1
|
Wimmer B, Schernthaner J, Edobor G, Friedrich A, Poeltner K, Temaj G, Wimmer M, Kronsteiner E, Pichler M, Gercke H, Huber R, Kaefer N, Rinnerthaler M, Karl T, Krauß J, Mohr T, Gerner C, Hintner H, Breitenbach M, Bauer JW, Rakers C, Kuhn D, von Hagen J, Müller N, Rathner A, Breitenbach-Koller H. RiboScreen TM Technology Delivers a Ribosomal Target and a Small-Molecule Ligand for Ribosome Editing to Boost the Production Levels of Tropoelastin, the Monomeric Unit of Elastin. Int J Mol Sci 2024; 25:8430. [PMID: 39125999 PMCID: PMC11312584 DOI: 10.3390/ijms25158430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Revised: 07/28/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024] Open
Abstract
Elastin, a key structural protein essential for the elasticity of the skin and elastogenic tissues, degrades with age. Replenishing elastin holds promise for anti-aging cosmetics and the supplementation of elastic activities of the cardiovascular system. We employed RiboScreenTM, a technology for identifying molecules that enhance the production of specific proteins, to target the production of tropoelastin. We make use of RiboScreenTM in two crucial steps: first, to pinpoint a target ribosomal protein (TRP), which acts as a switch to increase the production of the protein of interest (POI), and second, to identify small molecules that activate this ribosomal protein switch. Using RiboScreenTM, we identified ribosomal protein L40, henceforth eL40, as a TRP switch to boost tropoelastin production. Drug discovery identified a small-molecule hit that binds to eL40. In-cell treatment demonstrated activity of the eL40 ligand and delivered increased tropoelastin production levels in a dose-dependent manner. Thus, we demonstrate that RiboScreenTM can successfully identify a small-molecule hit capable of selectively enhancing tropoelastin production. This compound has the potential to be developed for topical or systemic applications to promote skin rejuvenation and to supplement elastic functionality within the cardiovascular system.
Collapse
Affiliation(s)
- Bjoern Wimmer
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria; (B.W.); (J.S.); (G.E.); (A.F.); (K.P.); (M.W.); (E.K.); (M.P.); (H.G.); (R.H.); (M.R.); (T.K.); (J.K.); (M.B.)
| | - Jan Schernthaner
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria; (B.W.); (J.S.); (G.E.); (A.F.); (K.P.); (M.W.); (E.K.); (M.P.); (H.G.); (R.H.); (M.R.); (T.K.); (J.K.); (M.B.)
| | - Genevieve Edobor
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria; (B.W.); (J.S.); (G.E.); (A.F.); (K.P.); (M.W.); (E.K.); (M.P.); (H.G.); (R.H.); (M.R.); (T.K.); (J.K.); (M.B.)
| | - Andreas Friedrich
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria; (B.W.); (J.S.); (G.E.); (A.F.); (K.P.); (M.W.); (E.K.); (M.P.); (H.G.); (R.H.); (M.R.); (T.K.); (J.K.); (M.B.)
| | - Katharina Poeltner
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria; (B.W.); (J.S.); (G.E.); (A.F.); (K.P.); (M.W.); (E.K.); (M.P.); (H.G.); (R.H.); (M.R.); (T.K.); (J.K.); (M.B.)
| | - Gazmend Temaj
- Human Genetics, Faculty of Pharmacy, College UBT, 10000 Pristina, Kosovo;
| | - Marlies Wimmer
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria; (B.W.); (J.S.); (G.E.); (A.F.); (K.P.); (M.W.); (E.K.); (M.P.); (H.G.); (R.H.); (M.R.); (T.K.); (J.K.); (M.B.)
| | - Elli Kronsteiner
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria; (B.W.); (J.S.); (G.E.); (A.F.); (K.P.); (M.W.); (E.K.); (M.P.); (H.G.); (R.H.); (M.R.); (T.K.); (J.K.); (M.B.)
| | - Mara Pichler
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria; (B.W.); (J.S.); (G.E.); (A.F.); (K.P.); (M.W.); (E.K.); (M.P.); (H.G.); (R.H.); (M.R.); (T.K.); (J.K.); (M.B.)
| | - Hanna Gercke
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria; (B.W.); (J.S.); (G.E.); (A.F.); (K.P.); (M.W.); (E.K.); (M.P.); (H.G.); (R.H.); (M.R.); (T.K.); (J.K.); (M.B.)
