Evolution of initiator tRNAs and selection of methionine as the initiating amino acid

Abstract

Transfer RNAs (tRNAs) have been important in shaping biomolecular evolution. Initiator tRNAs (tRNA i ), a special class of tRNAs, carry methionine (or its derivative, formyL-methionine) to ribosomes to start an enormously energy consuming but a highly regulated process of protein synthesis. The processes of tRNA i evolution, and selection of methionine as the universal initiating amino acid remain an enigmatic problem. We constructed phylogenetic trees using the whole sequence, the acceptor-TcC arm ('minihelix'), and the anticodon-dihydrouridine arm regions of tRNA i from 158 species belonging to all 3 domains of life. All the trees distinctly assembled into 3 domains of life. Large trees, generated using data for all the tRNAs of a vast number of species, fail to reveal the major evolutionary events and identity of the probable elongator tRNA sequences that could be ancestor of tRNA i . Therefore, we constructed trees using the minihelix or the whole sequence of species specific tRNAs, and iterated our analysis on 50 eubacterial species. We identified tRNA Pro , tRNA Glu , or tRNA Thr (but surprisingly not elongator tRNA Met ) as probable ancestors of tRNA i . We then determined the factors imposing selection of methionine as the initiating amino acid. Overall frequency of occurrence of methionine, whose metabolic cost of synthesis is the highest among all amino acids, remains almost unchanged across the 3 domains of life. Our correlation analysis shows that its high metabolic cost is independent of many physicochemical properties of the side chain. Our results indicate that selection of methionine, as the initiating amino acid was possibly a consequence of the evolution of one-carbon metabolism, which plays an important role in regulating translation initiation.

Understanding the Genetic Code

“…Initiation codons, acting with an initiation tRNA, usually encode formyl methionine (fMet) in bacteria, chloroplasts, and mitochondria or methionine (Met) in archaea and the cytosol of eukaryotes (34)(35)(36). The codon wobble position is P1, where the order of usage for prokaryotes is usually AUG Ͼ GUG Ͼ UUG Ͼ CUG.…”

Initiation of Protein Synthesis with Non‐Canonical Amino Acids In Vivo

“…Protein synthesis is initiated with methionine (Met) in all domains of life. [1] In E. coli,t ranslation initiates with N-formylmethionine (fMet) carried by the initiator methionyl-tRNA( Ec-tRNA fMet ;F igure 1). [2] Ec-tRNA fMet is the only tRNAa ble to initiate translation but is unable to elongate polypeptide chains.T his property arises from sequence motifs unique to initiator tRNAs (itRNAs), which allow binding to the ribosomal P-site,favor interactions with initiation factors,a nd preclude interactions with elongation factors.…”

Hijacking Translation Initiation for Synthetic Biology

“…Because of its early origin, the amino acid used for initiation must have been able to be synthesized via one‐carbon metabolism. Met and N 10 ‐formyltetrahydrofolate, the precursors of fMet, are perfect candidates providing a possible explanation for Met as the initiating amino acid …”