Fig 1.
The chess board pattern in the genetic code table.
When all SSN and WWN codon boxes are left out, a chess board pattern emerges (see text). In this representation it can immediately be seen that mixed SW/WS codon boxes with a middle-Y (U or C) are fourfold degenerate codon boxes, while mixed SW/WS codon boxes with a middle-R (A or G) are split codon boxes.
Fig 2.
Start of the genetic code with a single tRNA encoding a single amino acid (tentatively selected as Gly).
In the left hand panel the codons are indicated which are in efficient and unambiguous use. In the right hand panel the anticodons are indicated which perform the efficient and unambiguous decoding of these codons. The same division between left hand panel and right hand panel is used in Figs 3–6.
Fig 3.
The proposed 23 tRNA stage in the evolution of the standard genetic code.
Red, yellow, green, and blue are used to group codons together which are read by a single anticodon.
Fig 4.
The proposed 32 tRNA stage in the evolution of the standard genetic code.
The asterisks indicate anticodon first position modifications which are necessary to unambiguously read the respective codon box. At this stage there already is a distinction between initiator methionine and elongator methionine. Red, yellow, green, and blue are used to indicate the codons where changes happened compared to the situation in the previous figure.
Fig 5.
The proposed tRNA set of LUCA.
The asterisks indicate anticodon first position modifications which are necessary to unambiguously read the respective codon box. At this stage there already is a distinction between initiator methionine and elongator methionine. Red, yellow, green, and blue are used to indicate the codons where changes happened compared to the situation in the previous figure.
Fig 6.
The tRNA set of present-day Archaea.
The asterisks indicate anticodon first position modifications which are necessary to unambiguously read the respective codon box. The only difference with the proposed tRNA set of LUCA is the presence of the codon AUA in this codon repertoire (indicated by coloring with blue).
Fig 7.
Summary of the proposed three stages in the evolutionary development of the tRNA set in the standard genetic code.