A comparative genomics study on the effect of individual amino acids on ribosome stalling

Sabi and Tuller BMC Genomics 2015, 16(Suppl 10):S5 http://www.biomedcentral.com/1471-2164/16/S10/S5 RESEARCH Open Access A comparative genomics study on the effect of individual amino acids on ribosome stalling Renana Sabi1, Tamir Tuller1,2* From 13th Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics Frankfurt, Germany. 4-7 October 2015 Abstract Background: During protein synthesis, the nascent peptide chain emerges from the ribosome through the ribosomal exit tunnel. Biochemical interactions between the nascent peptide and the tunnel may stall the ribosome movement and thus affect the expression level of the protein being synthesized. Earlier studies focused on one model organism (S. cerevisiae), have suggested that certain amino acid sequences may be responsible for ribosome stalling; however, the stalling effect at the individual amino acid level across many organisms has not yet been quantified. Results: By analyzing multiple ribosome profiling datasets from different organisms (including prokaryotes and eukaryotes), we report for the first time the organism-specific amino acids that significantly lead to ribosome stalling. We show that the identity of the stalling amino acids vary across the tree of life. In agreement with previous studies, we observed a remarkable stalling signal of proline and arginine in S. cerevisiae. In addition, our analysis supports the conjecture that the stalling effect of positively charged amino acids is not universal and that in certain conditions, negative charge may also induce ribosome stalling. Finally, we show that the beginning part of the tunnel tends to undergo more interactions with the translated amino acids than other positions along the tunnel. Conclusions: The reported results support the conjecture that the ribosomal exit tunnel interacts with various amino acids and that the nature of these interactions varies among different organisms. Our findings should contribute towards better understanding of transcript and proteomic evolution and translation elongation regulation. Background mRNAs translation is a fundamental intracellular process which occurs in all living organisms. Translation elongation is an iterative stage of translation in which the ribosome scans the mRNA sequence and decodes it into a specific protein by adding one amino acid at the time to the growing peptide chain. It has been suggested that the speed by which ribosomes progress along the mRNA is affected by different local features of the coding sequence. One determinant of the translation elongation speed is the identity of the codon at the P-site; it has been suggested that the codon decoding rate is influenced by several factors related to the P-site, including: the cellular concentration of the * Correspondence: 1 Department of Biomedical Engineering, Tel Aviv University (TAU), Tel Aviv, Israel Full list of author information is available at the end of the article paired tRNA [1-6]; the efficiency of the codon-anticodon pairing which occurs non-optimally for wobble base pairing [7-9] and the efficiency of incorporation of the decoded amino acid into the polypeptide which is mainly poor in the case of proline [10-12]. Other coding sequence features thought to slow down ribosomes include: the folding energy of the mRNA sequence downstream from the ribosomal P-site [13-16]; the identity of the tRNA at the A-site [17]; and the charge of the amino acids in the exit tunnel [16,18,19]. The Ribosomal Exit Tunnel (RET) is the site through which nascent peptides leave the ribosome during translation. The non-uniform biochemical characteristics of the tunnel allow it to play an important role in affecting translation rates and protein folding rather than being a passive conduit for the nascent polypeptide. First, the overall electrostatic potential of the RET is negative and © 2015 Sabi and Tuller This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http:// creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/ zero/1.0/) applies to the data made available in this article, unless otherwise stated. Sabi and Tuller BMC Genomics 2015, 16(Suppl 10):S5 http://www.biomedcentral.com/1471-2164/16/S10/S5 varies in magnitude along the tunnel [19-23]; thus, it was suggested that a nascent peptide that contains charged amino acids may undergo electrostatic interaction with the exit tunnel [19]. Second, the diameter of the tunnel varies between 10A0 and 20A0 [24-27]; thus, the interaction between that nascent peptide and the exit tunnel may also be dictated by geometrical constraints. Although the expansion in diameter enables the partial folding of the translated peptide [28], the cramped dimensions of the tunnel prohibit a folding of whole protein domains and only tertiary/secondary structures of small segments are allowed [29]. Evidences of ribosome pausing mediated by nascent peptide have been manifested in several studies [30-36]. These studies, however, either conducted a small scale experiment or focused on one organism only. The development of the ribosome profiling technique has significantly broaden the comprehension of in vivo translation by enabling the detection of the momentary positions of ribosomes along the transcripts at nucleotide resolution [37]. During the past few years, the high throughput quantitative data obtained by ribosome profiling experiments has been widely used to study gene translation [10,16,18,38-51]. Specifically, ribosome profiling data was used to show that ribosome stalling is induced in response to the presence of certain amino acid [10,16,18]. Specifically, it has been suggested that positively charged amino acids are implicated in transient ribosomal pauses by interacting with the negatively charged exit tunnel [16,18,19]. A more recent study of Artieri and Fraiser [10], on the other hand, emphasized the possibility that the incorporation of proline into the nascent peptide has the major effect on ribosome stalling. In order to investigate the organism-specific influence of each individual amino acid on substantial ribosome stalling, we performed a large scale analysis based on multiple ribosome profiling datasets of 9 organisms including eukaryotes (H.sapiens, C.elegans, S.cerevisiae, S.pombe, A.thaliana, P.falciparum, D.melanogaster, M.musculus) and bacteria (C.crescentus). Results Ribosome profiling experiments include the following major stages (Figure 1A): cells are treated with cycloheximide (for example) to arrest translating ribosomes; then, RNA fragments protected by ribosomes from RNases are isolated and processed for high-throughput sequencing, resulting in reads of ribosomes protected footprints. As slowly (...truncated)