1
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Correia I, Oliveira C, Reis A, Guimarães AR, Aveiro S, Domingues P, Bezerra AR, Vitorino R, Moura G, Santos MAS. A proteogenomic pipeline for the analysis of protein biosynthesis errors in the human pathogen Candida albicans. Mol Cell Proteomics 2024:100818. [PMID: 39047911 DOI: 10.1016/j.mcpro.2024.100818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 03/20/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024] Open
Abstract
Candida albicans is a diploid pathogen known for its ability to live as a commensal fungus in healthy individuals, but causing both superficial infections and disseminated candidiasis in immunocompromised patients where it is associated with high morbidity and mortality. Its success in colonizing the human host is attributed to a wide range of virulence traits that modulate interactions between the host and the pathogen, such as optimal growth rate at 37 ºC, the ability to switch between yeast and hyphal forms and a remarkable genomic and phenotypic plasticity. A fascinating aspect of its biology is a prominent heterogeneous proteome that arises from frequent genomic rearrangements, high allelic variation, and high levels of amino acid misincorporations in proteins. This leads to increased morphological and physiological phenotypic diversity of high adaptive potential, but the scope of such protein mistranslation is poorly understood due to technical difficulties in detecting and quantifying amino acid misincorporation events in complex protein samples. We have developed and optimized mass spectrometry and bioinformatics pipelines capable of identifying rare amino acid misincorporation events at the proteome level. We have also analysed the proteomic profile of an engineered C. albicans strain that exhibits high level of leucine misincorporation at protein CUG sites and employed an in vivo quantitative gain-of-function fluorescence reporter system to validate our LC-MS/MS data. C. albicans misincorporates amino acids above the background level at protein sites of diverse codons, particularly at CUG, confirming our previous data on the quantification of leucine incorporation at single CUG sites of recombinant reporter proteins, but increasing misincorporation of Leucine at these sites does not alter the translational fidelity of the other codons. These findings indicate that the C. albicans statistical proteome exceeds prior estimates, suggesting that its highly plastic phenome may also be modulated by environmental factors due to translational ambiguity.
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Affiliation(s)
- Inês Correia
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences (DCM), University of Aveiro, Aveiro, Portugal.
| | - Carla Oliveira
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences (DCM), University of Aveiro, Aveiro, Portugal
| | - Andreia Reis
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences (DCM), University of Aveiro, Aveiro, Portugal
| | - Ana Rita Guimarães
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences (DCM), University of Aveiro, Aveiro, Portugal
| | - Susana Aveiro
- Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Pedro Domingues
- Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Ana Rita Bezerra
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences (DCM), University of Aveiro, Aveiro, Portugal
| | - Rui Vitorino
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences (DCM), University of Aveiro, Aveiro, Portugal
| | - Gabriela Moura
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences (DCM), University of Aveiro, Aveiro, Portugal
| | - Manuel A S Santos
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences (DCM), University of Aveiro, Aveiro, Portugal; Multidisciplinary Institute of Ageing (MIA-Portugal), University of Coimbra, Coimbra, Portugal.
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2
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Ević V, Rokov-Plavec J. Interplay between mistranslation and oxidative stress in Escherichia coli. Arh Hig Rada Toksikol 2024; 75:147-154. [PMID: 38963138 PMCID: PMC11223507 DOI: 10.2478/aiht-2024-75-3834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 03/01/2024] [Accepted: 05/01/2024] [Indexed: 07/05/2024] Open
Abstract
Mistakes in translation are mostly associated with toxic effects in the cell due to the production of functionally aberrant and misfolded proteins. However, under certain circumstances mistranslation can have beneficial effects and enable cells to preadapt to other stress conditions. Mistranslation may be caused by mistakes made by aminoacyl-tRNA synthetases, essential enzymes that link amino acids to cognate tRNAs. There is an Escherichia coli strain expressing isoleucyl-tRNA synthetase mutant variant with inactivated editing domain which produces mistranslated proteomes where valine (Val) and norvaline (Nva) are misincorporated into proteins instead of isoleucine. We compared this strain with the wild-type to determine the effects of such mistranslation on bacterial growth in oxidative stress conditions. When the cells were pre-incubated with 0.75 mmol/L Nva or 1.5 mmol/L Val or Nva and exposed to hydrogen peroxide, no beneficial effect of mistranslation was observed. However, when the editing-deficient strain was cultivated in medium supplemented with 0.75 mmol/L Val up to the early or mid-exponential phase of growth and then exposed to oxidative stress, it slightly outgrew the wild-type grown in the same conditions. Our results therefore show a modest adaptive effect of isoleucine mistranslation on bacterial growth in oxidative stress, but only in specific conditions. This points to a delicate balance between deleterious and beneficial effects of mistranslation.
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Affiliation(s)
- Valentina Ević
- University of Zagreb Faculty of Science, Department of Chemistry, Zagreb, Croatia
| | - Jasmina Rokov-Plavec
- University of Zagreb Faculty of Science, Department of Chemistry, Zagreb, Croatia
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3
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Ibba M. The Pros of changing tRNA identity. J Biol Chem 2023; 299:104974. [PMID: 37380073 PMCID: PMC10365949 DOI: 10.1016/j.jbc.2023.104974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/23/2023] [Indexed: 06/30/2023] Open
Abstract
The notion that errors in protein synthesis are universally harmful to the cell has been questioned by findings that suggest such mistakes may sometimes be beneficial. However, how often these beneficial mistakes arise from programmed changes in gene expression as opposed to reduced accuracy of the translation machinery is still unclear. A new study published in JBC shows that some bacteria have beneficially evolved the ability to mistranslate specific parts of the genetic code, a trait that allows improved antibiotic resistance.
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Affiliation(s)
- Michael Ibba
- Schmid College of Science and Technology, Chapman University, Orange, California, USA.
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4
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Lyu Z, Wilson C, Ling J. Translational Fidelity during Bacterial Stresses and Host Interactions. Pathogens 2023; 12:383. [PMID: 36986305 PMCID: PMC10057733 DOI: 10.3390/pathogens12030383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/22/2023] [Accepted: 02/24/2023] [Indexed: 03/05/2023] Open
Abstract
Translational fidelity refers to accuracy during protein synthesis and is maintained in all three domains of life. Translational errors occur at base levels during normal conditions and may rise due to mutations or stress conditions. In this article, we review our current understanding of how translational fidelity is perturbed by various environmental stresses that bacterial pathogens encounter during host interactions. We discuss how oxidative stress, metabolic stresses, and antibiotics affect various types of translational errors and the resulting effects on stress adaption and fitness. We also discuss the roles of translational fidelity during pathogen-host interactions and the underlying mechanisms. Many of the studies covered in this review will be based on work with Salmonella enterica and Escherichia coli, but other bacterial pathogens will also be discussed.
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Affiliation(s)
| | | | - Jiqiang Ling
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
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5
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Giegé R, Eriani G. The tRNA identity landscape for aminoacylation and beyond. Nucleic Acids Res 2023; 51:1528-1570. [PMID: 36744444 PMCID: PMC9976931 DOI: 10.1093/nar/gkad007] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 12/21/2022] [Accepted: 01/03/2023] [Indexed: 02/07/2023] Open
Abstract
tRNAs are key partners in ribosome-dependent protein synthesis. This process is highly dependent on the fidelity of tRNA aminoacylation by aminoacyl-tRNA synthetases and relies primarily on sets of identities within tRNA molecules composed of determinants and antideterminants preventing mischarging by non-cognate synthetases. Such identity sets were discovered in the tRNAs of a few model organisms, and their properties were generalized as universal identity rules. Since then, the panel of identity elements governing the accuracy of tRNA aminoacylation has expanded considerably, but the increasing number of reported functional idiosyncrasies has led to some confusion. In parallel, the description of other processes involving tRNAs, often well beyond aminoacylation, has progressed considerably, greatly expanding their interactome and uncovering multiple novel identities on the same tRNA molecule. This review highlights key findings on the mechanistics and evolution of tRNA and tRNA-like identities. In addition, new methods and their results for searching sets of multiple identities on a single tRNA are discussed. Taken together, this knowledge shows that a comprehensive understanding of the functional role of individual and collective nucleotide identity sets in tRNA molecules is needed for medical, biotechnological and other applications.
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Affiliation(s)
- Richard Giegé
- Correspondence may also be addressed to Richard Giegé.
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6
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Zhang Y, Guo Y, Luo Y, Du M, Yin X, Xu X, Zhang G. Integrated Metabolomics and Transcriptome Revealed the Effect of Fermented Lycium barbarum Residue Promoting Ovis aries Immunity. Front Immunol 2022; 13:889436. [PMID: 35464408 PMCID: PMC9024334 DOI: 10.3389/fimmu.2022.889436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 03/17/2022] [Indexed: 11/30/2022] Open
Abstract
Lycium barbarum residue contains abundant bioactive nutrients which can be used as feed supplement. The fermentation treatment of plant residue can promote the utilization of nutrients, rumen digestion, and the growth and immunity of animals. Based on ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) metabolomics and in-depth transcriptome analysis, the study tested the mechanisms of Lycium barbarum residue (RW) and fermented Lycium barbarum residue (RFW) on meat quality and immunity of sheep. Fifty-four Tan sheep were randomly divided into control, RFW or RW treatments. Data showed that RFW and RW increased the carcass weight, fat content, ash content and reduced the cooking loss of lamb. RFW performed more significant effects on activating immune-related genes than those of RW. The expression of chemokines and immune-related pathways, such as signaling pathways of interleukin-17 signaling pathway and NOD-like receptor signaling pathway, were elevated in sheep fed RFW. RW increased the diversity in rumen metabolites, especially compositions of lipids, organic acids and organ heterocyclic compounds. RFW affected numerous compounds which are closely correlated with the activation of immune genes. In conclusion, RFW could represent a valuable strategy to improve growth performance and immunity of sheep.
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Affiliation(s)
- Yajun Zhang
- Departments of Animal Science, School of Agriculture, Ningxia University, Yinchuan, China
| | - Yansheng Guo
- Departments of Animal Science, School of Agriculture, Ningxia University, Yinchuan, China
| | - Yulong Luo
- School of Food and Wine, Ningxia University, Yinchuan, China
| | - Min Du
- Nutrigenomics and Growth Biology Laboratory, Department of Animal Sciences, Washington State University, Pullman, WA, United States
| | - Xin Yin
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xiaochun Xu
- Collaborative Innovation Center for Food Production and Safety, North Minzu University, Yinchuan, China
| | - Guijie Zhang
- Departments of Animal Science, School of Agriculture, Ningxia University, Yinchuan, China
- *Correspondence: Guijie Zhang,
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7
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Lyu Z, Ling J. Increase in Ribosomal Fidelity Benefits Salmonella upon Bile Salt Exposure. Genes (Basel) 2022; 13:genes13020184. [PMID: 35205229 PMCID: PMC8872077 DOI: 10.3390/genes13020184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 02/04/2023] Open
Abstract
Translational fidelity is maintained by multiple quality control steps in all three domains of life. Increased translational errors (mistranslation) occur due to genetic mutations and external stresses. Severe mistranslation is generally harmful, but moderate levels of mistranslation may be favored under certain conditions. To date, little is known about the link between translational fidelity and host–pathogen interactions. Salmonella enterica can survive in the gall bladder during systemic or chronic infections due to bile resistance. Here we show that increased translational fidelity contributes to the fitness of Salmonella upon bile salt exposure, and the improved fitness depends on an increased level of intracellular adenosine triphosphate (ATP). Our work thus reveals a previously unknown linkage between translational fidelity and bacterial fitness under bile stress.
