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RNA Biology Volume 12, 2015 - Issue 9
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Research Paper

Rationally designed, heterologous S. cerevisiae transcripts expose novel expression determinants

Tuval Ben-YehezkelDepartment of Biomedical Engineering; Tel-Aviv University; Tel-Aviv, Israel;Department of Biological Chemistry; Weizmann Institute of Science; Rehovot, Israel;Department of Applied Mathematics and Computer Science; Weizmann Institute of Science; Rehovot, Israel;These authors equally contributed to this work.
,
Shimshi AtarDepartment of Biomedical Engineering; Tel-Aviv University; Tel-Aviv, Israel;These authors equally contributed to this work.
,
Hadas ZurDepartment of Biomedical Engineering; Tel-Aviv University; Tel-Aviv, Israel
,
Alon DiamentDepartment of Biomedical Engineering; Tel-Aviv University; Tel-Aviv, Israel
,
Eli GozDepartment of Biomedical Engineering; Tel-Aviv University; Tel-Aviv, Israel
,
Tzipy MarxDepartment of Biological Chemistry; Weizmann Institute of Science; Rehovot, Israel
,
Rafael CohenDepartment of Biological Chemistry; Weizmann Institute of Science; Rehovot, Israel
,
Alexandra DanaDepartment of Biomedical Engineering; Tel-Aviv University; Tel-Aviv, Israel
,
Anna FeldmanDepartment of Biomedical Engineering; Tel-Aviv University; Tel-Aviv, Israel
,
Ehud ShapiroDepartment of Biological Chemistry; Weizmann Institute of Science; Rehovot, Israel;Department of Applied Mathematics and Computer Science; Weizmann Institute of Science; Rehovot, Israel
&
Tamir TullerDepartment of Biomedical Engineering; Tel-Aviv University; Tel-Aviv, Israel;Sagol School of Neuroscience; Tel-Aviv University; Tel-Aviv, IsraelCorrespondence[email protected]
 show all
Pages 972-984 | Received 04 May 2015, Accepted 07 Jul 2015, Published online: 18 Sep 2015

