Rate-Limiting Steps in Yeast Protein Translation

Cited by (463)

Items 101–200 of 463

1. The Key Parameters that Govern Translation Efficiency
   Dan D. Erdmann-Pham, Khanh Dao Duc, Yun S. Song · 2020 · Cell Systems
2. Disrupting upstream translation in mRNAs is associated with human disease
   David S.M. Lee, Joseph Park, Andrew Kromer, Aris Baras, Daniel James Rader, Marylyn DeRiggi Ritchie, Louis R. Ghanem, Yoseph Barash · 2021 · Nature Communications
3. What, where, and how: Regulation of translation and the translational landscape in plants
   Hsin-Yen Larry Wu, Joey Jen, Polly Yingshan Hsu · 2023 · The Plant Cell
4. RNAi expression tuning, microfluidic screening, and genome recombineering for improved protein production in Saccharomyces cerevisiae
   Guokun Wang, Sara Björk, Mingtao Huang, Quanli Liu, Kate Campbell, Jens Nielsen, Haakan N. Joensson, Dina Petranović · 2019 · Proceedings of the National Academy of Sciences
5. Chloroplast translational regulation uncovers nonessential photosynthesis genes as key players in plant cold acclimation
   Yang Gao, Wolfram Thiele, Omar Saleh, Federico Scossa, Fayezeh Aarabi, Hongmou Zhang, Arun Sampathkumar, Kristina Kühn, Alisdair Robert Fernie, Ralph Bock et al. · 2022 · The Plant Cell
6. Computing the functional proteome: recent progress and future prospects for genome-scale models
   Edward J O’Brien, Bernhard Ørn Palsson · 2015 · Current Opinion in Biotechnology
7. Cellular growth defects triggered by an overload of protein localization processes
   Reiko Kintaka, Koji Makanae, Hisao Moriya · 2016 · Scientific Reports
8. Non-equilibrium coupling of protein structure and function to translation–elongation kinetics
   Ajeet K. Sharma, Edward P. O’Brien · 2018 · Current Opinion in Structural Biology
9. Highly efficient cellular expression of circular mRNA enables prolonged protein expression
   Mildred J. Unti, Samie R. Jaffrey · 2023 · Cell chemical biology
10. Translation Initiation Rate Determines the Impact of Ribosome Stalling on Bacterial Protein Synthesis
    Steven J. Hersch, Sara Elgamal, Assaf Katz, Michael Ibba, William Wiley Navarre · 2014 · Journal of Biological Chemistry
11. Codon usage optimization in pluripotent embryonic stem cells
    Susanne Bornelöv, Tommaso Selmi, Sophia Flad, Sabine Dietmann, Michaela Frye · 2019 · Genome biology
12. The effects of codon bias and optimality on mRNA and protein regulation
    Fabian Hia, Osamu Takeuchi · 2020 · Cellular and Molecular Life Sciences
13. Codon usage and protein length-dependent feedback from translation elongation regulates translation initiation and elongation speed
    Xueliang Lyu, Qian Yang, Fangzhou Zhao, Yi Liu · 2021 · Nucleic Acids Research
14. Translation complex profile sequencing to study the in vivo dynamics of mRNA–ribosome interactions during translation initiation, elongation and termination
    Nikolay E. Shirokikh, Stuart K. Archer, Traude Helene Beilharz, David Powell, Thomas Preiß · 2017 · Nature Protocols
15. Extensive and coordinated control of allele-specific expression by both transcription and translation in Candida albicans
    Dale Muzzey, Gavin Sherlock, Jonathan S. Weissman · 2014 · Genome Research
16. The translational landscape of Arabidopsis mitochondria
    Noelya Planchard, Pierre Bertin, Martine Quadrado, Céline Dargel-Graffin, Isabelle Hatin, Olivier Namy, Hakim Mireau · 2018 · Nucleic Acids Research
17. TASEP modelling provides a parsimonious explanation for the ability of a single uORF to derepress translation during the integrated stress response
    Dmitry E. Andreev, Maxim Dmitrievich Arnold, Stephen J. Kiniry, Gary Loughran, Audrey M. Michel, Dmitrii I. Rachinskii, Pavel V. Baranov · 2018 · eLife
18. Maximizing protein translation rate in the non-homogeneous ribosome flow model: a convex optimization approach
    Gilad Poker, Yoram Zarai, Michael Margaliot A, Tamir Tuller · 2014 · Journal of The Royal Society Interface
19. The radish Ogura fertility restorer impedes translation elongation along its cognate CMS-causing mRNA