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Affiliation(s)
- Zhihui Lyu
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
- Correspondence: (Z.L.); (J.L.)
| | - Jiqiang Ling
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
- Molecular and Cellular Biology, Bilogical Sciences Graduate Program, The University of Maryland, College Park, MD 20742, USA
- Correspondence: (Z.L.); (J.L.)
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8
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Han NC, Kavoor A, Ibba M. Characterizing the amino acid activation center of the naturally editing-deficient aminoacyl-tRNA synthetase PheRS in Mycoplasma mobile. FEBS Lett 2022; 596:947-957. [PMID: 35038769 DOI: 10.1002/1873-3468.14287] [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: 07/05/2021] [Revised: 01/06/2022] [Accepted: 01/09/2022] [Indexed: 11/09/2022]
Abstract
To ensure correct amino acids are incorporated during protein synthesis, aminoacyl-tRNA synthetases (aaRSs) employ proofreading mechanisms collectively referred to as editing. Although editing is important for viability, editing-deficient aaRSs have been identified in host-dependent organisms. In Mycoplasma mobile, editing-deficient PheRS and LeuRS have been identified. We characterized the amino acid activation site of MmPheRS and identified a previously unknown hyperaccurate mutation, L287F. Additionally, we report that m-Tyr, an oxidation byproduct of Phe which is toxic to editing-deficient cells, is poorly discriminated by MmPheRS activation and is not subjected to editing. Furthermore, expressing MmPheRS and the hyperaccurate variants renders Escherichia coli susceptible to m-Tyr stress, indicating that active site discrimination is insufficient in tolerating excess m-Tyr.
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Affiliation(s)
- Nien-Ching Han
- Department of Microbiology, The Ohio State University, Columbus, OH, 43220, USA
| | - Arundhati Kavoor
- Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, OH, 43220, USA
| | - Michael Ibba
- Department of Microbiology, The Ohio State University, Columbus, OH, 43220, USA.,Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, OH, 43220, USA.,Schmid College of Science and Technology, Chapman university, Orange, CA, 92866, USA
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9
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Abstract
Mycoplasmas are small, genome-reduced bacteria. They are obligate parasites that can be found in a wide range of host species, including the majority of livestock animals and humans. Colonization of the host can result in a wide spectrum of outcomes. In many cases, these successful parasites are considered commensal, as they are found in the microbiota of asymptomatic carriers. Conversely, mycoplasmas can also be pathogenic, as they are associated with a range of both acute and chronic inflammatory diseases which are problematic in veterinary and human medicine. The chronicity of mycoplasma infections and the ability of these bacteria to infect even recently vaccinated individuals clearly indicate that they are able to successfully evade their host’s humoral immune response. Over the years, multiple strategies of immune evasion have been identified in mycoplasmas, with a number of them aimed at generating important antigenic diversity. More recently, mycoplasma-specific anti-immunoglobulin strategies have also been characterized. Through the expression of the immunoglobulin-binding proteins protein M or mycoplasma immunoglobulin binding (MIB), mycoplasmas have the ability to target the host’s antibodies and to prevent them from interacting with their cognate antigens. In this review, we discuss how these discoveries shed new light on the relationship between mycoplasmas and their host’s immune system. We also propose that these strategies should be taken into consideration for future studies, as they are key to our understanding of mycoplasma diseases' chronic and inflammatory nature and are probably a contributing factor to reduce vaccine efficacy.
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10
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Zhang H, Wu J, Lyu Z, Ling J. Impact of alanyl-tRNA synthetase editing deficiency in yeast. Nucleic Acids Res 2021; 49:9953-9964. [PMID: 34500470 PMCID: PMC8464055 DOI: 10.1093/nar/gkab766] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/19/2021] [Accepted: 08/26/2021] [Indexed: 11/12/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are essential enzymes that provide the ribosome with aminoacyl-tRNA substrates for protein synthesis. Mutations in aaRSs lead to various neurological disorders in humans. Many aaRSs utilize editing to prevent error propagation during translation. Editing defects in alanyl-tRNA synthetase (AlaRS) cause neurodegeneration and cardioproteinopathy in mice and are associated with microcephaly in human patients. The cellular impact of AlaRS editing deficiency in eukaryotes remains unclear. Here we use yeast as a model organism to systematically investigate the physiological role of AlaRS editing. Our RNA sequencing and quantitative proteomics results reveal that AlaRS editing defects surprisingly activate the general amino acid control pathway and attenuate the heatshock response. We have confirmed these results with reporter and growth assays. In addition, AlaRS editing defects downregulate carbon metabolism and attenuate protein synthesis. Supplying yeast cells with extra carbon source partially rescues the heat sensitivity caused by AlaRS editing deficiency. These findings are in stark contrast with the cellular effects caused by editing deficiency in other aaRSs. Our study therefore highlights the idiosyncratic role of AlaRS editing compared with other aaRSs and provides a model for the physiological impact caused by the lack of AlaRS editing.
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Affiliation(s)
- Hong Zhang
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
| | - Jiang Wu
- 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
| | - Jiqiang Ling
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
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11
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Burgos R, Weber M, Gallo C, Lluch-Senar M, Serrano L. Widespread ribosome stalling in a genome-reduced bacterium and the need for translational quality control. iScience 2021; 24:102985. [PMID: 34485867 PMCID: PMC8403727 DOI: 10.1016/j.isci.2021.102985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/22/2021] [Accepted: 08/11/2021] [Indexed: 11/21/2022] Open
Abstract
Trans-translation is a ubiquitous bacterial mechanism of ribosome rescue mediated by a transfer-messenger RNA (tmRNA) that adds a degradation tag to the truncated nascent polypeptide. Here, we characterize this quality control system in a genome-reduced bacterium, Mycoplasma pneumoniae (MPN), and perform a comparative analysis of protein quality control components in slow and fast-growing prokaryotes. We show in vivo that in MPN the sole quality control cytoplasmic protease (Lon) degrades efficiently tmRNA-tagged proteins. Analysis of tmRNA-mutants encoding a tag resistant to proteolysis reveals extensive tagging activity under normal growth. Unlike knockout strains, these mutants are viable demonstrating the requirement of tmRNA-mediated ribosome recycling. Chaperone and Lon steady-state levels maintain proteostasis in these mutants suggesting a model in which co-evolution of Lon and their substrates offer simple mechanisms of regulation without specialized degradation machineries. Finally, comparative analysis shows relative increase in Lon/Chaperone levels in slow-growing bacteria suggesting physiological adaptation to growth demand. Lon degrades efficiently tmRNA-tagged proteins in a genome-reduced bacterium tmRNA-tag mutants are viable and reveal extensive tagging activity in M. pneumoniae Co-evolution of Lon and their substrates offer simple mechanisms of regulation Chaperone and Lon relative levels correlate with bacterial growth rates
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Affiliation(s)
- Raul Burgos
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Corresponding author
| | - Marc Weber
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Carolina Gallo
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Maria Lluch-Senar
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Pg. Lluis Companys 23, Barcelona 08010, Spain
- Corresponding author
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12
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Bacterial translation machinery for deliberate mistranslation of the genetic code. Proc Natl Acad Sci U S A 2021; 118:2110797118. [PMID: 34413202 DOI: 10.1073/pnas.2110797118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Inaccurate expression of the genetic code, also known as mistranslation, is an emerging paradigm in microbial studies. Growing evidence suggests that many microbial pathogens can deliberately mistranslate their genetic code to help invade a host or evade host immune responses. However, discovering different capacities for deliberate mistranslation remains a challenge because each group of pathogens typically employs a unique mistranslation mechanism. In this study, we address this problem by studying duplicated genes of aminoacyl-transfer RNA (tRNA) synthetases. Using bacterial prolyl-tRNA synthetase (ProRS) genes as an example, we identify an anomalous ProRS isoform, ProRSx, and a corresponding tRNA, tRNAProA, that are predominately found in plant pathogens from Streptomyces species. We then show that tRNAProA has an unusual hybrid structure that allows this tRNA to mistranslate alanine codons as proline. Finally, we provide biochemical, genetic, and mass spectrometric evidence that cells which express ProRSx and tRNAProA can translate GCU alanine codons as both alanine and proline. This dual use of alanine codons creates a hidden proteome diversity due to stochastic Ala→Pro mutations in protein sequences. Thus, we show that important plant pathogens are equipped with a tool to alter the identity of their sense codons. This finding reveals the initial example of a natural tRNA synthetase/tRNA pair for dedicated mistranslation of sense codons.
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13
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Guo J, Zhang Y, Mo J, Sun H, Li Q. Sulfamethoxazole-Altered Transcriptomein Green Alga Raphidocelis subcapitata Suggests Inhibition of Translation and DNA Damage Repair. Front Microbiol 2021; 12:541451. [PMID: 34349730 PMCID: PMC8326373 DOI: 10.3389/fmicb.2021.541451] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 06/08/2021] [Indexed: 02/05/2023] Open
Abstract
Occurrence of sulfonamide antibiotics has been reported in surface waters with the exposures ranging from < 1 ng L–1 to approximately 11 μg L–1, which may exert adverse effects on non-target algal species, inhibiting algal growth and further hindering the delivery of several ecosystem services. Yet the molecular mechanisms of sulfonamide in algae remain undetermined. The aims of the present work are: (1) to test the hypothesis whether sulfamethoxazole (SMX) inhibits the folate biosynthesis in a model green alga Raphidocelis subcapitata; and (2) to explore the effects of SMX at an environmentally relevant concentration on algal health. Here, transcriptomic analysis was applied to investigate the changes at the molecular levels in R. subcapitata treated with SMX at the concentrations of 5 and 300 μg L–1. After 7-day exposure, the algal density in the 5 μg L–1 group was not different from that in the controls, whereas a marked reduction of 63% in the high SMX group was identified. Using the adj p < 0.05 and absolute log2 fold change > 1 as a cutoff, we identified 1 (0 up- and 1 downregulated) and 1,103 (696 up- and 407 downregulated) differentially expressed genes (DEGs) in the 5 and 300 μg L–1 treatment groups, respectively. This result suggested that SMX at an environmentally relevant exposure may not damage algal health. In the 300 μg L–1 group, DEGs were primarily enriched in the DNA replication and repair, photosynthesis, and translation pathways. Particularly, the downregulation of base and nucleotide excision repair pathways suggested that SMX may be genotoxic and cause DNA damage in alga. However, the folate biosynthesis pathway was not enriched, suggesting that SMX does not necessarily inhibit the algal growth via its mode of action in bacteria. Taken together, this study revealed the molecular mechanism of action of SMX in algal growth inhibition.
