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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").