    Chuande Wang, Lina Lezhneva, Nadège Arnal, Martine Quadrado, Hakim Mireau · 2021 · Proceedings of the National Academy of Sciences
20. Single-Molecule Kinetics of the Eukaryotic Initiation Factor 4AI upon RNA Unwinding
    Yingjie Sun, Evrim Atas, Lisa Lindqvist, Nahum Sonenberg, Jerry Pelletier, Amit Meller · 2014 · Structure
21. Analysis of Ribosome-Associated mRNAs in Rice Reveals the Importance of Transcript Size and GC Content in Translation
    Dongyan Zhao, John P. Hamilton, Michael A. Hardigan, Dongmei Yin, Tao He, Brieanne Vaillancourt, Mauricio Alberto Reynoso, Germain C. Pauluzzi, Scott A. Funkhouser, Yuehua Cui et al. · 2016 · G3 Genes Genomes Genetics
22. The extent of ribosome queuing in budding yeast
    Alon Diament, Anna Feldman, Elisheva Schochet, Martin Kupiec, Yoav Arava, Tamir Tuller · 2018 · PLoS Computational Biology
23. Codon optimality controls differential mRNA translation during amino acid starvation
    Mridusmita Saikia, Xiaoyun Wang, Yuanhui Mao, Ji Wan, Tao Pan, Shu‐Bing Qian · 2016 · RNA
24. When mRNA translation meets decay
    Alicia A. Bicknell, Emiliano P. Ricci · 2017 · Biochemical Society Transactions
25. Excess ribosomal protein production unbalances translation in a model of Fragile X Syndrome
    Sang S. Seo, Susana R. Louros, Natasha J. Anstey, Miguel A. Gonzalez‐Lozano, Callista B. Harper, Nicholas Verity, Owen Dando, Sophie R. Thomson, Jennifer C. Darnell, Peter C. Kind et al. · 2022 · Nature Communications
26. Impact of C‐terminal amino acid composition on protein expression in bacteria
    Marc L Weber, Raul Burgos, Eva Yus, Jae‐Seong Yang, María Lluch‐Senar, Luis G. Serrano · 2020 · Molecular Systems Biology
27. Selectivity of mRNA degradation by autophagy in yeast
    Shiho Makino, Tomoko Kawamata, Shintaro Iwasaki, Yoshinori Ohsumi · 2021 · Nature Communications
28. CRISPR-RNAa: targeted activation of translation using dCas13 fusions to translation initiation factors
    Peter B. Otoupal, Brady F. Cress, Jennifer A. Doudna, Joseph S. Schoeniger · 2022 · Nucleic Acids Research
29. Critical reflections on synthetic gene design for recombinant protein expression
    Annabel H. A. Parret, Hüseyin Besir, Rob Meijers · 2016 · Current Opinion in Structural Biology
30. Beyond the Triplet Code: Context Cues Transform Translation
    Gloria Ann Brar · 2016 · Cell
31. Single-molecule imaging of microRNA-mediated gene silencing in cells
    Hotaka Kobayashi, Robert H. Singer · 2022 · Nature Communications
32. Predicting the translation efficiency of messenger RNA in mammalian cells
    Zheng, Dinghai, Persyn, Logan, Wang, Jun, Liu, Yue, Ulloa-Montoya, Fernando, Cenik, Can, Agarwal, Vikram · 2026 · Nature Biotechnology
33. High-yield secretory production of stable, active trypsin through engineering of the N-terminal peptide and self-degradation sites in Pichia pastoris
    Yunfeng Zhang, Hao Huang, Xinhui Yao, Guocheng Du, Jian Chen, Zhen Kang · 2017 · Bioresource Technology
34. Decoupling Yeast Cell Division and Stress Defense Implicates mRNA Repression in Translational Reallocation during Stress
    Yi‐Hsuan Ho, Evgenia Shishkova, James Hose, Joshua J. Coon, Audrey P. Gasch · 2018 · Current Biology
35. Toward a Kinetic Understanding of Eukaryotic Translation
    Masaaki Sokabe, Christopher S. Fraser · 2018 · Cold Spring Harbor Perspectives in Biology
36. Kinetic pathway of 40S ribosomal subunit recruitment to hepatitis C virus internal ribosome entry site
    Gabriele Fuchs, Alexey N. Petrov, Caleb D. Marceau, Lauren M. Popov, Jin Chen, Seán E. O’Leary, Richard Wang, Jan E. Carette, Peter Sarnow, Joseph Daniel Puglisi · 2014 · Proceedings of the National Academy of Sciences
37. Codon optimization underpins generalist parasitism in fungi
    Thomas Badet, Rémi Peyraud, Malick Mbengué, Olivier Navaud, Mark C. Derbyshire, Richard Peter Oliver, Adelin Barbacci, Sylvain Raffaele · 2017 · eLife
38. Inverted translational control of eukaryotic gene expression by ribosome collisions
