Ribosome signatures aid bacterial translation initiation site identification

Abstract

BackgroundWhile methods for annotation of genes are increasingly reliable, the exact identification of translation initiation sites remains a challenging problem. Since the N-termini of proteins often contain regulatory and targeting information, developing a robust method for start site identification is crucial. Ribosome profiling reads show distinct patterns of read length distributions around translation initiation sites. These patterns are typically lost in standard ribosome profiling analysis pipelines, when reads from footprints are adjusted to determine the specific codon being translated.ResultsUtilising these signatures in combination with nucleotide sequence information, we build a model capable of predicting translation initiation sites and demonstrate its high accuracy using N-terminal proteomics. Applying this to prokaryotic translatomes, we re-annotate translation initiation sites and provide evidence of N-terminal truncations and extensions of previously annotated coding sequences. These re-annotations are supported by the presence of structural and sequence-based features next to N-terminal peptide evidence. Finally, our model identifies 61 novel genes previously undiscovered in the Salmonella enterica genome.ConclusionsSignatures within ribosome profiling read length distributions can be used in combination with nucleotide sequence information to provide accurate genome-wide identification of translation initiation sites.Electronic supplementary materialThe online version of this article (doi:10.1186/s12915-017-0416-0) contains supplementary material, which is available to authorized users.

Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea

“…Finding translation initiation sites (TIS) for usual genes is challenging but relatively well addressed computationally and experimentally, contrary to internal/alternative TIS [32,33]. Therefore, we adopted the simplest working definition: the TIS is located at the nearest ATG or GTG start codon downstream of the iTSS.…”

DeepRibo: precise gene annotation of prokaryotes using deep learning and ribosome profiling data

“…Yet, the models' performances indicate this effect to be minimal. Moreover, recent studies have discovered genes with multiple translation initiation sites [41,14,12]. As this feature is not supported by current annotations, correct evaluation of the model in a multiple stop site setting is not possible.…”

“…chloramphenicol or tetracycline) preceding the ribo-seq protocol enriching for initiating ribosomes [12]. Recently, prediction methods based on machine learning algorithms have been devised to either delineate the ORF [13] or predict the TIS [14] based on a combination of ribosome profiling and sequence features for prokaryotic genomes. A multitude of tools are also available for eukaryotic samples [15,16,17,18,19,20].…”

Connecting Proteomics to Next‐Generation Sequencing: Proteogenomics and Its Current Applications in Biology

“…built a model to predict TISs by incorporating these signatures, which was later validated with N‐terminal proteomics. Consequently, they reannotated a number of TISs and verified N‐terminal truncations and extensions of previously annotated coding sequences in selected prokaryotes . Similarly, proteogenomics can be applied to detect unexpected translation termination.…”