Mistranslation and its control by tRNA synthetases

Abstract

Aminoacyl tRNA synthetases are ancient proteins that interpret the genetic material in all life forms. They are thought to have appeared during the transition from the RNA world to the theatre of proteins. During translation, they establish the rules of the genetic code, whereby each amino acid is attached to a tRNA that is cognate to the amino acid. Mistranslation occurs when an amino acid is attached to the wrong tRNA and subsequently is misplaced in a nascent protein. Mistranslation can be toxic to bacteria and mammalian cells, and can lead to heritable mutations. The great challenge for nature appears to be serine-for-alanine mistranslation, where even small amounts of this mistranslation cause severe neuropathologies in the mouse. To minimize serine-for-alanine mistranslation, powerful selective pressures developed to prevent mistranslation through a special editing activity imbedded within alanyl-tRNA synthetases (AlaRSs). However, serine-for-alanine mistranslation is so challenging that a separate, genome-encoded fragment of the editing domain of AlaRS is distributed throughout the Tree of Life to redundantly prevent serine-to-alanine mistranslation. Detailed X-ray structural and functional analysis shed light on why serine-for-alanine mistranslation is a universal problem, and on the selective pressures that engendered the appearance of AlaXps at the base of the Tree of Life.

Figure 1.

The universal Tree of Life with emergence of tRNA synthetases at the base of the Tree. LUCA, last universal common ancestor.

Figure 2.

Domains of AlaRS arranged in a linear fashion along the sequence. This arrangement of domains is conserved in all three kingdoms of the Tree of Life. The location of sti mutation associated with neurological degeneration in the mouse is noted.

Figure 3.

Active site of AlaRS with bound adenylate analogues (Ala-SA and Ser-SA). A universally conserved Asp carboxylate pins down the α-amino group of the bound adenylate. This same carboxylate makes a serendipitous H-bond with the sidechain -OH of bound serine.

Figure 4.

Schematic of the free-standing AlaXp editing domains (EDs) that is homologous to the ED and C-Ala portions of AlaRS (figure 2).

Figure 5.

(a) Schematic of the tRNA cloverleaf secondary structure (left) and its folding into an L-shaped three-dimensional structure (right). Common landmarks on the tRNA are noted. (b) Acceptor stems of bacterial, yeast and human tRNAs specific for alanine and the conserved G:U base pair that marks the tRNA for aminoacylation with alanine.

Figure 6.

Schematic of how the C-Ala domain of AlaXp carries the ED to Ser-tRNA^Ala. The C-domain binds to the outside corner of the L-shaped tRNA.

Figure 7.

(a) Schematic showing that C-Ala brings together aminoacylation and editing functions on the same tRNA. (b) The editing function of AlaRS is not sufficient by itself to maintain cell homeostasis and for that reason free-standing AlaXp's were retained to provide redundancy for clearing Ser-tRNA^Ala.