    Heungwon Park, Arvind Rasi Subramaniam · 2019 · PLoS Biology
39. On the Decoupling of Evolutionary Changes in mRNA and Protein Levels
    Daohan Jiang, Alexander L. Cope, Jianzhi Zhang, Matt Pennell · 2023 · Molecular Biology and Evolution
40. Genome-Wide and Experimental Resolution of Relative Translation Elongation Speed at Individual Gene Level in Human Cells
    Xin‐Lei Lian, Jiahui Guo, Wei Gu, Yizhi Cui, Jiayong Zhong, Jingjie Jin, Qing‐Yu He, Tong Wang, Gong Zhang · 2016 · PLoS Genetics
41. LARP4 mRNA codon-tRNA match contributes to LARP4 activity for ribosomal protein mRNA poly(A) tail length protection
    Sandy Mattijssen, Gopalakrishnan Aneeshkumar Arimbasseri, James Iben, Sergei Gaidamakov, Joowon Lee, Markus Hafner, Richard J Maraia · 2017 · eLife
42. Estimating Gene Expression and Codon-Specific Translational Efficiencies, Mutation Biases, and Selection Coefficients from Genomic Data Alone ‡
    Michael A. Gilchrist, Wei-Chen Chen, Premal Shah, Cedric Landerer, Russell Zaretzki · 2015 · Genome Biology and Evolution
43. Translation elongation and mRNA stability are coupled through the ribosomal A-site
    Gavin K. Hanson, Najwa Alhusaini, Nathan J. Morris, Thomas J. Sweet, Jeff Coller · 2018 · RNA
44. The diversity of Shine-Dalgarno sequences sheds light on the evolution of translation initiation
    Jin‐Der Wen, Syue-Ting Antony Kuo, Hsin-Hung David Chou · 2020 · RNA Biology
45. Scikit-ribo Enables Accurate Estimation and Robust Modeling of Translation Dynamics at Codon Resolution
    Han Fang, Yi-Fei Huang, Aditya Radhakrishnan, Adam C. Siepel, Gholson J. Lyon, Michael C. Schatz · 2018 · Cell Systems
46. On the Ribosomal Density that Maximizes Protein Translation Rate
    Yoram Zarai, Michael Margaliot A, Tamir Tuller · 2016 · PLoS ONE
47. Three distinct ribosome assemblies modulated by translation are the building blocks of polysomes
    Gabriella Viero, Lorenzo Lunelli, Andrea Passerini, Paolo Bianchini, Robert J.C. Gilbert, Paola Bernabò, Toma Tebaldi, Alberto Diaspro, Cecilia Pederzolli, Alessandro Quattrone · 2015 · The Journal of Cell Biology
48. Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression
    Enoch Antwi, Jurgen R. Haanstra, Gowthaman Ramasamy, Bryan C. Jensen, Dorothea Droll, Federico Rojas, Igor Minia, Monica Cristina Terrão, Clémentine Mercé, Keith R. Matthews et al. · 2016 · BMC Genomics
49. Computational resources for ribosome profiling: from database to Web server and software
    Hongwei Wang, Yan Wang, Zhi Xie · 2017 · Briefings in Bioinformatics
50. Kinetic modeling predicts a stimulatory role for ribosome collisions at elongation stall sites in bacteria
    Michael A. Ferrin, Arvind Rasi Subramaniam · 2017 · eLife
51. The link between adjacent codon pairs and mRNA stability
    Yuriko Harigaya, Roy Parker · 2017 · BMC Genomics
52. Translation at first sight: the influence of leading codons
    Ilya А. Osterman, Zoe S. Chervontseva, Sergey A Evfratov, Alena V Sorokina, Vladimir A Rodin, Maria P. Rubtsova, Ekaterina S. Komarova, Timofei S. Zatsepin, Marsel Rasimovich Kabilov, Alexey A. Bogdanov et al. · 2020 · Nucleic Acids Research
53. Trans-splicing enhances translational efficiency in C. elegans
    Yufei Yang, Xiaoqing Zhang, Xuehua Ma, Taolan Zhao, Qiushi Sun, Qing Huan, Shaohuan Wu, Zhuo Du, Wenfeng Qian · 2017 · Genome Research
54. Profiling of Small Ribosomal Subunits Reveals Modes and Regulation of Translation Initiation
    Adam P Giess, Yamila N. Torres Cleuren, Håkon Tjeldnes, Maximilian Krause, Teshome Tilahun Bizuayehu, Senna Hiensch, Aniekan M. Okon, Carston R. Wagner, Eivind Valen · 2020 · Cell Reports
55. The Herpes Simplex Virus 1 Virion Host Shutoff Protein Enhances Translation of Viral Late mRNAs by Preventing mRNA Overload
    Bianca Dauber, Holly A. Saffran, James R. Smiley · 2014 · Journal of Virology
56. Homeostasis in the Central Dogma of molecular biology: the importance of mRNA instability
    Pérez-Ortín, José E., Tordera, Vicente, Chávez, Sebastián · 2019 · RNA Biology
