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Snoeck S, Guidi C, De Mey M. "Metabolic burden" explained: stress symptoms and its related responses induced by (over)expression of (heterologous) proteins in Escherichia coli. Microb Cell Fact 2024; 23:96. [PMID: 38555441 PMCID: PMC10981312 DOI: 10.1186/s12934-024-02370-9] [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: 12/01/2023] [Accepted: 03/18/2024] [Indexed: 04/02/2024] Open
Abstract
BACKGROUND Engineering bacterial strains to redirect the metabolism towards the production of a specific product has enabled the development of industrial biotechnology. However, rewiring the metabolism can have severe implications for a microorganism, rendering cells with stress symptoms such as a decreased growth rate, impaired protein synthesis, genetic instability and an aberrant cell size. On an industrial scale, this is reflected in processes that are not economically viable. MAIN TEXT In literature, most stress symptoms are attributed to "metabolic burden", however the actual triggers and stress mechanisms involved are poorly understood. Therefore, in this literature review, we aimed to get a better insight in how metabolic engineering affects Escherichia coli and link the observed stress symptoms to its cause. Understanding the possible implications that chosen engineering strategies have, will help to guide the reader towards optimising the envisioned process more efficiently. CONCLUSION This review addresses the gap in literature and discusses the triggers and effects of stress mechanisms that can be activated when (over)expressing (heterologous) proteins in Escherichia coli. It uncovers that the activation of the different stress mechanisms is complex and that many are interconnected. The reader is shown that care has to be taken when (over)expressing (heterologous) proteins as the cell's metabolism is tightly regulated.
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Affiliation(s)
- Sofie Snoeck
- Department of Biotechnology, Centre for Synthetic Biology, Coupure Links 653, Gent, 9000, Belgium
| | - Chiara Guidi
- Department of Biotechnology, Centre for Synthetic Biology, Coupure Links 653, Gent, 9000, Belgium
| | - Marjan De Mey
- Department of Biotechnology, Centre for Synthetic Biology, Coupure Links 653, Gent, 9000, Belgium.
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2
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Vidal CM, Ouyang C, Qi Y, Mendez-Dorantes C, Coblentz A, Alva-Ornelas JA, Stark JM, Seewaldt VL, Ann DK. Arginine regulates HSPA5/BiP translation through ribosome pausing in triple-negative breast cancer cells. Br J Cancer 2023; 129:444-454. [PMID: 37386138 PMCID: PMC10403569 DOI: 10.1038/s41416-023-02322-x] [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: 12/13/2022] [Revised: 05/17/2023] [Accepted: 06/12/2023] [Indexed: 07/01/2023] Open
Abstract
BACKGROUND Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer with a high mortality rate due to a lack of therapeutic targets. Many TNBC cells are reliant on extracellular arginine for survival and express high levels of binding immunoglobin protein (BiP), a marker of metastasis and endoplasmic reticulum (ER) stress response. METHODS In this study, the effect of arginine shortage on BiP expression in the TNBC cell line MDA-MB-231 was evaluated. Two stable cell lines were generated in MDA-MB-231 cells: the first expressed wild-type BiP, and the second expressed a mutated BiP free of the two arginine pause-site codons, CCU and CGU, termed G-BiP. RESULTS The results showed that arginine shortage induced a non-canonical ER stress response by inhibiting BiP translation via ribosome pausing. Overexpression of G-BiP in MDA-MB-231 cells promoted cell resistance to arginine shortage compared to cells overexpressing wild-type BiP. Additionally, limiting arginine led to decreased levels of the spliced XBP1 in the G-BiP overexpressing cells, potentially contributing to their improved survival compared to the parental WT BiP overexpressing cells. CONCLUSION In conclusion, these findings suggest that the downregulation of BiP disrupts proteostasis during arginine shortage-induced non-canonical ER stress and plays a key role in cell growth inhibition, indicating BiP as a target of codon-specific ribosome pausing upon arginine shortage.
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Affiliation(s)
- Christina M Vidal
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
- Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Ching Ouyang
- Department of Computational and Quantitative Medicine, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Yue Qi
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Carlos Mendez-Dorantes
- Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Alaysia Coblentz
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Jackelyn A Alva-Ornelas
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Jeremy M Stark
- Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Victoria L Seewaldt
- Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - David K Ann
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA.
- Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA.
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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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Hsu DJ, Gao J, Yamaguchi N, Pinzaru A, Wu Q, Mandayam N, Liberti M, Heissel S, Alwaseem H, Tavazoie S, Tavazoie SF. Arginine limitation drives a directed codon-dependent DNA sequence evolution response in colorectal cancer cells. SCIENCE ADVANCES 2023; 9:eade9120. [PMID: 36608131 PMCID: PMC9821863 DOI: 10.1126/sciadv.ade9120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/01/2022] [Indexed: 05/18/2023]
Abstract
Utilization of specific codons varies between organisms. Cancer represents a model for understanding DNA sequence evolution and could reveal causal factors underlying codon evolution. We found that across human cancer, arginine codons are frequently mutated to other codons. Moreover, arginine limitation-a feature of tumor microenvironments-is sufficient to induce arginine codon-switching mutations in human colon cancer cells. Such DNA codon switching events encode mutant proteins with arginine residue substitutions. Mechanistically, arginine limitation caused rapid reduction of arginine transfer RNAs and the stalling of ribosomes over arginine codons. Such selective pressure against arginine codon translation induced an adaptive proteomic shift toward low-arginine codon-containing genes, including specific amino acid transporters, and caused mutational evolution away from arginine codons-reducing translational bottlenecks that occurred during arginine starvation. Thus, environmental availability of a specific amino acid can influence DNA sequence evolution away from its cognate codons and generate altered proteins.
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Affiliation(s)
- Dennis J. Hsu
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jenny Gao
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Norihiro Yamaguchi
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Alexandra Pinzaru
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Qiushuang Wu
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Nandan Mandayam
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Maria Liberti
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Søren Heissel
- Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Hanan Alwaseem
- Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Saeed Tavazoie
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Sohail F. Tavazoie
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
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5
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Hsu DJ, Gao J, Yamaguchi N, Pinzaru A, Mandayam N, Liberti M, Heissel S, Alwaseem H, Tavazoie S, Tavazoie SF. Arginine limitation causes a directed DNA sequence evolution response in colorectal cancer cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.02.521806. [PMID: 36711568 PMCID: PMC9881871 DOI: 10.1101/2023.01.02.521806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Utilization of specific codons varies significantly across organisms. Cancer represents a model for understanding DNA sequence evolution and could reveal causal factors underlying codon evolution. We found that across human cancer, arginine codons are frequently mutated to other codons. Moreover, arginine restriction-a feature of tumor microenvironments-is sufficient to induce arginine codon-switching mutations in human colon cancer cells. Such DNA codon switching events encode mutant proteins with arginine residue substitutions. Mechanistically, arginine limitation caused rapid reduction of arginine transfer RNAs and the stalling of ribosomes over arginine codons. Such selective pressure against arginine codon translation induced a proteomic shift towards low arginine codon containing genes, including specific amino acid transporters, and caused mutational evolution away from arginine codons-reducing translational bottlenecks that occurred during arginine starvation. Thus, environmental availability of a specific amino acid can influence DNA sequence evolution away from its cognate codons and generate altered proteins.
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Affiliation(s)
- Dennis J. Hsu
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jenny Gao
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Norihiro Yamaguchi
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Alexandra Pinzaru
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Nandan Mandayam
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Maria Liberti
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Søren Heissel
- Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Hanan Alwaseem
- Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Saeed Tavazoie
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY USA
| | - Sohail F. Tavazoie
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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6
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Leiva LE, Elgamal S, Leidel SA, Orellana O, Ibba M, Katz A. Oxidative stress strongly restricts the effect of codon choice on the efficiency of protein synthesis in Escherichia coli. Front Microbiol 2022; 13:1042675. [DOI: 10.3389/fmicb.2022.1042675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 11/04/2022] [Indexed: 11/30/2022] Open
Abstract
IntroductionThe response of enterobacteria to oxidative stress is usually considered to be regulated by transcription factors such as OxyR and SoxR. Nevertheless, several reports have shown that under oxidative stress the levels, modification and aminoacylation of tRNAs may be altered suggesting a role of codon bias in regulation of gene expression under this condition.MethodsIn order to characterize the effects of oxidative stress on translation elongation we constructed a library of 61 plasmids, each coding for the green fluorescent protein (GFP) translationally fused to a different set of four identical codons.ResultsUsing these reporters, we observed that GFP production levels vary widely (~15 fold) when Escherichia coli K-12 is cultured in minimal media as a consequence of codon choice variations. When bacteria are cultured under oxidative stress caused by paraquat the levels of GFP produced by most clones is reduced and, in contrast to control conditions, the range of GFP levels is restricted to a ~2 fold range. Restricting elongation of particular sequences does not increase the range of GFP production under oxidative stress, but altering translation initiation rates leads to an increase in this range.DiscussionAltogether, our results suggest that under normal conditions the speed of translation elongation is in the range of the speed of initiation and, consequently, codon choice impacts the speed of protein synthesis. In contrast, under oxidative stress translation initiation becomes much slower than elongation, limiting the speed of translation such that codon choice has at most only subtle effects on the overall output of translation.
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Komarova ES, Dontsova OA, Pyshnyi DV, Kabilov MR, Sergiev PV. Flow-Seq Method: Features and Application in Bacterial Translation Studies. Acta Naturae 2022; 14:20-37. [PMID: 36694903 PMCID: PMC9844084 DOI: 10.32607/actanaturae.11820] [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: 10/04/2022] [Accepted: 11/11/2022] [Indexed: 01/22/2023] Open
Abstract
The Flow-seq method is based on using reporter construct libraries, where a certain element regulating the gene expression of fluorescent reporter proteins is represented in many thousands of variants. Reporter construct libraries are introduced into cells, sorted according to their fluorescence level, and then subjected to next-generation sequencing. Therefore, it turns out to be possible to identify patterns that determine the expression efficiency, based on tens and hundreds of thousands of reporter constructs in one experiment. This method has become common in evaluating the efficiency of protein synthesis simultaneously by multiple mRNA variants. However, its potential is not confined to this area. In the presented review, a comparative analysis of the Flow-seq method and other alternative approaches used for translation efficiency evaluation of mRNA was carried out; the features of its application and the results obtained by Flow-seq were also considered.
