1
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McDonnell RT, Elcock AH. AutoRNC: An automated modeling program for building atomic models of ribosome-nascent chain complexes. Structure 2024; 32:621-629.e5. [PMID: 38428431 PMCID: PMC11073581 DOI: 10.1016/j.str.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 11/29/2023] [Accepted: 02/05/2024] [Indexed: 03/03/2024]
Abstract
The interpretation of experimental studies of co-translational protein folding often benefits from the use of computational methods that seek to model or simulate the nascent chain and its interactions with the ribosome. Building realistic 3D models of ribosome-nascent chain (RNC) constructs often requires expert knowledge, so to circumvent this issue, we describe here AutoRNC, an automated modeling program capable of constructing large numbers of plausible atomic models of RNCs within minutes. AutoRNC takes input from the user specifying any regions of the nascent chain that contain secondary or tertiary structure and attempts to build conformations compatible with those specifications-and with the constraints imposed by the ribosome-by sampling and progressively piecing together dipeptide conformations extracted from the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB). Despite using only modest computational resources, we show here that AutoRNC can build plausible conformations for a wide range of RNC constructs for which experimental data have already been reported.
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Affiliation(s)
- Robert T McDonnell
- Department of Biochemistry & Molecular Biology, University of Iowa, Iowa City, IA, USA
| | - Adrian H Elcock
- Department of Biochemistry & Molecular Biology, University of Iowa, Iowa City, IA, USA.
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2
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Zheng Z, Goncearenco A, Berezovsky IN. Back in time to the Gly-rich prototype of the phosphate binding elementary function. Curr Res Struct Biol 2024; 7:100142. [PMID: 38655428 PMCID: PMC11035071 DOI: 10.1016/j.crstbi.2024.100142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 03/31/2024] [Accepted: 04/03/2024] [Indexed: 04/26/2024] Open
Abstract
Binding of nucleotides and their derivatives is one of the most ancient elementary functions dating back to the Origin of Life. We review here the works considering one of the key elements in binding of (di)nucleotide-containing ligands - phosphate binding. We start from a brief discussion of major participants, conditions, and events in prebiotic evolution that resulted in the Origin of Life. Tracing back to the basic functions, including metal and phosphate binding, and, potentially, formation of primitive protein-protein interactions, we focus here on the phosphate binding. Critically assessing works on the structural, functional, and evolutionary aspects of phosphate binding, we perform a simple computational experiment reconstructing its most ancient and generic sequence prototype. The profiles of the phosphate binding signatures have been derived in form of position-specific scoring matrices (PSSMs), their peculiarities depending on the type of the ligands have been analyzed, and evolutionary connections between them have been delineated. Then, the apparent prototype that gave rise to all relevant phosphate-binding signatures had also been reconstructed. We show that two major signatures of the phosphate binding that discriminate between the binding of dinucleotide- and nucleotide-containing ligands are GxGxxG and GxxGxG, respectively. It appears that the signature archetypal for dinucleotide-containing ligands is more generic, and it can frequently bind phosphate groups in nucleotide-containing ligands as well. The reconstructed prototype's key signature GxGGxG underlies the role of glycine residues in providing flexibility and interactions necessary for binding the phosphate groups. The prototype also contains other ancient amino acids, valine, and alanine, showing versatility towards evolutionary design and functional diversification.
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Affiliation(s)
- Zejun Zheng
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, 138671, Singapore
| | | | - Igor N. Berezovsky
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, 138671, Singapore
- Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, 117579, Singapore
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3
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Chen X, Kaiser CM. AP profiling resolves co-translational folding pathway and chaperone interactions in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.01.555749. [PMID: 37693575 PMCID: PMC10491307 DOI: 10.1101/2023.09.01.555749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Natural proteins have evolved to fold robustly along specific pathways. Folding begins during synthesis, guided by interactions of the nascent protein with the ribosome and molecular chaperones. However, the timing and progression of co-translational folding remain largely elusive, in part because the process is difficult to measure in the natural environment of the cytosol. We developed a high-throughput method to quantify co-translational folding in live cells that we term Arrest Peptide profiling (AP profiling). We employed AP profiling to delineate co-translational folding for a set of GTPase domains with very similar structures, defining how topology shapes folding pathways. Genetic ablation of major nascent chain-binding chaperones resulted in localized folding changes that suggest how functional redundancies among chaperones are achieved by distinct interactions with the nascent protein. Collectively, our studies provide a window into cellular folding pathways of complex proteins and pave the way for systematic studies on nascent protein folding at unprecedented resolution and throughput.
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Affiliation(s)
- Xiuqi Chen
- CMDB Graduate Program, Johns Hopkins University, Baltimore, MD, United States
- Department of Biology, Johns Hopkins University, Baltimore, MD, United States
- Present address: Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Christian M. Kaiser
- Department of Biology, Johns Hopkins University, Baltimore, MD, United States
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, United States
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4
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Maheshwari AJ, Calles J, Waterton SK, Endy D. Engineering tRNA abundances for synthetic cellular systems. Nat Commun 2023; 14:4594. [PMID: 37524714 PMCID: PMC10390467 DOI: 10.1038/s41467-023-40199-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 07/13/2023] [Indexed: 08/02/2023] Open
Abstract
Routinizing the engineering of synthetic cells requires specifying beforehand how many of each molecule are needed. Physics-based tools for estimating desired molecular abundances in whole-cell synthetic biology are missing. Here, we use a colloidal dynamics simulator to make predictions for how tRNA abundances impact protein synthesis rates. We use rational design and direct RNA synthesis to make 21 synthetic tRNA surrogates from scratch. We use evolutionary algorithms within a computer aided design framework to engineer translation systems predicted to work faster or slower depending on tRNA abundance differences. We build and test the so-specified synthetic systems and find qualitative agreement between expected and observed systems. First principles modeling combined with bottom-up experiments can help molecular-to-cellular scale synthetic biology realize design-build-work frameworks that transcend tinker-and-test.
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Affiliation(s)
| | - Jonathan Calles
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Sean K Waterton
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Drew Endy
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.
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5
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McDonnell RT, Elcock AH. AutoRNC: an automated modeling program for building atomic models of ribosome-nascent chain complexes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.14.544999. [PMID: 37398297 PMCID: PMC10312685 DOI: 10.1101/2023.06.14.544999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The interpretation of experimental studies of co-translational protein folding often benefits from the use of computational methods that seek to model the nascent chain and its interactions with the ribosome. Ribosome-nascent chain (RNC) constructs studied experimentally can vary significantly in size and the extent to which they contain secondary and tertiary structure, and building realistic 3D models of them therefore often requires expert knowledge. To circumvent this issue, we describe here AutoRNC, an automated modeling program capable of constructing large numbers of plausible atomic models of RNCs within minutes. AutoRNC takes input from the user specifying any regions of the nascent chain that contain secondary or tertiary structure and attempts to build conformations compatible with those specifications - and with the constraints imposed by the ribosome - by sampling and progressively piecing together dipeptide conformations extracted from the RCSB. We first show that conformations of completely unfolded proteins built by AutoRNC in the absence of the ribosome have radii of gyration that match well with the corresponding experimental data. We then show that AutoRNC can build plausible conformations for a wide range of RNC constructs for which experimental data have already been reported. Since AutoRNC requires only modest computational resources, we anticipate that it will prove to be a useful hypothesis generator for experimental studies, for example, in providing indications of whether designed constructs are likely to be capable of folding, as well as providing useful starting points for downstream atomic or coarse-grained simulations of the conformational dynamics of RNCs.
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6
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Lauzon D, Vallée-Bélisle A. Functional advantages of building nanosystems using multiple molecular components. Nat Chem 2023; 15:458-467. [PMID: 36759713 DOI: 10.1038/s41557-022-01127-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 12/15/2022] [Indexed: 02/11/2023]
Abstract
Over half of all the natural nanomachines in living organisms are multimeric and likely exploit the self-assembly of their components to provide functional benefits. However, the advantages and disadvantages of building nanosystems using multiple molecular components remain relatively unexplored at the thermodynamic, kinetic and functional levels. In this study we used theory and a simple DNA-based model that forms the same nanostructures with different numbers of components to advance our knowledge in this area. Despite its lower assembly rate, we found that a system built with three components may undergo a more cooperative assembly transition from less preorganized components, which facilitates the emergence of functionalities. Using simple variations of its components, we also found that trimeric nanosystems display a much higher level of programmability than their dimeric counterparts because they can assemble with various levels of cooperativity, self-inhibition and time-dependent properties. We show here how two simple strategies (for example, cutting and adding components) can be employed to efficiently programme the regulatory function of a more complex, artificially selected, RNA-cleaving catalytic nanosystem.
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Affiliation(s)
- D Lauzon
- Laboratoire de Biosenseurs & Nanomachines, Département de Chimie, Université de Montréal, Montréal, Québec, Canada
| | - A Vallée-Bélisle
- Laboratoire de Biosenseurs & Nanomachines, Département de Chimie, Université de Montréal, Montréal, Québec, Canada.
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7
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Jaciuk M, Scherf D, Kaszuba K, Gaik M, Rau A, Kościelniak A, Krutyhołowa R, Rawski M, Indyka P, Graziadei A, Chramiec-Głąbik A, Biela A, Dobosz D, Lin TY, Abbassi NEH, Hammermeister A, Rappsilber J, Kosinski J, Schaffrath R, Glatt S. Cryo-EM structure of the fully assembled Elongator complex. Nucleic Acids Res 2023; 51:2011-2032. [PMID: 36617428 PMCID: PMC10018365 DOI: 10.1093/nar/gkac1232] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/22/2022] [Accepted: 12/09/2022] [Indexed: 01/10/2023] Open
Abstract
Transfer RNA (tRNA) molecules are essential to decode messenger RNA codons during protein synthesis. All known tRNAs are heavily modified at multiple positions through post-transcriptional addition of chemical groups. Modifications in the tRNA anticodons are directly influencing ribosome decoding and dynamics during translation elongation and are crucial for maintaining proteome integrity. In eukaryotes, wobble uridines are modified by Elongator, a large and highly conserved macromolecular complex. Elongator consists of two subcomplexes, namely Elp123 containing the enzymatically active Elp3 subunit and the associated Elp456 hetero-hexamer. The structure of the fully assembled complex and the function of the Elp456 subcomplex have remained elusive. Here, we show the cryo-electron microscopy structure of yeast Elongator at an overall resolution of 4.3 Å. We validate the obtained structure by complementary mutational analyses in vitro and in vivo. In addition, we determined various structures of the murine Elongator complex, including the fully assembled mouse Elongator complex at 5.9 Å resolution. Our results confirm the structural conservation of Elongator and its intermediates among eukaryotes. Furthermore, we complement our analyses with the biochemical characterization of the assembled human Elongator. Our results provide the molecular basis for the assembly of Elongator and its tRNA modification activity in eukaryotes.
