Skip to main content

Advertisement

Table 1 Concerted complementarity of 2nd bases in the acceptor stems of pairs of ancestral tRNAs with complementary anticodonsa

From: One ancestor for two codes viewed from the perspective of two complementary modes of tRNA aminoacylation

Amino acids Anticodons 2nd bases in acceptor Amino acids Anticodons 2nd bases in acceptor
  NAN × NUN    NGN × NCN  
1. Phe × Lys GAA × UUU S × G 17. Ser × Arg GGA × UCU G × Y
  GAA × UUU C × G   GGA × UCU C × G
  GAA × UUU C × C   AGA × UCU G/U × U/G
   C × G    S × S
   +    +
2. Phe × Glu GAA × UUC S × G/Y 18. Ser × Gly GGA × UCC G × C
  GAA × UUC C × C   GGA × UCC C × C
  GAA × UUC C × C   GGA × UCC G × C
   C × C    G × C
   -    +
3. Leu × Stop
(Leu × Gln)
UAA × UUG C × G 19. Ser × Stop
Ser × Arg
UGA × UCG G × C
  UAA × UUG C × G   UGA × UCG C × G
  UAA × UUG C × G   UGA × UCG Y/G × G
   C × G    S × S
   +    +
4. Leu × Gln CAA × UUG C × G 20. Ser × Arg CGA × UCG G × C
  CAA × UUG C × G   CGA × UCG C × G
  CAA × UUG C × G   CGA × UCG Y/G × G
   C × G    S × S
   +    +
5. Leu × Lys AAG × CUU C × G 21. Pro × Arg GGG × CCU G × C
  GAG × CUU C × G   GGG × CCU G × G
  AAG × CUU G × C   AGG × CCU G × C
   C × G    G × C
   +    +
6. Leu × Glu GAG × CUC C × G 22. Pro × Gly GGG × CCC G × C
  GAG × CUC C × C   GGG × CCC G × C
  GAG × CUC G × C   GGG × CCC x C
   S × S    G × C
   + ?    +
7. Leu × Stop UAG × CUG C × G 23. Pro × Trp UGG × CCA G × G
(Leu × Gln) UAG × CUG C × G   UGG × CCA G × G
  UAG × CUG G × G   UGG × CCA G × R
   C × G    G × G
   +    -
8. Leu × Gln CAG × CUG C × G 24. Pro × Arg CGG × CCG G × C
  CAG × CUG C × G   CGG × CCG G × G
  CAG × CUG U × G   CGG × CCG G × C
   C × G    G × C
   +    +
9. Ile × Asn GAU × GUU G × C 25. Thr × Ser AGU × RCU C × G
  GAU × GUU G × C   GGU × GCU C × C
  AAU × AUU G × C/U   AGU × ACU C × G
   G × C    C × G
   +    +
10. Ile × Asp GAU × GUC G × C 26. Thr × Gly GGU × GCC C × C
  GAU × GUC G × C   GGU × GCC C × C
  GAU × GUC G × C   GGU × GCC x C
   G × C    C × C
   +    -
11. Ile × Tyrb UAU × GUA C × G 27. Thr × Cys UGU × GCA C × G
  UAU × GUA x C   UGU × GCA C × C
  UAU × RUA C × C   UGU × RCA C × G
   ND    C × G
      +
12. Met × His CAU × GUG G × Y 28. Thr × Arg CGU × ACG C × G/C
  CAU × GUG G × C   CGU × GCG C × C
  CAU × GUG G × C   CGU × ACG C × G
   G × C    C × S
   +    - ?
13. Val × Asn GAC × GUU G × C 29. Ala × Ser GGC × GCU G × G
  GAC × GUU G × C   GGC × GCU G × C
  AAC × GUU G × N   AGC × GCU G × A/U
   G × C    G × N
   +    -
14. Val × Asp GAC × GUC G × C 30. Ala × Gly GGC × GCC G × C
  GAC × GUC G × C   GGC × GCC G × C
  GAC × GUC x C   GGC × GCC G × C
   G × C    G × C
   +    +
15. Val × Tyr UAC × GUA G - G 31. Ala × Cys UGC × GCA G × G
  UAC × GUA G × C   UGC × GCA G × C
  UAC × GUA G × C   UGC × GCA G × G
   G × S    G × G
   + ?    -
16. Val × His CAC × GUG G - Y 32. Ala × Arg CGC × GCG G × Y
  CAC × GUG G × C   CGC × GCG G × C
  CAC × GUG Y/G × C   CGC × GCG G × C
   G × C    G × C
   +    +
DC value for the presumed common ancestor of Bacteria, Archaea and Eukarya:
All pairs of complementary anticodons, i.e. NAN × NUN + NGN × NCN:
Total: DC = 24/31 = 0.77, p = 0.003
Stop codons excluded: DC = 21/28 = 0.75, p = 0.012
Only strictly complementary pairing allowed: DC = 19/24 = 0.79, p = 0.006
DC values for Bacteria, Archaea and Eukarya, all pooled together:
NAN × NUN pairs:
Total: DC = 34/44 = 0.77, p = 0.0004
Stop codons excluded: DC = 29/38 = 0.76, p = 0.0016
Only strictly complementary pairing allowed: DC = 17/24 = 0.71, p = 0.064
NGN × NCN pairs:
Total: DC = 31/46 = 0.67, p = 0.026
Stop codons excluded: DC = 28/43 = 0.65, p = 0.066
Only strictly complementary pairing allowed: DC = 23/31 = 0.74, p = 0.01
All pairs of complementary anticodons, i.e. NAN × NUN + NGN × NCN:
Total: DC = 65/90 = 0.72, p = 0.00002
Stop codons excluded: DC = 57/81 = 0.7, p = 0.0004
Only strictly complementary pairing allowed: DC = 40/55 = 0.73, p = 0.001
  1. a Shown are the ancestral second bases for pairs of tRNAs with complementary anticodons in Bacteria, Archaea, Eukarya and their presumed common ancestors (ordered from top to bottom for each pair). Plus and minus signs denote presence or absence of the concerted second base complementarity, respectively. There is an apparent deficiency of anticodons beginning with 5'A, especially in the domains of Bacteria and Archaea. As complementary partners, one can use (in such cases) anticodons that begin with 5'G, which allows a wobbling G-U pairing (in bold). Similarly, one can also include the three pairs with "nonsense" anticodons (bold and italicized). The four cases of coevolutionarily maintained dual complementarity, where the second bases change in different kingdoms, yet remain complementary in both tRNA partners are underlined. Question mark behind + or - means that the corresponding assignment is likely, but not certain. "Incomplete" entry in columns 3 and 6 (such as "× C" in column 6 for pair 22, third line) means that the corresponding tRNA was not found in the database. See Methods section for a detailed explanation of how DC values were calculated.
  2. b This pair (Ile × Tyr) was not used in the DC calculations because its status is uncertain due to the small number of tRNAs available ("ND" standing for "non-determined").