| | - Ronald Huber
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria; (B.W.); (J.S.); (G.E.); (A.F.); (K.P.); (M.W.); (E.K.); (M.P.); (H.G.); (R.H.); (M.R.); (T.K.); (J.K.); (M.B.)
| | - Niklas Kaefer
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria; (B.W.); (J.S.); (G.E.); (A.F.); (K.P.); (M.W.); (E.K.); (M.P.); (H.G.); (R.H.); (M.R.); (T.K.); (J.K.); (M.B.)
| | - Mark Rinnerthaler
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria; (B.W.); (J.S.); (G.E.); (A.F.); (K.P.); (M.W.); (E.K.); (M.P.); (H.G.); (R.H.); (M.R.); (T.K.); (J.K.); (M.B.)
| | - Thomas Karl
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria; (B.W.); (J.S.); (G.E.); (A.F.); (K.P.); (M.W.); (E.K.); (M.P.); (H.G.); (R.H.); (M.R.); (T.K.); (J.K.); (M.B.)
| | - Jan Krauß
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria; (B.W.); (J.S.); (G.E.); (A.F.); (K.P.); (M.W.); (E.K.); (M.P.); (H.G.); (R.H.); (M.R.); (T.K.); (J.K.); (M.B.)
| | - Thomas Mohr
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria; (T.M.); (C.G.)
| | - Christopher Gerner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria; (T.M.); (C.G.)
- Join Metabolome Facility, University of Vienna, Waehringer Str. 38, 1090 Vienna, Austria
| | - Helmut Hintner
- Department of Dermatology and Allergology, University Hospital Salzburg, Muellner Hauptstraße 48, 5020 Salzburg, Austria; (H.H.); (J.W.B.)
| | - Michael Breitenbach
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria; (B.W.); (J.S.); (G.E.); (A.F.); (K.P.); (M.W.); (E.K.); (M.P.); (H.G.); (R.H.); (M.R.); (T.K.); (J.K.); (M.B.)
| | - Johann W. Bauer
- Department of Dermatology and Allergology, University Hospital Salzburg, Muellner Hauptstraße 48, 5020 Salzburg, Austria; (H.H.); (J.W.B.)
| | - Christin Rakers
- Merck KGaA, Discovery & Development Technologies, Frankfurter Staße 250, 64293 Darmstadt, Germany (D.K.)
| | - Daniel Kuhn
- Merck KGaA, Discovery & Development Technologies, Frankfurter Staße 250, 64293 Darmstadt, Germany (D.K.)
| | - Joerg von Hagen
- Merck KGaA Healthcare, Frankfurter Straße 250, 64293 Darmstadt, Germany;
- ryon-Greentech Accelerator, Mainzer Straße 41, 64579 Gernsheim, Germany
| | - Norbert Müller
- Institute of Biochemistry, Johannes Kepler University, Altenbergerstraße 69, 4040 Linz, Austria;
- Department of Chemistry, Faculty of Science, University of South Bohemia in Českých Budějovicích, Branišovská 1760, 370 05 České Budějovice, Czech Republic
| | - Adriana Rathner
- Institute of Biochemistry, Johannes Kepler University, Altenbergerstraße 69, 4040 Linz, Austria;
| | - Hannelore Breitenbach-Koller
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria; (B.W.); (J.S.); (G.E.); (A.F.); (K.P.); (M.W.); (E.K.); (M.P.); (H.G.); (R.H.); (M.R.); (T.K.); (J.K.); (M.B.)
| |
Collapse
|
2
|
Weiss JL, Decker JC, Bolano A, Krahn N. Tuning tRNAs for improved translation. Front Genet 2024; 15:1436860. [PMID: 38983271 PMCID: PMC11231383 DOI: 10.3389/fgene.2024.1436860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 06/06/2024] [Indexed: 07/11/2024] Open
Abstract
Transfer RNAs have been extensively explored as the molecules that translate the genetic code into proteins. At this interface of genetics and biochemistry, tRNAs direct the efficiency of every major step of translation by interacting with a multitude of binding partners. However, due to the variability of tRNA sequences and the abundance of diverse post-transcriptional modifications, a guidebook linking tRNA sequences to specific translational outcomes has yet to be elucidated. Here, we review substantial efforts that have collectively uncovered tRNA engineering principles that can be used as a guide for the tuning of translation fidelity. These principles have allowed for the development of basic research, expansion of the genetic code with non-canonical amino acids, and tRNA therapeutics.