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Affiliation(s)
- Jiahua Guo
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, China
| | - Yibo Zhang
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, China.,School of Environmental Science and Engineering, Huazhong University of Science and Technology, Wuhan, China
| | - Jiezhang Mo
- Department of Chemistry, City University of Hong Kong, Hong Kong, China
| | - Haotian Sun
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, China
| | - Qi Li
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, China
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14
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De Ruysscher D, Pang L, Lenders SMG, Cappoen D, Cos P, Rozenski J, Strelkov SV, Weeks SD, Van Aerschot A. Synthesis and structure-activity studies of novel anhydrohexitol-based Leucyl-tRNA synthetase inhibitors. Eur J Med Chem 2020; 211:113021. [PMID: 33248851 DOI: 10.1016/j.ejmech.2020.113021] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/20/2020] [Accepted: 11/10/2020] [Indexed: 12/01/2022]
Abstract
Leucyl-tRNA synthetase (LeuRS) is a clinically validated target for the development of antimicrobials. This enzyme catalyzes the formation of charged tRNALeu molecules, an essential substrate for protein translation. In the first step of catalysis LeuRS activates leucine using ATP, forming a leucyl-adenylate intermediate. Bi-substrate inhibitors that mimic this chemically labile phosphoanhydride-linked nucleoside have proven to be potent inhibitors of different members of the aminoacyl-tRNA synthetase family but, to date, they have demonstrated poor antibacterial activity. We synthesized a small series of 1,5-anhydrohexitol-based analogues coupled to a variety of triazoles and performed detailed structure-activity relationship studies with bacterial LeuRS. In an in vitro assay, Kiapp values in the nanomolar range were demonstrated. Inhibitory activity differences between the compounds revealed that the polarity and size of the triazole substituents affect binding. X-ray crystallographic studies of N. gonorrhoeae LeuRS in complex with all the inhibitors highlighted the crucial interactions defining their relative enzyme inhibitory activities. We further examined their in vitro antimicrobial properties by screening against several bacterial and yeast strains. While only weak antibacterial activity against M. tuberculosis was detected, the extensive structural data which were obtained could make these LeuRS inhibitors a suitable starting point towards further antibiotic development.
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Affiliation(s)
- Dries De Ruysscher
- Medicinal Chemistry, Rega Institute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 - Box 1030, 3000, Leuven, Belgium
| | - Luping Pang
- Medicinal Chemistry, Rega Institute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 - Box 1030, 3000, Leuven, Belgium; Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 - Box 822, 3000, Leuven, Belgium
| | - Stijn M G Lenders
- Medicinal Chemistry, Rega Institute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 - Box 1030, 3000, Leuven, Belgium
| | - Davie Cappoen
- Laboratory of Microbiology, Parasitology and Hygiene, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Paul Cos
- Laboratory of Microbiology, Parasitology and Hygiene, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Jef Rozenski
- Medicinal Chemistry, Rega Institute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 - Box 1030, 3000, Leuven, Belgium
| | - Sergei V Strelkov
- Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 - Box 822, 3000, Leuven, Belgium
| | - Stephen D Weeks
- Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 - Box 822, 3000, Leuven, Belgium.
| | - Arthur Van Aerschot
- Medicinal Chemistry, Rega Institute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 - Box 1030, 3000, Leuven, Belgium.
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15
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Han NC, Kelly P, Ibba M. Translational quality control and reprogramming during stress adaptation. Exp Cell Res 2020; 394:112161. [PMID: 32619498 DOI: 10.1016/j.yexcr.2020.112161] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/26/2020] [Accepted: 06/29/2020] [Indexed: 12/18/2022]
Abstract
Organisms encounter stress throughout their lives, and therefore require the ability to respond rapidly to environmental changes. Although transcriptional responses are crucial for controlling changes in gene expression, regulation at the translational level often allows for a faster response at the protein levels which permits immediate adaptation. The fidelity and robustness of protein synthesis are actively regulated under stress. For example, mistranslation can be beneficial to cells upon environmental changes and also alters cellular stress responses. Additionally, stress modulates both global and selective translational regulation through mechanisms including the change of aminoacyl-tRNA activity, tRNA pool reprogramming and ribosome heterogeneity. In this review, we draw on studies from both the prokaryotic and eukaryotic systems to discuss current findings of cellular adaptation at the level of translation, specifically translational fidelity and activity changes in response to a wide array of environmental stressors including oxidative stress, nutrient depletion, temperature variation, antibiotics and host colonization.
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Affiliation(s)
- Nien-Ching Han
- Department of Microbiology, The Ohio State University, Columbus, OH, 43220, USA
| | - Paul Kelly
- The Ohio State University Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, OH, 43220, USA
| | - Michael Ibba
- Department of Microbiology, The Ohio State University, Columbus, OH, 43220, USA.
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16
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Abstract
The aminoacyl-tRNA synthetases are an essential and universally distributed family of enzymes that plays a critical role in protein synthesis, pairing tRNAs with their cognate amino acids for decoding mRNAs according to the genetic code. Synthetases help to ensure accurate translation of the genetic code by using both highly accurate cognate substrate recognition and stringent proofreading of noncognate products. While alterations in the quality control mechanisms of synthetases are generally detrimental to cellular viability, recent studies suggest that in some instances such changes facilitate adaption to stress conditions. Beyond their central role in translation, synthetases are also emerging as key players in an increasing number of other cellular processes, with far-reaching consequences in health and disease. The biochemical versatility of the synthetases has also proven pivotal in efforts to expand the genetic code, further emphasizing the wide-ranging roles of the aminoacyl-tRNA synthetase family in synthetic and natural biology.
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Affiliation(s)
- Miguel Angel Rubio Gomez
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Michael Ibba
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
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17
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Melnikov SV, Stevens DL, Fu X, Kwok HS, Zhang JT, Shen Y, Sabina J, Lee K, Lee H, Söll D. Exploiting evolutionary trade-offs for posttreatment management of drug-resistant populations. Proc Natl Acad Sci U S A 2020; 117:17924-17931. [PMID: 32661175 PMCID: PMC7395499 DOI: 10.1073/pnas.2003132117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Antibiotic resistance frequently evolves through fitness trade-offs in which the genetic alterations that confer resistance to a drug can also cause growth defects in resistant cells. Here, through experimental evolution in a microfluidics-based turbidostat, we demonstrate that antibiotic-resistant cells can be efficiently inhibited by amplifying the fitness costs associated with drug-resistance evolution. Using tavaborole-resistant Escherichia coli as a model, we show that genetic mutations in leucyl-tRNA synthetase (that underlie tavaborole resistance) make resistant cells intolerant to norvaline, a chemical analog of leucine that is mistakenly used by tavaborole-resistant cells for protein synthesis. We then show that tavaborole-sensitive cells quickly outcompete tavaborole-resistant cells in the presence of norvaline due to the amplified cost of the molecular defect of tavaborole resistance. This finding illustrates that understanding molecular mechanisms of drug resistance allows us to effectively amplify even small evolutionary vulnerabilities of resistant cells to potentially enhance or enable adaptive therapies by accelerating posttreatment competition between resistant and susceptible cells.
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Affiliation(s)
- Sergey V Melnikov
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520;
| | - David L Stevens
- Department of Chemistry, Yale University, New Haven, CT 06520
| | - Xian Fu
- Guangdong Provincial Key Laboratory of Genome Read and Write, 518120 Shenzhen, China
- BGI-Shenzhen, 518083 Shenzhen, China
- China National Genebank, BGI-Shenzhen, 518120 Shenzhen, China
| | - Hui Si Kwok
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - Jin-Tao Zhang
- BGI-Shenzhen, 518083 Shenzhen, China
- China National Genebank, BGI-Shenzhen, 518120 Shenzhen, China
| | - Yue Shen
- Guangdong Provincial Key Laboratory of Genome Read and Write, 518120 Shenzhen, China
- BGI-Shenzhen, 518083 Shenzhen, China
- China National Genebank, BGI-Shenzhen, 518120 Shenzhen, China
| | | | | | | | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520;
- Department of Chemistry, Yale University, New Haven, CT 06520
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18
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Chen H, Ercanbrack C, Wang T, Gan Q, Fan C. A Synthetic Reporter for Probing Mistranslation in Living Cells. Front Bioeng Biotechnol 2020; 8:623. [PMID: 32671035 PMCID: PMC7326783 DOI: 10.3389/fbioe.2020.00623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 05/21/2020] [Indexed: 01/13/2023] Open
Abstract
Aminoacyl-tRNA synthetases (AARSs) play key roles in maintaining high fidelity of protein synthesis. They charge cognate tRNAs with corresponding amino acids and hydrolyze mischarged tRNAs by editing mechanisms. Impairment of AARS editing activities can reduce the accuracy of tRNA aminoacylation to produce mischarged tRNAs, which cause mistranslation and cell damages. To evaluate the mistranslation rate of threonine codons in living cells, in this study, we designed a quantitative reporter derived from the green fluorescent protein (GFP). The original GFP has multiple threonine codons which could affect the accuracy of measurement, so we generated a GFP variant containing only one threonine residue to specifically quantify mistranslation at the threonine codon. To validate, we applied this single-threonine GFP reporter to evaluate mistranslation at the threonine codon with mutations or modifications of threonine-tRNA synthetase and compared it with other methods of mistranslation evaluation, which showed that this reporter is reliable and facile to use.
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Affiliation(s)
- Hao Chen
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, United States
| | - Carson Ercanbrack
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, United States
| | - Tony Wang
- Depratment of Biology, University of Arkansas, Fayetteville, AR, United States
| | - Qinglei Gan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, United States
| | - Chenguang Fan
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, United States.,Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, United States
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19
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Ostersetzer-Biran O, Klipcan L. Aminoacyl-tRNA synthetases and translational quality control in plant mitochondria. Mitochondrion 2020; 54:15-20. [PMID: 32580010 DOI: 10.1016/j.mito.2020.06.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 06/11/2020] [Accepted: 06/18/2020] [Indexed: 11/15/2022]
Abstract
Gene expression involves the transfer of information stored in the DNA to proteins by two sequential key steps: transcription and translation. Aminoacyl-tRNA synthetases (aaRSs), an ancient group of enzymes, are key to these processes as they catalyze the attachment of each of the 20 amino acids to their corresponding tRNA molecules. Yet, in addition to the 20 canonical amino acids, plants also produce numerous non-proteogenic amino acids (NPAAs), some of which are erroneously loaded into tRNAs, translated into non-functional or toxic proteins and may thereby disrupt essential cellular processes. While many studies have been focusing on plant organelle RNA metabolism, mitochondrial translation still lags behind its characterization in bacterial and eukaryotic systems. Notably, plant mitochondrial aaRSs generally have a dual location, residing also within the chloroplasts or cytosol. Currently, little is known about how mitochondrial aaRSs distinguish between amino acids and their closely related NPAAs. The organelle translation machineries in plants seem more susceptible to NPAAs due to protein oxidation by reactive oxygen species (ROS) and high rates of protein turnover. We speculate that plant organellar aaRSs have acquired high-affinities to their cognate amino acid substrates to reduce cytotoxic effects by NPAAs.
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Affiliation(s)
- Oren Ostersetzer-Biran
- Dept of Plant & Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| | - Liron Klipcan
- Gilat Research Center, Agricultural Research Organization, M.P Negev, 85280, Israel.