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Affiliation(s)
- E. S. Komarova
- Institute of Functional Genomics, Lomonosov Moscow State University, Moscow, 119234 Russia
| | - O. A. Dontsova
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119234 Russia
- Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234 Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117437 Russia
| | - D. V. Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - M. R. Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - P. V. Sergiev
- Institute of Functional Genomics, Lomonosov Moscow State University, Moscow, 119234 Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119234 Russia
- Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234 Russia
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The best of both worlds: Dual systems of reasoning in animals and AI. Cognition 2022; 225:105118. [PMID: 35453083 DOI: 10.1016/j.cognition.2022.105118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/29/2022] [Accepted: 04/01/2022] [Indexed: 11/20/2022]
Abstract
Much of human cognition involves two different types of reasoning that operate together. Type 1 reasoning systems are intuitive and fast, whereas Type 2 reasoning systems are reflective and slow. Why has our cognition evolved with these features? Both systems are coherent and in most ecological circumstances either alone is capable of coming up with the right answer most of the time. Neural tissue is costly, and thus far evolutionary models have struggled to identify a benefit of operating two systems of reasoning. To explore this issue we take a broad comparative perspective. We discuss how dual processes of cognition have enabled the emergence of selective attention in insects, transforming the learning capacities of these animals. Modern AIs using dual systems of learning are able to learn how their vast world works and how best to interact with it, allowing them to exceed human levels of performance in strategy games. We propose that the core benefits of dual processes of reasoning are to narrow down a problem space in order to focus cognitive resources most effectively.
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Kocaoglu B, Alexander WH. Degeneracy measures in biologically plausible random Boolean networks. BMC Bioinformatics 2022; 23:71. [PMID: 35164672 PMCID: PMC8845291 DOI: 10.1186/s12859-022-04601-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 01/31/2022] [Indexed: 11/10/2022] Open
Abstract
Background Degeneracy—the ability of structurally different elements to perform similar functions—is a property of many biological systems. Highly degenerate systems show resilience to perturbations and damage because the system can compensate for compromised function due to reconfiguration of the underlying network dynamics. Degeneracy thus suggests how biological systems can thrive despite changes to internal and external demands. Although degeneracy is a feature of network topologies and seems to be implicated in a wide variety of biological processes, research on degeneracy in biological networks is mostly limited to weighted networks. In this study, we test an information theoretic definition of degeneracy on random Boolean networks, frequently used to model gene regulatory networks. Random Boolean networks are discrete dynamical systems with binary connectivity and thus, these networks are well-suited for tracing information flow and the causal effects. By generating networks with random binary wiring diagrams, we test the effects of systematic lesioning of connections and perturbations of the network nodes on the degeneracy measure. Results Our analysis shows that degeneracy, on average, is the highest in networks in which ~ 20% of the connections are lesioned while 50% of the nodes are perturbed. Moreover, our results for the networks with no lesions and the fully-lesioned networks are comparable to the degeneracy measures from weighted networks, thus we show that the degeneracy measure is applicable to different networks. Conclusions Such a generalized applicability implies that degeneracy measures may be a useful tool for investigating a wide range of biological networks and, therefore, can be used to make predictions about the variety of systems’ ability to recover function. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04601-5.
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Affiliation(s)
- Basak Kocaoglu
- Center for Complex Systems and Brain Sciences, Florida Atlantic University, Boca Raton, FL, USA. .,The Brain Institute, Florida Atlantic University, Jupiter, FL, 33431, USA.
| | - William H Alexander
- Center for Complex Systems and Brain Sciences, Florida Atlantic University, Boca Raton, FL, USA.,Department of Psychology, Florida Atlantic University, Boca Raton, FL, USA.,The Brain Institute, Florida Atlantic University, Jupiter, FL, 33431, USA
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10
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Single-cell Ribo-seq reveals cell cycle-dependent translational pausing. Nature 2021; 597:561-565. [PMID: 34497418 DOI: 10.1038/s41586-021-03887-4] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 08/06/2021] [Indexed: 12/21/2022]
Abstract
Single-cell sequencing methods have enabled in-depth analysis of the diversity of cell types and cell states in a wide range of organisms. These tools focus predominantly on sequencing the genomes1, epigenomes2 and transcriptomes3 of single cells. However, despite recent progress in detecting proteins by mass spectrometry with single-cell resolution4, it remains a major challenge to measure translation in individual cells. Here, building on existing protocols5-7, we have substantially increased the sensitivity of these assays to enable ribosome profiling in single cells. Integrated with a machine learning approach, this technology achieves single-codon resolution. We validate this method by demonstrating that limitation for a particular amino acid causes ribosome pausing at a subset of the codons encoding the amino acid. Of note, this pausing is only observed in a sub-population of cells correlating to its cell cycle state. We further expand on this phenomenon in non-limiting conditions and detect pronounced GAA pausing during mitosis. Finally, we demonstrate the applicability of this technique to rare primary enteroendocrine cells. This technology provides a first step towards determining the contribution of the translational process to the remarkable diversity between seemingly identical cells.
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11
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Li J, Shen Z, Luo L, Ye D, Deng H, Gu S, Zhou C. tRNA Ini CAT inhibits proliferation and promotes apoptosis of laryngeal squamous cell carcinoma cells. J Clin Lab Anal 2021; 35:e23821. [PMID: 34048096 PMCID: PMC8274982 DOI: 10.1002/jcla.23821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Laryngeal squamous cell carcinoma (LSCC) brings a heavy blow to the patient's voice. Transfer RNA (tRNA) is a common RNA, the roles of tRNAs in LSCC are largely unknown. METHODS The tRNA expression profile in LSCC tissues and adjacent normal tissues was measured by a tRNA qRT-PCR array. The expression level of tRNAIni CAT in LSCC tissues and plasmas was detected by qRT-PCR. The receiver operating characteristic (ROC) curve was established. tRNAIni CAT was upregulated by a lentivirus vector in the LSCC cell line. Moreover, tRNAIni CAT was upregulated in LSCC xenograft nude mouse model and the xenografts were used for pathological analysis and transmission electron microscope (TEM) observation. RESULTS The top 10 upregulated tRNAs were tRNALys CTT -1, tRNALeu TAA , tRNAPhe GAA , tRNALeu CAG , tRNATyr ATA , tRNAMet CAT , tRNATyr GTA -1, tRNAThr CGT , tRNATyr GTA -2, tRNAAla AGC ; and the top 10 downregulated tRNAs were tRNAIni CAT , mt-tRNAGlu TTC , tRNAVal CAC -3, mt-tRNATrp TCA , mt-tRNATyr GTA , mt-tRNALys TTT , mt-tRNAThr TGT , mt-tRNAAsp GTC , mt-tRNAAsn GTT , mt-tRNAPro TGG . tRNAIni CAT was downregulated in LSCC tissues and plasma. The area under the ROC curve (AUC) in LSCC tissues and the plasma of patients with LSCC was 0.717 and 0.808, respectively. tRNAIni CAT inhibited LSCC cell proliferation and promoted apoptosis. The in vivo results showed that tRNAIni CAT inhibited the growth of the xenografts and promoted apoptosis. CONCLUSIONS This is the first study to provide tRNA expression profiles for LSCC tissues. tRNAIni CAT may be used as a new biomarker for the early diagnosis of LSCC. tRNAIni CAT inhibits cell proliferation and promotes apoptosis in vitro and in vivo.
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MESH Headings
- Animals
- Apoptosis/genetics
- Carcinoma, Squamous Cell/blood
- Carcinoma, Squamous Cell/diagnosis
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/pathology
- Cell Line, Tumor
- Cell Proliferation/genetics
- Female
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Green Fluorescent Proteins/metabolism
- Humans
- Laryngeal Neoplasms/blood
- Laryngeal Neoplasms/diagnosis
- Laryngeal Neoplasms/genetics
- Laryngeal Neoplasms/pathology
- Mice, Inbred BALB C
- Mice, Nude
- RNA, Transfer/blood
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- ROC Curve
- Up-Regulation/genetics
- Xenograft Model Antitumor Assays
- Mice
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Affiliation(s)
- Jun Li
- Department of Otorhinolaryngology, Head and Neck SurgeryThe Affiliated LiHuili HospitalNingbo UniversityNingboChina
- Department of Biochemistry and Molecular BiologyZhejiang Key Laboratory of PathophysiologyNingbo University School of MedicalNingboChina
| | - Zhisen Shen
- Department of Otorhinolaryngology, Head and Neck SurgeryThe Affiliated LiHuili HospitalNingbo UniversityNingboChina
| | - Lin Luo
- Department of Biochemistry and Molecular BiologyZhejiang Key Laboratory of PathophysiologyNingbo University School of MedicalNingboChina
| | - Dong Ye
- Department of Otorhinolaryngology, Head and Neck SurgeryThe Affiliated LiHuili HospitalNingbo UniversityNingboChina
| | - Hongxia Deng
- Department of Otorhinolaryngology, Head and Neck SurgeryThe Affiliated LiHuili HospitalNingbo UniversityNingboChina
| | - Shanshan Gu
- Department of Otorhinolaryngology, Head and Neck SurgeryThe Affiliated LiHuili HospitalNingbo UniversityNingboChina
| | - Chongchang Zhou
- Department of Otorhinolaryngology, Head and Neck SurgeryThe Affiliated LiHuili HospitalNingbo UniversityNingboChina
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Abstract
Increased proliferation and protein synthesis are characteristics of transformed and tumor cells. Although the components of the translation machinery are often dysregulated in cancer, the role of tRNAs in cancer cells has not been well studied. Nevertheless, the number of related studies has recently started increasing. With the development of high throughput technologies such as next-generation sequencing, genome-wide differential tRNA expression patterns in breast cancer-derived cell lines and breast tumors have been investigated. The genome-wide transcriptomics analyses have been linked with many studies for functional and phenotypic characterization, whereby tRNAs or tRNA-related fragments have been shown to play important roles in breast cancer regulation and as promising prognostic biomarkers. Here, we review their expression patterns, functions, prognostic value, and potential therapeutic use as well as related technologies.
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13
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Arella D, Dilucca M, Giansanti A. Codon usage bias and environmental adaptation in microbial organisms. Mol Genet Genomics 2021; 296:751-762. [PMID: 33818631 PMCID: PMC8144148 DOI: 10.1007/s00438-021-01771-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 02/22/2021] [Indexed: 01/01/2023]
Abstract
In each genome, synonymous codons are used with different frequencies; this general phenomenon is known as codon usage bias. It has been previously recognised that codon usage bias could affect the cellular fitness and might be associated with the ecology of microbial organisms. In this exploratory study, we investigated the relationship between codon usage bias, lifestyles (thermophiles vs. mesophiles; pathogenic vs. non-pathogenic; halophilic vs. non-halophilic; aerobic vs. anaerobic and facultative) and habitats (aquatic, terrestrial, host-associated, specialised, multiple) of 615 microbial organisms (544 bacteria and 71 archaea). Principal component analysis revealed that species with given phenotypic traits and living in similar environmental conditions have similar codon preferences, as represented by the relative synonymous codon usage (RSCU) index, and similar spectra of tRNA availability, as gauged by the tRNA gene copy number (tGCN). Moreover, by measuring the average tRNA adaptation index (tAI) for each genome, an index that can be associated with translational efficiency, we observed that organisms able to live in multiple habitats, including facultative organisms, mesophiles and pathogenic bacteria, are characterised by a reduced translational efficiency, consistently with their need to adapt to different environments. Our results show that synonymous codon choices might be under strong translational selection, which modulates the choice of the codons to differently match tRNA availability, depending on the organism's lifestyle needs. To our knowledge, this is the first large-scale study that examines the role of codon bias and translational efficiency in the adaptation of microbial organisms to the environment in which they live.