Collapse
Affiliation(s)
- Joshua L Weiss
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - J C Decker
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Ariadna Bolano
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Natalie Krahn
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| |
Collapse
|
3
|
Que Y, Qiu Y, Ding Z, Zhang S, Wei R, Xia J, Lin Y. The role of molecular chaperone CCT/TRiC in translation elongation: A literature review. Heliyon 2024; 10:e29029. [PMID: 38596045 PMCID: PMC11002246 DOI: 10.1016/j.heliyon.2024.e29029] [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: 01/12/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/11/2024] Open
Abstract
Protein synthesis from mRNA is an energy-intensive and strictly controlled biological process. Translation elongation is a well-coordinated and multifactorial step in translation that ensures the accurate and efficient addition of amino acids to a growing nascent-peptide chain encoded in the sequence of messenger RNA (mRNA). Which undergoes dynamic regulation due to cellular state and environmental determinants. An expanding body of research points to translational elongation as a crucial process that controls the translation of an mRNA through multiple feedback mechanisms. Molecular chaperones are key players in protein homeostasis to keep the balance between protein synthesis, folding, assembly, and degradation. Chaperonin-containing tailless complex polypeptide 1 (CCT) or tailless complex polypeptide 1 ring complex (TRiC) is an essential eukaryotic molecular chaperone that plays an essential role in assisting cellular protein folding and suppressing protein aggregation. In this review, we give an overview of the factors that influence translation elongation, focusing on different functions of molecular chaperones in translation elongation, including how they affect translation rates and post-translational modifications. We also provide an understanding of the mechanisms by which the molecular chaperone CCT plays multiple roles in the elongation phase of eukaryotic protein synthesis.
Collapse
Affiliation(s)
- Yueyue Que
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Yudan Qiu
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Zheyu Ding
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Shanshan Zhang
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Rong Wei
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Jianing Xia
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Yingying Lin
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| |
Collapse
|
4
|
Goldkamp AK, Hagen DE. Implications of tRNA abundance on translation elongation across bovine tissues. Front Genet 2023; 14:1308048. [PMID: 38174049 PMCID: PMC10763252 DOI: 10.3389/fgene.2023.1308048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 12/08/2023] [Indexed: 01/05/2024] Open
Abstract
Introduction: Translation is a crucial stage of gene expression. It may also act as an additional layer of regulation that plays an important role in gene expression and function. Highly expressed genes are believed to be codon-biased to support increased protein production, in which quickly translated codons correspond to highly abundant tRNAs. Synonymous SNPs, considered to be silent due to the degeneracy of the genetic code, may shift protein abundance and function through alterations in translational efficiency and suboptimal pairing to lowly abundant tRNAs. Methods: Here, we applied Quantitative Mature tRNA sequencing (QuantM-tRNAseq) and ribosome profiling across bovine tissues in order to investigate the relationship between tRNA expression and slowed translation. Results: Moreover, we have identified genes modulated at transcriptional and/or translational levels underlying tissue-specific biological processes. We have also successfully defined pausing sites that depict the regulatory information encoded within the open reading frame of transcripts, which could be related to translation rate and facilitate proper protein folding. This work offers an atlas of distinctive pausing sites across three bovine tissues, which provides an opportunity to predict codon optimality and understand tissue-specific mechanisms of regulating protein synthesis.
Collapse
Affiliation(s)
| | - Darren E. Hagen
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, United States
| |
Collapse
|
5
|
Barros GC, Guerrero S, Silva GM. The central role of translation elongation in response to stress. Biochem Soc Trans 2023; 51:959-969. [PMID: 37318088 PMCID: PMC11160351 DOI: 10.1042/bst20220584] [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: 02/06/2023] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/16/2023]
Abstract
Protein synthesis is essential to support homeostasis, and thus, must be highly regulated during cellular response to harmful environments. All stages of translation are susceptible to regulation under stress, however, the mechanisms involved in translation regulation beyond initiation have only begun to be elucidated. Methodological advances enabled critical discoveries on the control of translation elongation, highlighting its important role in translation repression and the synthesis of stress-response proteins. In this article, we discuss recent findings on mechanisms of elongation control mediated by ribosome pausing and collisions and the availability of tRNAs and elongation factors. We also discuss how elongation intersects with distinct modes of translation control, further supporting cellular viability and gene expression reprogramming. Finally, we highlight how several of these pathways are reversibly regulated, emphasizing the dynamics of translation control during stress-response progression. A comprehensive understanding of translation regulation under stress will produce fundamental knowledge of protein dynamics while opening new avenues and strategies to overcome dysregulated protein production and cellular sensitivity to stress.
