Saturday, September 02, 2006

A 'Nucleic Acids Research' Article Review

An article entitled 'Comparison of characteristics and function of translation termination signals between and within prokaryotic and eukaryotic organisms' appeared in 'Nucleic Acids Research.' A review follows.

Research, focused on six prokaryotic and five eukaryotic genomes, was the basis for determining whether the termination signal for protein synthesis has common determinants. In the words of the authors: "Four of the six prokaryotic and all of the eukaryotic genomes investigated demonstrated a similar pattern of nucleotide bias both 5' and 3' of the stop codon. A preferred core signal of 4 nt was evident, encompassing the stop codon and the following nucleotide. Codons decoded by hyper-modified tRNAs were over-represented in the region 5' to the stop codon in genes from both kingdoms."

Experiments were aimed at determining whether there existed a correlation between termination efficiency and signal abundance bias. Escherichia coli, one of the prokaryotic organisms studied, showed a correlation between termination efficiency and signal abundance as related to the stop codons UAA and UGA. Such was not the case with mammalian cells.

The paper notes the interactive nature of protein synthesis termination. There is evolutionary significance to the data. There are differences between prokaryotes and eukaryotes with regard to translation termination. As noted in the paper, protein synthesis termination involves release factors (RFs). The function of these RF proteins entails release of the polypeptide chain from the ribosome. Whereas prokaryotes contain two release factors eukaryotes only contain one. As expected the decoding capacity of the eukaryotic RF extends to all three stop codons. The two prokaryotic RFs are both effective with the UAA stop codon but RF1 only decodes UAG and RF2, UGA.

[An article entitled 'Endless possibilities: translation termination and stop codon recognition' provides some background information about release factors that could be helpful. The following passage is from this cited article.]

During translation termination, a stop codon located in the ribosomal A-site is recognized by a release factor or release factor complex, which binds the ribosome and triggers release of the nascent peptide. In eukaryotes, translation is terminated by a heterodimer consisting of two proteins, release factors eRF1 and eRF3, which interact in vivo (Frolova et al., 1994 ; Zhouravleva et al., 1995 ; Stansfield et al., 1995 ). eRF1 recognizes all three stop codons and triggers peptidyl-tRNA hydrolysis by the ribosome, releasing the nascent peptide (Frolova et al., 1994 ; Drugeon et al., 1997 ). Eukaryote termination efficiency is enhanced by the GTPase release factor eRF3, the second component of the heterodimer eRF complex. In response to a stop codon in the ribosomal A-site, formation of a quaternary complex comprising the ribosome, eRF1, GTP and eRF3 triggers GTP hydrolysis and enhances the rate of peptidyl release

In contrast to eukaryotes, the role of stop codon recognition during translation termination in eubacteria is divided between two so-called class 1 release factors, RF1 and RF2, which in Escherichia coli are encoded by the essential prfA and prfB genes, respectively (Scolnick et al., 1968 ; Caskey et al., 1984 ; Weiss et al., 1984 ). RF1 catalyses translation termination at UAA and UAG codons, and RF2 at UAA and UGA codons


[Back to the review]

The authors state that the differences in prokaryotic/eukaryotic release factors are consistent with independent evolution. The absence of sequence and structural homology among the prokaryotic and eukaryotic release factors is additional data in support of their conclusion.

The paper devotes attention to the issue of termination efficiency. Experimental evidence was cited testing nucleotide sequence changes in E.coli- both 5' and 3' of stop codons.

Results indicate that there is bias in occurence of specific nucleotide sequences which affects bacterial termination efficiency. Translation termination efficiency was also studied in yeast and mammalian cells. In the words of the authors- "these studies have revealed that the nucleotide sequences both 5' and 3' of the stop codon can modulate termination efficiency."

The prokaryotic and eukaryotic genomes studied both shared similar relationships in their level of gene expression and nucleotide sequence bias. Highly expressed genes show nucleotide bias in the area around stop codons while the bias of genes with the lowest expression was insignificant. Specific nucleotide biases have been identified- TAAT (E.coli K12 and M.genitalium), TAAA and TAAT (B.subtilis), TAGC (M.tuberculosis) and in the words of the authors: "All five eukaryotic genomes showed preferred tetra-nucleotide signals of a stop codon followed by a purine (G or A)."


The paper states that a correlation exists between tRNA abundance and translation efficiency for both prokaryotes and eukaryotes. However, insofar as termination efficiency was concerned the data gave differing interpretations for prokaryotes and eukaryotes. The number of termination codons UAA, UGA and UAG are not equally abundant in E.coli; UAG terminating the smallest percentage of genes. There was a correlation observed in the abundance of termination signals and the efficiency of termination in E.coli. Inefficient signals in E.coli were linked to gene expression. This was most pronounced with low mRNA levels and smaller genes where termination and initiation signals were closer. Initiation of mRNA was said to be influenced by ribosomal pausing and queuing which in turn can result from inefficient termination.

In contrast the same relationship between abundance of termination codons and efficiency of termination was not found in the eukaryotes studied. As the authors stated:

"Indeed, the abundant UAA signal was the least efficient and, generally, the rare signals were among the most efficient."


There were efforts made to determine the importance of release factors to stop signal efficiency. To do so the concentration of RF was increased by as much as five-fold and a dramatic increase in termination efficiency at rare signals was observed. More abundant signals were not as impacted. The authors had this to say about RFs and protein synthesis termination:


The recognition and binding of the decoding RFs for termination of protein synthesis may be the major, if not the sole determinant of the extended length of the stop signal in prokaryotes. In prokaryotes, transcription and translation are spatially and temporally linked, and efficient recognition of stop codons by the decoding factors is correlated with translation rate.


As was the case with prokaryotes increased concentration of decoding RF resulted in improved signal efficiency for eukaryotes and even influenced gene expression with reference to particular genes. Eukaryotic signal sequences were investigated to determine termination efficiency and in the words of the authors:


The results indicated that differences in the nucleotide sequences in both 3' and 5' contexts could affect signal efficiency but this did not correlate with bias and/or abundance.



I found interesting the analysis related to an observation of a lack of direct correlation between termination efficiency in eukaryotes and the bias 5' and 3' of stop codons. The implication, according to the authors, is that the function of the translation termination signal is broader than termination of protein synthesis. They then speculate that the translation termination sequence may be connected with an mRNA recycling loop which lessens the rate of mRNA decay and increases protein expression efficiency. The existence of extended termination signals may be a means by which mature and premature stop codons are distinguished.

In concluding remarks the authors noted that greater regulation of gene expression exists in eukaryotic organisms. New roles for eukaryotic translation termination mechanisms exist that are not found in prokaryotes. The authors surmise that this may explain some of the divergence in translational termination signals.

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