Alternative Translational Initiation Database

Besides providing researchers with information on alternative translational start sites and their protein products, we also made a general statistics. We systematically analyzed the nucleotide contexts of alternative initiation sites and the characteristics of isoelectric point value (pI) and molecular weight (Mw) of the translated isoforms in eukaryotes. For genes with the same name but from different species, only one of them was included. 140 genes in eukaryotes (including 301 alternatively translated protein products with complete amino acid sequences available) formed the material of the statistical analyses.

The nucleotide contexts of 140 first starting codons encoding full-length isoforms and 161 downstream in-frame alternative starting codons initiating N-term truncated isoforms were considered in subplot A and subplot B respectively. For a case-control study, we randomly selected 1000 non-homological genes of Homo sapiens that are not subject to alternative translational initiation events (ATIEs). The nucleotide contexts of initiation sites, in-frame ATG sequences and out-of-frame ATG sequences in these 1000 genes were calculated in subplot C, D and E, respectively. The nucleotide context logos ranged from upstream nucleotide position -12 to downstream position +15 adjacent to the starting codon. Kozak consensus context (GCC(A/G)CC***G) in which the most important features are the G at downstream position +4 adjacent to the starting codon and the A/G at upstream position -3 is conserved in subfigure C. In-frame ATG and out-of-frame ATG are located in a suboptimal context, as shown in subplot D and E. Initiation only proceeds efficiently if the starting codon occurs within the Kozak consensus context. However, Kozak consensus context is less conserved surrounding the in-frame alternative initiation sites that are subject to ATIEs than the initiation sites that are not subject to ATIEs (Subplot B). In many (not most) cases of alternative initiation the context of the first start codon was optimal (Subplot A). Due to this interesting result, we suppose a new undiscovered mechanism leading to alternative translational initiation might exist besides "leaky scanning".

Figure 1: The nucleotide context logos. The figure showed the context logos of first initiation sites (Subplot A) and the downstream in-frame alternative initiation sites (Subplot B) in ATIEs. Also, for a case-control study, the logos of initiation sites, in-frame ATG sequences and out-of-frame ATG sequences that are not subject to ATIEs were listed in subplot C, D and E, respectively.

The molecular weights (Mws) and isoelectric point (pI) values are important to describe the basis protein features. Statistical plots on theoretical pI values and Mws of N-term truncated isoforms vs. full-length isoforms were shown in figure 2. The Mws of N-term amino acids fragment truncated range between 1% and 79% of Mws of full-length isoforms. And each N-term truncated isoform tends to change its pI value to a new pH at which the protein has an equal number of positive and negative charges.

Figure2: Statistics on isoelectric point values and molecular weights of alternative isoforms in eukaryotes.

The variable of y-axis in the right plot denotes the ratio of Mw of N-term truncated isoform vs. Mw of full-length isoform. Its value is limited in the range of 21% to 99%.

Abbreviations: Kda, kilodalton; pI, isoelectric point; Mw, molecular weight.

We systematically analyzed the impact of ATIEs on biological diversification from the viewpoint of the alteration of domain contents and subcellular localizations.In our result, alternative isoforms in 120 out of the 140 ATIEs reside in different cellular compartments or function in distinct domain contents. The synthesis of alternative proteins having different domain contents or subcellular relocations potentially confers on these isoforms distinct functions. Detailed conclusions can be found in our paper "alteration of protein subcellular location and domain formation by alternative translational initiation" accepted by the journal of PROTEINs: Structure, Function, and Bioinformatics [1].

Reference:

1. J. Cai, Y. Huang, F. Li and Y. Li. Alteration of protein subcellular location and domain formation by alternative translational initiation. PROTEINS: Structure, Function, and Bioinformatics, in press.