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20
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Kuncha SK, Venkadasamy VL, Amudhan G, Dahate P, Kola SR, Pottabathini S, Kruparani SP, Shekar PC, Sankaranarayanan R. Genomic innovation of ATD alleviates mistranslation associated with multicellularity in Animalia. eLife 2020; 9:58118. [PMID: 32463355 PMCID: PMC7302879 DOI: 10.7554/elife.58118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 05/27/2020] [Indexed: 12/26/2022] Open
Abstract
The emergence of multicellularity in Animalia is associated with increase in ROS and expansion of tRNA-isodecoders. tRNA expansion leads to misselection resulting in a critical error of L-Ala mischarged onto tRNAThr, which is proofread by Animalia-specific-tRNA Deacylase (ATD) in vitro. Here we show that in addition to ATD, threonyl-tRNA synthetase (ThrRS) can clear the error in cellular scenario. This two-tier functional redundancy for translation quality control breaks down during oxidative stress, wherein ThrRS is rendered inactive. Therefore, ATD knockout cells display pronounced sensitivity through increased mistranslation of threonine codons leading to cell death. Strikingly, we identify the emergence of ATD along with the error inducing tRNA species starting from Choanoflagellates thus uncovering an important genomic innovation required for multicellularity that occurred in unicellular ancestors of animals. The study further provides a plausible regulatory mechanism wherein the cellular fate of tRNAs can be switched from protein biosynthesis to non-canonical functions. The first animals evolved around 750 million years ago from single-celled ancestors that were most similar to modern-day organisms called the Choanoflagellates. As animals evolved they developed more complex body plans consisting of multiple cells organized into larger structures known as tissues and organs. Over time cells also evolved increased levels of molecules called reactive oxygen species, which are involved in many essential cell processes but are toxic at high levels. Animal cells also contain more types of molecules known as transfer ribonucleic acids, or tRNAs for short, than Choanoflagellate cells and other single-celled organisms. These molecules deliver building blocks known as amino acids to the machinery that produces new proteins. To ensure the proteins are made correctly, it is important that tRNAs deliver specific amino acids to the protein-building machinery in the right order. Each type of tRNA usually only pairs with a specific type of amino acid, but sometimes the enzymes involved in this process can make mistakes. Therefore, cells contain proofreading enzymes that help remove incorrect amino acids on tRNAs. One such enzyme – called ATD – is only found in animals. Experiments in test tubes reported that ATD removes an amino acid called alanine from tRNAs that are supposed to carry threonine, but its precise role in living cells remained unclear. To address this question, Kuncha et al. studied proofreading enzymes in human kidney cells. The experiments showed that, in addition to ATD, a second enzyme known as ThrRS was also able to correct alanine substitutions for threonines on tRNAs. However, reactive oxygen species inactivated the proofreading ability of ThrRS, suggesting ATD plays an essential role in correcting errors in cells containing high levels of reactive oxygen species. These findings suggest that as organisms evolved multiple cells and the levels of tRNA and oxidative stress increased, this led to the appearance of a new proofreading enzyme. Further studies found that ATD originated around 900 million years ago, before Choanoflagellates and animals diverged, indicating these enzymes might have helped to shape the evolution of animals. The next step following on from this work will be to understand the role of ATD in the cells of organs that are known to have particularly high levels of reactive oxygen species, such as testis and ovaries.
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Affiliation(s)
- Santosh Kumar Kuncha
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | | | | | - Priyanka Dahate
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Sankara Rao Kola
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | | | - P Chandra Shekar
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
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21
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Weitzel CS, Li L, Zhang C, Eilts KK, Bretz NM, Gatten AL, Whitaker RJ, Martinis SA. Duplication of leucyl-tRNA synthetase in an archaeal extremophile may play a role in adaptation to variable environmental conditions. J Biol Chem 2020; 295:4563-4576. [PMID: 32102848 DOI: 10.1074/jbc.ra118.006481] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 02/25/2020] [Indexed: 12/23/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are ancient enzymes that play a fundamental role in protein synthesis. They catalyze the esterification of specific amino acids to the 3'-end of their cognate tRNAs and therefore play a pivotal role in protein synthesis. Although previous studies suggest that aaRS-dependent errors in protein synthesis can be beneficial to some microbial species, evidence that reduced aaRS fidelity can be adaptive is limited. Using bioinformatics analyses, we identified two distinct leucyl-tRNA synthetase (LeuRS) genes within all genomes of the archaeal family Sulfolobaceae. Remarkably, one copy, designated LeuRS-I, had key amino acid substitutions within its editing domain that would be expected to disrupt hydrolytic editing of mischarged tRNALeu and to result in variation within the proteome of these extremophiles. We found that another copy, LeuRS-F, contains canonical active sites for aminoacylation and editing. Biochemical and genetic analyses of the paralogs within Sulfolobus islandicus supported the hypothesis that LeuRS-F, but not LeuRS-I, functions as an essential tRNA synthetase that accurately charges leucine to tRNALeu for protein translation. Although LeuRS-I was not essential, its expression clearly supported optimal S. islandicus growth. We conclude that LeuRS-I may have evolved to confer a selective advantage under the extreme and fluctuating environmental conditions characteristic of the volcanic hot springs in which these archaeal extremophiles reside.
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Affiliation(s)
| | - Li Li
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801.,Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, Illinois 61801
| | - Changyi Zhang
- Department of Microbiology, University of Illinois, Urbana, Illinois 61801.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801
| | - Kristen K Eilts
- Department of Chemistry, Illinois State University, Normal, Illinois 61761
| | - Nicholas M Bretz
- Department of Chemistry, Illinois State University, Normal, Illinois 61761
| | - Alex L Gatten
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801
| | - Rachel J Whitaker
- Department of Microbiology, University of Illinois, Urbana, Illinois 61801.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801
| | - Susan A Martinis
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801.,Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, Illinois 61801
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22
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Alanyl-tRNA Synthetase Quality Control Prevents Global Dysregulation of the Escherichia coli Proteome. mBio 2019; 10:mBio.02921-19. [PMID: 31848288 PMCID: PMC6918089 DOI: 10.1128/mbio.02921-19] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Mechanisms have evolved to prevent errors in replication, transcription, and translation of genetic material, with translational errors occurring most frequently. Errors in protein synthesis can occur at two steps, during tRNA aminoacylation and ribosome decoding. Recent advances in protein mass spectrometry have indicated that previous reports of translational errors have potentially underestimated the frequency of these events, but also that the majority of translational errors occur during ribosomal decoding, suggesting that aminoacylation errors are evolutionarily less tolerated. Despite that interpretation, there is evidence that some aminoacylation errors may be regulated, and thus provide a benefit to the cell, while others are clearly detrimental. Here, we show that while it has been suggested that regulated Thr-to-Ser substitutions may be beneficial, there is a threshold beyond which these errors are detrimental. In contrast, we show that errors mediated by alanyl-tRNA synthetase (AlaRS) are not well tolerated and induce a global stress response that leads to gross perturbation of the Escherichia coli proteome, with potentially catastrophic effects on fitness and viability. Tolerance for Ala mistranslation appears to be much lower than with other translational errors, consistent with previous reports of multiple proofreading mechanisms targeting mischarged tRNAAla These results demonstrate the essential role of aminoacyl-tRNA proofreading in optimizing cellular fitness and suggest that any potentially beneficial effects of mistranslation may be confined to specific amino acid substitutions.IMPORTANCE Errors in protein synthesis have historically been assumed to be detrimental to the cell. While there are many reports that translational errors are consequential, there is a growing body of evidence that some mistranslation events may be tolerated or even beneficial. Using two models of mistranslation, we compare the direct phenotypic effects of these events in Escherichia coli This work provides insight into the threshold for tolerance of specific mistranslation events that were previously predicted to be broadly neutral to proteome integrity. Furthermore, these data reveal the effects of mistranslation beyond the general unfolded stress response, leading to global translational reprogramming.
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23
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Berg MD, Zhu Y, Genereaux J, Ruiz BY, Rodriguez-Mias RA, Allan T, Bahcheli A, Villén J, Brandl CJ. Modulating Mistranslation Potential of tRNA Ser in Saccharomyces cerevisiae. Genetics 2019; 213:849-863. [PMID: 31484688 PMCID: PMC6827378 DOI: 10.1534/genetics.119.302525] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 09/01/2019] [Indexed: 12/15/2022] Open
Abstract
Transfer RNAs (tRNAs) read the genetic code, translating nucleic acid sequence into protein. For tRNASer the anticodon does not specify its aminoacylation. For this reason, mutations in the tRNASer anticodon can result in amino acid substitutions, a process called mistranslation. Previously, we found that tRNASer with a proline anticodon was lethal to cells. However, by incorporating secondary mutations into the tRNA, mistranslation was dampened to a nonlethal level. The goal of this work was to identify second-site substitutions in tRNASer that modulate mistranslation to different levels. Targeted changes to putative identity elements led to total loss of tRNA function or significantly impaired cell growth. However, through genetic selection, we identified 22 substitutions that allow nontoxic mistranslation. These secondary mutations are primarily in single-stranded regions or substitute G:U base pairs for Watson-Crick pairs. Many of the variants are more toxic at low temperature and upon impairing the rapid tRNA decay pathway. We suggest that the majority of the secondary mutations affect the stability of the tRNA in cells. The temperature sensitivity of the tRNAs allows conditional mistranslation. Proteomic analysis demonstrated that tRNASer variants mistranslate to different extents with diminished growth correlating with increased mistranslation. When combined with a secondary mutation, other anticodon substitutions allow serine mistranslation at additional nonserine codons. These mistranslating tRNAs have applications in synthetic biology, by creating "statistical proteins," which may display a wider range of activities or substrate specificities than the homogenous form.
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Affiliation(s)
- Matthew D Berg
- Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Yanrui Zhu
- Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Julie Genereaux
- Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Bianca Y Ruiz
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
| | | | - Tyler Allan
- Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Alexander Bahcheli
- Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Judit Villén
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
| | - Christopher J Brandl
- Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
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24
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Zhang P, Ma S. Recent development of leucyl-tRNA synthetase inhibitors as antimicrobial agents. MEDCHEMCOMM 2019; 10:1329-1341. [PMID: 31534653 PMCID: PMC6727470 DOI: 10.1039/c9md00139e] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 05/26/2019] [Indexed: 12/14/2022]
Abstract
Aminoacyl-tRNA synthetases (aaRSs) widely exist in organisms and mediate protein synthesis. Inhibiting these synthetases can lead to the termination of protein synthesis and subsequently achieve antibacterial and antiparasitic purposes. Moreover, the structures of aaRSs found in eukaryotes have considerable structural differences compared to those in prokaryotes, based on which it is possible to develop highly selective inhibitors. Leucyl-tRNA synthetase (LeuRS) with unique synthesis and editing sites is one of 20 kinds of aaRSs. Many inhibitors targeting LeuRS have been designed and synthesized, some of which have entered clinical use. For example, the benzoxaborole compound AN2690 has been approved by the FDA for the treatment of onychomycosis. AN3365 is suspended in the phase II clinical trial due to the rapid development of AN3365 resistance, but it may be used in combination with other antibiotics. The aaRSs, especially LeuRS, are being considered as targets of new potential anti-infective drugs for the treatment of not only bacterial or fungal infections but also infections by trypanosomes and malaria parasites. This review mainly describes the development of LeuRS inhibitors, focusing on their mechanisms of action, structure-activity relationships (SARs), and in vitro and in vivo activities.