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Affiliation(s)
- Davide Arella
- Department of Physics, Sapienza University of Rome, 00185, Rome, Italy.
| | - Maddalena Dilucca
- Department of Physics, Sapienza University of Rome, 001885, Rome, Italy
| | - Andrea Giansanti
- Department of Physics, Sapienza University of Rome, 00185, Rome, Italy
- INFN, Roma1 Unit, 00185, Rome, Italy
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14
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Balbontín R, Frazão N, Gordo I. DNA Breaks-Mediated Fitness Cost Reveals RNase HI as a New Target for Selectively Eliminating Antibiotic-Resistant Bacteria. Mol Biol Evol 2021; 38:3220-3234. [PMID: 33830249 PMCID: PMC8321526 DOI: 10.1093/molbev/msab093] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Antibiotic resistance often generates defects in bacterial growth called fitness cost. Understanding the causes of this cost is of paramount importance, as it is one of the main determinants of the prevalence of resistances upon reducing antibiotics use. Here we show that the fitness costs of antibiotic resistance mutations that affect transcription and translation in Escherichia coli strongly correlate with DNA breaks, which are generated via transcription–translation uncoupling, increased formation of RNA–DNA hybrids (R-loops), and elevated replication–transcription conflicts. We also demonstrated that the mechanisms generating DNA breaks are repeatedly targeted by compensatory evolution, and that DNA breaks and the cost of resistance can be increased by targeting the RNase HI, which specifically degrades R-loops. We further show that the DNA damage and thus the fitness cost caused by lack of RNase HI function drive resistant clones to extinction in populations with high initial frequency of resistance, both in laboratory conditions and in a mouse model of gut colonization. Thus, RNase HI provides a target specific against resistant bacteria, which we validate using a repurposed drug. In summary, we revealed key mechanisms underlying the fitness cost of antibiotic resistance mutations that can be exploited to specifically eliminate resistant bacteria.
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Affiliation(s)
| | | | - Isabel Gordo
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
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15
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do Couto Bordignon P, Pechmann S. Inferring translational heterogeneity from Saccharomyces cerevisiae ribosome profiling. FEBS J 2021; 288:4541-4559. [PMID: 33539640 DOI: 10.1111/febs.15748] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 01/27/2021] [Accepted: 02/02/2021] [Indexed: 11/30/2022]
Abstract
Translation of mRNAs into proteins by the ribosome is the most important step of protein biosynthesis. Accordingly, translation is tightly controlled and heavily regulated to maintain cellular homeostasis. Ribosome profiling (Ribo-seq) has revolutionized the study of translation by revealing many of its underlying mechanisms. However, equally many aspects of translation remain mysterious, in part also due to persisting challenges in the interpretation of data obtained from Ribo-seq experiments. Here, we show that some of the variability observed in Ribo-seq data has biological origins and reflects programmed heterogeneity of translation. Through a comparative analysis of Ribo-seq data from Saccharomyces cerevisiae, we systematically identify short 3-codon sequences that are differentially translated (DT) across mRNAs, that is, identical sequences that are translated sometimes fast and sometimes slowly beyond what can be attributed to variability between experiments. Remarkably, the thus identified DT sequences link to mechanisms known to regulate translation elongation and are enriched in genes important for protein and organelle biosynthesis. Our results thus highlight examples of translational heterogeneity that are encoded in the genomic sequences and tuned to optimizing cellular homeostasis. More generally, our work highlights the power of Ribo-seq to understand the complexities of translation regulation.
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16
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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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17
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Samatova E, Daberger J, Liutkute M, Rodnina MV. Translational Control by Ribosome Pausing in Bacteria: How a Non-uniform Pace of Translation Affects Protein Production and Folding. Front Microbiol 2021; 11:619430. [PMID: 33505387 PMCID: PMC7829197 DOI: 10.3389/fmicb.2020.619430] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/11/2020] [Indexed: 11/23/2022] Open
Abstract
Protein homeostasis of bacterial cells is maintained by coordinated processes of protein production, folding, and degradation. Translational efficiency of a given mRNA depends on how often the ribosomes initiate synthesis of a new polypeptide and how quickly they read the coding sequence to produce a full-length protein. The pace of ribosomes along the mRNA is not uniform: periods of rapid synthesis are separated by pauses. Here, we summarize recent evidence on how ribosome pausing affects translational efficiency and protein folding. We discuss the factors that slow down translation elongation and affect the quality of the newly synthesized protein. Ribosome pausing emerges as important factor contributing to the regulatory programs that ensure the quality of the proteome and integrate the cellular and environmental cues into regulatory circuits of the cell.
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Affiliation(s)
- Ekaterina Samatova
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Jan Daberger
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Marija Liutkute
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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18
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Katz A, Leidel SA, Ibba M. Editorial: Microbial Regulation of Translation. Front Genet 2020; 11:616946. [PMID: 33329755 PMCID: PMC7719694 DOI: 10.3389/fgene.2020.616946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 10/26/2020] [Indexed: 12/04/2022] Open
Affiliation(s)
- Assaf Katz
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomèdicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Sebastian A Leidel
- Research Group for RNA Biochemistry, Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Michael Ibba
- Schmid College of Science and Technology, Chapman University, Orange, CA, United States
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19
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Banh RS, Biancur DE, Yamamoto K, Sohn ASW, Walters B, Kuljanin M, Gikandi A, Wang H, Mancias JD, Schneider RJ, Pacold ME, Kimmelman AC. Neurons Release Serine to Support mRNA Translation in Pancreatic Cancer. Cell 2020; 183:1202-1218.e25. [PMID: 33142117 DOI: 10.1016/j.cell.2020.10.016] [Citation(s) in RCA: 135] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 08/31/2020] [Accepted: 10/06/2020] [Indexed: 12/23/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) tumors have a nutrient-poor, desmoplastic, and highly innervated tumor microenvironment. Although neurons can release stimulatory factors to accelerate PDAC tumorigenesis, the metabolic contribution of peripheral axons has not been explored. We found that peripheral axons release serine (Ser) to support the growth of exogenous Ser (exSer)-dependent PDAC cells during Ser/Gly (glycine) deprivation. Ser deprivation resulted in ribosomal stalling on two of the six Ser codons, TCC and TCT, and allowed the selective translation and secretion of nerve growth factor (NGF) by PDAC cells to promote tumor innervation. Consistent with this, exSer-dependent PDAC tumors grew slower and displayed enhanced innervation in mice on a Ser/Gly-free diet. Blockade of compensatory neuronal innervation using LOXO-101, a Trk-NGF inhibitor, further decreased PDAC tumor growth. Our data indicate that axonal-cancer metabolic crosstalk is a critical adaptation to support PDAC growth in nutrient poor environments.
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Affiliation(s)
- Robert S Banh
- Department of Radiation Oncology, Perlmutter Cancer Center, New York University Medical Center, New York, NY 10016, USA
| | - Douglas E Biancur
- Department of Radiation Oncology, Perlmutter Cancer Center, New York University Medical Center, New York, NY 10016, USA
| | - Keisuke Yamamoto
- Department of Radiation Oncology, Perlmutter Cancer Center, New York University Medical Center, New York, NY 10016, USA
| | - Albert S W Sohn
- Department of Radiation Oncology, Perlmutter Cancer Center, New York University Medical Center, New York, NY 10016, USA
| | - Beth Walters
- Department of Microbiology and Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Miljan Kuljanin
- Division of Genomic Stability and DNA Repair, Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Hale Family Pancreatic Cancer Research Center, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Ajami Gikandi
- Division of Genomic Stability and DNA Repair, Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Hale Family Pancreatic Cancer Research Center, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Huamin Wang
- Department of Anatomical Pathology, M.D. Anderson Cancer Center, University of Texas, Houston, TX 77030, USA
| | - Joseph D Mancias
- Division of Genomic Stability and DNA Repair, Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Hale Family Pancreatic Cancer Research Center, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Robert J Schneider
- Department of Radiation Oncology, Perlmutter Cancer Center, New York University Medical Center, New York, NY 10016, USA; Department of Microbiology and Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Michael E Pacold
- Department of Radiation Oncology, Perlmutter Cancer Center, New York University Medical Center, New York, NY 10016, USA
| | - Alec C Kimmelman
- Department of Radiation Oncology, Perlmutter Cancer Center, New York University Medical Center, New York, NY 10016, USA.
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20
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Leiva LE, Pincheira A, Elgamal S, Kienast SD, Bravo V, Leufken J, Gutiérrez D, Leidel SA, Ibba M, Katz A. Modulation of Escherichia coli Translation by the Specific Inactivation of tRNA Gly Under Oxidative Stress. Front Genet 2020; 11:856. [PMID: 33014012 PMCID: PMC7461829 DOI: 10.3389/fgene.2020.00856] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 07/14/2020] [Indexed: 11/17/2022] Open
Abstract
Bacterial oxidative stress responses are generally controlled by transcription factors that modulate the synthesis of RNAs with the aid of some sRNAs that control the stability, and in some cases the translation, of specific mRNAs. Here, we report that oxidative stress additionally leads to inactivation of tRNAGly in Escherichia coli, inducing a series of physiological changes. The observed inactivation of tRNAGly correlated with altered efficiency of translation of Gly codons, suggesting a possible mechanism of translational control of gene expression under oxidative stress. Changes in translation also depended on the availability of glycine, revealing a mechanism whereby bacteria modulate the response to oxidative stress according to the prevailing metabolic state of the cells.
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Affiliation(s)
- Lorenzo Eugenio Leiva
- Programa de Biología Celular y Molecular, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Andrea Pincheira
- Programa de Biología Celular y Molecular, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Sara Elgamal
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH, United States
| | - Sandra D Kienast
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Cells-in-Motion Cluster of Excellence and Faculty of Medicine, University of Münster, Münster, Germany.,Research Group for RNA Biochemistry, Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Verónica Bravo
- Unidad de Microbiología, Escuela de Medicina, Facultad de Ciencias Médicas, Universidad de Santiago de Chile, Santiago, Chile
| | - Johannes Leufken
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Cells-in-Motion Cluster of Excellence and Faculty of Medicine, University of Münster, Münster, Germany.,Research Group for RNA Biochemistry, Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Daniela Gutiérrez
- Programa de Biología Celular y Molecular, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Sebastian A Leidel
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Cells-in-Motion Cluster of Excellence and Faculty of Medicine, University of Münster, Münster, Germany.,Research Group for RNA Biochemistry, Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Michael Ibba
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH, United States
| | - Assaf Katz
- Programa de Biología Celular y Molecular, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
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21
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Parker DJ, Lalanne JB, Kimura S, Johnson GE, Waldor MK, Li GW. Growth-Optimized Aminoacyl-tRNA Synthetase Levels Prevent Maximal tRNA Charging. Cell Syst 2020; 11:121-130.e6. [PMID: 32726597 DOI: 10.1016/j.cels.2020.07.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 05/07/2020] [Accepted: 07/02/2020] [Indexed: 01/28/2023]
Abstract
Aminoacyl-tRNA synthetases (aaRSs) serve a dual role in charging tRNAs. Their enzymatic activities both provide protein synthesis flux and reduce uncharged tRNA levels. Although uncharged tRNAs can negatively impact bacterial growth, substantial concentrations of tRNAs remain deacylated even under nutrient-rich conditions. Here, we show that tRNA charging in Bacillus subtilis is not maximized due to optimization of aaRS production during rapid growth, which prioritizes demands in protein synthesis over charging levels. The presence of uncharged tRNAs is alleviated by precisely tuned translation kinetics and the stringent response, both insensitive to aaRS overproduction but sharply responsive to underproduction, allowing for just enough aaRS production atop a "fitness cliff." Notably, we find that the stringent response mitigates fitness defects at all aaRS underproduction levels even without external starvation. Thus, adherence to minimal, flux-satisfying protein production drives limited tRNA charging and provides a basis for the sensitivity and setpoints of an integrated growth-control network.