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Affiliation(s)
- Marcin Jaciuk
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - David Scherf
- Institute for Biology, Department for Microbiology, University of Kassel, Kassel 34132, Germany
| | - Karol Kaszuba
- European Molecular Biology Laboratory Hamburg, Hamburg 22607, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg 22607, Germany
| | - Monika Gaik
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - Alexander Rau
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin 13355, Germany
| | - Anna Kościelniak
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - Rościsław Krutyhołowa
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - Michał Rawski
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
- National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, Krakow 30-387, Poland
| | - Paulina Indyka
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
- National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, Krakow 30-387, Poland
| | - Andrea Graziadei
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin 13355, Germany
| | | | - Anna Biela
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - Dominika Dobosz
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - Ting-Yu Lin
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - Nour-el-Hana Abbassi
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw 02-091, Poland
| | - Alexander Hammermeister
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
- Institute for Biology, Department for Microbiology, University of Kassel, Kassel 34132, Germany
| | - Juri Rappsilber
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin 13355, Germany
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Jan Kosinski
- European Molecular Biology Laboratory Hamburg, Hamburg 22607, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg 22607, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Raffael Schaffrath
- Institute for Biology, Department for Microbiology, University of Kassel, Kassel 34132, Germany
| | - Sebastian Glatt
- To whom correspondence should be addressed. Tel: +48 12 664 6321; Fax: +48 12 664 6902;
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8
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Moreira-Ramos S, Arias L, Flores R, Katz A, Levicán G, Orellana O. Synonymous mutations in the phosphoglycerate kinase 1 gene induce an altered response to protein misfolding in Schizosaccharomyces pombe. Front Microbiol 2023; 13:1074741. [PMID: 36713198 PMCID: PMC9875302 DOI: 10.3389/fmicb.2022.1074741] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 12/20/2022] [Indexed: 01/13/2023] Open
Abstract
Background Proteostasis refers to the processes that regulate the biogenesis, folding, trafficking, and degradation of proteins. Any alteration in these processes can lead to cell malfunction. Protein synthesis, a key proteostatic process, is highly-regulated at multiple levels to ensure adequate adaptation to environmental and physiological challenges such as different stressors, proteotoxic conditions and aging, among other factors. Because alterations in protein translation can lead to protein misfolding, examining how protein translation is regulated may also help to elucidate in part how proteostasis is controlled. Codon usage bias has been implicated in the fine-tuning of translation rate, as more-frequent codons might be read faster than their less-frequent counterparts. Thus, alterations in codon usage due to synonymous mutations may alter translation kinetics and thereby affect the folding of the nascent polypeptide, without altering its primary structure. To date, it has been difficult to predict the effect of synonymous mutations on protein folding and cellular fitness due to a scarcity of relevant data. Thus, the purpose of this work was to assess the effect of synonymous mutations in discrete regions of the gene that encodes the highly-expressed enzyme 3-phosphoglycerate kinase 1 (pgk1) in the fission yeast Schizosaccharomyces pombe. Results By means of systematic replacement of synonymous codons along pgk1, we found slightly-altered protein folding and activity in a region-specific manner. However, alterations in protein aggregation, heat stress as well as changes in proteasome activity occurred independently of the mutated region. Concomitantly, reduced mRNA levels of the chaperones Hsp9 and Hsp16 were observed. Conclusion Taken together, these data suggest that codon usage bias of the gene encoding this highly-expressed protein is an important regulator of protein function and proteostasis.
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Affiliation(s)
- Sandra Moreira-Ramos
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Loreto Arias
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Rodrigo Flores
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Assaf Katz
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Gloria Levicán
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Omar Orellana
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile,*Correspondence: Omar Orellana,
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9
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Bui PT, Hoang TX. The protein escape process at the ribosomal exit tunnel has conserved mechanisms across the domains of life. J Chem Phys 2023; 158:015102. [PMID: 36610950 DOI: 10.1063/5.0129532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The ribosomal exit tunnel is the primary structure affecting the release of nascent proteins at the ribosome. The ribosomal exit tunnels from different species have elements of conservation and differentiation in structural and physico-chemical properties. In this study, by simulating the elongation and escape processes of nascent proteins at the ribosomal exit tunnels of four different organisms, we show that the escape process has conserved mechanisms across the domains of life. Specifically, it is found that the escape process of proteins follows the diffusion mechanism given by a simple diffusion model, and the median escape time positively correlates with the number of hydrophobic residues and the net charge of a protein for all the exit tunnels considered. These properties hold for 12 distinct proteins considered in two slightly different and improved Gō-like models. It is also found that the differences in physico-chemical properties of the tunnels lead to quantitative differences in the protein escape times. In particular, the relatively strong hydrophobicity of E. coli's tunnel and the unusually high number of negatively charged amino acids on the tunnel's surface of H. marismortui lead to substantially slower escapes of proteins at these tunnels than at those of S. cerevisiae and H. sapiens.
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Affiliation(s)
- Phuong Thuy Bui
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 11307, Vietnam
| | - Trinh Xuan Hoang
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 11307, Vietnam
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10
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Yu S, Srebnik S, Dao Duc K. Geometric differences in the ribosome exit tunnel impact the escape of small nascent proteins. Biophys J 2023; 122:20-29. [PMID: 36463403 PMCID: PMC9822834 DOI: 10.1016/j.bpj.2022.11.2945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 11/14/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
The exit tunnel is the subcompartment of the ribosome that contains the nascent polypeptide chain and, as such, is involved in various vital functions, including regulation of translation and protein folding. As the geometry of the tunnel shows important differences across species, we focus on key geometrical features of eukaryote and prokaryote tunnels. We used a simple coarse-grained molecular dynamics model to study the role of the tunnel geometry in the post-translational escape of short proteins (short open reading frames [sORFs]) with lengths ranging from 6 to 56 amino acids. We found that the probability of escape for prokaryotes is one for all but the 12-mer chains. Moreover, proteins of this length have an extremely low escape probability in eukaryotes. A detailed examination of the associated single trajectories and energy profiles showed that these variations can be explained by the interplay between the protein configurational space and the confinement effects introduced by the constriction sites of the ribosome exit tunnel. For certain lengths, either one or both of the constriction sites can lead to the trapping of the protein in the "pocket" regions preceding these sites. As the distribution of existing sORFs indicates some bias in length that is consistent with our findings, we finally suggest that the constraints imposed by the tunnel geometry have impacted the evolution of sORFs.
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Affiliation(s)
- Shiqi Yu
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Simcha Srebnik
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Khanh Dao Duc
- Department of Mathematics, University of British Columbia, Vancouver, British Columbia, Canada.
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11
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Yang CI, Kim J, Shan SO. Ribosome-nascent chain interaction regulates N-terminal protein modification. J Mol Biol 2022; 434:167535. [PMID: 35278477 PMCID: PMC9126151 DOI: 10.1016/j.jmb.2022.167535] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 03/01/2022] [Accepted: 03/04/2022] [Indexed: 01/02/2023]
Abstract
Numerous proteins initiate their folding, localization, and modifications early during translation, and emerging data show that the ribosome actively participates in diverse protein biogenesis pathways. Here we show that the ribosome imposes an additional layer of substrate selection during N-terminal methionine excision (NME), an essential protein modification in bacteria. Biochemical analyses show that cotranslational NME is exquisitely sensitive to a hydrophobic signal sequence or transmembrane domain near the N terminus of the nascent polypeptide. The ability of the nascent chain to access the active site of NME enzymes dictates NME efficiency, which is inhibited by confinement of the nascent chain on the ribosome surface and exacerbated by signal recognition particle. In vivo measurements corroborate the inhibition of NME by an N-terminal hydrophobic sequence, suggesting the retention of formylmethionine on a substantial fraction of the secretory and membrane proteome. Our work demonstrates how molecular features of a protein regulate its cotranslational modification and highlights the active participation of the ribosome in protein biogenesis pathways via interactions of the ribosome surface with the nascent protein.
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12
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The folding and misfolding mechanisms of multidomain proteins. MEDICINE IN DRUG DISCOVERY 2022. [DOI: 10.1016/j.medidd.2022.100126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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13
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Tao P, Xiao Y. Role of cotranslational folding for β-sheet-enriched proteins: A perspective from molecular dynamics simulations. Phys Rev E 2022; 105:024402. [PMID: 35291071 DOI: 10.1103/physreve.105.024402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 01/14/2022] [Indexed: 06/14/2023]
Abstract
The formations of correct three-dimensional structures of proteins are essential to their functions. Cotranslational folding is vital for proteins to form correct structures in vivo. Although some experiments have shown that cotranslational folding can improve the efficiency of folding, its microscopic mechanism is not yet clear. Previously, we built a model of the ribosomal exit tunnel and investigated the cotranslational folding of a three-helix protein by using all-atom molecular dynamics simulations. Here we study the cotranslational folding of three β-sheet-enriched proteins using the same method. The results show that cotranslational folding can enhance the helical population in most cases and reduce non-native long-range contacts before emerging from the ribosomal exit tunnel. After exiting the tunnel, all proteins fall into local minimal states and the structural ensembles of cotranslational folding show more helical conformations than those of free folding. In particular, for one of the three proteins, the GTT WW domain, we find that one local minimum state of the cotranslational folding is the known folding intermediate, which is not found in free folding. This result suggests that the cotranslational folding may increase the folding efficiency by accelerating the sampling more than by avoiding the misfolded state, which is presently a mainstream viewpoint.
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Affiliation(s)
- Peng Tao
- School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Yi Xiao
- School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
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14
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Sorokina I, Mushegian AR, Koonin EV. Is Protein Folding a Thermodynamically Unfavorable, Active, Energy-Dependent Process? Int J Mol Sci 2022; 23:521. [PMID: 35008947 PMCID: PMC8745595 DOI: 10.3390/ijms23010521] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/30/2021] [Accepted: 12/31/2021] [Indexed: 02/04/2023] Open
Abstract
The prevailing current view of protein folding is the thermodynamic hypothesis, under which the native folded conformation of a protein corresponds to the global minimum of Gibbs free energy G. We question this concept and show that the empirical evidence behind the thermodynamic hypothesis of folding is far from strong. Furthermore, physical theory-based approaches to the prediction of protein folds and their folding pathways so far have invariably failed except for some very small proteins, despite decades of intensive theory development and the enormous increase of computer power. The recent spectacular successes in protein structure prediction owe to evolutionary modeling of amino acid sequence substitutions enhanced by deep learning methods, but even these breakthroughs provide no information on the protein folding mechanisms and pathways. We discuss an alternative view of protein folding, under which the native state of most proteins does not occupy the global free energy minimum, but rather, a local minimum on a fluctuating free energy landscape. We further argue that ΔG of folding is likely to be positive for the majority of proteins, which therefore fold into their native conformations only through interactions with the energy-dependent molecular machinery of living cells, in particular, the translation system and chaperones. Accordingly, protein folding should be modeled as it occurs in vivo, that is, as a non-equilibrium, active, energy-dependent process.