Collapse
Affiliation(s)
| | | | - Gustavo M. Silva
- Department of Biology, Duke University, Durham, NC, USA
- Lead contact
| |
Collapse
|
6
|
Raymond WS, Ghaffari S, Aguilera LU, Ron E, Morisaki T, Fox ZR, May MP, Stasevich TJ, Munsky B. Using mechanistic models and machine learning to design single-color multiplexed nascent chain tracking experiments. Front Cell Dev Biol 2023; 11:1151318. [PMID: 37325568 PMCID: PMC10267835 DOI: 10.3389/fcell.2023.1151318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 05/09/2023] [Indexed: 06/17/2023] Open
Abstract
mRNA translation is the ubiquitous cellular process of reading messenger-RNA strands into functional proteins. Over the past decade, large strides in microscopy techniques have allowed observation of mRNA translation at a single-molecule resolution for self-consistent time-series measurements in live cells. Dubbed Nascent chain tracking (NCT), these methods have explored many temporal dynamics in mRNA translation uncaptured by other experimental methods such as ribosomal profiling, smFISH, pSILAC, BONCAT, or FUNCAT-PLA. However, NCT is currently restricted to the observation of one or two mRNA species at a time due to limits in the number of resolvable fluorescent tags. In this work, we propose a hybrid computational pipeline, where detailed mechanistic simulations produce realistic NCT videos, and machine learning is used to assess potential experimental designs for their ability to resolve multiple mRNA species using a single fluorescent color for all species. Our simulation results show that with careful application this hybrid design strategy could in principle be used to extend the number of mRNA species that could be watched simultaneously within the same cell. We present a simulated example NCT experiment with seven different mRNA species within the same simulated cell and use our ML labeling to identify these spots with 90% accuracy using only two distinct fluorescent tags. We conclude that the proposed extension to the NCT color palette should allow experimentalists to access a plethora of new experimental design possibilities, especially for cell Signaling applications requiring simultaneous study of multiple mRNAs.
Collapse
Affiliation(s)
- William S Raymond
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO, United States
| | - Sadaf Ghaffari
- Department of Computer Science, Colorado State University, Fort Collins, CO, United States
| | - Luis U Aguilera
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, United States
| | - Eric Ron
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO, United States
| | - Tatsuya Morisaki
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, United States
| | - Zachary R Fox
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO, United States
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Michael P May
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO, United States
| | - Timothy J Stasevich
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, United States
- World Research Hub Initiative and Cell Biology Unit, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Brian Munsky
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO, United States
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, United States
| |
Collapse
|
7
|
Zhang D, Zhu L, Wang F, Li P, Wang Y, Gao Y. Molecular mechanisms of eukaryotic translation fidelity and their associations with diseases. Int J Biol Macromol 2023; 242:124680. [PMID: 37141965 DOI: 10.1016/j.ijbiomac.2023.124680] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 04/27/2023] [Indexed: 05/06/2023]
Abstract
Converting genetic information into functional proteins is a complex, multi-step process, with each step being tightly regulated to ensure the accuracy of translation, which is critical to cellular health. In recent years, advances in modern biotechnology, especially the development of cryo-electron microscopy and single-molecule techniques, have enabled a clearer understanding of the mechanisms of protein translation fidelity. Although there are many studies on the regulation of protein translation in prokaryotes, and the basic elements of translation are highly conserved in prokaryotes and eukaryotes, there are still great differences in the specific regulatory mechanisms. This review describes how eukaryotic ribosomes and translation factors regulate protein translation and ensure translation accuracy. However, a certain frequency of translation errors does occur in translation, so we describe diseases that arise when the rate of translation errors reaches or exceeds a threshold of cellular tolerance.