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Affiliation(s)
- Darren J Parker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jean-Benoît Lalanne
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Satoshi Kimura
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Grace E Johnson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Matthew K Waldor
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Gene-Wei Li
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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22
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Jores T, Tonnies J, Dorrity MW, Cuperus JT, Fields S, Queitsch C. Identification of Plant Enhancers and Their Constituent Elements by STARR-seq in Tobacco Leaves. THE PLANT CELL 2020; 32:2120-2131. [PMID: 32409318 PMCID: PMC7346570 DOI: 10.1105/tpc.20.00155] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/30/2020] [Accepted: 05/13/2020] [Indexed: 05/04/2023]
Abstract
Genetic engineering of cis-regulatory elements in crop plants is a promising strategy to ensure food security. However, such engineering is currently hindered by our limited knowledge of plant cis-regulatory elements. Here, we adapted self-transcribing active regulatory region sequencing (STARR-seq)-a technology for the high-throughput identification of enhancers-for its use in transiently transformed tobacco (Nicotiana benthamiana) leaves. We demonstrate that the optimal placement in the reporter construct of enhancer sequences from a plant virus, pea (Pisum sativum) and wheat (Triticum aestivum), was just upstream of a minimal promoter and that none of these four known enhancers was active in the 3' untranslated region of the reporter gene. The optimized assay sensitively identified small DNA regions containing each of the four enhancers, including two whose activity was stimulated by light. Furthermore, we coupled the assay to saturation mutagenesis to pinpoint functional regions within an enhancer, which we recombined to create synthetic enhancers. Our results describe an approach to define enhancer properties that can be performed in potentially any plant species or tissue transformable by Agrobacterium and that can use regulatory DNA derived from any plant genome.
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Affiliation(s)
- Tobias Jores
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
| | - Jackson Tonnies
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
- Graduate Program in Biology, University of Washington, Seattle, Washington 98195
| | - Michael W Dorrity
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
| | - Stanley Fields
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
- Department of Medicine, University of Washington, Seattle, Washington 98195
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
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23
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Luo Z, Hoffmann SA, Jiang S, Cai Y, Dai J. Probing eukaryotic genome functions with synthetic chromosomes. Exp Cell Res 2020; 390:111936. [PMID: 32165165 DOI: 10.1016/j.yexcr.2020.111936] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 02/25/2020] [Accepted: 02/29/2020] [Indexed: 02/07/2023]
Abstract
The ability to redesign and reconstruct a cell at whole-genome level provides new platforms for biological study. The international synthetic yeast genome project-Sc2.0, designed by interrogating knowledge amassed by the yeast community to date, exemplifies how a classical synthetic biology "design-build-test-learn" engineering cycle can effectively test hypotheses about various genome fundamentals. The genome reshuffling SCRaMbLE system implemented in synthetic yeast strains also provides unprecedented diversified resources for genotype-phenotype study and yeast metabolic engineering. Further development of genome synthesis technology will shed new lights on complex biological processes in higher eukaryotes.
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Affiliation(s)
- Zhouqing Luo
- Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Key Laboratory of Synthetic Genomics, Center for Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Stefan A Hoffmann
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, M1 7DN, Manchester, UK
| | - Shuangying Jiang
- Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Key Laboratory of Synthetic Genomics, Center for Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Yizhi Cai
- Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Key Laboratory of Synthetic Genomics, Center for Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, M1 7DN, Manchester, UK.
| | - Junbiao Dai
- Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Key Laboratory of Synthetic Genomics, Center for Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518055, China.
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24
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Jack BR, Boutz DR, Paff ML, Smith BL, Wilke CO. Transcript degradation and codon usage regulate gene expression in a lytic phage. Virus Evol 2019; 5:vez055. [PMID: 31908847 PMCID: PMC6938266 DOI: 10.1093/ve/vez055] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Many viral genomes are small, containing only single- or double-digit numbers of genes and relatively few regulatory elements. Yet viruses successfully execute complex regulatory programs as they take over their host cells. Here, we propose that some viruses regulate gene expression via a carefully balanced interplay between transcription, translation, and transcript degradation. As our model system, we employ bacteriophage T7, whose genome of approximately sixty genes is well annotated and for which there is a long history of computational models of gene regulation. We expand upon prior modeling work by implementing a stochastic gene expression simulator that tracks individual transcripts, polymerases, ribosomes, and ribonucleases participating in the transcription, translation, and transcript-degradation processes occurring during a T7 infection. By combining this detailed mechanistic modeling of a phage infection with high-throughput gene expression measurements of several strains of bacteriophage T7, evolved and engineered, we can show that both the dynamic interplay between transcription and transcript degradation, and between these two processes and translation, appear to be critical components of T7 gene regulation. Our results point to targeted degradation as a generic gene regulation strategy that may have evolved in many other viruses. Further, our results suggest that detailed mechanistic modeling may uncover the biological mechanisms at work in both evolved and engineered virus variants.
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Affiliation(s)
- Benjamin R Jack
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
| | - Daniel R Boutz
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Matthew L Paff
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
| | - Bartram L Smith
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
| | - Claus O Wilke
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
- Corresponding author: E-mail:
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25
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Kriner MA, Subramaniam AR. The serine transporter SdaC prevents cell lysis upon glucose depletion in Escherichia coli. Microbiologyopen 2019; 9:e960. [PMID: 31680488 PMCID: PMC7002108 DOI: 10.1002/mbo3.960] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/25/2019] [Accepted: 10/09/2019] [Indexed: 11/10/2022] Open
Abstract
The amino acid serine plays diverse metabolic roles, yet bacteria actively degrade exogenously provided serine via deamination to pyruvate. Serine deamination is thought to be a detoxification mechanism due to the ability of serine to inhibit several biosynthetic reactions, but this pathway remains highly active even in nutrient-replete conditions. While investigating the physiological roles of serine deamination in different growth conditions, we discovered that Escherichia coli cells lacking the sdaCB operon, which encodes the serine transporter SdaC and the serine deaminase SdaB, lyse upon glucose depletion in a medium containing no exogenous serine but all other amino acids and nucleobases. Unexpectedly, this lysis phenotype can be recapitulated by deleting sdaC alone and can be rescued by heterologous expression of SdaC. Lysis of ΔsdaC cells can be prevented by omitting glycine from the medium, inhibiting the glycine cleavage system, or by increasing alanine availability. Together, our results reveal that the serine transporter SdaC plays a critical role in maintaining amino acid homeostasis during shifts in nutrient availability in E. coli.
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Affiliation(s)
- Michelle A Kriner
- Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Arvind R Subramaniam
- Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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26
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Greenwich J, Reverdy A, Gozzi K, Di Cecco G, Tashjian T, Godoy-Carter V, Chai Y. A Decrease in Serine Levels during Growth Transition Triggers Biofilm Formation in Bacillus subtilis. J Bacteriol 2019; 201:e00155-19. [PMID: 31138626 PMCID: PMC6620397 DOI: 10.1128/jb.00155-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 05/17/2019] [Indexed: 12/12/2022] Open
Abstract
Biofilm development in Bacillus subtilis is regulated at multiple levels. While a number of known signals that trigger biofilm formation do so through the activation of one or more sensory histidine kinases, it was discovered that biofilm activation is also coordinated by sensing intracellular metabolic signals, including serine starvation. Serine starvation causes ribosomes to pause on specific serine codons, leading to a decrease in the translation rate of sinR, which encodes a master repressor for biofilm matrix genes and ultimately triggers biofilm induction. How serine levels change in different growth stages, how B. subtilis regulates intracellular serine levels, and how serine starvation triggers ribosomes to pause on selective serine codons remain unknown. Here, we show that serine levels decrease as cells enter stationary phase and that unlike most other amino acid biosynthesis genes, expression of serine biosynthesis genes decreases upon the transition into stationary phase. The deletion of the gene for a serine deaminase responsible for converting serine to pyruvate led to a delay in biofilm formation, further supporting the idea that serine levels are a critical intracellular signal for biofilm activation. Finally, we show that levels of all five serine tRNA isoacceptors are decreased in stationary phase compared with exponential phase. However, the three isoacceptors recognizing UCN serine codons are reduced to a much greater extent than the two that recognize AGC and AGU serine codons. Our findings provide evidence for a link between serine homeostasis and biofilm development in B. subtilisIMPORTANCE In Bacillus subtilis, biofilm formation is triggered in response to environmental and cellular signals. It was proposed that serine limitation acts as a proxy for nutrient status and triggers biofilm formation at the onset of biofilm entry through a novel signaling mechanism caused by global ribosome pausing on selective serine codons. In this study, we reveal that serine levels decrease at the biofilm entry due to catabolite control and a serine shunt mechanism. We also show that levels of five serine tRNA isoacceptors are differentially decreased in stationary phase compared with exponential phase; three isoacceptors recognizing UCN serine codons are reduced much more than the two recognizing AGC and AGU codons. This finding indicates a possible mechanism for selective ribosome pausing.
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Affiliation(s)
- Jennifer Greenwich
- Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | - Alicyn Reverdy
- Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | - Kevin Gozzi
- Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | - Grace Di Cecco
- Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | - Tommy Tashjian
- Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | | | - Yunrong Chai
- Department of Biology, Northeastern University, Boston, Massachusetts, USA
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27
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Fan Y, Thompson L, Lyu Z, Cameron TA, De Lay NR, Krachler AM, Ling J. Optimal translational fidelity is critical for Salmonella virulence and host interactions. Nucleic Acids Res 2019; 47:5356-5367. [PMID: 30941426 PMCID: PMC6547416 DOI: 10.1093/nar/gkz229] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/19/2019] [Accepted: 03/24/2019] [Indexed: 01/09/2023] Open
Abstract
Translational fidelity is required for accurate flow of genetic information, but is frequently altered by genetic changes and environmental stresses. To date, little is known about how translational fidelity affects the virulence and host interactions of bacterial pathogens. Here we show that surprisingly, either decreasing or increasing translational fidelity impairs the interactions of the enteric pathogen Salmonella Typhimurium with host cells and its fitness in zebrafish. Host interactions are mediated by Salmonella pathogenicity island 1 (SPI-1). Our RNA sequencing and quantitative RT-PCR results demonstrate that SPI-1 genes are among the most down-regulated when translational fidelity is either increased or decreased. Further, this down-regulation of SPI-1 genes depends on the master regulator HilD, and altering translational fidelity destabilizes HilD protein via enhanced degradation by Lon protease. Our work thus reveals that optimal translational fidelity is pivotal for adaptation of Salmonella to the host environment, and provides important mechanistic insights into this process.