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Affiliation(s)
| | - Arcady R. Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, Alexandria, VA 22314, USA;
- Clare Hall College, University of Cambridge, Cambridge CB3 9AL, UK
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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15
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Joiret M, Kerff F, Rapino F, Close P, Geris L. Ribosome exit tunnel electrostatics. Phys Rev E 2022; 105:014409. [PMID: 35193250 DOI: 10.1103/physreve.105.014409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
The impact of ribosome exit tunnel electrostatics on the protein elongation rate or on forces acting upon the nascent polypeptide chain are currently not fully elucidated. In the past, researchers have measured the electrostatic potential inside the ribosome polypeptide exit tunnel at a limited number of spatial points, at least in rabbit reticulocytes. Here we present a basic electrostatic model of the exit tunnel of the ribosome, providing a quantitative physical description of the tunnel interaction with the nascent proteins at all centro-axial points inside the tunnel. We show that a strong electrostatic screening is due to water molecules (not mobile ions) attracted to the ribosomal nucleic acid phosphate moieties buried in the immediate vicinity of the tunnel wall. We also show how the tunnel wall components and local ribosomal protein protrusions impact on the electrostatic potential profile and impede charged amino acid residues from progressing through the tunnel, affecting the elongation rate in a range of -40% to +85% when compared to the average elongation rate. The time spent by the ribosome to decode the genetic encrypted message is constrained accordingly. We quantitatively derive, at single-residue resolution, the axial forces acting on the nascent peptide from its particular sequence embedded in the tunnel. The model sheds light on how the experimental data point measurements of the potential are linked to the local structural chemistry of the inner wall, shape, and size of the tunnel. The model consistently connects experimental observations coming from different fields in molecular biology, x-ray crystallography, physical chemistry, biomechanics, and synthetic and multiomics biology. Our model should be a valuable tool to gain insight into protein synthesis dynamics, translational control, and the role of the ribosome's mechanochemistry in the cotranslational protein folding.
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Affiliation(s)
- Marc Joiret
- Biomechanics Research Unit, GIGA In Silico Medicine, Liège University, CHU-B34(+5) 1 Avenue de l'Hôpital, 4000 Liège, Belgium
| | - Frederic Kerff
- UR InBios, Centre d'Ingénierie des Protéines, Bât B6a, Allée du 6 Août, 19, B-4000 Liège, Belgium
| | - Francesca Rapino
- Cancer Signaling, GIGA Stem Cells, CHU-B34(+2) 1 Avenue de l'Hôpital, B-4000 Liège, Belgium
| | - Pierre Close
- Cancer Signaling, GIGA Stem Cells, CHU-B34(+2) 1 Avenue de l'Hôpital, B-4000 Liège, Belgium
| | - Liesbet Geris
- Biomechanics Research Unit, GIGA In Silico Medicine, Liège University, CHU-B34(+5) 1 Avenue de l'Hôpital, 4000 Liège, Belgium
- Skeletal Biology & Engineering Research Center, KU Leuven, ON I Herestraat 49 - box 813, 3000 Leuven, Belgium
- Biomechanics Section, KU Leuven, Celestijnenlaan 300C box 2419, B-3001 Heverlee, Belgium
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16
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Tirumalai MR, Anane-Bediakoh D, Rajesh S, Fox GE. Net Charges of the Ribosomal Proteins of the S10 and spc Clusters of Halophiles Are Inversely Related to the Degree of Halotolerance. Microbiol Spectr 2021; 9:e0178221. [PMID: 34908470 PMCID: PMC8672879 DOI: 10.1128/spectrum.01782-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/24/2021] [Indexed: 11/20/2022] Open
Abstract
Net positive charge(s) on ribosomal proteins (r-proteins) have been reported to influence the assembly and folding of ribosomes. A high percentage of r-proteins from extremely halophilic archaea are known to be acidic or even negatively charged. Those proteins that remain positively charged are typically far less positively charged. Here, the analysis is extended to non-archaeal halophilic bacteria, eukaryotes, and halotolerant archaea. The net charges (pH 7.4) of the r-proteins that comprise the S10-spc operon/cluster from individual microbial and eukaryotic genomes were estimated and intercompared. It was observed that, as a general rule, the net charges of individual proteins remained mostly basic as the salt tolerance of the bacterial strains increased from 5 to 15%. The most striking exceptions were the extremely halophilic bacterial strains, Salinibacter ruber SD01, Acetohalobium arabaticum DSM 5501 and Selenihalanaerobacter shriftii ATCC BAA-73, which are reported to require a minimum of 18% to 21% salt for their growth. All three strains have higher numbers of acidic S10-spc cluster r-proteins than what is seen in the moderate halophiles or the halotolerant strains. Of the individual proteins, only uL2 never became acidic. uS14 and uL16 also seldom became acidic. The net negative charges on several of the S10-spc cluster r-proteins are a feature generally shared by all extremely halophilic archaea and bacteria. The S10-spc cluster r-proteins of halophilic fungi and algae (eukaryotes) were exceptions: these were positively charged despite the halophilicity of the organisms. IMPORTANCE The net charges (at pH 7.4) of the ribosomal proteins (r-proteins) that comprise the S10-spc cluster show an inverse relationship with the halophilicity/halotolerance levels in both bacteria and archaea. In non-halophilic bacteria, the S10-spc cluster r-proteins are generally basic (positively charged), while the rest of the proteomes in these strains are generally acidic. On the other hand, the whole proteomes of the extremely halophilic strains are overall negatively charged, including the S10-spc cluster r-proteins. Given that the distribution of charged residues in the ribosome exit tunnel influences cotranslational folding, the contrasting charges observed in the S10-spc cluster r-proteins have potential implications for the rate of passage of these proteins through the ribosomal exit tunnel. Furthermore, the universal protein uL2, which lies in the oldest part of the ribosome, is always positively charged irrespective of the strain/organism it belongs to. This has implications for its role in the prebiotic context.
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Affiliation(s)
- Madhan R. Tirumalai
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | | | - Sidharth Rajesh
- Clements High School (Class of 2023), Fort Bend Independent School District, Sugar Land, Texas, USA
| | - George E. Fox
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
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17
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Perach M, Zafrir Z, Tuller T, Lewinson O. Identification of conserved slow codons that are important for protein expression and function. RNA Biol 2021; 18:2296-2307. [PMID: 33691590 PMCID: PMC8632084 DOI: 10.1080/15476286.2021.1901185] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 02/28/2021] [Accepted: 03/06/2021] [Indexed: 10/21/2022] Open
Abstract
ABSTRASTDue to the redundancy of the genetic code most amino acids are encoded by several 'synonymous' codons. These codons are used unevenly, and each organism demonstrates its own unique codon usage bias, where the 'preferred' codons are associated with tRNAs that are found in high concentrations. Therefore, for decades, the prevailing view had been that preferred and non-preferred codons are linked to high or slow translation rates, respectively.However, this simplified view is contrasted by the frequent failures of codon-optimization efforts and by evidence of non-preferred (i.e. 'slow') codons having specific roles important for efficient production of functional proteins. One such specific role of slower codons is the regulation of co-translational protein folding, a complex biophysical process that is very challenging to model or to measure.Here, we combined a genome-wide approach with experiments to investigate the role of slow codons in protein production and co-translational folding. We analysed homologous gene groups from divergent bacteria and identified positions of inter-species conservation of bias towards slow codons. We then generated mutants where the conserved slow codons are substituted with 'fast' ones, and experimentally studied the effects of these codon substitutions. Using cellular and biochemical approaches we find that at certain locations, slow-to-fast codon substitutions reduce protein expression, increase protein aggregation, and impair protein function.This report provides an approach for identifying functionally relevant regions with slower codons and demonstrates that such codons are important for protein expression and function.
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Affiliation(s)
- Michal Perach
- Department of Molecular Microbiology, the Bruce and Ruth Rappaport Faculty of Medicine, The Technion-Israel Institute of Technology, Haifa, Israel
| | - Zohar Zafrir
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Oded Lewinson
- Department of Molecular Microbiology, the Bruce and Ruth Rappaport Faculty of Medicine, The Technion-Israel Institute of Technology, Haifa, Israel
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18
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Bui PT, Hoang TX. Hydrophobic and electrostatic interactions modulate protein escape at the ribosomal exit tunnel. Biophys J 2021; 120:4798-4808. [PMID: 34555360 DOI: 10.1016/j.bpj.2021.09.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 08/04/2021] [Accepted: 09/15/2021] [Indexed: 11/17/2022] Open
Abstract
After translation, nascent proteins must escape the ribosomal exit tunnel to attain complete folding to their native states. This escape process also frees up the ribosome tunnel for a new translation job. In this study, we investigate the impacts of energetic interactions between the ribosomal exit tunnel and nascent proteins on the protein escape process by molecular dynamics simulations using partially coarse-grained models that incorporate hydrophobic and electrostatic interactions of the ribosome tunnel of Haloarcula marismortui with nascent proteins. We find that, in general, attractive interactions slow down the protein escape process, whereas repulsive interactions speed it up. For the small globular proteins considered, the median escape time correlates with both the number of hydrophobic residues, Nh, and the net charge, Q, of a nascent protein. A correlation coefficient exceeding 0.96 is found for the relation between the median escape time and a combined quantity of Nh + 5.9Q, suggesting that it is ∼6 times more efficient to modulate the escape time by changing the total charge than the number of hydrophobic residues. The estimated median escape times are found in the submillisecond-to-millisecond range, indicating that the escape does not delay the ribosome recycling. For various types of the tunnel model, with and without hydrophobic and electrostatic interactions, the escape time distribution always follows a simple diffusion model that describes the escape process as a downhill drift of a Brownian particle, suggesting that nascent proteins escape along barrier-less pathways at the ribosome tunnel.
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Affiliation(s)
- Phuong Thuy Bui
- Institute of Theoretical and Applied Research, Duy Tan University, Hanoi, Vietnam; Faculty of Pharmacy, Duy Tan University, Da Nang, Vietnam
| | - Trinh Xuan Hoang
- Institute of Physics, Vietnam Academy of Science and Technology, Ba Dinh, Hanoi, Vietnam; Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Cau Giay, Hanoi, Vietnam.