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Eyal Cohen, Zohar Zafrir & Tamir Tuller. (2018) A code for transcription elongation speed. RNA Biology 15:1, pages 81-94.
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Martin Seeger, Max Flöttmann & Edda Klipp. (2023) A dynamical stochastic model of yeast translation across the cell cycle. Heliyon 9:2, pages e13101.
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Dong Jae Kim, Jiwoo Kim, Dong Hyun Lee, Jongwuk Lee & Han Min Woo. (2022) DeepTESR: A Deep Learning Framework to Predict the Degree of Translational Elongation Short Ramp for Gene Expression Control. ACS Synthetic Biology 11:5, pages 1719-1726.
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Tamar Neumann & Tamir Tuller. (2022) Modeling the ribosomal small subunit dynamic in Saccharomyces cerevisiae based on TCP-seq data . Nucleic Acids Research 50:3, pages 1297-1316.
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Stav Carmel Ezra & Tamir Tuller. (2022) Modeling the effect of rRNA-mRNA interactions and mRNA folding on mRNA translation in chloroplasts. Computational and Structural Biotechnology Journal 20, pages 2521-2538.
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Bikash K. Bhandari, Chun Shen Lim, Daniela M. Remus, Augustine Chen, Craig van Dolleweerd & Paul P. Gardner. (2021) Analysis of 11,430 recombinant protein production experiments reveals that protein yield is tunable by synonymous codon changes of translation initiation sites. PLOS Computational Biology 17:10, pages e1009461.
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Kuidong Xu, Yi Tong, Yi Li, Jin Tao, Jianghua Li, Jingwen Zhou & Song Liu. (2021) Rational Design of the N-Terminal Coding Sequence for Regulating Enzyme Expression in Bacillus subtilis . ACS Synthetic Biology 10:2, pages 265-276.
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Michael Peeri & Tamir Tuller. (2020) High-resolution modeling of the selection on local mRNA folding strength in coding sequences across the tree of life. Genome Biology 21:1.
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Wesley D. Penn, Haley R. Harrington, Jonathan P. Schlebach & Suchetana Mukhopadhyay. (2020) Regulators of Viral Frameshifting: More Than RNA Influences Translation Events. Annual Review of Virology 7:1, pages 219-238.
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Shir Bahiri-Elitzur & Tamir Tuller. (2020) Computational discovery and modeling of novel gene expression rules encoded in the mRNA. Biochemical Society Transactions 48:4, pages 1519-1528.
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Shaked Bergman & Tamir Tuller. (2020) Widespread non-modular overlapping codes in the coding regions*. Physical Biology 17:3, pages 031002.
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Dan D. Erdmann-Pham, Khanh Dao Duc & Yun S. Song. (2020) The Key Parameters that Govern Translation Efficiency. Cell Systems 10:2, pages 183-192.e6.
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Jingyi Jessica Li, Guo-Liang Chew & Mark Douglas Biggin. (2019) Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes. Genome Biology 20:1.
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Alon Diament, Iddo Weiner, Noam Shahar, Shira Landman, Yael Feldman, Shimshi Atar, Meital Avitan, Shira Schweitzer, Iftach Yacoby & Tamir Tuller. (2019) ChimeraUGEM: unsupervised gene expression modeling in any given organism. Bioinformatics 35:18, pages 3365-3371.
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Renana Sabi & Tamir Tuller. (2019) Novel insights into gene expression regulation during meiosis revealed by translation elongation dynamics. npj Systems Biology and Applications 5:1.
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Wentao Ding, Jian Cheng, Dan Guo, Ling Mao, Jingwei Li, Lina Lu, Yunxin Zhang, Jiangke Yang & Huifeng Jiang. (2018) Engineering the 5′ UTR-Mediated Regulation of Protein Abundance in Yeast Using Nucleotide Sequence Activity Relationships. ACS Synthetic Biology 7:12, pages 2709-2714.
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Bo Zheng, Xiaoyan Ma, Ning Wang, Tingting Ding, Liwei Guo, Xiaorong Zhang, Yu Yang, Chun Li & Yi-Xin Huo. (2018) Utilization of rare codon-rich markers for screening amino acid overproducers. Nature Communications 9:1.
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Marc Torrent, Guilhem ChalanconNatalia S. de Groot, Arthur Wuster & M. Madan Babu. (2018) Cells alter their tRNA abundance to selectively regulate protein synthesis during stress conditions. Science Signaling 11:546.
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Søren D Petersen, Jie Zhang, Jae S Lee, Tadas Jakočiūnas, Lise M Grav, Helene F Kildegaard, Jay D Keasling & Michael K Jensen. (2018) Modular 5′-UTR hexamers for context-independent tuning of protein expression in eukaryotes. Nucleic Acids Research.
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Marcel Noßmann, Jana Pieper, Falk Hillmann, Axel A. Brakhage & Thomas Munder. (2017) Generation of an arginine-tRNA-adapted Saccharomyces cerevisiae strain for effective heterologous protein expression. Current Genetics 64:3, pages 589-598.
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Charlotte Mignon, Natacha Mariano, Gustavo Stadthagen, Adrien Lugari, Priscillia Lagoutte, Stéphanie Donnat, Sylvie Chenavas, Cyril Perot, Régis Sodoyer & Bettina Werle. (2018) Codon harmonization – going beyond the speed limit for protein expression. FEBS Letters 592:9, pages 1554-1564.
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Iddo Weiner, Shimshi Atar, Shira Schweitzer, Haviva Eilenberg, Yael Feldman, Meital Avitan, Mor Blau, Avihai Danon, Tamir Tuller & Iftach Yacoby. (2018) Enhancing heterologous expression in Chlamydomonas reinhardtii by transcript sequence optimization . The Plant Journal 94:1, pages 22-31.
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Alon Diament, Anna Feldman, Elisheva Schochet, Martin Kupiec, Yoav Arava & Tamir Tuller. (2018) The extent of ribosome queuing in budding yeast. PLOS Computational Biology 14:1, pages e1005951.
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Yoram Zarai, Michael Margaliot & Tamir Tuller. 2018. Systems Biology. Systems Biology 275 300 .
Yoram Zarai, Michael Margaliot & Tamir Tuller. (2017) Optimal Down Regulation of mRNA Translation. Scientific Reports 7:1.
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Thomas Beuchert Kallehauge, Shangzhong Li, Lasse Ebdrup Pedersen, Tae Kwang Ha, Daniel Ley, Mikael Rørdam Andersen, Helene Faustrup Kildegaard, Gyun Min Lee & Nathan E. Lewis. (2017) Ribosome profiling-guided depletion of an mRNA increases cell growth rate and protein secretion. Scientific Reports 7:1.
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Alexander Churkin, Matan Drory Retwitzer, Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl & Danny Barash. (2017) Design of RNAs: comparing programs for inverse RNA folding. Briefings in Bioinformatics, pages bbw120.
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Eli Goz, Hadas Zur & Tamir Tuller. 2017. Evolutionary Biology: Self/Nonself Evolution, Species and Complex Traits Evolution, Methods and Concepts. Evolutionary Biology: Self/Nonself Evolution, Species and Complex Traits Evolution, Methods and Concepts 87 110 .
Alon Diament & Tamir Tuller. (2016) Estimation of ribosome profiling performance and reproducibility at various levels of resolution. Biology Direct 11:1.
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Yoram Zarai, Michael Margaliot, Eduardo D. Sontag & Tamir Tuller. (2016) Controlling the ribosomal density profile in mRNA translation. Controlling the ribosomal density profile in mRNA translation.
Hadas Zur & Tamir Tuller. (2016) Predictive biophysical modeling and understanding of the dynamics of mRNA translation and its evolution. Nucleic Acids Research, pages gkw764.
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Zohar Zafrir, Hadas Zur & Tamir Tuller. (2016) Selection for reduced translation costs at the intronic 5′ end in fungi. DNA Research 23:4, pages 377-394.
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Armando Fernandes & Susana Vinga. (2016) Improving Protein Expression Prediction Using Extra Features and Ensemble Averaging. PLOS ONE 11:3, pages e0150369.
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Alon Raveh, Michael Margaliot, Eduardo D. Sontag & Tamir Tuller. (2016) A model for competition for ribosomes in the cell. Journal of The Royal Society Interface 13:116, pages 20151062.
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Gilad Poker, Michael Margaliot & Tamir Tuller. (2015) Sensitivity of mRNA Translation. Scientific Reports 5:1.
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