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Affiliation(s)
- Yongqiang Fan
- College of Life and Health Sciences, Northeastern University, Shenyang 110819, People's Republic of China
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
- Shenyang National Laboratory for Materials Science, Northeastern University, Shenyang 110819, People's Republic of China
| | - Laurel Thompson
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Zhihui Lyu
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
| | - Todd A Cameron
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Nicholas R De Lay
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Anne Marie Krachler
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Jiqiang Ling
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
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28
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Darnell AM, Subramaniam AR, O'Shea EK. Translational Control through Differential Ribosome Pausing during Amino Acid Limitation in Mammalian Cells. Mol Cell 2019; 71:229-243.e11. [PMID: 30029003 DOI: 10.1016/j.molcel.2018.06.041] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 05/07/2018] [Accepted: 06/26/2018] [Indexed: 12/22/2022]
Abstract
Limitation for amino acids is thought to regulate translation in mammalian cells primarily by signaling through the kinases mTORC1 and GCN2. We find that a selective loss of arginine tRNA charging during limitation for arginine regulates translation through ribosome pausing at two of six arginine codons. Surprisingly, limitation for leucine, an essential and abundant amino acid in protein, results in little or no ribosome pausing. Chemical and genetic perturbation of mTORC1 and GCN2 signaling revealed that their robust response to leucine limitation prevents ribosome pausing, while an insufficient response to arginine limitation leads to loss of tRNA charging and ribosome pausing. Ribosome pausing decreases protein production and triggers premature ribosome termination without reducing mRNA levels. Together, our results suggest that amino acids that are not optimally sensed by the mTORC1 and GCN2 pathways still regulate translation through an evolutionarily conserved mechanism based on codon-specific ribosome pausing.
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Affiliation(s)
- Alicia M Darnell
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Arvind R Subramaniam
- Basic Sciences Division and Computational Biology Program of Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
| | - Erin K O'Shea
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA; Department of Chemistry and Chemical Biology and Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.
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29
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Du MZ, Wei W, Qin L, Liu S, Zhang AY, Zhang Y, Zhou H, Guo FB. Co-adaption of tRNA gene copy number and amino acid usage influences translation rates in three life domains. DNA Res 2018; 24:623-633. [PMID: 28992099 PMCID: PMC5726483 DOI: 10.1093/dnares/dsx030] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 06/15/2017] [Indexed: 12/01/2022] Open
Abstract
Although more and more entangled participants of translation process were realized, how they cooperate and co-determine the final translation efficiency still lacks details. Here, we reasoned that the basic translation components, tRNAs and amino acids should be consistent to maximize the efficiency and minimize the cost. We firstly revealed that 310 out of 410 investigated genomes of three domains had significant co-adaptions between the tRNA gene copy numbers and amino acid compositions, indicating that maximum efficiency constitutes ubiquitous selection pressure on protein translation. Furthermore, fast-growing and larger bacteria are found to have significantly better co-adaption and confirmed the effect of this pressure. Within organism, highly expressed proteins and those connected to acute responses have higher co-adaption intensity. Thus, the better co-adaption probably speeds up the growing of cells through accelerating the translation of special proteins. Experimentally, manipulating the tRNA gene copy number to optimize co-adaption between enhanced green fluorescent protein (EGFP) and tRNA gene set of Escherichia coli indeed lifted the translation rate (speed). Finally, as a newly confirmed translation rate regulating mechanism, the co-adaption reflecting translation rate not only deepens our understanding on translation process but also provides an easy and practicable method to improve protein translation rates and productivity.
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Affiliation(s)
| | - Wen Wei
- School of Life Science and Technology
| | - Lei Qin
- School of Life Science and Technology
| | - Shuo Liu
- School of Life Science and Technology
| | - An-Ying Zhang
- School of Life Science and Technology.,Centre for Informational Biology
| | - Yong Zhang
- School of Life Science and Technology.,Centre for Informational Biology
| | - Hong Zhou
- School of Life Science and Technology.,Centre for Informational Biology
| | - Feng-Biao Guo
- School of Life Science and Technology.,Centre for Informational Biology.,Key Laboratory for Neuroinformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, China
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30
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Abstract
The pool of transfer RNA (tRNA) molecules in cells allows the ribosome to decode genetic information. This repertoire of molecular decoders is positioned in the crossroad of the genome, the transcriptome, and the proteome. Omics and systems biology now allow scientists to explore the entire repertoire of tRNAs of many organisms, revealing basic exciting biology. The tRNA gene set of hundreds of species is now characterized, in addition to the tRNA genes of organelles and viruses. Genes encoding tRNAs for certain anticodon types appear in dozens of copies in a genome, while others are universally absent from any genome. Transcriptome measurement of tRNAs is challenging, but in recent years new technologies have allowed researchers to determine the dynamic expression patterns of tRNAs. These advances reveal that availability of ready-to-translate tRNA molecules is highly controlled by several transcriptional and posttranscriptional regulatory processes. This regulation shapes the proteome according to the cellular state. The tRNA pool profoundly impacts many aspects of cellular and organismal life, including protein expression level, translation accuracy, adequacy of folding, and even mRNA stability. As a result, the shape of the tRNA pool affects organismal health and may participate in causing conditions such as cancer and neurological conditions.
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Affiliation(s)
- Roni Rak
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100 Israel;
| | - Orna Dahan
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100 Israel;
| | - Yitzhak Pilpel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100 Israel;
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31
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Li SHJ, Li Z, Park JO, King CG, Rabinowitz JD, Wingreen NS, Gitai Z. Escherichia coli translation strategies differ across carbon, nitrogen and phosphorus limitation conditions. Nat Microbiol 2018; 3:939-947. [PMID: 30038306 DOI: 10.1038/s41564-018-0199-2] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 06/15/2018] [Indexed: 11/09/2022]
Abstract
For cells to grow faster they must increase their protein production rate. Microorganisms have traditionally been thought to accomplish this increase by producing more ribosomes to enhance protein synthesis capacity, leading to the linear relationship between ribosome level and growth rate observed under most growth conditions previously examined. Past studies have suggested that this linear relationship represents an optimal resource allocation strategy for each growth rate, independent of any specific nutrient state. Here we investigate protein production strategies in continuous cultures limited for carbon, nitrogen and phosphorus, which differentially impact substrate supply for protein versus nucleic acid metabolism. Unexpectedly, we find that at slow growth rates, Escherichia coli achieves the same protein production rate using three different strategies under the three different nutrient limitations. Under phosphorus (P) limitation, translation is slow due to a particularly low abundance of ribosomes, which are RNA-rich and thus particularly costly for phosphorous-limited cells. Under nitrogen (N) limitation, translation elongation is slowed by processes including ribosome stalling at glutamine codons. Under carbon (C) limitation, translation is slowed by accumulation of inactive ribosomes not bound to messenger RNA. These extra ribosomes enable rapid growth acceleration during nutrient upshift. Thus, bacteria tune ribosome usage across different limiting nutrients to enable balanced nutrient-limited growth while also preparing for future nutrient upshifts.
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Affiliation(s)
| | - Zhiyuan Li
- Princeton Center for Theoretical Science, Princeton University, Princeton, NJ, USA
| | - Junyoung O Park
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.,Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA.,Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA, USA
| | | | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.,Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Ned S Wingreen
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA. .,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
| | - Zemer Gitai
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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32
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Rojas J, Castillo G, Leiva LE, Elgamal S, Orellana O, Ibba M, Katz A. Codon usage revisited: Lack of correlation between codon usage and the number of tRNA genes in enterobacteria. Biochem Biophys Res Commun 2018; 502:450-455. [PMID: 29859934 DOI: 10.1016/j.bbrc.2018.05.168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 05/25/2018] [Indexed: 01/01/2023]
Abstract
It is widely believed that if a high number of genes are found for any tRNA in a rapidly replicating bacteria, then the cytoplasmic levels of that tRNA will be high and an open reading frame containing a higher frequency of the complementary codon will be translated faster. This idea is based on correlations between the number of tRNA genes, tRNA concentration and the frequency of codon usage observed in a limited number of strains as well as from the fact that artificially changing the number of tRNA genes alters translation efficiency and consequently the amount of properly folded protein synthesized. tRNA gene number may greatly vary in a genome due to duplications, deletions and lateral transfer which in turn would alter the levels and functionality of many proteins. Such changes are potentially deleterious for fitness and as a result it is expected that changes in tRNA gene numbers should be accompanied by a modification of the frequency of codon usage. In contrast to this model, when comparing the number of tRNA genes and the frequency of codon usage of several Salmonella enterica and Escherichia coli strains we found that changes in the number of tRNA genes are not correlated to changes in codon usage. Furthermore, these changes are not correlated with a change in the efficiency of codon translation. These results suggest that once a genome gains or loses tRNA genes, it responds by modulating the concentrations of tRNAs rather than modifying its frequency of codon usage.
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Affiliation(s)
- Joaquín Rojas
- Programa de Biología Celular y Molecular, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, 8380453, Chile
| | - Gabriel Castillo
- Programa de Biología Celular y Molecular, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, 8380453, Chile
| | - Lorenzo Eugenio Leiva
- Programa de Biología Celular y Molecular, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, 8380453, Chile
| | - Sara Elgamal
- Department of Microbiology and The Center for RNA Biology, Ohio State University, Columbus, OH, 43210, USA
| | - Omar Orellana
- Programa de Biología Celular y Molecular, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, 8380453, Chile
| | - Michael Ibba
- Department of Microbiology and The Center for RNA Biology, Ohio State University, Columbus, OH, 43210, USA
| | - Assaf Katz
- Programa de Biología Celular y Molecular, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, 8380453, Chile.
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33
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Codon usage of highly expressed genes affects proteome-wide translation efficiency. Proc Natl Acad Sci U S A 2018; 115:E4940-E4949. [PMID: 29735666 DOI: 10.1073/pnas.1719375115] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although the genetic code is redundant, synonymous codons for the same amino acid are not used with equal frequencies in genomes, a phenomenon termed "codon usage bias." Previous studies have demonstrated that synonymous changes in a coding sequence can exert significant cis effects on the gene's expression level. However, whether the codon composition of a gene can also affect the translation efficiency of other genes has not been thoroughly explored. To study how codon usage bias influences the cellular economy of translation, we massively converted abundant codons to their rare synonymous counterpart in several highly expressed genes in Escherichia coli This perturbation reduces both the cellular fitness and the translation efficiency of genes that have high initiation rates and are naturally enriched with the manipulated codon, in agreement with theoretical predictions. Interestingly, we could alleviate the observed phenotypes by increasing the supply of the tRNA for the highly demanded codon, thus demonstrating that the codon usage of highly expressed genes was selected in evolution to maintain the efficiency of global protein translation.