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19
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Komar AA. A Code Within a Code: How Codons Fine-Tune Protein Folding in the Cell. BIOCHEMISTRY (MOSCOW) 2021; 86:976-991. [PMID: 34488574 DOI: 10.1134/s0006297921080083] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The genetic code sets the correspondence between the sequence of a given nucleotide triplet in an mRNA molecule, called a codon, and the amino acid that is added to the growing polypeptide chain during protein synthesis. With four bases (A, G, U, and C), there are 64 possible triplet codons: 61 sense codons (encoding amino acids) and 3 nonsense codons (so-called, stop codons that define termination of translation). In most organisms, there are 20 common/standard amino acids used in protein synthesis; thus, the genetic code is redundant with most amino acids (with the exception of Met and Trp) are being encoded by more than one (synonymous) codon. Synonymous codons were initially presumed to have entirely equivalent functions, however, the finding that synonymous codons are not present at equal frequencies in mRNA suggested that the specific codon choice might have functional implications beyond coding for amino acid. Observation of nonequivalent use of codons in mRNAs implied a possibility of the existence of auxiliary information in the genetic code. Indeed, it has been found that genetic code contains several layers of such additional information and that synonymous codons are strategically placed within mRNAs to ensure a particular translation kinetics facilitating and fine-tuning co-translational protein folding in the cell via step-wise/sequential structuring of distinct regions of the polypeptide chain emerging from the ribosome at different points in time. This review summarizes key findings in the field that have identified the role of synonymous codons and their usage in protein folding in the cell.
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Affiliation(s)
- Anton A Komar
- Center for Gene Regulation in Health and Disease and Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH 44115, USA. .,Department of Biochemistry and Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH 44106, USA.,Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.,DAPCEL, Inc., Cleveland, OH 44106, USA
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20
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Fernández A. Artificial Intelligence Deconstructs Drug Targeting In Vivo by Leveraging a Transformer Platform. ACS Med Chem Lett 2021; 12:1052-1055. [PMID: 34267868 DOI: 10.1021/acsmedchemlett.1c00237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Lead optimization in structure-based drug design ultimately requires that the therapeutic agent be evaluated in the cellular context. However, the in vivo control of the target structure remains unyielding to computational modeling. This situation may change as transformer technologies enable a deconstruction of in vivo cooperativity steering drug-induced protein folding.
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Affiliation(s)
- Ariel Fernández
- Daruma Institute for AI in Pharmaceutical Research, AF Innovation Pharma Consultancy, GmbH, 4000 Pemberton Court, Winston-Salem, North Carolina 27106, United States
- CONICET/INQUISUR, National Research Council for Science and Technology, Buenos Aires 1033, Argentina
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21
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Tian G, Hu C, Yun Y, Yang W, Dubiel W, Cheng Y, Wolf DA. Dual roles of HSP70 chaperone HSPA1 in quality control of nascent and newly synthesized proteins. EMBO J 2021; 40:e106183. [PMID: 34010456 PMCID: PMC8246255 DOI: 10.15252/embj.2020106183] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 04/06/2021] [Accepted: 04/15/2021] [Indexed: 12/22/2022] Open
Abstract
Exposure to heat stress triggers a well‐defined acute response marked by HSF1‐dependent transcriptional upregulation of heat shock proteins. Cells allowed to recover acquire thermotolerance, but this adaptation is poorly understood. By quantitative proteomics, we discovered selective upregulation of HSP70‐family chaperone HSPA1 and its co‐factors, HSPH1 and DNAJB1, in MCF7 breast cancer cells acquiring thermotolerance. HSPA1 was found to have dual function during heat stress response: (i) During acute stress, it promotes the recruitment of the 26S proteasome to translating ribosomes, thus poising cells for rapid protein degradation and resumption of protein synthesis upon recovery; (ii) during thermotolerance, HSPA1 together with HSPH1 maintains ubiquitylated nascent/newly synthesized proteins in a soluble state required for their efficient proteasomal clearance. Consistently, deletion of HSPH1 impedes thermotolerance and esophageal tumor growth in mice, thus providing a potential explanation for the poor prognosis of digestive tract cancers with high HSPH1 and nominating HSPH1 as a cancer drug target. We propose dual roles of HSPA1 either alone or in complex with HSPH1 and DNAJB1 in promoting quality control of nascent/newly synthesized proteins and cellular thermotolerance.
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Affiliation(s)
- Guiyou Tian
- School of Pharmaceutical Sciences, State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen, China
| | - Cheng Hu
- School of Pharmaceutical Sciences, State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen, China
| | - Yun Yun
- School of Pharmaceutical Sciences, State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen, China
| | - Wensheng Yang
- Department of Pathology, Chenggong Hospital of Xiamen University, Xiamen, China
| | - Wolfgang Dubiel
- School of Pharmaceutical Sciences, State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen, China.,Institute of Experimental Internal Medicine, Medical Faculty, Otto von Guericke University, Magdeburg, Germany
| | - Yabin Cheng
- School of Pharmaceutical Sciences, State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen, China
| | - Dieter A Wolf
- School of Pharmaceutical Sciences, State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen, China
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22
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Maciuba K, Rajasekaran N, Chen X, Kaiser CM. Co-translational folding of nascent polypeptides: Multi-layered mechanisms for the efficient biogenesis of functional proteins. Bioessays 2021; 43:e2100042. [PMID: 33987870 PMCID: PMC8262109 DOI: 10.1002/bies.202100042] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/02/2021] [Accepted: 04/07/2021] [Indexed: 11/09/2022]
Abstract
The coupling of protein synthesis and folding is a crucial yet poorly understood aspect of cellular protein folding. Over the past few years, it has become possible to experimentally follow and define protein folding on the ribosome, revealing principles that shape co-translational folding and distinguish it from refolding in solution. Here, we highlight some of these recent findings from biochemical and biophysical studies and their potential significance for cellular protein biogenesis. In particular, we focus on nascent chain interactions with the ribosome, interactions within the nascent protein, modulation of translation elongation rates, and the role of mechanical force that accompanies nascent protein folding. The ability to obtain mechanistic insight in molecular detail has set the stage for exploring the intricate process of nascent protein folding. We believe that the aspects discussed here will be generally important for understanding how protein synthesis and folding are coupled and regulated.
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Affiliation(s)
- Kevin Maciuba
- CMDB Graduate Program, Johns Hopkins University, Baltimore, Maryland, USA
| | | | - Xiuqi Chen
- CMDB Graduate Program, Johns Hopkins University, Baltimore, Maryland, USA
| | - Christian M Kaiser
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA.,Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
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23
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Tao P, Wang E, Xiao Y. Pathway regulation mechanism revealed by cotranslational folding of villin headpiece subdomain HP35. Phys Rev E 2021; 101:052403. [PMID: 32575289 DOI: 10.1103/physreve.101.052403] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 04/13/2020] [Indexed: 01/07/2023]
Abstract
Cotranslational folding is one of the most important features of protein folding in vivo. Although many studies have shown that the folding pathways of cotranslational folding are different from free folding in vitro, the detailed mechanism of folding dynamics is lacking. Here we combine all-atom molecular simulations with an ideal ribosome tunnel model to investigate the cotranslational folding of villin headpiece subdomain HP35. By comparing the folding dynamics between cotranslational folding and free folding, we found that cotranslational folding tends to fold along the pathway that is easier to fold into native state in the latter. In addition, the roles of the ribosome tunnel and sequential folding are analyzed separately. Our results show that the ribosome can prevent the untimely folding of the C segment of HP35 to reduce the non-native interactions, while the translation speed can regulate the amounts of native and non-native interactions and the balance between them. Overall, these results give insights into the general mechanisms of cotranslational protein folding.
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Affiliation(s)
- Peng Tao
- School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Ercheng Wang
- School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China.,College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Yi Xiao
- School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
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24
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Fernández A. Artificial Intelligence Set to Reverse Engineer Drug Targeting in the Cell. ACS Pharmacol Transl Sci 2021; 4:1256-1259. [PMID: 34151218 DOI: 10.1021/acsptsci.1c00107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Indexed: 11/28/2022]
Abstract
Therapeutic drugs are required to target proteins in the cell, not in vitro. Yet, drug-induced protein folding in vivo is off limits to computational modeling efforts. This situation may change as artificial intelligence empowers molecular dynamics and enables the deconstruction of in vivo cooperativity for structural adaptation.
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Affiliation(s)
- Ariel Fernández
- Daruma Institute for AI in Pharmaceutical Research, AF Innovation Pharma Consultancy, GmbH, 4000 Pemberton Court, Winston-Salem, North Carolina 27106, United States.,CONICET, Argentine National Research Council, Buenos Aires 1033, Argentina
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25
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Terrey M, Adamson SI, Chuang JH, Ackerman SL. Defects in translation-dependent quality control pathways lead to convergent molecular and neurodevelopmental pathology. eLife 2021; 10:e66904. [PMID: 33899734 PMCID: PMC8075583 DOI: 10.7554/elife.66904] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/05/2021] [Indexed: 12/27/2022] Open
Abstract
Translation-dependent quality control pathways such as no-go decay (NGD), non-stop decay (NSD), and nonsense-mediated decay (NMD) govern protein synthesis and proteostasis by resolving non-translating ribosomes and preventing the production of potentially toxic peptides derived from faulty and aberrant mRNAs. However, how translation is altered and the in vivo defects that arise in the absence of these pathways are poorly understood. Here, we show that the NGD/NSD factors Pelo and Hbs1l are critical in mice for cerebellar neurogenesis but expendable for survival of these neurons after development. Analysis of mutant mouse embryonic fibroblasts revealed translational pauses, alteration of signaling pathways, and translational reprogramming. Similar effects on signaling pathways, including mTOR activation, the translatome and mouse cerebellar development were observed upon deletion of the NMD factor Upf2. Our data reveal that these quality control pathways that function to mitigate errors at distinct steps in translation can evoke similar cellular responses.
