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. 2008 Sep;14(9):1730-6.
doi: 10.1261/rna.1037108. Epub 2008 Jul 24.

All translation elongation factors and the e, f, and h subunits of translation initiation factor 3 are encoded by 5'-terminal oligopyrimidine (TOP) mRNAs

Valentina Iadevaia  1 , Sara Caldarola, Elisa Tino, Francesco Amaldi, Fabrizio Loreni
Affiliations

All translation elongation factors and the e, f, and h subunits of translation initiation factor 3 are encoded by 5'-terminal oligopyrimidine (TOP) mRNAs

Valentina Iadevaia et al. RNA. 2008 Sep.

Abstract

Terminal oligopyrimidine (TOP) mRNAs (encoded by the TOP genes) are identified by a sequence of 6-12 pyrimidines at the 5' end and by a growth-associated translational regulation. All vertebrate genes for the 80 ribosomal proteins and some other genes involved, directly or indirectly, in translation, are TOP genes. Among the numerous translation factors, only eEF1A and eEF2 are known to be encoded by TOP genes, most of the others having not been analyzed. Here, we report a systematic analysis of the human genes for translation factors. Our results show that: (1) all five elongation factors are encoded by TOP genes; and (2) among the initiation and termination factors analyzed, only eIF3e, eIF3f, and eIF3h exhibit the characteristics of TOP genes. Interestingly, these three polypeptides have been recently shown to constitute a specific subgroup among eIF3 subunits. In fact, eIF3e, eIF3f, and eIF3h are the part of the functional core of eIF3 that is not conserved in Saccharomyces cerevisiae. It has been hypothesized that they are regulatory subunits, and the fact that they are encoded by TOP genes may be relevant for their function.

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Figures

FIGURE 1.
FIGURE 1.
Primer extension. A 5′ end-labeled primer (specific for the indicated mRNAs) was annealed to 20 μg of total RNA from HeLa cells and then extended with reverse transcriptase. Extension products were separated on 6% polyacrylamide gel and exposed for autoradiography. The major extension band is indicated by the arrow. The nucleotide corresponding to the major extension band is indicated by an “*” in the sequence reported in the lower part of each panel which include the surrounding of the tss. M, 10-bp size marker; seq, unrelated sequence ladder; PE, primer extension products.
FIGURE 2.
FIGURE 2.
Polysomal mRNA profile in different growth conditions. HeLa (H), HEK293 (K), and NIH3T3 (N) cells were incubated in medium lacking serum (−serum) and then stimulated for 1 h with complete medium without (+serum) or with (+rap+serum) rapamycin. Cytoplasmic extracts were separated on sucrose gradients, and fractions were collected while absorbance was monitored at 260 nm. (A) Examples of absorbance profiles from HeLa cells are outlined with black arrows indicating the positions of the 80S ribosomes; the first fraction corresponds to the bottom of the gradient. (B) RNA extracted from each fraction was analyzed on Northern blots with the indicated probes. (C) Quantification of the signals is reported as a column plot of the percentage of mRNA on polysomes, obtained by adding up the values of fractions 1–5.
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