57. Mechanisms governing codon usage bias and the implications for protein expression in the chloroplast of Chlamydomonas reinhardtii
    Maxime Fages‐Lartaud, Kristoffer Hundvin, Martin F. Hohmann‐Marriott · 2022 · The Plant Journal
58. Factors That Shape Eukaryotic tRNAomes: Processing, Modification and Anticodon–Codon Use
    Richard J Maraia, Gopalakrishnan Aneeshkumar Arimbasseri · 2017 · Biomolecules
59. Ribosome reinitiation can explain length-dependent translation of messenger RNA
    David W. Rogers, Marvin A. Böttcher, Arne Traulsen, Duncan Greig · 2017 · PLoS Computational Biology
60. Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes
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61. Isoform-level ribosome occupancy estimation guided by transcript abundance with Ribomap
    Hao Wang, C. Joel McManus, Carl Kingsford · 2016 · Bioinformatics
62. mRNA translation and protein synthesis: an analysis of different modelling methodologies and a new PBN based approach
    Yun‐Bo Zhao, J. Krishnan · 2014 · BMC Systems Biology
63. Pateamine A-sensitive ribosome profiling reveals the scope of translation in mouse embryonic stem cells
    Alexandra Popa, Kévin Lebrigand, Pascal Barbry, Rainer Waldmann · 2016 · BMC Genomics
64. Translation Stress Regulates Ribosome Synthesis and Cell Proliferation
    Sivakumar Vadivel Gnanasundram, Robin Fåhræus · 2018 · International Journal of Molecular Sciences
65. Modeling Protein Destiny in Developing Fruit
    Isma Belouah, Christine Nazaret, Pierre Pétriacq, Sylvain Prigent, Camille Bénard, Virginie Mengin, Mélisande Blein‐Nicolas, Alisandra K. Denton, Thierry Balliau, Ségolène Augé et al. · 2019 · PLANT PHYSIOLOGY
66. Novel mRNA-specific effects of ribosome drop-off on translation rate and polysome profile
    Pierre Bonnin, Norbert Kern, Neil T. Young, Ian Stansfield, Maria Carmen Romano · 2017 · PLoS Computational Biology
67. Adaptation of mRNA structure to control protein folding
    Guilhem Faure, Aleksey Y. Ogurtsov, Svetlana A. Shabalina, Eugene V. Koonin · 2017 · RNA Biology
68. Widespread non-modular overlapping codes in the coding regions*
    Shaked Bergman, Tamir Tuller · 2020 · Physical Biology
69. Ribosomal stalk proteins RPLP1 and RPLP2 promote biogenesis of flaviviral and cellular multi-pass transmembrane proteins
    Rafael Kroon Campos, H. R. Sagara Wijeratne, Premal Shah, Mariano A. García-Blanco, Shelton S. Bradrick · 2020 · Nucleic Acids Research
70. Synonymous codons, ribosome speed, and eukaryotic gene expression regulation
    Daniel Tarrant, Tobias von der Haar · 2014 · Cellular and Molecular Life Sciences
71. Optimizing the dynamics of protein expression
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72. riboviz: analysis and visualization of ribosome profiling datasets
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73. Inferring efficiency of translation initiation and elongation from ribosome profiling
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74. Rational Design of the N-Terminal Coding Sequence for Regulating Enzyme Expression in Bacillus subtilis
    Kuidong Xu, Yi Tong, Yi Li, Jin Tao, Jianghua Li, Jingwen Zhou, Song Liu · 2021 · ACS Synthetic Biology
75. Harnessing anti-inflammatory pathways and macrophage nano delivery to treat inflammatory and fibrotic disorders
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76. A System for Gene Expression Noise Control in Yeast
    Max Mundt, Alexander Anders, Séan Murray, Victor Sourjik · 2018 · ACS Synthetic Biology
77. Experimental determination of evolutionary barriers to horizontal gene transfer
    Hande Acar Kirit, Mato Lagator, Jonathan P. Bollback · 2020 · BMC Microbiology
78. Decoding the effects of synonymous variants
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79. Unbiased Quantitative Models of Protein Translation Derived from Ribosome Profiling Data
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80. Extensive allele‐specific translational regulation in hybrid mice