Collapse
Affiliation(s)
- Dejiu Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Lei Zhu
- College of Basic Medical, Qingdao Binhai University, Qingdao, China
| | - Fei Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.
| | - Yanyan Gao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.
| |
Collapse
|
8
|
Rong Y, Jensen SI, Lindorff-Larsen K, Nielsen AT. Folding of heterologous proteins in bacterial cell factories: Cellular mechanisms and engineering strategies. Biotechnol Adv 2023; 63:108079. [PMID: 36528238 DOI: 10.1016/j.biotechadv.2022.108079] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 11/20/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022]
Abstract
The expression of correctly folded and functional heterologous proteins is important in many biotechnological production processes, whether it is enzymes, biopharmaceuticals or biosynthetic pathways for production of sustainable chemicals. For industrial applications, bacterial platform organisms, such as E. coli, are still broadly used due to the availability of tools and proven suitability at industrial scale. However, expression of heterologous proteins in these organisms can result in protein aggregation and low amounts of functional protein. This review provides an overview of the cellular mechanisms that can influence protein folding and expression, such as co-translational folding and assembly, chaperone binding, as well as protein quality control, across different model organisms. The knowledge of these mechanisms is then linked to different experimental methods that have been applied in order to improve functional heterologous protein folding, such as codon optimization, fusion tagging, chaperone co-production, as well as strain and protein engineering strategies.
Collapse
Affiliation(s)
- Yixin Rong
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Sheila Ingemann Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark.
| |
Collapse
|
9
|
Raymond WS, Ghaffari S, Aguilera LU, Ron E, Morisaki T, Fox ZR, May MP, Stasevich TJ, Munsky B. Using Mechanistic Models and Machine Learning to Design Single-Color Multiplexed Nascent Chain Tracking Experiments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.25.525583. [PMID: 36747627 PMCID: PMC9900927 DOI: 10.1101/2023.01.25.525583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
mRNA translation is the ubiquitous cellular process of reading messenger-RNA strands into functional proteins. Over the past decade, large strides in microscopy techniques have allowed observation of mRNA translation at a single-molecule resolution for self-consistent time-series measurements in live cells. Dubbed Nascent chain tracking (NCT), these methods have explored many temporal dynamics in mRNA translation uncaptured by other experimental methods such as ribosomal profiling, smFISH, pSILAC, BONCAT, or FUNCAT-PLA. However, NCT is currently restricted to the observation of one or two mRNA species at a time due to limits in the number of resolvable fluorescent tags. In this work, we propose a hybrid computational pipeline, where detailed mechanistic simulations produce realistic NCT videos, and machine learning is used to assess potential experimental designs for their ability to resolve multiple mRNA species using a single fluorescent color for all species. Through simulation, we show that with careful application, this hybrid design strategy could in principle be used to extend the number of mRNA species that could be watched simultaneously within the same cell. We present a simulated example NCT experiment with seven different mRNA species within the same simulated cell and use our ML labeling to identify these spots with 90% accuracy using only two distinct fluorescent tags. The proposed extension to the NCT color palette should allow experimentalists to access a plethora of new experimental design possibilities, especially for cell signalling applications requiring simultaneous study of multiple mRNAs.
Collapse
Affiliation(s)
- William S. Raymond
- School of Biomedical Engineering, Colorado State University, Fort Collins, Colorado, USA
| | - Sadaf Ghaffari
- Department of Computer Science, Colorado State University, Fort Collins, Colorado, USA
| | - Luis U. Aguilera
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, Colorado, USA
| | - Eric Ron
- School of Biomedical Engineering, Colorado State University, Fort Collins, Colorado, USA
| | - Tatsuya Morisaki
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Zachary R. Fox
- School of Biomedical Engineering, Colorado State University, Fort Collins, Colorado, USA,Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Michael P. May
- School of Biomedical Engineering, Colorado State University, Fort Collins, Colorado, USA
| | - Timothy J. Stasevich
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA,Cell Biology Unit, Institute of Innovative Research, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, Japan
| | - Brian Munsky
- School of Biomedical Engineering, Colorado State University, Fort Collins, Colorado, USA,Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, Colorado, USA,Corresponding Author: Brian Munsky -
| |
Collapse
|
10
|
Salimi K, Alvandi M, Saberi Pirouz M, Rakhshan K, Howatson G. Regulating eEF2 and eEF2K in skeletal muscle by exercise. Arch Physiol Biochem 2023:1-12. [PMID: 36633938 DOI: 10.1080/13813455.2023.2164898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 12/15/2022] [Accepted: 12/29/2022] [Indexed: 01/13/2023]
Abstract
Skeletal muscle is a flexible and adaptable tissue that strongly responds to exercise training. The skeletal muscle responds to exercise by increasing muscle protein synthesis (MPS) when energy is available. One of protein synthesis's major rate-limiting and critical regulatory steps is the translation elongation pathway. The process of translation elongation in skeletal muscle is highly regulated. It requires elongation factors that are intensely affected by various physiological stimuli such as exercise and the total available energy of cells. Studies have shown that exercise involves the elongation pathway by numerous signalling pathways. Since the elongation pathway, has been far less studied than the other translation steps, its comprehensive prospect and quantitative understanding remain in the dark. This study highlights the current understanding of the effect of exercise training on the translation elongation pathway focussing on the molecular factors affecting the pathway, including Ca2+, AMPK, PKA, mTORC1/P70S6K, MAPKs, and myostatin. We further discussed the mode and volume of exercise training intervention on the translation elongation pathway.What is the topic of this review? This review summarises the impacts of exercise training on the translation elongation pathway in skeletal muscle focussing on eEF2 and eEF2K.What advances does it highlight? This review highlights mechanisms and factors that profoundly influence the translation elongation pathway and argues that exercise might modulate the response. This review also combines the experimental observations focussing on the regulation of translation elongation during and after exercise. The findings widen our horizon to the notion of mechanisms involved in muscle protein synthesis (MPS) through translation elongation response to exercise training.