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34
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Pan T. Modifications and functional genomics of human transfer RNA. Cell Res 2018; 28:395-404. [PMID: 29463900 PMCID: PMC5939049 DOI: 10.1038/s41422-018-0013-y] [Citation(s) in RCA: 225] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 12/27/2017] [Indexed: 11/18/2022] Open
Abstract
Transfer RNA (tRNA) is present at tens of millions of transcripts in a human cell and is the most abundant RNA in moles among all cellular RNAs. tRNA is also the most extensively modified RNA with, on an average, 13 modifications per molecule. The primary function of tRNA as the adaptor of amino acids and the genetic code in protein synthesis is well known. tRNA modifications play multi-faceted roles in decoding and other cellular processes. The abundance, modification, and aminoacylation (charging) levels of tRNAs contribute to mRNA decoding in ways that reflect the cell type and its environment; however, how these factors work together to maximize translation efficiency remains to be understood. tRNAs also interact with many proteins not involved in translation and this may coordinate translation activity and other processes in the cell. This review focuses on the modifications and the functional genomics of human tRNA and discusses future perspectives on the explorations of human tRNA biology.
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Affiliation(s)
- Tao Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA.
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35
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Kwon NH, Lee MR, Kong J, Park SK, Hwang BJ, Kim BG, Lee ES, Moon HG, Kim S. Transfer-RNA-mediated enhancement of ribosomal proteins S6 kinases signaling for cell proliferation. RNA Biol 2018; 15:635-648. [PMID: 28816616 PMCID: PMC6103689 DOI: 10.1080/15476286.2017.1356563] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
While transfer-RNAs (tRNAs) are known to transport amino acids to ribosome, new functions are being unveiled from tRNAs and their fragments beyond protein synthesis. Here we show that phosphorylation of 90-kDa RPS6K (ribosomal proteins S6 kinase) was enhanced by tRNALeu overexpression under amino acids starvation condition. The phosphorylation of 90-kDa RPS6K was decreased by siRNA specific to tRNALeu and was independent to mTOR (mammalian target of rapamycin) signaling. Among the 90-kDa RPS6K family, RSK1 (ribosomal S6 kinase 1) and MSK2 (mitogen-and stress-activated protein kinase 2) were the major kinases phosphorylated by tRNALeu overexpression. Through SILAC (stable isotope labeling by/with amino acids in cell culture) and combined mass spectrometry analysis, we identified EBP1 (ErbB3-binding protein 1) as the tRNALeu-binding protein. We suspected that the overexpression of free tRNALeu would reinforce ErbB2/ErbB3 signaling pathway by disturbing the interaction between ErbB3 and EBP1, resulting in RSK1/MSK2 phosphorylation, improving cell proliferation and resistance to death. Analysis of samples from patients with breast cancer also indicated an association between tRNALeu overexpression and the ErbB2-positive population. Our results suggested a possible link between tRNALeu overexpression and RSK1/MSK2 activation and ErbB2/ErbB3 signaling.
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Affiliation(s)
- Nam Hoon Kwon
- a Medicinal Bioconvergence Research Center , Seoul National University , Suwon , Gyeonggi , Korea
| | - Mi Ran Lee
- a Medicinal Bioconvergence Research Center , Seoul National University , Suwon , Gyeonggi , Korea
| | - Jiwon Kong
- a Medicinal Bioconvergence Research Center , Seoul National University , Suwon , Gyeonggi , Korea.,b Department of Pharmacy , Seoul National University , Seoul , Korea
| | - Seung Kyun Park
- c Department of Molecular Bioscience , College of Biomedical Science, Kangwon National University , Chuncheon , Kangwon , Korea
| | - Byung Joon Hwang
- c Department of Molecular Bioscience , College of Biomedical Science, Kangwon National University , Chuncheon , Kangwon , Korea
| | - Byung Gyu Kim
- a Medicinal Bioconvergence Research Center , Seoul National University , Suwon , Gyeonggi , Korea
| | - Eun-Shin Lee
- d Department of Surgery , Seoul National University College of Medicine , Seoul , Korea
| | - Hyeong-Gon Moon
- d Department of Surgery , Seoul National University College of Medicine , Seoul , Korea
| | - Sunghoon Kim
- a Medicinal Bioconvergence Research Center , Seoul National University , Suwon , Gyeonggi , Korea.,e Department of Molecular Medicine and Biopharmaceutical Sciences , Graduate School of Convergence Science and Technology, Seoul National University , Suwon , Gyeonggi , Korea
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36
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Willis IM, Moir RD. Signaling to and from the RNA Polymerase III Transcription and Processing Machinery. Annu Rev Biochem 2018; 87:75-100. [PMID: 29328783 DOI: 10.1146/annurev-biochem-062917-012624] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
RNA polymerase (Pol) III has a specialized role in transcribing the most abundant RNAs in eukaryotic cells, transfer RNAs (tRNAs), along with other ubiquitous small noncoding RNAs, many of which have functions related to the ribosome and protein synthesis. The high energetic cost of producing these RNAs and their central role in protein synthesis underlie the robust regulation of Pol III transcription in response to nutrients and stress by growth regulatory pathways. Downstream of Pol III, signaling impacts posttranscriptional processes affecting tRNA function in translation and tRNA cleavage into smaller fragments that are increasingly attributed with novel cellular activities. In this review, we consider how nutrients and stress control Pol III transcription via its factors and its negative regulator, Maf1. We highlight recent work showing that the composition of the tRNA population and the function of individual tRNAs is dynamically controlled and that unrestrained Pol III transcription can reprogram central metabolic pathways.
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Affiliation(s)
- Ian M Willis
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA; , .,Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Robyn D Moir
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA; ,
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37
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Fan Y, Evans CR, Barber KW, Banerjee K, Weiss KJ, Margolin W, Igoshin OA, Rinehart J, Ling J. Heterogeneity of Stop Codon Readthrough in Single Bacterial Cells and Implications for Population Fitness. Mol Cell 2017; 67:826-836.e5. [PMID: 28781237 PMCID: PMC5591071 DOI: 10.1016/j.molcel.2017.07.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 05/22/2017] [Accepted: 07/07/2017] [Indexed: 12/30/2022]
Abstract
Gene expression noise (heterogeneity) leads to phenotypic diversity among isogenic individual cells. Our current understanding of gene expression noise is mostly limited to transcription, as separating translational noise from transcriptional noise has been challenging. It also remains unclear how translational heterogeneity originates. Using a transcription-normalized reporter system, we discovered that stop codon readthrough is heterogeneous among single cells, and individual cells with higher UGA readthrough grow faster from stationary phase. Our work also revealed that individual cells with lower protein synthesis levels exhibited higher UGA readthrough, which was confirmed with ribosome-targeting antibiotics (e.g., chloramphenicol). Further experiments and mathematical modeling suggest that varied competition between ternary complexes and release factors perturbs the UGA readthrough level. Our results indicate that fluctuations in the concentrations of translational components lead to UGA readthrough heterogeneity among single cells, which enhances phenotypic diversity of the genetically identical population and facilitates its adaptation to changing environments.
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MESH Headings
- Bacterial Proteins/biosynthesis
- Bacterial Proteins/genetics
- Codon, Terminator
- Escherichia coli/genetics
- Escherichia coli/growth & development
- Escherichia coli/metabolism
- Escherichia coli Proteins/biosynthesis
- Escherichia coli Proteins/genetics
- Gene Expression Regulation, Bacterial
- Genes, Reporter
- Genetic Fitness
- Genotype
- Kinetics
- Luminescent Proteins/biosynthesis
- Luminescent Proteins/genetics
- Microscopy, Fluorescence
- Models, Genetic
- One-Carbon Group Transferases
- Phenotype
- RNA, Bacterial/biosynthesis
- RNA, Bacterial/genetics
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- Transcription, Genetic
- Red Fluorescent Protein
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Affiliation(s)
- Yongqiang Fan
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Christopher R Evans
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Karl W Barber
- Department of Cellular & Molecular Physiology, Yale University, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Kinshuk Banerjee
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
| | - Kalyn J Weiss
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - William Margolin
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Oleg A Igoshin
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA; Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Jesse Rinehart
- Department of Cellular & Molecular Physiology, Yale University, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Jiqiang Ling
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, Houston, TX 77030, USA.
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38
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Evans ME, Clark WC, Zheng G, Pan T. Determination of tRNA aminoacylation levels by high-throughput sequencing. Nucleic Acids Res 2017; 45:e133. [PMID: 28586482 PMCID: PMC5737633 DOI: 10.1093/nar/gkx514] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/15/2017] [Accepted: 05/31/2017] [Indexed: 01/03/2023] Open
Abstract
Transfer RNA (tRNA) decodes mRNA codons when aminoacylated (charged) with an amino acid at its 3' end. Charged tRNAs turn over rapidly in cells, and variations in charged tRNA fractions are known to be a useful parameter in cellular responses to stress. tRNA charging fractions can be measured for individual tRNA species using acid denaturing gels, or comparatively at the genome level using microarrays. These hybridization-based approaches cannot be used for high resolution analysis of mammalian tRNAs due to their large sequence diversity. Here we develop a high-throughput sequencing method that enables accurate determination of charged tRNA fractions at single-base resolution (Charged DM-tRNA-seq). Our method takes advantage of the recently developed DM-tRNA-seq method, but includes additional chemical steps that specifically remove the 3'A residue in uncharged tRNA. Charging fraction is obtained by counting the fraction of A-ending reads versus A+C-ending reads for each tRNA species in the same sequencing reaction. In HEK293T cells, most cytosolic tRNAs are charged at >80% levels, whereas tRNASer and tRNAThr are charged at lower levels. These low charging levels were validated using acid denaturing gels. Our method should be widely applicable for investigations of tRNA charging as a parameter in biological regulation.
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Affiliation(s)
- Molly E. Evans
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Wesley C. Clark
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Guanqun Zheng
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Tao Pan
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL 60637, USA
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39
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Ferrin MA, Subramaniam AR. Kinetic modeling predicts a stimulatory role for ribosome collisions at elongation stall sites in bacteria. eLife 2017; 6. [PMID: 28498106 PMCID: PMC5446239 DOI: 10.7554/elife.23629] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 05/10/2017] [Indexed: 02/01/2023] Open
Abstract
Ribosome stalling on mRNAs can decrease protein expression. To decipher ribosome kinetics at stall sites, we induced ribosome stalling at specific codons by starving the bacterium Escherichia coli for the cognate amino acid. We measured protein synthesis rates from a reporter library of over 100 variants that encoded systematic perturbations of translation initiation rate, the number of stall sites, and the distance between stall sites. Our measurements are quantitatively inconsistent with two widely-used kinetic models for stalled ribosomes: ribosome traffic jams that block initiation, and abortive (premature) termination of stalled ribosomes. Rather, our measurements support a model in which collision with a trailing ribosome causes abortive termination of the stalled ribosome. In our computational analysis, ribosome collisions selectively stimulate abortive termination without fine-tuning of kinetic rate parameters at ribosome stall sites. We propose that ribosome collisions serve as a robust timer for translational quality control pathways to recognize stalled ribosomes.