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Affiliation(s)
- Markus Terrey
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, Division of Biological Sciences, University of California San DiegoLa JollaUnited States
- Graduate School of Biomedical Sciences and Engineering, University of MaineOronoUnited States
| | - Scott I Adamson
- The Jackson Laboratory for Genomic MedicineFarmingtonUnited States
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn HealthFarmingtonUnited States
| | - Jeffrey H Chuang
- The Jackson Laboratory for Genomic MedicineFarmingtonUnited States
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn HealthFarmingtonUnited States
| | - Susan L Ackerman
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, Division of Biological Sciences, University of California San DiegoLa JollaUnited States
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26
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Rapino F, Zhou Z, Roncero Sanchez AM, Joiret M, Seca C, El Hachem N, Valenti G, Latini S, Shostak K, Geris L, Li P, Huang G, Mazzucchelli G, Baiwir D, Desmet CJ, Chariot A, Georges M, Close P. Wobble tRNA modification and hydrophilic amino acid patterns dictate protein fate. Nat Commun 2021; 12:2170. [PMID: 33859181 PMCID: PMC8050329 DOI: 10.1038/s41467-021-22254-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 03/05/2021] [Indexed: 02/07/2023] Open
Abstract
Regulation of mRNA translation elongation impacts nascent protein synthesis and integrity and plays a critical role in disease establishment. Here, we investigate features linking regulation of codon-dependent translation elongation to protein expression and homeostasis. Using knockdown models of enzymes that catalyze the mcm5s2 wobble uridine tRNA modification (U34-enzymes), we show that gene codon content is necessary but not sufficient to predict protein fate. While translation defects upon perturbation of U34-enzymes are strictly dependent on codon content, the consequences on protein output are determined by other features. Specific hydrophilic motifs cause protein aggregation and degradation upon codon-dependent translation elongation defects. Accordingly, the combination of codon content and the presence of hydrophilic motifs define the proteome whose maintenance relies on U34-tRNA modification. Together, these results uncover the mechanism linking wobble tRNA modification to mRNA translation and aggregation to maintain proteome homeostasis.
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Affiliation(s)
- Francesca Rapino
- Laboratory of Cancer Signaling, University of Liège, Liège, Belgium.
- GIGA-Institute, University of Liège, Liège, Belgium.
- University of Liège, Liège, Belgium.
- Department of Radiation Oncology (Maastro), GROW School for Oncology and Developmental Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands.
| | - Zhaoli Zhou
- Laboratory of Cancer Signaling, University of Liège, Liège, Belgium
- GIGA-Institute, University of Liège, Liège, Belgium
- University of Liège, Liège, Belgium
- Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Ana Maria Roncero Sanchez
- Laboratory of Cancer Signaling, University of Liège, Liège, Belgium
- GIGA-Institute, University of Liège, Liège, Belgium
- University of Liège, Liège, Belgium
| | - Marc Joiret
- Laboratory of Cancer Signaling, University of Liège, Liège, Belgium
- GIGA-Institute, University of Liège, Liège, Belgium
- University of Liège, Liège, Belgium
- Biomechanics Research Unit, University of Liège, Liège, Belgium
| | - Christian Seca
- Laboratory of Cancer Signaling, University of Liège, Liège, Belgium
- GIGA-Institute, University of Liège, Liège, Belgium
- University of Liège, Liège, Belgium
| | - Najla El Hachem
- Laboratory of Cancer Signaling, University of Liège, Liège, Belgium
- GIGA-Institute, University of Liège, Liège, Belgium
- University of Liège, Liège, Belgium
| | - Gianluca Valenti
- University of Liège, Liège, Belgium
- Unité de Recherche Transitions, University of Liège, Liège, Belgium
| | - Sara Latini
- Laboratory of Cancer Signaling, University of Liège, Liège, Belgium
- GIGA-Institute, University of Liège, Liège, Belgium
- University of Liège, Liège, Belgium
| | - Kateryna Shostak
- GIGA-Institute, University of Liège, Liège, Belgium
- University of Liège, Liège, Belgium
- Laboratory of Medical Chemistry, University of Liège, Liège, Belgium
| | - Liesbet Geris
- GIGA-Institute, University of Liège, Liège, Belgium
- University of Liège, Liège, Belgium
- Biomechanics Research Unit, University of Liège, Liège, Belgium
| | - Ping Li
- Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Gang Huang
- Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Gabriel Mazzucchelli
- GIGA-Institute, University of Liège, Liège, Belgium
- University of Liège, Liège, Belgium
- Mass Spectrometry Laboratory, System Biology and Chemical Biology, University of Liège, Liège, Belgium
| | - Dominique Baiwir
- GIGA-Institute, University of Liège, Liège, Belgium
- University of Liège, Liège, Belgium
- Mass Spectrometry Laboratory, System Biology and Chemical Biology, University of Liège, Liège, Belgium
| | - Christophe J Desmet
- GIGA-Institute, University of Liège, Liège, Belgium
- University of Liège, Liège, Belgium
- Laboratory of Cellular and Molecular Immunology, University of Liège, Liège, Belgium
- Faculty of Veterinary Medicine, University of Liege, Liege, Belgium
| | - Alain Chariot
- GIGA-Institute, University of Liège, Liège, Belgium
- University of Liège, Liège, Belgium
- Laboratory of Medical Chemistry, University of Liège, Liège, Belgium
- WELBIO, University of Liege, Liege, Belgium
| | - Michel Georges
- GIGA-Institute, University of Liège, Liège, Belgium
- University of Liège, Liège, Belgium
- Faculty of Veterinary Medicine, University of Liege, Liege, Belgium
- Unit of Animal Genomics, University of Liège, Liège, Belgium
| | - Pierre Close
- Laboratory of Cancer Signaling, University of Liège, Liège, Belgium.
- GIGA-Institute, University of Liège, Liège, Belgium.
- University of Liège, Liège, Belgium.
- WELBIO, University of Liege, Liege, Belgium.
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27
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Bui PT, Hoang TX. Protein escape at the ribosomal exit tunnel: Effect of the tunnel shape. J Chem Phys 2021; 153:045105. [PMID: 32752708 DOI: 10.1063/5.0008292] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We study the post-translational escape of nascent proteins at the ribosomal exit tunnel with the consideration of a real shape atomistic tunnel based on the Protein Data Bank structure of the large ribosome subunit of archeon Haloarcula marismortui. Molecular dynamics simulations employing the Go-like model for the proteins show that at intermediate and high temperatures, including a presumable physiological temperature, the protein escape process at the atomistic tunnel is quantitatively similar to that at a cylinder tunnel of length L = 72 Å and diameter d = 16 Å. At low temperatures, the atomistic tunnel, however, yields an increased probability of protein trapping inside the tunnel, while the cylinder tunnel does not cause the trapping. All-β proteins tend to escape faster than all-α proteins, but this difference is blurred on increasing the protein's chain length. A 29-residue zinc-finger domain is shown to be severely trapped inside the tunnel. Most of the single-domain proteins considered, however, can escape efficiently at the physiological temperature with the escape time distribution following the diffusion model proposed in our previous works. An extrapolation of the simulation data to a realistic value of the friction coefficient for amino acids indicates that the escape times of globular proteins are at the sub-millisecond scale. It is argued that this time scale is short enough for the smooth functioning of the ribosome by not allowing nascent proteins to jam the ribosome tunnel.
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Affiliation(s)
- Phuong Thuy Bui
- Institute of Theoretical and Applied Research, Duy Tan University, Hanoi 100000, Vietnam
| | - Trinh Xuan Hoang
- Institute of Physics, Vietnam Academy of Science and Technology, 10 Dao Tan, Ba Dinh, Hanoi 11108, Vietnam
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28
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Nissley DA, Carbery A, Chonofsky M, Deane CM. Ribosome occupancy profiles are conserved between structurally and evolutionarily related yeast domains. Bioinformatics 2021; 37:1853-1859. [PMID: 33483722 PMCID: PMC8317121 DOI: 10.1093/bioinformatics/btab020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 12/11/2020] [Accepted: 01/12/2021] [Indexed: 02/05/2023] Open
Abstract
Motivation Protein synthesis is a non-equilibrium process, meaning that the speed of translation can influence the ability of proteins to fold and function. Assuming that structurally similar proteins fold by similar pathways, the profile of translation speed along an mRNA should be evolutionarily conserved between related proteins to direct correct folding and downstream function. The only evidence to date for such conservation of translation speed between homologous proteins has used codon rarity as a proxy for translation speed. There are, however, many other factors including mRNA structure and the chemistry of the amino acids in the A- and P-sites of the ribosome that influence the speed of amino acid addition. Results Ribosome profiling experiments provide a signal directly proportional to the underlying translation times at the level of individual codons. We compared ribosome occupancy profiles (extracted from five different large-scale yeast ribosome profiling studies) between related protein domains to more directly test if their translation schedule was conserved. Our analysis reveals that the ribosome occupancy profiles of paralogous domains tend to be significantly more similar to one another than to profiles of non-paralogous domains. This trend does not depend on domain length, structural classes, amino acid composition or sequence similarity. Our results indicate that entire ribosome occupancy profiles and not just rare codon locations are conserved between even distantly related domains in yeast, providing support for the hypothesis that translation schedule is conserved between structurally related domains to retain folding pathways and facilitate efficient folding. Availability and implementation Python3 code is available on GitHub at https://github.com/DanNissley/Compare-ribosome-occupancy. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Daniel A Nissley
- Department of Statistics, University of Oxford, Oxford, OX1 3LB, UK
| | - Anna Carbery
- Department of Statistics, University of Oxford, Oxford, OX1 3LB, UK
| | - Mark Chonofsky
- Department of Statistics, University of Oxford, Oxford, OX1 3LB, UK
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29
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Liu Y, Yang Q, Zhao F. Synonymous but Not Silent: The Codon Usage Code for Gene Expression and Protein Folding. Annu Rev Biochem 2021; 90:375-401. [PMID: 33441035 DOI: 10.1146/annurev-biochem-071320-112701] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Codon usage bias, the preference for certain synonymous codons, is found in all genomes. Although synonymous mutations were previously thought to be silent, a large body of evidence has demonstrated that codon usage can play major roles in determining gene expression levels and protein structures. Codon usage influences translation elongation speed and regulates translation efficiency and accuracy. Adaptation of codon usage to tRNA expression determines the proteome landscape. In addition, codon usage biases result in nonuniform ribosome decoding rates on mRNAs, which in turn influence the cotranslational protein folding process that is critical for protein function in diverse biological processes. Conserved genome-wide correlations have also been found between codon usage and protein structures. Furthermore, codon usage is a major determinant of mRNA levels through translation-dependent effects on mRNA decay and translation-independent effects on transcriptional and posttranscriptional processes. Here, we discuss the multifaceted roles and mechanisms of codon usage in different gene regulatory processes.
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Affiliation(s)
- Yi Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA;
| | - Qian Yang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA;
| | - Fangzhou Zhao
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA;
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30
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Clusan L, Le Goff P, Flouriot G, Pakdel F. A Closer Look at Estrogen Receptor Mutations in Breast Cancer and Their Implications for Estrogen and Antiestrogen Responses. Int J Mol Sci 2021; 22:ijms22020756. [PMID: 33451133 PMCID: PMC7828590 DOI: 10.3390/ijms22020756] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/29/2020] [Accepted: 12/31/2020] [Indexed: 02/06/2023] Open
Abstract
Breast cancer (BC) is the most common cancer among women worldwide. More than 70% of BC cases express estrogen receptor alpha (ERα), a central transcription factor that stimulates the proliferation of breast cancer cells, usually in the presence of estrogen. While most cases of ER-positive BC initially respond to antiestrogen therapies, a high percentage of cases develop resistance to treatment over time. The recent discovery of mutated forms of ERα that result in constitutively active forms of the receptor in the metastatic-resistance stage of BC has provided a strong rationale for the development of new antiestrogens. These molecules targeting clinically relevant ERα mutants and a combination with other pharmacological inhibitors of specific pathways may constitute alternative treatments to improve clinical practice in the fight against metastatic-resistant ER-positive BC. In this review, we summarize the latest advances regarding the particular involvement of point mutations of ERα in endocrine resistance. We also discuss the involvement of synonymous ERα mutations with respect to co-translational folding of the receptor and ribosome biogenesis in breast carcinogenesis.
