyl-tRNA synthetases [9], or having comparable affinities for aminoacyl-tRNA such that there is sufficient competition with elongation factor EF-Tu [5].  
tRNA-dependent ribosome-independent peptide bond formation is catalyzed by a family of enzymes called aminoacyl-tRNA protein transferases, which are expressed in very diverse organisms and are involved in N-end rule protein degradation pathways. Aminoacyl-tRNA protein transferases are a class of enzymes that transfer amino acids from an aminoacyl-tRNA to the N-terminus of a protein, which either marks it for degradation by the cellular machinery or alters the proteins' function. These enzymes are found in eubacteria [12], yeast [13], plants [14], and animals [15]. It has been demonstrated that aminoacyl-tRNA protein transferases in eukaryotes have a large range of physiological functions _in vivo_, including heart development [16], G-protein signalling [17; 18], gametogenesis [19], and apoptosis [20; 21; 22; 23; 24] (see review for more details [25]).