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Affiliation(s)
- Michael A Ferrin
- Basic Sciences Division and Computational Biology Program of Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Arvind R Subramaniam
- Basic Sciences Division and Computational Biology Program of Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States
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40
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When mRNA translation meets decay. Biochem Soc Trans 2017; 45:339-351. [DOI: 10.1042/bst20160243] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Revised: 12/19/2016] [Accepted: 01/11/2017] [Indexed: 12/26/2022]
Abstract
Messenger RNA (mRNA) translation and mRNA degradation are important determinants of protein output, and they are interconnected. Previously, it was thought that translation of an mRNA, as a rule, prevents its degradation. mRNA surveillance mechanisms, which degrade mRNAs as a consequence of their translation, were considered to be exceptions to this rule. Recently, however, it has become clear that many mRNAs are degraded co-translationally, and it has emerged that codon choice, by influencing the rate of ribosome elongation, affects the rate of mRNA decay. In this review, we discuss the links between translation and mRNA stability, with an emphasis on emerging data suggesting that codon optimality may regulate mRNA degradation.
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41
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Maraia RJ, Arimbasseri AG. Factors That Shape Eukaryotic tRNAomes: Processing, Modification and Anticodon-Codon Use. Biomolecules 2017; 7:biom7010026. [PMID: 28282871 PMCID: PMC5372738 DOI: 10.3390/biom7010026] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 02/24/2017] [Indexed: 01/24/2023] Open
Abstract
Transfer RNAs (tRNAs) contain sequence diversity beyond their anticodons and the large variety of nucleotide modifications found in all kingdoms of life. Some modifications stabilize structure and fit in the ribosome whereas those to the anticodon loop modulate messenger RNA (mRNA) decoding activity more directly. The identities of tRNAs with some universal anticodon loop modifications vary among distant and parallel species, likely to accommodate fine tuning for their translation systems. This plasticity in positions 34 (wobble) and 37 is reflected in codon use bias. Here, we review convergent evidence that suggest that expansion of the eukaryotic tRNAome was supported by its dedicated RNA polymerase III transcription system and coupling to the precursor-tRNA chaperone, La protein. We also review aspects of eukaryotic tRNAome evolution involving G34/A34 anticodon-sparing, relation to A34 modification to inosine, biased codon use and regulatory information in the redundancy (synonymous) component of the genetic code. We then review interdependent anticodon loop modifications involving position 37 in eukaryotes. This includes the eukaryote-specific tRNA modification, 3-methylcytidine-32 (m3C32) and the responsible gene, TRM140 and homologs which were duplicated and subspecialized for isoacceptor-specific substrates and dependence on i6A37 or t6A37. The genetics of tRNA function is relevant to health directly and as disease modifiers.
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Affiliation(s)
- Richard J Maraia
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA.
- Commissioned Corps, U.S. Public Health Service, Rockville, MD, 20016, USA.
| | - Aneeshkumar G Arimbasseri
- Molecular Genetics Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India.
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42
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Frumkin I, Schirman D, Rotman A, Li F, Zahavi L, Mordret E, Asraf O, Wu S, Levy SF, Pilpel Y. Gene Architectures that Minimize Cost of Gene Expression. Mol Cell 2016; 65:142-153. [PMID: 27989436 DOI: 10.1016/j.molcel.2016.11.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 10/10/2016] [Accepted: 11/01/2016] [Indexed: 11/30/2022]
Abstract
Gene expression burdens cells by consuming resources and energy. While numerous studies have investigated regulation of expression level, little is known about gene design elements that govern expression costs. Here, we ask how cells minimize production costs while maintaining a given protein expression level and whether there are gene architectures that optimize this process. We measured fitness of ∼14,000 E. coli strains, each expressing a reporter gene with a unique 5' architecture. By comparing cost-effective and ineffective architectures, we found that cost per protein molecule could be minimized by lowering transcription levels, regulating translation speeds, and utilizing amino acids that are cheap to synthesize and that are less hydrophobic. We then examined natural E. coli genes and found that highly expressed genes have evolved more forcefully to minimize costs associated with their expression. Our study thus elucidates gene design elements that improve the economy of protein expression in natural and heterologous systems.
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Affiliation(s)
- Idan Frumkin
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Dvir Schirman
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Aviv Rotman
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Fangfei Li
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA; Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Liron Zahavi
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Ernest Mordret
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Omer Asraf
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Song Wu
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Sasha F Levy
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA; Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Yitzhak Pilpel
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel.
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43
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Goodarzi H, Nguyen HCB, Zhang S, Dill BD, Molina H, Tavazoie SF. Modulated Expression of Specific tRNAs Drives Gene Expression and Cancer Progression. Cell 2016; 165:1416-1427. [PMID: 27259150 DOI: 10.1016/j.cell.2016.05.046] [Citation(s) in RCA: 307] [Impact Index Per Article: 38.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 04/04/2016] [Accepted: 05/13/2016] [Indexed: 01/01/2023]
Abstract
Transfer RNAs (tRNAs) are primarily viewed as static contributors to gene expression. By developing a high-throughput tRNA profiling method, we find that specific tRNAs are upregulated in human breast cancer cells as they gain metastatic activity. Through loss-of-function, gain-of-function, and clinical-association studies, we implicate tRNAGluUUC and tRNAArgCCG as promoters of breast cancer metastasis. Upregulation of these tRNAs enhances stability and ribosome occupancy of transcripts enriched for their cognate codons. Specifically, tRNAGluUUC promotes metastatic progression by directly enhancing EXOSC2 expression and enhancing GRIPAP1-constituting an "inducible" pathway driven by a tRNA. The cellular proteomic shift toward a pro-metastatic state mirrors global tRNA shifts, allowing for cell-state and cell-type transgene expression optimization through codon content quantification. TRNA modulation represents a mechanism by which cells achieve altered expression of specific transcripts and proteins. TRNAs are thus dynamic regulators of gene expression and the tRNA codon landscape can causally and specifically impact disease progression.
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Affiliation(s)
- Hani Goodarzi
- Laboratory of Systems Cancer Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
| | - Hoang C B Nguyen
- Laboratory of Systems Cancer Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Steven Zhang
- Laboratory of Systems Cancer Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Brian D Dill
- Proteome Resource Center, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Henrik Molina
- Proteome Resource Center, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Sohail F Tavazoie
- Laboratory of Systems Cancer Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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44
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tRNA-mediated codon-biased translation in mycobacterial hypoxic persistence. Nat Commun 2016; 7:13302. [PMID: 27834374 PMCID: PMC5114619 DOI: 10.1038/ncomms13302] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 09/21/2016] [Indexed: 02/07/2023] Open
Abstract
Microbial pathogens adapt to the stress of infection by regulating transcription, translation and protein modification. We report that changes in gene expression in hypoxia-induced non-replicating persistence in mycobacteria—which models tuberculous granulomas—are partly determined by a mechanism of tRNA reprogramming and codon-biased translation. Mycobacterium bovis BCG responded to each stage of hypoxia and aerobic resuscitation by uniquely reprogramming 40 modified ribonucleosides in tRNA, which correlate with selective translation of mRNAs from families of codon-biased persistence genes. For example, early hypoxia increases wobble cmo5U in tRNAThr(UGU), which parallels translation of transcripts enriched in its cognate codon, ACG, including the DosR master regulator of hypoxic bacteriostasis. Codon re-engineering of dosR exaggerates hypoxia-induced changes in codon-biased DosR translation, with altered dosR expression revealing unanticipated effects on bacterial survival during hypoxia. These results reveal a coordinated system of tRNA modifications and translation of codon-biased transcripts that enhance expression of stress response proteins in mycobacteria. Mycobacteria can adapt to the stress of human infection by entering a dormant state. Here the authors show that hypoxia-induced dormancy in M. bovis BCG involves the reprogramming of tRNA wobble modifications and copy numbers, coupled with biased use of synonymous codons in survival genes.
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45
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Man M, Zhang Y, Ma G, Friston K, Liu S. Quantification of degeneracy in Hodgkin-Huxley neurons on Newman-Watts small world network. J Theor Biol 2016; 402:62-74. [PMID: 27155043 DOI: 10.1016/j.jtbi.2016.05.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 04/29/2016] [Accepted: 05/02/2016] [Indexed: 01/22/2023]
Abstract
Degeneracy is a fundamental source of biological robustness, complexity and evolvability in many biological systems. However, degeneracy is often confused with redundancy. Furthermore, the quantification of degeneracy has not been addressed for realistic neuronal networks. The objective of this paper is to characterize degeneracy in neuronal network models via quantitative mathematic measures. Firstly, we establish Hodgkin-Huxley neuronal networks with Newman-Watts small world network architectures. Secondly, in order to calculate the degeneracy, redundancy and complexity in the ensuing networks, we use information entropy to quantify the information a neuronal response carries about the stimulus - and mutual information to measure the contribution of each subset of the neuronal network. Finally, we analyze the interdependency of degeneracy, redundancy and complexity - and how these three measures depend upon network architectures. Our results suggest that degeneracy can be applied to any neuronal network as a formal measure, and degeneracy is distinct from redundancy. Qualitatively degeneracy and complexity are more highly correlated over different network architectures, in comparison to redundancy. Quantitatively, the relationship between both degeneracy and redundancy depends on network coupling strength: both degeneracy and redundancy increase with complexity for small coupling strengths; however, as coupling strength increases, redundancy decreases with complexity (in contrast to degeneracy, which is relatively invariant). These results suggest that the degeneracy is a general topologic characteristic of neuronal networks, which could be applied quantitatively in neuroscience and connectomics.
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Affiliation(s)
- Menghua Man
- Electrostatic and Electromagnetic Protection Institute, Mechanical Engineering College, Shijiazhuang, China.
| | - Ya Zhang
- Electrostatic and Electromagnetic Protection Institute, Mechanical Engineering College, Shijiazhuang, China
| | - Guilei Ma
- Electrostatic and Electromagnetic Protection Institute, Mechanical Engineering College, Shijiazhuang, China
| | - Karl Friston
- The Wellcome Trust Centre for Neuroimaging, Institute of Neurology, University College London, Queen Square, London, United Kingdom
| | - Shanghe Liu
- Electrostatic and Electromagnetic Protection Institute, Mechanical Engineering College, Shijiazhuang, China
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46
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Acevedo-Rocha CG, Budisa N. Xenomicrobiology: a roadmap for genetic code engineering. Microb Biotechnol 2016; 9:666-76. [PMID: 27489097 PMCID: PMC4993186 DOI: 10.1111/1751-7915.12398] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 07/12/2016] [Indexed: 11/27/2022] Open
Abstract
Biology is an analytical and informational science that is becoming increasingly dependent on chemical synthesis. One example is the high‐throughput and low‐cost synthesis of DNA, which is a foundation for the research field of synthetic biology (SB). The aim of SB is to provide biotechnological solutions to health, energy and environmental issues as well as unsustainable manufacturing processes in the frame of naturally existing chemical building blocks. Xenobiology (XB) goes a step further by implementing non‐natural building blocks in living cells. In this context, genetic code engineering respectively enables the re‐design of genes/genomes and proteins/proteomes with non‐canonical nucleic (XNAs) and amino (ncAAs) acids. Besides studying information flow and evolutionary innovation in living systems, XB allows the development of new‐to‐nature therapeutic proteins/peptides, new biocatalysts for potential applications in synthetic organic chemistry and biocontainment strategies for enhanced biosafety. In this perspective, we provide a brief history and evolution of the genetic code in the context of XB. We then discuss the latest efforts and challenges ahead for engineering the genetic code with focus on substitutions and additions of ncAAs as well as standard amino acid reductions. Finally, we present a roadmap for the directed evolution of artificial microbes for emancipating rare sense codons that could be used to introduce novel building blocks. The development of such xenomicroorganisms endowed with a ‘genetic firewall’ will also allow to study and understand the relation between code evolution and horizontal gene transfer.