Collapse
Affiliation(s)
- Kia Salimi
- Department of Exercise Physiology, Faculty of Sport and Exercise Sciences, University of Tehran, Tehran, Iran
| | - Masoomeh Alvandi
- Department of Biological Science in Sport and Health, University of Shahid Beheshti, Tehran, Iran
| | - Mahdi Saberi Pirouz
- Student Research Committee, Iran University of Medical Sciences, Tehran, Iran
| | - Kamran Rakhshan
- Department of Medical Physiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Electrophysiology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Glyn Howatson
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
- Water Research Group, North West University, Potchefstroom, South Africa
| |
Collapse
|
11
|
Ayalew H, Peiris S, Chiluwal A, Kumar R, Tiwari M, Ostmeyer T, Bean S, Jagadish SVK. Stable sorghum grain quality QTL were identified using SC35 × RTx430 mapping population. THE PLANT GENOME 2022; 15:e20227. [PMID: 35880472 DOI: 10.1002/tpg2.20227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 04/18/2022] [Indexed: 06/15/2023]
Abstract
Understanding the genetic control and inheritance of grain quality traits is instrumental in facilitating end-use quality improvement. This study was conducted to identify and map quantitative trait loci (QTL) controlling protein, starch, and amylose content in grain sorghum [Sorghum bicolor (L.) Moench] grown under variable environmental conditions. A recombinant inbred line (RIL) population derived from a cross between RTx430 and SC35 was evaluated in six environments across Hays and Manhattan, KS. Significant variation was observed in genotype, environment, and genotype × environment interaction for all three quality traits. Unlike the RILs, the two parental lines did not show significant differences for these traits. However, significant transgressive segregation was observed for all traits resulting in phenotypic performance extending beyond the two parents. A total of seven protein, 10 starch, and 10 amylose content QTL were identified. Chromosomal regions and phenotypic variation (PVE) of QTL were variable across growing conditions. Quantitative trait loci hotspots for all three traits were detected on chromosomes 1 (115.2-119.2 cM) and 2 (118.2-127.4 cM). Candidate gene analysis indicated that these QTL hotspots were conditioned by several transcription factors, such as Cytochrome P450 and basic helix-loop-helix DNA binding protein, which regulate starch and protein accumulation in the grain. The identified genomic regions and underlying candidate genes provide a starting point for further validation and marker-assisted gene pyramiding to improve sorghum grain quality.