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81. Deciphering mRNA Sequence Determinants of Protein Production Rate
    Juraj Szavits-Nossan, Luca Ciandrini, Maria Carmen Romano · 2018 · Physical Review Letters
82. Co-adaption of tRNA gene copy number and amino acid usage influences translation rates in three life domains
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83. RNA-tethering assay and eIF4G:eIF4A obligate dimer design uncovers multiple eIF4F functional complexes
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84. Accurate Recovery of Ribosome Positions Reveals Slow Translation of Wobble-Pairing Codons in Yeast
    Hao Wang, C. Joel McManus, Carl Kingsford · 2016 · Journal of Computational Biology
85. Calibrated ribosome profiling assesses the dynamics of ribosomal flux on transcripts
    Kotaro Tomuro, Mari Mito, Hirotaka Toh, Naohiro Kawamoto, Takahito Miyake, Siu Yu A. Chow, Masao Doi, Yoshiho Ikeuchi, Yuichi Shichino, Shintaro Iwasaki · 2024 · Nature Communications
86. Translation and Co-translational Membrane Engagement of Plastid-encoded Chlorophyll-binding Proteins Are Not Influenced by Chlorophyll Availability in Maize
    Reimo Zoschke, Prakitchai Chotewutmontri, Alice Barkan · 2017 · Frontiers in Plant Science
87. The Lsm1-7/Pat1 complex binds to stress-activated mRNAs and modulates the response to hyperosmotic shock
    Elena Garré, Vicent Pelechano, Manuel M. Sánchez del Pino, Paula M. Alepuz, Per Sunnerhagen · 2018 · PLoS Genetics
88. Comparative Loss-of-Function Screens Reveal ABCE1 as an Essential Cellular Host Factor for Efficient Translation of Paramyxoviridae and Pneumoviridae
    Danielle E. Anderson, Kristin Pfeffermann, So Young Kim, Bevan Sawatsky, James L. Pearson, Mikhail Kovtun, David L. Corcoran, Yvonne Krebs, Kristmundur Sigmundsson, Sharon F. Jamison et al. · 2019 · mBio
89. So close, no matter how far: multiple paths connecting transcription to mRNA translation in eukaryotes
    Boris Slobodin, Rivka Dikstein · 2020 · EMBO Reports
90. Quantitative studies of mRNA recruitment to the eukaryotic ribosome
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91. In Planta Single-Molecule Pull-Down Reveals Tetrameric Stoichiometry of HD-ZIPIII:LITTLE ZIPPER Complexes
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92. Length-dependent translation initiation benefits the functional proteome of human cells
    Jieming Guo, Xin‐Lei Lian, Jiayong Zhong, Tong Wang, Gong Zhang · 2014 · Molecular BioSystems
93. The landscape of transcriptional and translational changes over 22 years of bacterial adaptation
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94. Positive Charge Loading at Protein Termini Is Due to Membrane Protein Topology, Not a Translational Ramp
    Catherine A. Charneski, Laurence D. Hurst · 2013 · Molecular Biology and Evolution
95. The Impact of Selection at the Amino Acid Level on the Usage of Synonymous Codons
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96. NoRC Recruitment by H2A.X Deposition at rRNA Gene Promoter Limits Embryonic Stem Cell Proliferation
    Boris Eleuteri, Sergi Aranda, Patrik Ernfors · 2018 · Cell Reports
97. Osmotic regulation and tissue localization of the myo‐inositol biosynthesis pathway in tilapia (Oreochromis mossambicus) larvae
    Romina Sacchi, Alison M. Gardell, Nicole Chang, Dietmar Kültz · 2014 · Journal of Experimental Zoology Part A Ecological Genetics and Physiology
98. Genetic profiling of protein burden and nuclear export overload
    Reiko Kintaka, Koji Makanae, Shotaro Namba, Hisaaki Kato, Keiji Kito, Shinsuke Ohnuki, Yoshikazu Ohya, Brenda Andrews, Charles M. Boone, Hisao Moriya · 2020 · eLife
99. Translational buffering by ribosome stalling in upstream open reading frames
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100. Quantifying codon usage in signal peptides: Gene expression and amino acid usage explain apparent selection for inefficient codons
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