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Affiliation(s)
- Panpan Zhang
- Department of Medicinal Chemistry , Key Laboratory of Chemical Biology , Ministry of Education , School of Pharmaceutical Sciences , Shandong University , 44, West Culture Road , Jinan 250012 , P. R. China . E mail:
| | - Shutao Ma
- Department of Medicinal Chemistry , Key Laboratory of Chemical Biology , Ministry of Education , School of Pharmaceutical Sciences , Shandong University , 44, West Culture Road , Jinan 250012 , P. R. China . E mail:
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25
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Steiner RE, Ibba M. Regulation of tRNA-dependent translational quality control. IUBMB Life 2019; 71:1150-1157. [PMID: 31135095 DOI: 10.1002/iub.2080] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/01/2019] [Accepted: 05/14/2019] [Indexed: 02/06/2023]
Abstract
Translation is the most error-prone process in protein synthesis; however, it is important that accuracy is maintained because erroneous translation has been shown to affect all domains of life. Translational quality control is maintained by both proteins and RNA through intricate processes. The aminoacyl-tRNA synthetases help maintain high levels of translational accuracy through the esterification of tRNA and proofreading mechanisms. tRNA is often recognized by an aminoacyl-tRNA synthetase in a sequence and structurally dependent manner, sometimes involving modified nucleotides. Additionally, some proofreading mechanisms of aminoacyl-tRNA synthetases require tRNA elements for hydrolysis of a noncognate aminoacyl-tRNA. Finally, tRNA is also important for proper decoding of the mRNA message by codon and anticodon pairing. Here, recent developments regarding the importance of tRNA in maintenance of translational accuracy are reviewed. © 2019 IUBMB Life, 2019 © 2019 IUBMB Life, 71(8):1150-1157, 2019.
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Affiliation(s)
- Rebecca E Steiner
- The Ohio State University Biochemistry Program, The Ohio State University, Columbus, OH, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Michael Ibba
- The Ohio State University Biochemistry Program, The Ohio State University, Columbus, OH, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH, USA.,Department of Microbiology, The Ohio State University, Columbus, OH, USA
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26
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Ou X, Cao J, Cheng A, Peppelenbosch MP, Pan Q. Errors in translational decoding: tRNA wobbling or misincorporation? PLoS Genet 2019; 15:e1008017. [PMID: 30921315 PMCID: PMC6438450 DOI: 10.1371/journal.pgen.1008017] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
As the central dogma of molecular biology, genetic information flows from DNA through transcription into RNA followed by translation of the message into protein by transfer RNAs (tRNAs). However, mRNA translation is not always perfect, and errors in the amino acid composition may occur. Mistranslation is generally well tolerated, but once it reaches superphysiological levels, it can give rise to a plethora of diseases. The key causes of mistranslation are errors in translational decoding of the codons in mRNA. Such errors mainly derive from tRNA misdecoding and misacylation, especially when certain codon-paired tRNA species are missing. Substantial progress has recently been made with respect to the mechanistic basis of erroneous mRNA decoding as well as the resulting consequences for physiology and pathology. Here, we aim to review this progress with emphasis on viral evolution and cancer development.
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Affiliation(s)
- Xumin Ou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, the Netherlands
| | - Jingyu Cao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- * E-mail: (AC); (QP)
| | - Maikel P. Peppelenbosch
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, the Netherlands
| | - Qiuwei Pan
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, the Netherlands
- * E-mail: (AC); (QP)
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27
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Differential responses to stress of two Mycoplasma hyopneumoniae strains. J Proteomics 2019; 199:67-76. [PMID: 30862566 DOI: 10.1016/j.jprot.2019.03.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 02/18/2019] [Accepted: 03/07/2019] [Indexed: 12/14/2022]
Abstract
Mycoplasma hyopneumoniae is a respiratory pathogen, causing porcine enzootic pneumonia. To survive in the porcine respiratory tract, M. hyopneumoniae must cope with both oxidative and heat stress imposed by the host. To get insights into M. hyopneumoniae stress responses and pathogenicity mechanisms, the protein profiles of two M. hyopneumoniae strains, pathogenic 7448 strain and non-pathogenic strain J, were surveyed under oxidative (OS) or heat (HS) stress. M. hyopneumoniae strains were submitted to OS (0.5% hydrogen peroxide) or HS (temperature shifts to 42 °C) conditions and protein profiling was carried out by LC-MS/MS and label-free quantitative analyses. Data are available via ProteomeXchange with identifier PXD012742. Qualitative and quantitative differences involving 40-60 M. hyopneumoniae proteins were observed for both strains when comparing bacteria exposed to OS or HS to non-treated controls. However, no differences in abundance were found in proteins classically related to stress responses, as peroxidases and chaperones, suggesting that these proteins would be constitutively present in both strains in the tested conditions. Interestingly, under stress conditions, more virulence-related proteins were detected in M. hyopneumoniae 7448 differentially represented proteins than in M. hyopneumoniae J, suggesting that stress may trigger a differential response of the corresponding genes, shared by both strains.
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Francklyn CS, Mullen P. Progress and challenges in aminoacyl-tRNA synthetase-based therapeutics. J Biol Chem 2019; 294:5365-5385. [PMID: 30670594 DOI: 10.1074/jbc.rev118.002956] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Aminoacyl-tRNA synthetases (ARSs) are universal enzymes that catalyze the attachment of amino acids to the 3' ends of their cognate tRNAs. The resulting aminoacylated tRNAs are escorted to the ribosome where they enter protein synthesis. By specifically matching amino acids to defined anticodon sequences in tRNAs, ARSs are essential to the physical interpretation of the genetic code. In addition to their canonical role in protein synthesis, ARSs are also involved in RNA splicing, transcriptional regulation, translation, and other aspects of cellular homeostasis. Likewise, aminoacylated tRNAs serve as amino acid donors for biosynthetic processes distinct from protein synthesis, including lipid modification and antibiotic biosynthesis. Thanks to the wealth of details on ARS structures and functions and the growing appreciation of their additional roles regulating cellular homeostasis, opportunities for the development of clinically useful ARS inhibitors are emerging to manage microbial and parasite infections. Exploitation of these opportunities has been stimulated by the discovery of new inhibitor frameworks, the use of semi-synthetic approaches combining chemistry and genome engineering, and more powerful techniques for identifying leads from the screening of large chemical libraries. Here, we review the inhibition of ARSs by small molecules, including the various families of natural products, as well as inhibitors developed by either rational design or high-throughput screening as antibiotics and anti-parasitic therapeutics.
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Affiliation(s)
- Christopher S Francklyn
- From the Department of Biochemistry, College of Medicine, University of Vermont, Burlington, Vermont 05405
| | - Patrick Mullen
- From the Department of Biochemistry, College of Medicine, University of Vermont, Burlington, Vermont 05405
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Melnikov SV, van den Elzen A, Stevens DL, Thoreen CC, Söll D. Loss of protein synthesis quality control in host-restricted organisms. Proc Natl Acad Sci U S A 2018; 115:E11505-E11512. [PMID: 30455292 PMCID: PMC6298100 DOI: 10.1073/pnas.1815992115] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Intracellular organisms, such as obligate parasites and endosymbionts, typically possess small genomes due to continuous genome decay caused by an environment with alleviated natural selection. Previously, a few species with highly reduced genomes, including the intracellular pathogens Mycoplasma and Microsporidia, have been shown to carry degenerated editing domains in aminoacyl-tRNA synthetases. These defects in the protein synthesis machinery cause inaccurate translation of the genetic code, resulting in significant statistical errors in protein sequences that are thought to help parasites to escape immune response of a host. In this study we analyzed 10,423 complete bacterial genomes to assess conservation of the editing domains in tRNA synthetases, including LeuRS, IleRS, ValRS, ThrRS, AlaRS, and PheRS. We found that, while the editing domains remain intact in free-living species, they are degenerated in the overwhelming majority of host-restricted bacteria. Our work illustrates that massive genome erosion triggered by an intracellular lifestyle eradicates one of the most fundamental components of a living cell: the system responsible for proofreading of amino acid selection for protein synthesis. This finding suggests that inaccurate translation of the genetic code might be a general phenomenon among intercellular organisms with reduced genomes.
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Affiliation(s)
- Sergey V Melnikov
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511
| | - Antonia van den Elzen
- Department of Cellular and Molecular Physiology, Yale University, New Haven, CT 06520
| | - David L Stevens
- Department of Chemistry, Yale University, New Haven, CT 06511
| | - Carson C Thoreen
- Department of Cellular and Molecular Physiology, Yale University, New Haven, CT 06520
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511;
- Department of Chemistry, Yale University, New Haven, CT 06511
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30
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Zimmerman SM, Kon Y, Hauke AC, Ruiz BY, Fields S, Phizicky EM. Conditional accumulation of toxic tRNAs to cause amino acid misincorporation. Nucleic Acids Res 2018; 46:7831-7843. [PMID: 30007351 PMCID: PMC6125640 DOI: 10.1093/nar/gky623] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 06/22/2018] [Accepted: 07/01/2018] [Indexed: 12/16/2022] Open
Abstract
To develop a system for conditional amino acid misincorporation, we engineered tRNAs in the yeast Saccharomyces cerevisiae to be substrates of the rapid tRNA decay (RTD) pathway, such that they accumulate when RTD is turned off. We used this system to test the effects on growth of a library of tRNASer variants with all possible anticodons, and show that many are lethal when RTD is inhibited and the tRNA accumulates. Using mass spectrometry, we measured serine misincorporation in yeast containing each of six tRNA variants, and for five of them identified hundreds of peptides with serine substitutions at the targeted amino acid sites. Unexpectedly, we found that there is not a simple correlation between toxicity and the level of serine misincorporation; in particular, high levels of serine misincorporation can occur at cysteine residues without obvious growth defects. We also showed that toxic tRNAs can be used as a tool to identify sequence variants that reduce tRNA function. Finally, we generalized this method to another tRNA species, and generated conditionally toxic tRNATyr variants in a similar manner. This method should facilitate the study of tRNA biology and provide a tool to probe the effects of amino acid misincorporation on cellular physiology.