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31
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Terrey M, Adamson SI, Gibson AL, Deng T, Ishimura R, Chuang JH, Ackerman SL. GTPBP1 resolves paused ribosomes to maintain neuronal homeostasis. eLife 2020; 9:e62731. [PMID: 33186095 PMCID: PMC7665888 DOI: 10.7554/elife.62731] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 10/26/2020] [Indexed: 12/14/2022] Open
Abstract
Ribosome-associated quality control pathways respond to defects in translational elongation to recycle arrested ribosomes and degrade aberrant polypeptides and mRNAs. Loss of a tRNA gene leads to ribosomal pausing that is resolved by the translational GTPase GTPBP2, and in its absence causes neuron death. Here, we show that loss of the homologous protein GTPBP1 during tRNA deficiency in the mouse brain also leads to codon-specific ribosome pausing and neurodegeneration, suggesting that these non-redundant GTPases function in the same pathway to mitigate ribosome pausing. As observed in Gtpbp2-/- mice (Ishimura et al., 2016), GCN2-mediated activation of the integrated stress response (ISR) was apparent in the Gtpbp1-/- brain. We observed decreased mTORC1 signaling which increased neuronal death, whereas ISR activation was neuroprotective. Our data demonstrate that GTPBP1 functions as an important quality control mechanism during translation elongation and suggest that translational signaling pathways intricately interact to regulate neuronal homeostasis during defective elongation.
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Affiliation(s)
- Markus Terrey
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, Division of Biological Sciences, University of California, San DiegoSan DiegoUnited States
- Graduate School of Biomedical Sciences and Engineering, University of MaineOronoUnited States
| | - Scott I Adamson
- The Jackson Laboratory for Genomic MedicineFarmingtonUnited States
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn HealthFarmingtonUnited States
| | - Alana L Gibson
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, Division of Biological Sciences, University of California, San DiegoSan DiegoUnited States
| | - Tianda Deng
- Division of Biological Sciences, Section of Molecular Biology, University of California, San DiegoSan DiegoUnited States
| | - Ryuta Ishimura
- The Jackson Laboratory for Mammalian GeneticsBar HarborUnited States
| | - Jeffrey H Chuang
- The Jackson Laboratory for Genomic MedicineFarmingtonUnited States
| | - Susan L Ackerman
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, Division of Biological Sciences, University of California, San DiegoSan DiegoUnited States
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32
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Liu Y. A code within the genetic code: codon usage regulates co-translational protein folding. Cell Commun Signal 2020; 18:145. [PMID: 32907610 PMCID: PMC7488015 DOI: 10.1186/s12964-020-00642-6] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 08/10/2020] [Indexed: 01/05/2023] Open
Abstract
The genetic code is degenerate, and most amino acids are encoded by two to six synonymous codons. Codon usage bias, the preference for certain synonymous codons, is a universal feature of all genomes examined. Synonymous codon mutations were previously thought to be silent; however, a growing body evidence now shows that codon usage regulates protein structure and gene expression through effects on co-translational protein folding, translation efficiency and accuracy, mRNA stability, and transcription. Codon usage regulates the speed of translation elongation, resulting in non-uniform ribosome decoding rates on mRNAs during translation that is adapted to co-translational protein folding process. Biochemical and genetic evidence demonstrate that codon usage plays an important role in regulating protein folding and function in both prokaryotic and eukaryotic organisms. Certain protein structural types are more sensitive than others to the effects of codon usage on protein folding, and predicted intrinsically disordered domains are more prone to misfolding caused by codon usage changes than other domain types. Bioinformatic analyses revealed that gene codon usage correlates with different protein structures in diverse organisms, indicating the existence of a codon usage code for co-translational protein folding. This review focuses on recent literature on the role and mechanism of codon usage in regulating translation kinetics and co-translational protein folding. Video abstract
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Affiliation(s)
- Yi Liu
- Department of Physiology, ND13.214A, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390-9040, USA.
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33
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Does proteostasis get lost in translation? Implications for protein aggregation across the lifespan. Ageing Res Rev 2020; 62:101119. [PMID: 32603841 DOI: 10.1016/j.arr.2020.101119] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 06/05/2020] [Accepted: 06/17/2020] [Indexed: 02/06/2023]
Abstract
Protein aggregation is a phenomenon of major relevance in neurodegenerative and neuromuscular disorders, cataracts, diabetes and many other diseases. Research has unveiled that proteins also aggregate in multiple tissues during healthy aging yet, the biological and biomedical relevance of this apparently asymptomatic phenomenon remains to be understood. It is known that proteome homeostasis (proteostasis) is maintained by a balanced protein synthesis rate, high protein synthesis accuracy, efficient protein folding and continual tagging of damaged proteins for degradation, suggesting that protein aggregation during healthy aging may be associated with alterations in both protein synthesis and the proteostasis network (PN) pathways. In particular, dysregulation of protein synthesis and alterations in translation fidelity are hypothesized to lead to the production of misfolded proteins which could explain the occurrence of age-related protein aggregation. Nevertheless, some data on this topic is controversial and the biological mechanisms that lead to widespread protein aggregation remain to be elucidated. We review the recent literature about the age-related decline of proteostasis, highlighting the need to build an integrated view of protein synthesis rate, fidelity and quality control pathways in order to better understand the proteome alterations that occur during aging and in age-related diseases.
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Shishido H, Yoon JS, Yang Z, Skach WR. CFTR trafficking mutations disrupt cotranslational protein folding by targeting biosynthetic intermediates. Nat Commun 2020; 11:4258. [PMID: 32848127 PMCID: PMC7450043 DOI: 10.1038/s41467-020-18101-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 08/04/2020] [Indexed: 02/03/2023] Open
Abstract
Protein misfolding causes a wide spectrum of human disease, and therapies that target misfolding are transforming the clinical care of cystic fibrosis. Despite this success, however, very little is known about how disease-causing mutations affect the de novo folding landscape. Here we show that inherited, disease-causing mutations located within the first nucleotide-binding domain (NBD1) of the cystic fibrosis transmembrane conductance regulator (CFTR) have distinct effects on nascent polypeptides. Two of these mutations (A455E and L558S) delay compaction of the nascent NBD1 during a critical window of synthesis. The observed folding defect is highly dependent on nascent chain length as well as its attachment to the ribosome. Moreover, restoration of the NBD1 cotranslational folding defect by second site suppressor mutations also partially restores folding of full-length CFTR. These findings demonstrate that nascent folding intermediates can play an important role in disease pathogenesis and thus provide potential targets for pharmacological correction.
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Affiliation(s)
- Hideki Shishido
- CFFT Lab, Cystic Fibrosis Foundation, 44 Hartwell Ave, Lexington, MA, 02421, USA
| | - Jae Seok Yoon
- CFFT Lab, Cystic Fibrosis Foundation, 44 Hartwell Ave, Lexington, MA, 02421, USA
| | - Zhongying Yang
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, 3181 S.W. Sam Jackson Park Rd, Portland, OR, 97239, USA
| | - William R Skach
- Cystic Fibrosis Foundation, 4550 Montgomery Ave., Suite 1100N, Bethesda, MD, 20814, USA.
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35
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Washburn RS, Zuber PK, Sun M, Hashem Y, Shen B, Li W, Harvey S, Acosta Reyes FJ, Gottesman ME, Knauer SH, Frank J. Escherichia coli NusG Links the Lead Ribosome with the Transcription Elongation Complex. iScience 2020; 23:101352. [PMID: 32726726 PMCID: PMC7390762 DOI: 10.1016/j.isci.2020.101352] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 06/04/2020] [Accepted: 07/03/2020] [Indexed: 02/07/2023] Open
Abstract
It has been known for more than 50 years that transcription and translation are physically coupled in bacteria, but whether or not this coupling may be mediated by the two-domain protein N-utilization substance (Nus) G in Escherichia coli is still heavily debated. Here, we combine integrative structural biology and functional analyses to provide conclusive evidence that NusG can physically link transcription with translation by contacting both RNA polymerase and the ribosome. We present a cryo-electron microscopy structure of a NusG:70S ribosome complex and nuclear magnetic resonance spectroscopy data revealing simultaneous binding of NusG to RNAP and the intact 70S ribosome, providing the first direct structural evidence for NusG-mediated coupling. Furthermore, in vivo reporter assays show that recruitment of NusG occurs late in transcription and strongly depends on translation. Thus, our data suggest that coupling occurs initially via direct RNAP:ribosome contacts and is then mediated by NusG.
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Affiliation(s)
- Robert S Washburn
- Department of Microbiology & Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Philipp K Zuber
- Biochemistry IV - Biopolymers, University of Bayreuth, 95447 Bayreuth, Germany
| | - Ming Sun
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Yaser Hashem
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Bingxin Shen
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Wen Li
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Sho Harvey
- University of Michigan, Ann Arbor, MI 48109, USA
| | - Francisco J Acosta Reyes
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Max E Gottesman
- Department of Microbiology & Immunology, Columbia University Medical Center, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA.
| | - Stefan H Knauer
- Biochemistry IV - Biopolymers, University of Bayreuth, 95447 Bayreuth, Germany.
| | - Joachim Frank
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA.
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36
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Non-conservation of folding rates in the thioredoxin family reveals degradation of ancestral unassisted-folding. Biochem J 2020; 476:3631-3647. [PMID: 31750876 PMCID: PMC6906118 DOI: 10.1042/bcj20190739] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/19/2019] [Accepted: 11/21/2019] [Indexed: 01/04/2023]
Abstract
Evolution involves not only adaptation, but also the degradation of superfluous features. Many examples of degradation at the morphological level are known (vestigial organs, for instance). However, the impact of degradation on molecular evolution has been rarely addressed. Thioredoxins serve as general oxidoreductases in all cells. Here, we report extensive mutational analyses on the folding of modern and resurrected ancestral bacterial thioredoxins. Contrary to claims from recent literature, in vitro folding rates in the thioredoxin family are not evolutionarily conserved, but span at least a ∼100-fold range. Furthermore, modern thioredoxin folding is often substantially slower than ancestral thioredoxin folding. Unassisted folding, as probed in vitro, thus emerges as an ancestral vestigial feature that underwent degradation, plausibly upon the evolutionary emergence of efficient cellular folding assistance. More generally, our results provide evidence that degradation of ancestral features shapes, not only morphological evolution, but also the evolution of individual proteins.
