Abstract
Although translation is the key step during gene expression, it remains poorly characterized at the level of individual genes. For this reason, we developed Transimulation – a web service measuring translational activity of genes in three model organisms: Escherichia coli, Saccharomyces cerevisiae and Homo sapiens. The calculations are based on our previous computational model of translation and experimental data sets. Transimulation quantifies mean translation initiation and elongation time (expressed in SI units), and the number of proteins produced per transcript. It also approximates the number of ribosomes that typically occupy a transcript during translation, and simulates their propagation. The simulation of ribosomes’ movement is interactive and allows modifying the coding sequence on the fly. It also enables uploading any coding sequence and simulating its translation in one of three model organisms. In such a case, ribosomes propagate according to mean codon elongation times of the host organism, which may prove useful for heterologous expression. Transimulation was used to examine evolutionary conservation of translational parameters of orthologous genes. Transimulation may be accessed at http://nexus.ibb.waw.pl/Transimulation (requires Java version 1.7 or higher). Its manual and source code, distributed under the GPL-2.0 license, is freely available at the website.
Highlights
For many years, it was believed that gene expression regulation takes place mainly at the level of transcription
We decided to extend the set of results by applying the model to two additional organisms: Escherichia coli and Homo sapiens (HeLa cell line), for which high quality data sets on mRNA relative abundance, ribosome footprints, and tRNAs decoding specificities are available
To facilitate access to the results, we developed Transimulation – a web service simulating protein biosynthesis from individual genes for the three studied organisms
Summary
It was believed that gene expression regulation takes place mainly at the level of transcription. Deeper insight into protein biosynthesis seems crucial to better integrate transcriptomic and proteomic data [6,7,8], the process is still poorly characterized at the level of individual proteins, mainly due to difficulties in experimental determination of absolute translation rates. For this reason, we have developed [9] a model measuring translational activity at the level of individual genes, and implemented it genome-wide in Saccharomyces cerevisiae. By combining these results with data on mRNA stabilities, we determined the number of proteins produced from each transcript during its lifetime
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