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Affiliation(s)
- Carlos G Acevedo-Rocha
- Biosyntia ApS, 2970, Hørsholm, Denmark.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970, Hørsholm, Denmark
| | - Nediljko Budisa
- Department of Chemistry, Technical University Berlin, Müller-Breslau-Str. 10, Berlin, 10623, Germany
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47
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Benureau Y, Colin P, Staropoli I, Gonzalez N, Garcia-Perez J, Alcami J, Arenzana-Seisdedos F, Lagane B. Guidelines for cloning, expression, purification and functional characterization of primary HIV-1 envelope glycoproteins. J Virol Methods 2016; 236:184-195. [PMID: 27451265 DOI: 10.1016/j.jviromet.2016.07.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 07/13/2016] [Accepted: 07/19/2016] [Indexed: 12/14/2022]
Abstract
The trimeric HIV-1 envelope (Env) glycoproteins gp120 and gp41 mediate virus entry into target cells by engaging CD4 and the coreceptors CCR5 or CXCR4 at the cell surface and driving membrane fusion. Receptor/gp120 interactions regulate the virus life cycle, HIV infection transmission and pathogenesis. Env is also the target of neutralizing antibodies. Efforts have thus been made to produce soluble HIV-1 glycoproteins to develop vaccines and study the role and mechanisms of HIV/receptor interactions. However, production and purification of Env glycoproteins and their functional assessment has to cope with multiple obstacles. These include difficulties in amplifying and cloning env sequences and setting up receptor binding assays that are suitable for studies on large collections of glycoproteins, flexible enough to adapt to Env and receptor structural heterogeneities, and allow recapitulating the receptor binding properties of virion-associated Env trimers. Here we identify these difficulties and present protocols to produce primary gp120 and determination of their binding properties to receptors. The receptor binding assays confirmed that the produced glycoproteins are competent for binding CD4 and undergo proper CD4-induced conformational changes required for interaction with CCR5. These assays may help elucidate the role of gp120/receptor interactions in the pathophysiology of HIV infection and develop HIV-1 entry inhibitors.
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Affiliation(s)
- Yann Benureau
- INSERM U1108, Institut Pasteur, 75015 Paris, France; Viral Pathogenesis Unit, Department of Virology, Institut Pasteur, 75015 Paris, France.
| | - Philippe Colin
- INSERM U1108, Institut Pasteur, 75015 Paris, France; Viral Pathogenesis Unit, Department of Virology, Institut Pasteur, 75015 Paris, France.
| | - Isabelle Staropoli
- INSERM U1108, Institut Pasteur, 75015 Paris, France; Viral Pathogenesis Unit, Department of Virology, Institut Pasteur, 75015 Paris, France.
| | - Nuria Gonzalez
- AIDS Immunopathogenesis Unit, Instituto de Salud Carlos III, 28220, Majadahonda, Madrid, Spain.
| | - Javier Garcia-Perez
- AIDS Immunopathogenesis Unit, Instituto de Salud Carlos III, 28220, Majadahonda, Madrid, Spain.
| | - Jose Alcami
- AIDS Immunopathogenesis Unit, Instituto de Salud Carlos III, 28220, Majadahonda, Madrid, Spain.
| | - Fernando Arenzana-Seisdedos
- INSERM U1108, Institut Pasteur, 75015 Paris, France; Viral Pathogenesis Unit, Department of Virology, Institut Pasteur, 75015 Paris, France.
| | - Bernard Lagane
- INSERM U1108, Institut Pasteur, 75015 Paris, France; Viral Pathogenesis Unit, Department of Virology, Institut Pasteur, 75015 Paris, France.
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48
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Katz A, Elgamal S, Rajkovic A, Ibba M. Non-canonical roles of tRNAs and tRNA mimics in bacterial cell biology. Mol Microbiol 2016; 101:545-58. [PMID: 27169680 DOI: 10.1111/mmi.13419] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2016] [Indexed: 12/27/2022]
Abstract
Transfer RNAs (tRNAs) are the macromolecules that transfer activated amino acids from aminoacyl-tRNA synthetases to the ribosome, where they are used for the mRNA guided synthesis of proteins. Transfer RNAs are ancient molecules, perhaps even predating the existence of the translation machinery. Albeit old, these molecules are tremendously conserved, a characteristic that is well illustrated by the fact that some bacterial tRNAs are efficient and specific substrates of eukaryotic aminoacyl-tRNA synthetases and ribosomes. Considering their ancient origin and high structural conservation, it is not surprising that tRNAs have been hijacked during evolution for functions outside of translation. These roles beyond translation include synthetic, regulatory and information functions within the cell. Here we provide an overview of the non-canonical roles of tRNAs and their mimics in bacteria, and discuss some of the common themes that arise when comparing these different functions.
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Affiliation(s)
- Assaf Katz
- Programa de Biología Celular y Molecular, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, 8380453, Chile
| | - Sara Elgamal
- Department of Microbiology and The Center for RNA Biology, Ohio State University, Columbus, Ohio, 43210, USA
| | - Andrei Rajkovic
- Department of Microbiology and The Center for RNA Biology, Ohio State University, Columbus, Ohio, 43210, USA
| | - Michael Ibba
- Department of Microbiology and The Center for RNA Biology, Ohio State University, Columbus, Ohio, 43210, USA
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49
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Radhakrishnan A, Green R. Connections Underlying Translation and mRNA Stability. J Mol Biol 2016; 428:3558-64. [PMID: 27261255 DOI: 10.1016/j.jmb.2016.05.025] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 05/03/2016] [Accepted: 05/18/2016] [Indexed: 10/21/2022]
Abstract
Gene expression and regulation in organisms minimally depends on transcription by RNA polymerase and on the stability of the RNA product (for both coding and non-coding RNAs). For coding RNAs, gene expression is further influenced by the amount of translation by the ribosome and by the stability of the protein product. The stabilities of these two classes of RNA, non-coding and coding, vary considerably: tRNAs and rRNAs tend to be long lived while mRNAs tend to be more short lived. Even among mRNAs, however, there is a considerable range in stability (ranging from seconds to hours in bacteria and up to days in metazoans), suggesting a significant role for stability in the regulation of gene expression. Here, we review recent experiments from bacteria, yeast and metazoans indicating that the stability of most mRNAs is broadly impacted by the actions of ribosomes that translate them. Ribosomal recognition of defective mRNAs triggers "mRNA surveillance" pathways that target the mRNA for degradation [Shoemaker and Green (2012) ]. More generally, even the stability of perfectly functional mRNAs appears to be dictated by overall rates of translation by the ribosome [Herrick et al. (1990), Presnyak et al. (2015) ]. Given that mRNAs are synthesized for the purpose of being translated into proteins, it is reassuring that such intimate connections between mRNA and the ribosome can drive biological regulation. In closing, we consider the likelihood that these connections between protein synthesis and mRNA stability are widespread or whether other modes of regulation dominate the mRNA stability landscape in higher organisms.
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Affiliation(s)
- Aditya Radhakrishnan
- Program in Molecular Biophysics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Johns Hopkins School of Medicine, Department of Molecular Biology and Genetics, Baltimore, MD 21205, USA
| | - Rachel Green
- Howard Hughes Medical Institute, Johns Hopkins School of Medicine, Department of Molecular Biology and Genetics, Baltimore, MD 21205, USA.
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50
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Yan Q, Philmus B, Hesse C, Kohen M, Chang JH, Loper JE. The Rare Codon AGA Is Involved in Regulation of Pyoluteorin Biosynthesis in Pseudomonas protegens Pf-5. Front Microbiol 2016; 7:497. [PMID: 27148187 PMCID: PMC4836200 DOI: 10.3389/fmicb.2016.00497] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 03/27/2016] [Indexed: 11/24/2022] Open
Abstract
The soil bacterium Pseudomonas protegens Pf-5 can colonize root and seed surfaces of many plants, protecting them from infection by plant pathogenic fungi and oomycetes. The capacity to suppress disease is attributed to Pf-5's production of a large spectrum of antibiotics, which is controlled by complex regulatory circuits operating at the transcriptional and post-transcriptional levels. In this study, we analyzed the genomic sequence of Pf-5 for codon usage patterns and observed that the six rarest codons in the genome are present in all seven known antibiotic biosynthesis gene clusters. In particular, there is an abundance of rare codons in pltR, which encodes a member of the LysR transcriptional regulator family that controls the expression of pyoluteorin biosynthetic genes. To test the hypothesis that rare codons in pltR influence pyoluteorin production, we generated a derivative of Pf-5 in which 23 types of rare codons in pltR were substituted with synonymous preferred codons. The resultant mutant produced pyoluteorin at levels 15 times higher than that of the wild-type Pf-5. Accordingly, the promoter activity of the pyoluteorin biosynthetic gene pltL was 20 times higher in the codon-modified stain than in the wild-type. pltR has six AGA codons, which is the rarest codon in the Pf-5 genome. Substitution of all six AGA codons with preferred Arg codons resulted in a variant of pltR that conferred increased pyoluteorin production and pltL promoter activity. Furthermore, overexpression of tRNAUCUArg, the cognate tRNA for the AGA codon, significantly increased pyoluteorin production by Pf-5. A bias in codon usage has been linked to the regulation of many phenotypes in eukaryotes and prokaryotes but, to our knowledge, this is the first example of the role of a rare codon in the regulation of antibiotic production by a Gram-negative bacterium.
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Affiliation(s)
- Qing Yan
- Department of Botany and Plant Pathology, Oregon State University Corvallis, OR, USA
| | | | - Cedar Hesse
- Horticultural Crops Research Laboratory, US Department of Agriculture, Agricultural Research Service Corvallis, OR, USA
| | - Max Kohen
- Department of Botany and Plant Pathology, Oregon State University Corvallis, OR, USA
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University Corvallis, OR, USA
| | - Joyce E Loper
- Department of Botany and Plant Pathology, Oregon State UniversityCorvallis, OR, USA; Horticultural Crops Research Laboratory, US Department of Agriculture, Agricultural Research ServiceCorvallis, OR, USA
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