Collapse
Affiliation(s)
- Habtamu Ayalew
- Dep. of Agronomy, Kansas State Univ., Manhattan, KS, 66506, USA
| | - Shantha Peiris
- Grain Quality and Structure Research Unit, CGAHR, USDA-ARS, Manhattan, KS, 66502, USA
| | - Anuj Chiluwal
- Dep. of Agronomy, Kansas State Univ., Manhattan, KS, 66506, USA
| | - Ritesh Kumar
- Dep. of Agronomy, Kansas State Univ., Manhattan, KS, 66506, USA
| | - Manish Tiwari
- Dep. of Agronomy, Kansas State Univ., Manhattan, KS, 66506, USA
| | - Troy Ostmeyer
- Dep. of Agronomy, Kansas State Univ., Manhattan, KS, 66506, USA
| | - Scott Bean
- Grain Quality and Structure Research Unit, CGAHR, USDA-ARS, Manhattan, KS, 66502, USA
| | | |
Collapse
|
12
|
Cacioppo R, Lindon C. Regulating the regulator: a survey of mechanisms from transcription to translation controlling expression of mammalian cell cycle kinase Aurora A. Open Biol 2022; 12:220134. [PMID: 36067794 PMCID: PMC9448500 DOI: 10.1098/rsob.220134] [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] [Indexed: 11/12/2022] Open
Abstract
Aurora Kinase A (AURKA) is a positive regulator of mitosis with a strict cell cycle-dependent expression pattern. Recently, novel oncogenic roles of AURKA have been uncovered that are independent of the kinase activity and act within multiple signalling pathways, including cell proliferation, survival and cancer stem cell phenotypes. For this, cellular abundance of AURKA protein is per se crucial and must be tightly fine-tuned. Indeed, AURKA is found overexpressed in different cancers, typically as a result of gene amplification or enhanced transcription. It has however become clear that impaired processing, decay and translation of AURKA mRNA can also offer the basis for altered AURKA levels. Accordingly, the involvement of gene expression mechanisms controlling AURKA expression in human diseases is increasingly recognized and calls for much more research. Here, we explore and create an integrated view of the molecular processes regulating AURKA expression at the level of transcription, post-transcription and translation, intercalating discussion on how impaired regulation underlies disease. Given that targeting AURKA levels might affect more functions compared to inhibiting the kinase activity, deeper understanding of its gene expression may aid the design of alternative and therapeutically more successful ways of suppressing the AURKA oncogene.
Collapse
Affiliation(s)
- Roberta Cacioppo
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, UK
| | - Catherine Lindon
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, UK
| |
Collapse
|
13
|
Dastidar SG, Nair D. A Ribosomal Perspective on Neuronal Local Protein Synthesis. Front Mol Neurosci 2022; 15:823135. [PMID: 35283723 PMCID: PMC8904363 DOI: 10.3389/fnmol.2022.823135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 01/17/2022] [Indexed: 11/15/2022] Open
Abstract
Continued mRNA translation and protein production are critical for various neuronal functions. In addition to the precise sorting of proteins from cell soma to distant locations, protein synthesis allows a dynamic remodeling of the local proteome in a spatially variable manner. This spatial heterogeneity of protein synthesis is shaped by several factors such as injury, guidance cues, developmental cues, neuromodulators, and synaptic activity. In matured neurons, thousands of synapses are non-uniformly distributed throughout the dendritic arbor. At any given moment, the activity of individual synapses varies over a wide range, giving rise to the variability in protein synthesis. While past studies have primarily focused on the translation factors or the identity of translated mRNAs to explain the source of this variation, the role of ribosomes in this regard continues to remain unclear. Here, we discuss how several stochastic mechanisms modulate ribosomal functions, contributing to the variability in neuronal protein expression. Also, we point out several underexplored factors such as local ion concentration, availability of tRNA or ATP during translation, and molecular composition and organization of a compartment that can influence protein synthesis and its variability in neurons.
Collapse
|
14
|
Garin S, Levi O, Forrest ME, Antonellis A, Arava YS. Comprehensive characterization of mRNAs associated with yeast cytosolic aminoacyl-tRNA synthetases. RNA Biol 2021; 18:2605-2616. [PMID: 34039240 PMCID: PMC8632134 DOI: 10.1080/15476286.2021.1935116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/18/2021] [Accepted: 05/21/2021] [Indexed: 12/27/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are a conserved family of enzymes with an essential role in protein synthesis: ligating amino acids to cognate tRNA molecules for translation. In addition to their role in tRNA charging, aaRSs have acquired non-canonical functions, including post-transcriptional regulation of mRNA expression. Yet, the extent and mechanisms of these post-transcriptional functions are largely unknown. Herein, we performed a comprehensive transcriptome analysis to define the mRNAs that are associated with almost all aaRSs present in S. cerevisiae cytosol. Nineteen (out of twenty) isogenic strains of GFP-tagged cytosolic aaRSs were subjected to immunoprecipitation with anti-GFP beads along with an untagged control. mRNAs associated with each aaRS were then identified by RNA-seq. The extent of mRNA association varied significantly between aaRSs, from MetRS in which none appeared to be statistically significant, to PheRS that binds hundreds of different mRNAs. Interestingly, many target mRNAs are bound by multiple aaRSs, suggesting co-regulation by this family of enzymes. Gene Ontology analyses for aaRSs with a considerable number of target mRNAs discovered an enrichment for pathways of amino acid metabolism and of ribosome biosynthesis. Furthermore, sequence and structure motif analysis revealed for some aaRSs an enrichment for motifs that resemble the anticodon stem loop of cognate tRNAs. These data suggest that aaRSs coordinate mRNA expression in response to amino acid availability and may utilize RNA elements that mimic their canonical tRNA binding partners.