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Affiliation(s)
| | - Yoshiko Kon
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine, Rochester, NY 14642, USA
| | - Alayna C Hauke
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine, Rochester, NY 14642, USA
| | - Bianca Y Ruiz
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Stanley Fields
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Eric M Phizicky
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine, Rochester, NY 14642, USA
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Noutahi E, Calderon V, Blanchette M, Lang FB, El-Mabrouk N. CoreTracker: accurate codon reassignment prediction, applied to mitochondrial genomes. Bioinformatics 2018; 33:3331-3339. [PMID: 28655158 DOI: 10.1093/bioinformatics/btx421] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/23/2017] [Indexed: 11/13/2022] Open
Abstract
Motivation Codon reassignments have been reported across all domains of life. With the increasing number of sequenced genomes, the development of systematic approaches for genetic code detection is essential for accurate downstream analyses. Three automated prediction tools exist so far: FACIL, GenDecoder and Bagheera; the last two respectively restricted to metazoan mitochondrial genomes and CUG reassignments in yeast nuclear genomes. These tools can only analyze a single genome at a time and are often not followed by a validation procedure, resulting in a high rate of false positives. Results We present CoreTracker, a new algorithm for the inference of sense-to-sense codon reassignments. CoreTracker identifies potential codon reassignments in a set of related genomes, then uses statistical evaluations and a random forest classifier to predict those that are the most likely to be correct. Predicted reassignments are then validated through a phylogeny-aware step that evaluates the impact of the new genetic code on the protein alignment. Handling simultaneously a set of genomes in a phylogenetic framework, allows tracing back the evolution of each reassignment, which provides information on its underlying mechanism. Applied to metazoan and yeast genomes, CoreTracker significantly outperforms existing methods on both precision and sensitivity. Availability and implementation CoreTracker is written in Python and available at https://github.com/UdeM-LBIT/CoreTracker. Contact mabrouk@iro.umontreal.ca. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Emmanuel Noutahi
- Département d'Informatique et de Recherche Opérationnelle (DIRO), Université de Montréal, Montréal, QC CP 6128, Canada
| | - Virginie Calderon
- Département d'Informatique et de Recherche Opérationnelle (DIRO), Université de Montréal, Montréal, QC CP 6128, Canada
| | - Mathieu Blanchette
- School of Computer Science, McGill University, McConnell Engineering Bldg., Montréal, QC H3A 0E9, Canada
| | - Franz B Lang
- Département de Biochimie, Centre Robert Cedergren, Université de Montréal, Montréal, QC CP 6128, Canada
| | - Nadia El-Mabrouk
- Département d'Informatique et de Recherche Opérationnelle (DIRO), Université de Montréal, Montréal, QC CP 6128, Canada
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32
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Errors during Gene Expression: Single-Cell Heterogeneity, Stress Resistance, and Microbe-Host Interactions. mBio 2018; 9:mBio.01018-18. [PMID: 29970467 PMCID: PMC6030554 DOI: 10.1128/mbio.01018-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Gene expression has been considered a highly accurate process, and deviation from such fidelity has been shown previously to be detrimental for the cell. More recently, increasing evidence has supported the notion that the accuracy of gene expression is indeed flexibly variable. The levels of errors during gene expression differ from condition to condition and even from cell to cell within genetically identical populations grown under the same conditions. The different levels of errors resulting from inaccurate gene expression are now known to play key roles in regulating microbial stress responses and host interactions. This minireview summarizes the recent development in understanding the level, regulation, and physiological impact of errors during gene expression. Gene expression has been considered a highly accurate process, and deviation from such fidelity has been shown previously to be detrimental for the cell. More recently, increasing evidence has supported the notion that the accuracy of gene expression is indeed flexibly variable.
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33
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Error-prone protein synthesis in parasites with the smallest eukaryotic genome. Proc Natl Acad Sci U S A 2018; 115:E6245-E6253. [PMID: 29915081 DOI: 10.1073/pnas.1803208115] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Microsporidia are parasitic fungi-like organisms that invade the interior of living cells and cause chronic disorders in a broad range of animals, including humans. These pathogens have the tiniest known genomes among eukaryotic species, for which they serve as a model for exploring the phenomenon of genome reduction in obligate intracellular parasites. Here we report a case study to show an apparent effect of overall genome reduction on the primary structure and activity of aminoacyl-tRNA synthetases, indispensable cellular proteins required for protein synthesis. We find that most microsporidian synthetases lack regulatory and eukaryote-specific appended domains and have a high degree of sequence variability in tRNA-binding and catalytic domains. In one synthetase, LeuRS, an apparent sequence degeneration annihilates the editing domain, a catalytic center responsible for the accurate selection of leucine for protein synthesis. Unlike accurate LeuRS synthetases from other eukaryotic species, microsporidian LeuRS is error-prone: apart from leucine, it occasionally uses its near-cognate substrates, such as norvaline, isoleucine, valine, and methionine. Mass spectrometry analysis of the microsporidium Vavraia culicis proteome reveals that nearly 6% of leucine residues are erroneously replaced by other amino acids. This remarkably high frequency of mistranslation is not limited to leucine codons and appears to be a general property of protein synthesis in microsporidian parasites. Taken together, our findings reveal that the microsporidian protein synthesis machinery is editing-deficient, and that the proteome of microsporidian parasites is more diverse than would be anticipated based on their genome sequences.
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34
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The emerging complexity of the tRNA world: mammalian tRNAs beyond protein synthesis. Nat Rev Mol Cell Biol 2017; 19:45-58. [PMID: 28875994 DOI: 10.1038/nrm.2017.77] [Citation(s) in RCA: 272] [Impact Index Per Article: 38.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The discovery of the genetic code and tRNAs as decoders of the code transformed life science. However, after establishing the role of tRNAs in protein synthesis, the field moved to other parts of the RNA world. Now, tRNA research is blooming again, with demonstration of the involvement of tRNAs in various other pathways beyond translation and in adapting translation to environmental cues. These roles are linked to the presence of tRNA sequence variants known as isoacceptors and isodecoders, various tRNA base modifications, the versatility of protein binding partners and tRNA fragmentation events, all of which collectively create an incalculable complexity. This complexity provides a vast repertoire of tRNA species that can serve various functions in cellular homeostasis and in adaptation of cellular functions to changing environments, and it likely arose from the fundamental role of RNAs in early evolution.
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35
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Translational fidelity and mistranslation in the cellular response to stress. Nat Microbiol 2017; 2:17117. [PMID: 28836574 DOI: 10.1038/nmicrobiol.2017.117] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 06/20/2017] [Indexed: 11/08/2022]
Abstract
Faithful translation of mRNA into the corresponding polypeptide is a complex multistep process, requiring accurate amino acid selection, transfer RNA (tRNA) charging and mRNA decoding on the ribosome. Key players in this process are aminoacyl-tRNA synthetases (aaRSs), which not only catalyse the attachment of cognate amino acids to their respective tRNAs, but also selectively hydrolyse incorrectly activated non-cognate amino acids and/or misaminoacylated tRNAs. This aaRS proofreading provides quality control checkpoints that exclude non-cognate amino acids during translation, and in so doing helps to prevent the formation of an aberrant proteome. However, despite the intrinsic need for high accuracy during translation, and the widespread evolutionary conservation of aaRS proofreading pathways, requirements for translation quality control vary depending on cellular physiology and changes in growth conditions, and translation errors are not always detrimental. Recent work has demonstrated that mistranslation can also be beneficial to cells, and some organisms have selected for a higher degree of mistranslation than others. The aims of this Review Article are to summarize the known mechanisms of protein translational fidelity and explore the diversity and impact of mistranslation events as a potentially beneficial response to environmental and cellular stress.
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36
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Mistranslation can enhance fitness through purging of deleterious mutations. Nat Commun 2017; 8:15410. [PMID: 28524864 PMCID: PMC5454534 DOI: 10.1038/ncomms15410] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 03/20/2017] [Indexed: 01/01/2023] Open
Abstract
Phenotypic mutations are amino acid changes caused by mistranslation. How phenotypic mutations affect the adaptive evolution of new protein functions is unknown. Here we evolve the antibiotic resistance protein TEM-1 towards resistance on the antibiotic cefotaxime in an Escherichia coli strain with a high mistranslation rate. TEM-1 populations evolved in such strains endow host cells with a general growth advantage, not only on cefotaxime but also on several other antibiotics that ancestral TEM-1 had been unable to deactivate. High-throughput sequencing of TEM-1 populations shows that this advantage is associated with a lower incidence of weakly deleterious genotypic mutations. Our observations show that mistranslation is not just a source of noise that delays adaptive evolution. It could even facilitate adaptive evolution by exacerbating the effects of deleterious mutations and leading to their more efficient purging. The ubiquity of mistranslation and its effects render mistranslation an important factor in adaptive protein evolution. Mistranslation results in amino acid changes in proteins known as phenotypic mutations and these occur at a much higher rate than DNA mutations. Here, the authors show that mistranslation can increase the response to directional selection by exacerbating the fitness effects of deleterious DNA mutations.
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37
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Kermgard E, Yang Z, Michel AM, Simari R, Wong J, Ibba M, Lazazzera BA. Quality Control by Isoleucyl-tRNA Synthetase of Bacillus subtilis Is Required for Efficient Sporulation. Sci Rep 2017; 7:41763. [PMID: 28139725 PMCID: PMC5282499 DOI: 10.1038/srep41763] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 12/22/2016] [Indexed: 11/11/2022] Open
Abstract
Isoleucyl-tRNA synthetase (IleRS) is an aminoacyl-tRNA synthetase whose essential function is to aminoacylate tRNAIle with isoleucine. Like some other aminoacyl-tRNA synthetases, IleRS can mischarge tRNAIle and correct this misacylation through a separate post-transfer editing function. To explore the biological significance of this editing function, we created a ileS(T233P) mutant of Bacillus subtilis that allows tRNAIle mischarging while retaining wild-type Ile-tRNAIle synthesis activity. As seen in other species defective for aminoacylation quality control, the growth rate of the ileS(T233P) strain was not significantly different from wild-type. When the ileS(T233P) strain was assessed for its ability to promote distinct phenotypes in response to starvation, the ileS(T233P) strain was observed to exhibit a significant defect in formation of environmentally resistant spores. The sporulation defect ranged from 3-fold to 30-fold and was due to a delay in activation of early sporulation genes. The loss of aminoacylation quality control in the ileS(T233P) strain resulted in the inability to compete with a wild-type strain under selective conditions that required sporulation. These data show that the quality control function of IleRS is required in B. subtilis for efficient sporulation and suggests that editing by aminoacyl-tRNA synthetases may be important for survival under starvation/nutrient limitation conditions.