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37
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Addabbo RM, Dalphin MD, Mecha MF, Liu Y, Staikos A, Guzman-Luna V, Cavagnero S. Complementary Role of Co- and Post-Translational Events in De Novo Protein Biogenesis. J Phys Chem B 2020; 124:6488-6507. [DOI: 10.1021/acs.jpcb.0c03039] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Rayna M. Addabbo
- Biophysics Graduate Degree Program, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Matthew D. Dalphin
- Biophysics Graduate Degree Program, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Miranda F. Mecha
- Biophysics Graduate Degree Program, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Yue Liu
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Alexios Staikos
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Valeria Guzman-Luna
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Silvia Cavagnero
- Biophysics Graduate Degree Program, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
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38
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Rojano-Nisimura AM, Haning K, Janovsky J, Vasquez KA, Thompson JP, Contreras LM. Codon Selection Affects Recruitment of Ribosome-Associating Factors during Translation. ACS Synth Biol 2020; 9:329-342. [PMID: 31769967 DOI: 10.1021/acssynbio.9b00344] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An intriguing aspect of protein synthesis is how cotranslational events are managed inside the cell. In this study, we developed an in vivo bimolecular fluorescence complementation assay coupled to SecM stalling (BiFC-SecM) to study how codon usage influences the interactions of ribosome-associating factors that occur cotranslationally. We profiled ribosomal associations of a number of proteins, and observed differential association of chaperone proteins TF, DnaK, GroEL, and translocation factor Ffh as a result of introducing synonymous codon substitutions that change the affinity of the translating sequence to the ribosomal anti-Shine-Dalgarno (aSD) sequence. The use of pausing sequences within proteins regulates their transit within the translating ribosome. Our results indicate that the dynamics between cellular factors and the new polypeptide chain are affected by how codon composition is designed. Furthermore, associating factors may play a role in processes including protein quality control (folding and degradation) and cellular respiration.
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Affiliation(s)
- Alejandra M. Rojano-Nisimura
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Stop A4800, Austin, Texas 78712, United States
| | - Katie Haning
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, Texas 78712, United States
| | - Justin Janovsky
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Stop A4800, Austin, Texas 78712, United States
| | - Kevin A. Vasquez
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, Texas 78712, United States
| | - Jeffrey P. Thompson
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, Texas 78712, United States
| | - Lydia M. Contreras
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, Texas 78712, United States
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39
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Engineering Biology to Construct Microbial Chassis for the Production of Difficult-to-Express Proteins. Int J Mol Sci 2020; 21:ijms21030990. [PMID: 32024292 PMCID: PMC7037952 DOI: 10.3390/ijms21030990] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/28/2020] [Accepted: 01/31/2020] [Indexed: 12/12/2022] Open
Abstract
A large proportion of the recombinant proteins manufactured today rely on microbe-based expression systems owing to their relatively simple and cost-effective production schemes. However, several issues in microbial protein expression, including formation of insoluble aggregates, low protein yield, and cell death are still highly recursive and tricky to optimize. These obstacles are usually rooted in the metabolic capacity of the expression host, limitation of cellular translational machineries, or genetic instability. To this end, several microbial strains having precisely designed genomes have been suggested as a way around the recurrent problems in recombinant protein expression. Already, a growing number of prokaryotic chassis strains have been genome-streamlined to attain superior cellular fitness, recombinant protein yield, and stability of the exogenous expression pathways. In this review, we outline challenges associated with heterologous protein expression, some examples of microbial chassis engineered for the production of recombinant proteins, and emerging tools to optimize the expression of heterologous proteins. In particular, we discuss the synthetic biology approaches to design and build and test genome-reduced microbial chassis that carry desirable characteristics for heterologous protein expression.
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40
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Robinson PJ, Kanemura S, Cao X, Bulleid NJ. Protein secondary structure determines the temporal relationship between folding and disulfide formation. J Biol Chem 2020; 295:2438-2448. [PMID: 31953323 PMCID: PMC7039548 DOI: 10.1074/jbc.ra119.011983] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/16/2020] [Indexed: 11/06/2022] Open
Abstract
How and when disulfide bonds form in proteins relative to the stage of their folding is a fundamental question in cell biology. Two models describe this relationship: the folded precursor model, in which a nascent structure forms before disulfides do, and the quasi-stochastic model, where disulfides form prior to folding. Here we investigated oxidative folding of three structurally diverse substrates, β2-microglobulin, prolactin, and the disintegrin domain of ADAM metallopeptidase domain 10 (ADAM10), to understand how these mechanisms apply in a cellular context. We used a eukaryotic cell-free translation system in which we could identify disulfide isomers in stalled translation intermediates to characterize the timing of disulfide formation relative to translocation into the endoplasmic reticulum and the presence of non-native disulfides. Our results indicate that in a domain lacking secondary structure, disulfides form before conformational folding through a process prone to nonnative disulfide formation, whereas in proteins with defined secondary structure, native disulfide formation occurs after partial folding. These findings reveal that the nascent protein structure promotes correct disulfide formation during cotranslational folding.
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Affiliation(s)
- Philip J Robinson
- Institute of Molecular, Cell, and Systems Biology, College of Medical Veterinary and Life Sciences, Davidson Building, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Shingo Kanemura
- Kwansei Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337, Japan
| | - Xiaofei Cao
- Institute of Molecular, Cell, and Systems Biology, College of Medical Veterinary and Life Sciences, Davidson Building, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Neil J Bulleid
- Institute of Molecular, Cell, and Systems Biology, College of Medical Veterinary and Life Sciences, Davidson Building, University of Glasgow, Glasgow G12 8QQ, United Kingdom.
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42
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Abstract
Large proteins composed of multiple domains are abundant in all proteomes, but their folding and structural dynamics remain poorly understood. Using single-molecule force spectroscopy, we have defined how stabilizing interfaces among the domains of elongation factor G (EF-G) shape its folding pathway. Contrary to the expectation that multidomain proteins fold sequentially as they emerge from the ribosome, we find that folding cannot be completed until the full protein has been synthesized. This posttranslational folding mechanism results in a propensity for misfolding. It is dictated by an energetic coupling among domains that enables conformational flexibility crucial for EF-G function. EF-G thus provides an example of how distinct biological ends—robust folding and functionally important flexibility—come into conflict during protein biogenesis. Large proteins with multiple domains are thought to fold cotranslationally to minimize interdomain misfolding. Once folded, domains interact with each other through the formation of extensive interfaces that are important for protein stability and function. However, multidomain protein folding and the energetics of domain interactions remain poorly understood. In elongation factor G (EF-G), a highly conserved protein composed of 5 domains, the 2 N-terminal domains form a stably structured unit cotranslationally. Using single-molecule optical tweezers, we have defined the steps leading to fully folded EF-G. We find that the central domain III of EF-G is highly dynamic and does not fold upon emerging from the ribosome. Surprisingly, a large interface with the N-terminal domains does not contribute to the stability of domain III. Instead, it requires interactions with its folded C-terminal neighbors to be stably structured. Because of the directionality of protein synthesis, this energetic dependency of domain III on its C-terminal neighbors disrupts cotranslational folding and imposes a posttranslational mechanism on the folding of the C-terminal part of EF-G. As a consequence, unfolded domains accumulate during synthesis, leading to the extensive population of misfolded species that interfere with productive folding. Domain III flexibility enables large-scale conformational transitions that are part of the EF-G functional cycle during ribosome translocation. Our results suggest that energetic tuning of domain stabilities, which is likely crucial for EF-G function, complicates the folding of this large multidomain protein.
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43
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Krutyhołowa R, Hammermeister A, Zabel R, Abdel-Fattah W, Reinhardt-Tews A, Helm M, Stark MJR, Breunig KD, Schaffrath R, Glatt S. Kti12, a PSTK-like tRNA dependent ATPase essential for tRNA modification by Elongator. Nucleic Acids Res 2019; 47:4814-4830. [PMID: 30916349 PMCID: PMC6511879 DOI: 10.1093/nar/gkz190] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/14/2019] [Accepted: 03/11/2019] [Indexed: 01/08/2023] Open
Abstract
Posttranscriptional RNA modifications occur in all domains of life. Modifications of anticodon bases are of particular importance for ribosomal decoding and proteome homeostasis. The Elongator complex modifies uridines in the wobble position and is highly conserved in eukaryotes. Despite recent insights into Elongator's architecture, the structure and function of its regulatory factor Kti12 have remained elusive. Here, we present the crystal structure of Kti12′s nucleotide hydrolase domain trapped in a transition state of ATP hydrolysis. The structure reveals striking similarities to an O-phosphoseryl-tRNA kinase involved in the selenocysteine pathway. Both proteins employ similar mechanisms of tRNA binding and show tRNASec-dependent ATPase activity. In addition, we demonstrate that Kti12 binds directly to Elongator and that ATP hydrolysis is crucial for Elongator to maintain proper tRNA anticodon modification levels in vivo. In summary, our data reveal a hitherto uncharacterized link between two translational control pathways that regulate selenocysteine incorporation and affect ribosomal tRNA selection via specific tRNA modifications.
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Affiliation(s)
- Rościsław Krutyhołowa
- Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.,Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Rene Zabel
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Wael Abdel-Fattah
- Institut für Biologie, FG Mikrobiologie, Universität Kassel, Kassel, Germany
| | | | - Mark Helm
- Institut für Pharmazie und Biochemie, Universität Mainz, Mainz, Germany
| | - Michael J R Stark
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, UK
| | - Karin D Breunig
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Raffael Schaffrath
- Institut für Biologie, FG Mikrobiologie, Universität Kassel, Kassel, Germany
| | - Sebastian Glatt
- Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
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44
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Dao Duc K, Batra SS, Bhattacharya N, Cate JHD, Song YS. Differences in the path to exit the ribosome across the three domains of life. Nucleic Acids Res 2019; 47:4198-4210. [PMID: 30805621 PMCID: PMC6486554 DOI: 10.1093/nar/gkz106] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 02/22/2019] [Indexed: 01/07/2023] Open
Abstract
The ribosome exit tunnel is an important structure involved in the regulation of translation and other essential functions such as protein folding. By comparing 20 recently obtained cryo-EM and X-ray crystallography structures of the ribosome from all three domains of life, we here characterize the key similarities and differences of the tunnel across species. We first show that a hierarchical clustering of tunnel shapes closely reflects the species phylogeny. Then, by analyzing the ribosomal RNAs and proteins, we explain the observed geometric variations and show direct association between the conservations of the geometry, structure and sequence. We find that the tunnel is more conserved in the upper part close to the polypeptide transferase center, while in the lower part, it is substantially narrower in eukaryotes than in bacteria. Furthermore, we provide evidence for the existence of a second constriction site in eukaryotic exit tunnels. Overall, these results have several evolutionary and functional implications, which explain certain differences between eukaryotes and prokaryotes in their translation mechanisms. In particular, they suggest that major co-translational functions of bacterial tunnels were externalized in eukaryotes, while reducing the tunnel size provided some other advantages, such as facilitating the nascent chain elongation and enabling antibiotic resistance.
