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Protein synthesis is an important process in cell (Smith and Szathmary, 1999).
During translation, amino acids are brought to the site of synthesis by tRNA molecules in the
form of aminoacyl tRNA. Rate of polypeptide synthesis in the cell is influenced by the rate
at which the cognate aminoacyl tRNA appears at the site of protein synthesis, which
is determined by the relative abundance of tRNA molecules in the cytosol. Correct
pairing between the codon and anticodon in the ribosome stimulates the hydrolysis of GTP,
resulting in a conformational change in the ribosome, followed by accommodation of the
tRNA molecule (Ogle et al., 2003). During a codon-anticodon pairing, the
1st and 2nd nucleotides of the codon pair with the
3rd and 2nd nucleotides respectively of the anticodon follow
the principle of Watson-Crick pairing, whereas the pairing between the
3rd nucleotide of the codon with the
1st nucleotide of the anticodon is also influenced by wobble pairing.
Because of this, more than one codon can be decoded by one tRNA molecule. The exact reason
for wobble pairing at the 3rd position of codons is not known. However, it has been
speculated that the position of the anticodon in the anticodon stem loop prohibits a perfectly
linear alignment with the corresponding mRNA codon, causing wobble pairing at this
position (Brown, 2002). The wobble pairing at the
3rd nucleotide position of a codon might
have evolved to enhance the efficiency of translation. Had there been no wobble pairing, for
61 sense codons, there would have been a requirement of tRNAs with as many
different anticodons. Wobble pairing has reduced this requirement. Appearance of cognate
tRNA molecule at the `A' site in the ribosome during translation would obviously become
much easier and hence faster, if the choice of tRNA is to be made from a pool of less
diverse tRNA population than from a more diverse larger one. This also explains why
synonymous codons are not randomly present in the genetic code. It seems, wobble pairing and
non-randomness of synonymous codons are the consequences of a coevolutionary process
leading to an increased efficiency in the translation rate (Das
et al., 2006).
According to the standard wobble rule (Osawa
et al., 1992), a minimum of 32 different tRNA molecules are sufficient for decoding all 61 sense codons. Many bacterial
genomes have been completely sequenced till date and the information regarding the occurrence
of different tRNA molecules present in the genomes is available in the databases.
The availability of the genome sequences presents an opportunity to address some key
issues in evolutionary genomics. In a recent analysis, it has been observed that tRNA
number present in a cell is negatively correlated with bacterial generation time irrespective
of genome GC% (Rocha, 2004). Cells having shorter generation time have more number
of tRNA genes but having lesser number of different anticodons. It has been suggested
that due to the higher tRNA number, translation process is more efficient, so cell division
is quicker in these cells (Rocha, 2004). The question of the factors determining genome
GC content is one such problem. Number of different tRNA genes is found to be often
more than 32 and these numbers are different among different bacteria. In this study, we
analyzed the occurrence of the tRNA genes in different bacterial genomes in the context of
the following issues: (i) presence of a complete set of tRNA genes capable of decoding all
61 codons on the basis of the standard wobble rule; (ii) commonality in features in the
genomes, if any, which might influence the occurrence of tRNA genes; and (iii) probable
correlation between genome GC% and occurrence of
tRNA gene. |