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Affiliation(s)
- Elizabeth Kermgard
- Department of Microbiology, Immunology and Molecular Genetics University of California, Los Angeles, California 90095, USA
| | - Zhou Yang
- Department of Microbiology, Immunology and Molecular Genetics University of California, Los Angeles, California 90095, USA
| | - Annika-Marisa Michel
- Department of Microbiology, Immunology and Molecular Genetics University of California, Los Angeles, California 90095, USA.,Technische Universität Braunschweig, Institut of Microbiology, Braunschweig, Germany
| | - Rachel Simari
- Ohio State Biochemistry Program, Ohio State University, Columbus, Ohio 43210, USA
| | - Jacqueline Wong
- Department of Microbiology, Immunology and Molecular Genetics University of California, Los Angeles, California 90095, USA
| | - Michael Ibba
- Ohio State Biochemistry Program, Ohio State University, Columbus, Ohio 43210, USA.,Department of Microbiology, Ohio State University, Columbus, Ohio 43210, USA.,Center for RNA Biology, Ohio State University, Columbus, Ohio 43210, USA
| | - Beth A Lazazzera
- Department of Microbiology, Immunology and Molecular Genetics University of California, Los Angeles, California 90095, USA.,Molecular Biology Institute, University of California, Los Angeles, California 90095, USA
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Mistranslation: from adaptations to applications. Biochim Biophys Acta Gen Subj 2017; 1861:3070-3080. [PMID: 28153753 DOI: 10.1016/j.bbagen.2017.01.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/23/2017] [Accepted: 01/24/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND The conservation of the genetic code indicates that there was a single origin, but like all genetic material, the cell's interpretation of the code is subject to evolutionary pressure. Single nucleotide variations in tRNA sequences can modulate codon assignments by altering codon-anticodon pairing or tRNA charging. Either can increase translation errors and even change the code. The frozen accident hypothesis argued that changes to the code would destabilize the proteome and reduce fitness. In studies of model organisms, mistranslation often acts as an adaptive response. These studies reveal evolutionary conserved mechanisms to maintain proteostasis even during high rates of mistranslation. SCOPE OF REVIEW This review discusses the evolutionary basis of altered genetic codes, how mistranslation is identified, and how deviations to the genetic code are exploited. We revisit early discoveries of genetic code deviations and provide examples of adaptive mistranslation events in nature. Lastly, we highlight innovations in synthetic biology to expand the genetic code. MAJOR CONCLUSIONS The genetic code is still evolving. Mistranslation increases proteomic diversity that enables cells to survive stress conditions or suppress a deleterious allele. Genetic code variants have been identified by genome and metagenome sequence analyses, suppressor genetics, and biochemical characterization. GENERAL SIGNIFICANCE Understanding the mechanisms of translation and genetic code deviations enables the design of new codes to produce novel proteins. Engineering the translation machinery and expanding the genetic code to incorporate non-canonical amino acids are valuable tools in synthetic biology that are impacting biomedical research. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.
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Mohler K, Aerni HR, Gassaway B, Ling J, Ibba M, Rinehart J. MS-READ: Quantitative measurement of amino acid incorporation. Biochim Biophys Acta Gen Subj 2017; 1861:3081-3088. [PMID: 28130155 DOI: 10.1016/j.bbagen.2017.01.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 01/18/2017] [Indexed: 10/20/2022]
Abstract
Ribosomal protein synthesis results in the genetically programmed incorporation of amino acids into a growing polypeptide chain. Faithful amino acid incorporation that accurately reflects the genetic code is critical to the structure and function of proteins as well as overall proteome integrity. Errors in protein synthesis are generally detrimental to cellular processes yet emerging evidence suggest that proteome diversity generated through mistranslation may be beneficial under certain conditions. Cumulative translational error rates have been determined at the organismal level, however codon specific error rates and the spectrum of misincorporation errors from system to system remain largely unexplored. In particular, until recently technical challenges have limited the ability to detect and quantify comparatively rare amino acid misincorporation events, which occur orders of magnitude less frequently than canonical amino acid incorporation events. We now describe a technique for the quantitative analysis of amino acid incorporation that provides the sensitivity necessary to detect mistranslation events during translation of a single codon at frequencies as low as 1 in 10,000 for all 20 proteinogenic amino acids, as well as non-proteinogenic and modified amino acids. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.
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Affiliation(s)
- Kyle Mohler
- Department of Microbiology, The Ohio State University, 318 West 12th Avenue, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
| | - Hans-Rudolf Aerni
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Cellular & Molecular Physiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Brandon Gassaway
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Cellular & Molecular Physiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jiqiang Ling
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Michael Ibba
- Department of Microbiology, The Ohio State University, 318 West 12th Avenue, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
| | - Jesse Rinehart
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Cellular & Molecular Physiology, Yale University School of Medicine, New Haven, CT 06520, USA.
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40
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Rewiring protein synthesis: From natural to synthetic amino acids. Biochim Biophys Acta Gen Subj 2017; 1861:3024-3029. [PMID: 28095316 DOI: 10.1016/j.bbagen.2017.01.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 01/11/2017] [Accepted: 01/12/2017] [Indexed: 11/21/2022]
Abstract
BACKGROUND The protein synthesis machinery uses 22 natural amino acids as building blocks that faithfully decode the genetic information. Such fidelity is controlled at multiple steps and can be compromised in nature and in the laboratory to rewire protein synthesis with natural and synthetic amino acids. SCOPE OF REVIEW This review summarizes the major quality control mechanisms during protein synthesis, including aminoacyl-tRNA synthetases, elongation factors, and the ribosome. We will discuss evolution and engineering of such components that allow incorporation of natural and synthetic amino acids at positions that deviate from the standard genetic code. MAJOR CONCLUSIONS The protein synthesis machinery is highly selective, yet not fixed, for the correct amino acids that match the mRNA codons. Ambiguous translation of a codon with multiple amino acids or complete reassignment of a codon with a synthetic amino acid diversifies the proteome. GENERAL SIGNIFICANCE Expanding the genetic code with synthetic amino acids through rewiring protein synthesis has broad applications in synthetic biology and chemical biology. Biochemical, structural, and genetic studies of the translational quality control mechanisms are not only crucial to understand the physiological role of translational fidelity and evolution of the genetic code, but also enable us to better design biological parts to expand the proteomes of synthetic organisms. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.
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41
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Schwartz MH, Pan T. Function and origin of mistranslation in distinct cellular contexts. Crit Rev Biochem Mol Biol 2017; 52:205-219. [PMID: 28075177 DOI: 10.1080/10409238.2016.1274284] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Mistranslation describes errors during protein synthesis that prevent the amino acid sequences specified in the genetic code from being reflected within proteins. For a long time, mistranslation has largely been considered an aberrant cellular process that cells actively avoid at all times. However, recent evidence has demonstrated that cells from all three domains of life not only tolerate certain levels and forms of mistranslation, but actively induce mistranslation under certain circumstances. To this end, dedicated biological mechanisms have recently been found to reduce translational fidelity, which indicates that mistranslation is not exclusively an erroneous process and can even benefit cells in particular cellular contexts. There currently exists a spectrum of mistranslational processes that differ not only in their origins, but also in their molecular and cellular effects. These findings suggest that the optimal degree of translational fidelity largely depends on a specific cellular context. This review aims to conceptualize the basis and functional consequence of the diverse types of mistranslation that have been described so far.
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Affiliation(s)
- Michael H Schwartz
- a Department of Biochemistry and Molecular Biology , University of Chicago, Chicago , IL , USA
| | - Tao Pan
- a Department of Biochemistry and Molecular Biology , University of Chicago, Chicago , IL , USA
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42
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Structural characterization of antibiotic self-immunity tRNA synthetase in plant tumour biocontrol agent. Nat Commun 2016; 7:12928. [PMID: 27713402 PMCID: PMC5059758 DOI: 10.1038/ncomms12928] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 08/16/2016] [Indexed: 01/08/2023] Open
Abstract
Antibiotic-producing microbes evolved self-resistance mechanisms to avoid suicide. The biocontrol Agrobacterium radiobacter K84 secretes the Trojan Horse antibiotic agrocin 84 that is selectively transported into the plant pathogen A. tumefaciens and processed into the toxin TM84. We previously showed that TM84 employs a unique tRNA-dependent mechanism to inhibit leucyl-tRNA synthetase (LeuRS), while the TM84-producer prevents self-poisoning by expressing a resistant LeuRS AgnB2. We now identify a mechanism by which the antibiotic-producing microbe resists its own toxin. Using a combination of structural, biochemical and biophysical approaches, we show that AgnB2 evolved structural changes so as to resist the antibiotic by eliminating the tRNA-dependence of TM84 binding. Mutagenesis of key resistance determinants results in mutants adopting an antibiotic-sensitive phenotype. This study illuminates the evolution of resistance in self-immunity genes and provides mechanistic insights into a fascinating tRNA-dependent antibiotic with applications for the development of anti-infectives and the prevention of biocontrol emasculation.
The bacterium Agrobacterium radiobacter K84 secretes an antibiotic that is transported into the plant pathogen A. tumefaciens and processed into the toxin TM84. Here, the authors identify a mechanism whereby the antibiotic-producing microbe resists its own toxin.
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Schwartz MH, Waldbauer JR, Zhang L, Pan T. Global tRNA misacylation induced by anaerobiosis and antibiotic exposure broadly increases stress resistance in Escherichia coli. Nucleic Acids Res 2016; 44:10292-10303. [PMID: 27672035 PMCID: PMC5137444 DOI: 10.1093/nar/gkw856] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 09/14/2016] [Accepted: 09/16/2016] [Indexed: 12/22/2022] Open
Abstract
High translational fidelity is commonly considered a requirement for optimal cellular health and protein function. However, recent findings have shown that inducible mistranslation specifically with methionine engendered at the tRNA charging level occurs in mammalian cells, yeast and archaea, yet it was unknown whether bacteria were capable of mounting a similar response. Here, we demonstrate that Escherichia coli misacylates non-methionyl-tRNAs with methionine in response to anaerobiosis and antibiotic exposure via the methionyl–tRNA synthetase (MetRS). Two MetRS succinyl-lysine modifications independently confer high tRNA charging fidelity to the otherwise promiscuous, unmodified enzyme. Strains incapable of tRNA mismethionylation are less adept at growth in the presence of antibiotics and stressors. The presence of tRNA mismethionylation and its potential role in mistranslation within the bacterial domain establishes this response as a pervasive biological mechanism and connects it to diverse cellular functions and modes of fitness.
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Affiliation(s)
- Michael H Schwartz
- Department of Biochemistry and Molecular Biology, University of Chicago, 929 E. 57th St., Chicago, IL 60637, USA.,Committee on Microbiology, University of Chicago, 929 E. 57th St., Chicago, IL 60637, USA
| | - Jacob R Waldbauer
- Department of Geophysical Sciences, University of Chicago, 5734 S. Ellis Ave., Chicago, IL 60637, USA
| | - Lichun Zhang
- Department of Geophysical Sciences, University of Chicago, 5734 S. Ellis Ave., Chicago, IL 60637, USA
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, 929 E. 57th St., Chicago, IL 60637, USA .,Committee on Microbiology, University of Chicago, 929 E. 57th St., Chicago, IL 60637, USA
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The essential mycobacterial amidotransferase GatCAB is a modulator of specific translational fidelity. Nat Microbiol 2016; 1:16147. [PMID: 27564922 DOI: 10.1038/nmicrobiol.2016.147] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 07/19/2016] [Indexed: 01/14/2023]
Abstract
Although regulation of translation fidelity is an essential process1-7, diverse organisms and organelles have differing requirements of translational accuracy8-15, and errors in gene translation serve an adaptive function under certain conditions16-20. Therefore, optimal levels of fidelity may vary according to context. Most bacteria utilize a two-step pathway for the specific synthesis of aminoacylated glutamine and/or asparagine tRNAs, involving the glutamine amidotransferase GatCAB21-25, but it had not been appreciated that GatCAB may play a role in modulating mistranslation rates. Here, by using a forward genetic screen, we show that the mycobacterial GatCAB enzyme complex mediates the translational fidelity of glutamine and asparagine codons. We identify mutations in gatA that cause partial loss of function in the holoenzyme, with a consequent increase in rates of mistranslation. By monitoring single-cell transcription dynamics, we demonstrate that reduced gatCAB expression leads to increased mistranslation rates, which result in enhanced rifampicin-specific phenotypic resistance. Consistent with this, strains with mutations in gatA from clinical isolates of Mycobacterium tuberculosis show increased mistranslation, with associated antibiotic tolerance, suggesting a role for mistranslation as an adaptive strategy in tuberculosis. Together, our findings demonstrate a potential role for the indirect tRNA aminoacylation pathway in regulating translational fidelity and adaptive mistranslation.