Collapse
Affiliation(s)
- Shahar Garin
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Ofri Levi
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Megan E. Forrest
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Anthony Antonellis
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Neurology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Yoav S. Arava
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| |
Collapse
|
15
|
Gobet C, Naef F. Ribo-DT: An automated pipeline for inferring codon dwell times from ribosome profiling data. Methods 2021; 203:10-16. [PMID: 34673173 DOI: 10.1016/j.ymeth.2021.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 11/16/2022] Open
Abstract
Protein synthesis is an energy consuming process characterised as a pivotal and highly regulated step in gene expression. The net protein output is dictated by a combination of translation initiation, elongation and termination rates that have remained difficult to measure. Recently, the development of ribosome profiling has enabled the inference of translation parameters through modelling, as this method informs on the ribosome position along the mRNA. Here, we present an automated, reproducible and portable computational pipeline to infer relative single-codon and codon-pair dwell times as well as gene flux from raw ribosome profiling sequencing data. As a case study, we applied our workflow to a publicly available yeast ribosome profiling dataset consisting of 57 independent gene knockouts related to RNA and tRNA modifications. We uncovered the effects of those modifications on translation elongation and codon selection during decoding. In particular, knocking out mod5 and trm7 increases codon-specific dwell times which indicates their potential tRNA targets, and highlights effects of nucleotide modifications on ribosome decoding rate.
Collapse
Affiliation(s)
- Cédric Gobet
- Institute of Bioengineering (IBI), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Félix Naef
- Institute of Bioengineering (IBI), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| |
Collapse
|
16
|
The radish Ogura fertility restorer impedes translation elongation along its cognate CMS-causing mRNA. Proc Natl Acad Sci U S A 2021; 118:2105274118. [PMID: 34433671 DOI: 10.1073/pnas.2105274118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The control of messenger RNA (mRNA) translation has been increasingly recognized as a key regulatory step for gene control, but clear examples in eukaryotes are still scarce. Nucleo-cytoplasmic male sterilities (CMS) represent ideal genetic models to dissect genetic interactions between the mitochondria and the nucleus in plants. This trait is determined by specific mitochondrial genes and is associated with a pollen sterility phenotype that can be suppressed by nuclear genes known as restorer-of-fertility (Rf). In this study, we focused on the Ogura CMS system in rapeseed and showed that reversion to male sterility by the PPR-B fertility restorer (also called Rfo) occurs through a specific translation inhibition of the mitochondria-encoded CMS-causing mRNA orf138 We also demonstrate that PPR-B binds within the coding sequence of orf138 and acts as a ribosome blocker to specifically impede translation elongation along the orf138 mRNA. Rfo is the first recognized fertility restorer shown to act this way. These observations will certainly facilitate the development of synthetic fertility restorers for CMS systems in which efficient natural Rfs are lacking.
Collapse
|
17
|
Yadav V, Ullah Irshad I, Kumar H, Sharma AK. Quantitative Modeling of Protein Synthesis Using Ribosome Profiling Data. Front Mol Biosci 2021; 8:688700. [PMID: 34262940 PMCID: PMC8274658 DOI: 10.3389/fmolb.2021.688700] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/25/2021] [Indexed: 12/12/2022] Open
Abstract
Quantitative prediction on protein synthesis requires accurate translation initiation and codon translation rates. Ribosome profiling data, which provide steady-state distribution of relative ribosome occupancies along a transcript, can be used to extract these rate parameters. Various methods have been developed in the past few years to measure translation-initiation and codon translation rates from ribosome profiling data. In the review, we provide a detailed analysis of the key methods employed to extract the translation rate parameters from ribosome profiling data. We further discuss how these approaches were used to decipher the role of various structural and sequence-based features of mRNA molecules in the regulation of gene expression. The utilization of these accurate rate parameters in computational modeling of protein synthesis may provide new insights into the kinetic control of the process of gene expression.
Collapse
Affiliation(s)
- Vandana Yadav
- Department of Physics, Indian Institute of Technology Madras, Chennai, India
| | | | - Hemant Kumar
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Ajeet K Sharma
- Department of Physics, Indian Institute of Technology Jammu, Jammu, India
| |
Collapse
|