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Ribosome Traffic on mRNAs Maps to Gene Ontology: Genome-wide Quantification of Translation Initiation Rates and Polysome Size Regulation

Figure 8

Initiation rate: summary of the findings.

(A) For a given ‘physiological’ number of ribosomes we found mRNA-specific initiation rates, distributed over a broad range of values (Figure 2). Different regions of the distributions can be mapped to certain GO annotations. For example, mRNAs with small physiological initiation rate are regulatory proteins while genes involved in translation have a larger initiation rate. (B) Changes in initiation (induced, for instance, by variations in the ribosomal pool, e.g. available ribosomes increase to a value of ) are estimated by our modelling and theoretically perceived by the transcript in different ways, according to their current-initiation relationship . In particular, some mRNAs have a large gearing factor , such as regulatory proteins, while other messengers, such as translation associated ones, are less sensitive to changes of the initiation rate. (C) For very large initiation rates the protein production rates reach a maximal elongation-limited value, i.e. only depending on the sequence of codons. We discover that translation associated genes have a larger maximal production rate when compared to other mRNAs, such as regulatory proteins, whose production might need to be capped. (D) In general we find two main groups of sequences classified according to their current-initiation relationship . Abrupt sequences, usually regulatory proteins, present an abrupt ‘kink’ in , meaning that the protein production rate can quickly saturate above specific values (sequence-dependent) of the initiation rate. Genes involved in translation like ribosomal proteins are instead classified as smooth sequences, since their sequences are such that this abrupt crossover does not exist.

doi: https://doi.org/10.1371/journal.pcbi.1002866.g008