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Affiliation(s)
- Khanh Dao Duc
- Computer Science Division, University of California, Berkeley, CA 94720, USA
| | - Sanjit S Batra
- Computer Science Division, University of California, Berkeley, CA 94720, USA
| | | | - Jamie H D Cate
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.,Department of Chemistry, University of California, Berkeley, CA 94720, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yun S Song
- Computer Science Division, University of California, Berkeley, CA 94720, USA.,Department of Statistics, University of California, Berkeley, CA 94720, USA.,Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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45
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Leipheimer J, Bloom ALM, Campomizzi CS, Salei Y, Panepinto JC. Translational Regulation Promotes Oxidative Stress Resistance in the Human Fungal Pathogen Cryptococcus neoformans. mBio 2019; 10:e02143-19. [PMID: 31719175 PMCID: PMC6851278 DOI: 10.1128/mbio.02143-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/09/2019] [Indexed: 01/08/2023] Open
Abstract
Cryptococcus neoformans is one of the few environmental fungi that can survive within a mammalian host and cause disease. Although many of the factors responsible for establishing virulence have been recognized, how they are expressed in response to certain host-derived cellular stresses is rarely addressed. Here, we characterize the temporal translational response of C. neoformans to oxidative stress. We find that translation is largely inhibited through the phosphorylation of the critical initiation factor eIF2α (α subunit of eukaryotic initiation factor 2) by a sole kinase. Preventing eIF2α-mediated translational suppression resulted in growth sensitivity to hydrogen peroxide (H2O2). Our work suggests that translational repression in response to H2O2 partly facilitates oxidative stress adaptation by accelerating the decay of abundant non-stress-related transcripts while facilitating the proper expression levels of select oxidative stress response factors. Our results illustrate translational suppression as a critical determinant of select mRNA decay, gene expression, and subsequent survival in response to oxidative stress.IMPORTANCE Fungal survival in a mammalian host requires the coordinated expression and downregulation of a large cohort of genes in response to cellular stresses. Initial infection with C. neoformans occurs in the lungs, where it interacts with host macrophages. Surviving macrophage-derived cellular stresses, such as the production of reactive oxygen and nitrogen species, is believed to promote dissemination into the central nervous system. Therefore, investigating how an oxidative stress-resistant phenotype is brought about in C. neoformans not only furthers our understanding of fungal pathogenesis but also unveils mechanisms of stress-induced gene reprogramming. We discovered that H2O2-derived oxidative stress resulted in severe translational suppression and that this suppression was necessary for the accelerated decay and expression of tested transcripts.
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Affiliation(s)
- Jay Leipheimer
- Department of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, University at Buffalo, SUNY, Buffalo, New York, USA
| | - Amanda L M Bloom
- Department of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, University at Buffalo, SUNY, Buffalo, New York, USA
| | | | - Yana Salei
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida, USA
| | - John C Panepinto
- Department of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, University at Buffalo, SUNY, Buffalo, New York, USA
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46
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Haase N, Holtkamp W, Lipowsky R, Rodnina M, Rudorf S. Decomposition of time-dependent fluorescence signals reveals codon-specific kinetics of protein synthesis. Nucleic Acids Res 2019; 46:e130. [PMID: 30107440 PMCID: PMC6294494 DOI: 10.1093/nar/gky740] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/03/2018] [Indexed: 12/12/2022] Open
Abstract
During protein synthesis, the nascent peptide chain traverses the peptide exit tunnel of the ribosome. We monitor the co-translational movement of the nascent peptide using a fluorescent probe attached to the N-terminus of the nascent chain. Due to fluorophore quenching, the time-dependent fluorescence signal emitted by an individual peptide is determined by co-translational events, such as secondary structure formation and peptide-tunnel interactions. To obtain information on these individual events, the measured ensemble fluorescence signal has to be decomposed into position-dependent intensities. Here, we describe mRNA translation as a Markov process with specific fluorescence intensities assigned to the different states of the process. Combining the computed stochastic time evolution of the translation process with a sequence of observed ensemble fluorescence time courses, we compute the unknown position-specific intensities and obtain detailed information on the kinetics of the translation process. In particular, we find that translation of poly(U) mRNAs dramatically slows down at the fourth UUU codon. The method presented here detects subtle differences in the position-specific fluorescence intensities and thus provides a novel approach to study translation kinetics in ensemble experiments.
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Affiliation(s)
- Nadin Haase
- Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany
| | - Wolf Holtkamp
- Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany
| | - Reinhard Lipowsky
- Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany
| | - Marina Rodnina
- Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany
| | - Sophia Rudorf
- Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany
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47
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Dauden MI, Jaciuk M, Weis F, Lin TY, Kleindienst C, Abbassi NEH, Khatter H, Krutyhołowa R, Breunig KD, Kosinski J, Müller CW, Glatt S. Molecular basis of tRNA recognition by the Elongator complex. SCIENCE ADVANCES 2019; 5:eaaw2326. [PMID: 31309145 PMCID: PMC6620098 DOI: 10.1126/sciadv.aaw2326] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 06/03/2019] [Indexed: 05/17/2023]
Abstract
The highly conserved Elongator complex modifies transfer RNAs (tRNAs) in their wobble base position, thereby regulating protein synthesis and ensuring proteome stability. The precise mechanisms of tRNA recognition and its modification reaction remain elusive. Here, we show cryo-electron microscopy structures of the catalytic subcomplex of Elongator and its tRNA-bound state at resolutions of 3.3 and 4.4 Å. The structures resolve details of the catalytic site, including the substrate tRNA, the iron-sulfur cluster, and a SAM molecule, which are all validated by mutational analyses in vitro and in vivo. tRNA binding induces conformational rearrangements, which precisely position the targeted anticodon base in the active site. Our results provide the molecular basis for substrate recognition of Elongator, essential to understand its cellular function and role in neurodegenerative diseases and cancer.
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Affiliation(s)
- Maria I. Dauden
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Marcin Jaciuk
- Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Felix Weis
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Ting-Yu Lin
- Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Carolin Kleindienst
- Institute of Biology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Nour El Hana Abbassi
- Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Postgraduate School of Molecular Medicine, Warsaw, Poland
| | - Heena Khatter
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Rościsław Krutyhołowa
- Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Karin D. Breunig
- Institute of Biology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Jan Kosinski
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Hamburg, Germany
| | - Christoph W. Müller
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Sebastian Glatt
- Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
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48
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Two Old Dogs, One New Trick: A Review of RNA Polymerase and Ribosome Interactions during Transcription-Translation Coupling. Int J Mol Sci 2019; 20:ijms20102595. [PMID: 31137816 PMCID: PMC6566652 DOI: 10.3390/ijms20102595] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/22/2019] [Accepted: 05/24/2019] [Indexed: 12/14/2022] Open
Abstract
The coupling of transcription and translation is more than mere translation of an mRNA that is still being transcribed. The discovery of physical interactions between RNA polymerase and ribosomes has spurred renewed interest into this long-standing paradigm of bacterial molecular biology. Here, we provide a concise presentation of recent insights gained from super-resolution microscopy, biochemical, and structural work, including cryo-EM studies. Based on the presented data, we put forward a dynamic model for the interaction between RNA polymerase and ribosomes, in which the interactions are repeatedly formed and broken. Furthermore, we propose that long intervening nascent RNA will loop out and away during the forming the interactions between the RNA polymerase and ribosomes. By comparing the effect of the direct interactions between RNA polymerase and ribosomes with those that transcription factors NusG and RfaH mediate, we submit that two distinct modes of coupling exist: Factor-free and factor-mediated coupling. Finally, we provide a possible framework for transcription-translation coupling and elude to some open questions in the field.
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49
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Co-translational assembly of mammalian nuclear multisubunit complexes. Nat Commun 2019; 10:1740. [PMID: 30988355 PMCID: PMC6465333 DOI: 10.1038/s41467-019-09749-y] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 03/29/2019] [Indexed: 01/07/2023] Open
Abstract
Cells dedicate significant energy to build proteins often organized in multiprotein assemblies with tightly regulated stoichiometries. As genes encoding subunits assembling in a multisubunit complex are dispersed in the genome of eukaryotes, it is unclear how these protein complexes assemble. Here, we show that mammalian nuclear transcription complexes (TFIID, TREX-2 and SAGA) composed of a large number of subunits, but lacking precise architectural details are built co-translationally. We demonstrate that dimerization domains and their positions in the interacting subunits determine the co-translational assembly pathway (simultaneous or sequential). The lack of co-translational interaction can lead to degradation of the partner protein. Thus, protein synthesis and complex assembly are linked in building mammalian multisubunit complexes, suggesting that co-translational assembly is a general principle in mammalian cells to avoid non-specific interactions and protein aggregation. These findings will also advance structural biology by defining endogenous co-translational building blocks in the architecture of multisubunit complexes. Genes encoding protein complex subunits are often dispersed in the genome of eukaryotes, raising the question how these protein complexes assemble. Here, the authors provide evidence that mammalian nuclear transcription complexes are formed co-translationally to ensure specific and functional interactions.
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50
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Sabi R, Tuller T. Novel insights into gene expression regulation during meiosis revealed by translation elongation dynamics. NPJ Syst Biol Appl 2019; 5:12. [PMID: 30962948 PMCID: PMC6449359 DOI: 10.1038/s41540-019-0089-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 03/20/2019] [Indexed: 01/14/2023] Open
Abstract
The ability to dynamically control mRNA translation has a great impact on many intracellular processes. Whereas it is believed that translational control in eukaryotes occurs mainly at initiation, the condition-specific changes at the elongation level and their potential regulatory role remain unclear. Using computational approaches applied to ribosome profiling data, we show that elongation rate is dynamic and can change considerably during the yeast meiosis to facilitate the selective translation of stage-specific transcripts. We observed unique elongation changes during meiosis II, including a global inhibition of translation elongation at the onset of anaphase II accompanied by a sharp shift toward increased elongation for genes required at this meiotic stage. We also show that ribosomal proteins counteract the global decreased elongation by maintaining high initiation rates. Our findings provide new insights into gene expression regulation during meiosis and demonstrate that codon usage evolved, among others, to optimize timely translation.
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Affiliation(s)
- Renana Sabi
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
- The Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv, Israel
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