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Zhou XL, Chen Y, Fang ZP, Ruan ZR, Wang Y, Liu RJ, Xue MQ, Wang ED. Translational Quality Control by Bacterial Threonyl-tRNA Synthetases. J Biol Chem 2016; 291:21208-21221. [PMID: 27542414 DOI: 10.1074/jbc.m116.740472] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Indexed: 11/06/2022] Open
Abstract
Translational fidelity mediated by aminoacyl-tRNA synthetases ensures the generation of the correct aminoacyl-tRNAs, which is critical for most species. Threonyl-tRNA synthetase (ThrRS) contains multiple domains, including an N2 editing domain. Of the ThrRS domains, N1 is the last to be assigned a function. Here, we found that ThrRSs from Mycoplasma species exhibit differences in their domain composition and editing active sites compared with the canonical ThrRSs. The Mycoplasma mobile ThrRS, the first example of a ThrRS naturally lacking the N1 domain, displays efficient post-transfer editing activity. In contrast, the Mycoplasma capricolum ThrRS, which harbors an N1 domain and a degenerate N2 domain, is editing-defective. Only editing-capable ThrRSs were able to support the growth of a yeast thrS deletion strain (ScΔthrS), thus suggesting that ScΔthrS is an excellent tool for studying the in vivo editing of introduced bacterial ThrRSs. On the basis of the presence or absence of an N1 domain, we further revealed the crucial importance of the only absolutely conserved residue within the N1 domain in regulating editing by mediating an N1-N2 domain interaction in Escherichia coli ThrRS. Our results reveal the translational quality control of various ThrRSs and the role of the N1 domain in translational fidelity.
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Affiliation(s)
- Xiao-Long Zhou
- From the State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China and
| | - Yun Chen
- From the State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China and
| | - Zhi-Peng Fang
- From the State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China and
| | - Zhi-Rong Ruan
- From the State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China and
| | - Yong Wang
- the School of Life Science and Technology, ShanghaiTech University, 200031 Shanghai, China
| | - Ru-Juan Liu
- From the State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China and
| | - Mei-Qin Xue
- From the State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China and
| | - En-Duo Wang
- From the State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China and the School of Life Science and Technology, ShanghaiTech University, 200031 Shanghai, China
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Fan Y, Evans CR, Ling J. Reduced Protein Synthesis Fidelity Inhibits Flagellar Biosynthesis and Motility. Sci Rep 2016; 6:30960. [PMID: 27468805 PMCID: PMC4965754 DOI: 10.1038/srep30960] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/12/2016] [Indexed: 01/02/2023] Open
Abstract
Accurate translation of the genetic information from DNA to protein is maintained by multiple quality control steps from bacteria to mammals. Genetic and environmental alterations have been shown to compromise translational quality control and reduce fidelity during protein synthesis. The physiological impact of increased translational errors is not fully understood. While generally considered harmful, translational errors have recently been shown to benefit cells under certain stress conditions. In this work, we describe a novel regulatory pathway in which reduced translational fidelity downregulates expression of flagellar genes and suppresses bacterial motility. Electron microscopy imaging shows that the error-prone Escherichia coli strain lacks mature flagella. Further genetic analyses reveal that translational errors upregulate expression of a small RNA DsrA through enhancing its transcription, and deleting DsrA from the error-prone strain restores motility. DsrA regulates expression of H-NS and RpoS, both of which regulate flagellar genes. We demonstrate that an increased level of DsrA in the error-prone strain suppresses motility through the H-NS pathway. Our work suggests that bacteria are capable of switching on and off the flagellar system by altering translational fidelity, which may serve as a previously unknown mechanism to improve fitness in response to environmental cues.
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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
| | - 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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Wang X, Pan T. Stress Response and Adaptation Mediated by Amino Acid Misincorporation during Protein Synthesis. Adv Nutr 2016; 7:773S-9S. [PMID: 27422514 PMCID: PMC4942860 DOI: 10.3945/an.115.010991] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Translation of genetic information into functional proteins is critical for all cellular life. Accurate protein synthesis relies on proper aminoacylation of transfer RNAs (tRNAs) and decoding of mRNAs by the ribosome with the use of aminoacyl-tRNAs. Mistranslation can lead to pathologic consequences. All cells contain elaborate quality control mechanisms in translation, although translational fidelity may be regulated by various factors such as nutrient limitation or reactive oxygen species. Translation fidelity is maintained via the accuracy of tRNA aminoacylation by the aminoacyl-tRNA synthetases and matching of the mRNA codon with the tRNA anticodon by the ribosome. Stringent substrate discrimination and proofreading are critical in aminoacylating tRNAs with their cognate amino acid to maintain high accuracy of translation. Although the composition of the cellular proteome generally adheres to the genetic code, accumulating evidence indicates that cells can also deliberately mistranslate; they synthesize mutant proteins that deviate from the genetic code in response to stress or environmental changes. Mistranslation with tRNA charged with noncognate amino acids can expand the proteome to enhance stress response and help adaptation. Here, we review current knowledge on mistranslation through tRNA misacylation and describe advances in our understanding of translational control in the regulation of stress response and human diseases.
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Affiliation(s)
- Xiaoyun Wang
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL
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Moghal A, Hwang L, Faull K, Ibba M. Multiple Quality Control Pathways Limit Non-protein Amino Acid Use by Yeast Cytoplasmic Phenylalanyl-tRNA Synthetase. J Biol Chem 2016; 291:15796-805. [PMID: 27226603 DOI: 10.1074/jbc.m116.726828] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Indexed: 11/06/2022] Open
Abstract
Non-protein amino acids, particularly isomers of the proteinogenic amino acids, present a threat to proteome integrity if they are mistakenly inserted into proteins. Quality control during aminoacyl-tRNA synthesis reduces non-protein amino acid incorporation by both substrate discrimination and proofreading. For example phenylalanyl-tRNA synthetase (PheRS) proofreads the non-protein hydroxylated phenylalanine derivative m-Tyr after its attachment to tRNA(Phe) We now show in Saccharomyces cerevisiae that PheRS misacylation of tRNA(Phe) with the more abundant Phe oxidation product o-Tyr is limited by kinetic discrimination against o-Tyr-AMP in the transfer step followed by o-Tyr-AMP release from the synthetic active site. This selective rejection of a non-protein aminoacyl-adenylate is in addition to known kinetic discrimination against certain non-cognates in the activation step as well as catalytic hydrolysis of mispaired aminoacyl-tRNA(Phe) species. We also report an unexpected resistance to cytotoxicity by a S. cerevisiae mutant with ablated post-transfer editing activity when supplemented with o-Tyr, cognate Phe, or Ala, the latter of which is not a substrate for activation by this enzyme. Our phenotypic, metabolomic, and kinetic analyses indicate at least three modes of discrimination against non-protein amino acids by S. cerevisiae PheRS and support a non-canonical role for SccytoPheRS post-transfer editing in response to amino acid stress.
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Affiliation(s)
- Adil Moghal
- From the Ohio State Biochemistry Program, Department of Microbiology, The Ohio State University, Columbus, Ohio 43210 and
| | - Lin Hwang
- Pasarow Mass Spectrometry Laboratory, Semel Institute of Neuroscience and Human Behavior, University of California, Los Angeles, California 90095
| | - Kym Faull
- Pasarow Mass Spectrometry Laboratory, Semel Institute of Neuroscience and Human Behavior, University of California, Los Angeles, California 90095
| | - Michael Ibba
- From the Ohio State Biochemistry Program, Department of Microbiology, The Ohio State University, Columbus, Ohio 43210 and
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Clues to tRNA Evolution from the Distribution of Class II tRNAs and Serine Codons in the Genetic Code. Life (Basel) 2016; 6:life6010010. [PMID: 26927183 PMCID: PMC4810241 DOI: 10.3390/life6010010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/20/2016] [Accepted: 02/22/2016] [Indexed: 11/30/2022] Open
Abstract
We have previously proposed that tRNAGly was the first tRNA and glycine was the first amino acid incorporated into the genetic code. The next two amino acids incorporated would have been the other two small hydrophilic amino acids serine and aspartic acid, which occurred through the duplication of the tRNAGly sequence, followed by mutation of its anticodon by single C to U transition mutations, possibly through spontaneous deamination. Interestingly, however, tRNASer has a different structure than most other tRNAs, possessing a long variable arm; because of this tRNASer is classified as a class II tRNA. Also, serine codons are found not only in the bottom right-hand corner of the genetic code table next to those for glycine and aspartic acid, but also in the top row of the table, next to those for two of the most hydrophobic amino acids, leucine and phenylalanine. In the following, I propose that the class II tRNA structure of tRNASer and the arrangement of serine codons in the genetic code provide clues to the early evolution of tRNA and the genetic code. In addition, I address Di Giulio’s recent criticism of our proposal that tRNAGly was the first tRNA, and discuss how early peptides produced from a restricted amino acid alphabet of glycine, serine and aspartic acid might have possessed proteolytic activity, which is possibly important for the early recycling of amino acid monomers.
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Translation quality control is critical for bacterial responses to amino acid stress. Proc Natl Acad Sci U S A 2016; 113:2252-7. [PMID: 26858451 DOI: 10.1073/pnas.1525206113] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Gene expression relies on quality control for accurate transmission of genetic information. One mechanism that prevents amino acid misincorporation errors during translation is editing of misacylated tRNAs by aminoacyl-tRNA synthetases. In the absence of editing, growth is limited upon exposure to excess noncognate amino acid substrates and other stresses, but whether these physiological effects result solely from mistranslation remains unclear. To explore if translation quality control influences cellular processes other than protein synthesis, an Escherichia coli strain defective in Tyr-tRNA(Phe) editing was used. In the absence of editing, cellular levels of aminoacylated tRNA(Phe) were elevated during amino acid stress, whereas in the wild-type strain these levels declined under the same growth conditions. In the editing-defective strain, increased levels of aminoacylated tRNA(Phe) led to continued synthesis of the PheL leader peptide and attenuation of pheA transcription under amino acid stress. Consequently, in the absence of editing, activation of the phenylalanine biosynthetic operon becomes less responsive to phenylalanine limitation. In addition to raising aminoacylated tRNA levels, the absence of editing lowered the amount of deacylated tRNA(Phe) in the cell. This reduction in deacylated tRNA was accompanied by decreased synthesis of the second messenger guanosine tetraphosphate and limited induction of stringent response-dependent gene expression in editing-defective cells during amino acid stress. These data show that a single quality-control mechanism, the editing of misacylated aminoacyl-tRNAs, provides a critical checkpoint both for maintaining the accuracy of translation and for determining the sensitivity of transcriptional responses to amino acid stress.
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