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Baker M, Zhang X, Maciel-Guerra A, Babaarslan K, Dong Y, Wang W, Hu Y, Renney D, Liu L, Li H, Hossain M, Heeb S, Tong Z, Pearcy N, Zhang M, Geng Y, Zhao L, Hao Z, Senin N, Chen J, Peng Z, Li F, Dottorini T. Convergence of resistance and evolutionary responses in Escherichia coli and Salmonella enterica co-inhabiting chicken farms in China. Nat Commun 2024; 15:206. [PMID: 38182559 PMCID: PMC10770378 DOI: 10.1038/s41467-023-44272-1] [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: 04/04/2023] [Accepted: 12/06/2023] [Indexed: 01/07/2024] Open
Abstract
Sharing of genetic elements among different pathogens and commensals inhabiting same hosts and environments has significant implications for antimicrobial resistance (AMR), especially in settings with high antimicrobial exposure. We analysed 661 Escherichia coli and Salmonella enterica isolates collected within and across hosts and environments, in 10 Chinese chicken farms over 2.5 years using data-mining methods. Most isolates within same hosts possessed the same clinically relevant AMR-carrying mobile genetic elements (plasmids: 70.6%, transposons: 78%), which also showed recent common evolution. Supervised machine learning classifiers revealed known and novel AMR-associated mutations and genes underlying resistance to 28 antimicrobials, primarily associated with resistance in E. coli and susceptibility in S. enterica. Many were essential and affected same metabolic processes in both species, albeit with varying degrees of phylogenetic penetration. Multi-modal strategies are crucial to investigate the interplay of mobilome, resistance and metabolism in cohabiting bacteria, especially in ecological settings where community-driven resistance selection occurs.
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Affiliation(s)
- Michelle Baker
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Loughborough, Leicestershire, LE12 5RD, UK
| | - Xibin Zhang
- Shandong New Hope Liuhe Group Co. Ltd. and Qingdao Key Laboratory of Animal Feed Safety, Qingdao, Shandong, 266000, P.R. China
| | - Alexandre Maciel-Guerra
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Loughborough, Leicestershire, LE12 5RD, UK
| | - Kubra Babaarslan
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Loughborough, Leicestershire, LE12 5RD, UK
| | - Yinping Dong
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, P. R. China
| | - Wei Wang
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, P. R. China
| | - Yujie Hu
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, P. R. China
| | - David Renney
- Nimrod Veterinary Products Limited, 2, Wychwood Court, Cotswold Business Village, Moreton-in-Marsh, GL56 0JQ, London, UK
| | - Longhai Liu
- Shandong Kaijia Food Co. Ltd, Weifang, P. R. China
| | - Hui Li
- Luoyang Center for Disease Control and Prevention, No. 9, Zhenghe Road, Luolong District, Luoyang City, Henan Province, Luolong, 471000, P. R. China
| | - Maqsud Hossain
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Loughborough, Leicestershire, LE12 5RD, UK
| | - Stephan Heeb
- School of Life Sciences, University of Nottingham, East Drive, Nottingham, Nottinghamshire, NG7 2RD, UK
| | - Zhiqin Tong
- Luoyang Center for Disease Control and Prevention, No. 9, Zhenghe Road, Luolong District, Luoyang City, Henan Province, Luolong, 471000, P. R. China
| | - Nicole Pearcy
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Loughborough, Leicestershire, LE12 5RD, UK
- School of Life Sciences, University of Nottingham, East Drive, Nottingham, Nottinghamshire, NG7 2RD, UK
| | - Meimei Zhang
- Liaoning Provincial Center for Disease Control and Prevention, No. 168, Jinfeng Street, Hunnan District, Shenyang City, Liaoning Province, 110072, P. R. China
| | - Yingzhi Geng
- Liaoning Provincial Center for Disease Control and Prevention, No. 168, Jinfeng Street, Hunnan District, Shenyang City, Liaoning Province, 110072, P. R. China
| | - Li Zhao
- Agricultural Biopharmaceutical Laboratory, College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, No. 700 Changcheng Road, Chengyang District, Qingdao City, Shandong Province, 266109, P. R. China
| | - Zhihui Hao
- Chinese Veterinary Medicine Innovation Center, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing City, 100193, P. R. China
| | - Nicola Senin
- Department of Engineering, University of Perugia, Perugia, I06125, Italy
| | - Junshi Chen
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, P. R. China
| | - Zixin Peng
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, P. R. China.
| | - Fengqin Li
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, P. R. China.
| | - Tania Dottorini
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Loughborough, Leicestershire, LE12 5RD, UK.
- Centre for Smart Food Research, Nottingham Ningbo China Beacons of Excellence Research and Innovation Institute, University of Nottingham Ningbo China, Ningbo, 315100, P. R. China.
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2
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Barros GC, Guerrero S, Silva GM. The central role of translation elongation in response to stress. Biochem Soc Trans 2023; 51:959-969. [PMID: 37318088 PMCID: PMC11160351 DOI: 10.1042/bst20220584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/16/2023]
Abstract
Protein synthesis is essential to support homeostasis, and thus, must be highly regulated during cellular response to harmful environments. All stages of translation are susceptible to regulation under stress, however, the mechanisms involved in translation regulation beyond initiation have only begun to be elucidated. Methodological advances enabled critical discoveries on the control of translation elongation, highlighting its important role in translation repression and the synthesis of stress-response proteins. In this article, we discuss recent findings on mechanisms of elongation control mediated by ribosome pausing and collisions and the availability of tRNAs and elongation factors. We also discuss how elongation intersects with distinct modes of translation control, further supporting cellular viability and gene expression reprogramming. Finally, we highlight how several of these pathways are reversibly regulated, emphasizing the dynamics of translation control during stress-response progression. A comprehensive understanding of translation regulation under stress will produce fundamental knowledge of protein dynamics while opening new avenues and strategies to overcome dysregulated protein production and cellular sensitivity to stress.
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Affiliation(s)
| | | | - Gustavo M. Silva
- Department of Biology, Duke University, Durham, NC, USA
- Lead contact
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3
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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: 6] [Impact Index Per Article: 6.0] [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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4
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Fu Y, Zhang L, Song H, Liao J, Lin L, Jiang W, Wu X, Wang G. Acetylome and Succinylome Profiling of Edwardsiella tarda Reveals Key Roles of Both Lysine Acylations in Bacterial Antibiotic Resistance. Antibiotics (Basel) 2022; 11:841. [PMID: 35884095 PMCID: PMC9312108 DOI: 10.3390/antibiotics11070841] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/17/2022] [Accepted: 06/20/2022] [Indexed: 11/20/2022] Open
Abstract
The antibiotic resistance of Edwardsiella tarda is becoming increasingly prevalent, and thus novel antimicrobial strategies are being sought. Lysine acylation has been demonstrated to play an important role in bacterial physiological functions, while its role in bacterial antibiotic resistance remains largely unclear. In this study, we investigated the lysine acetylation and succinylation profiles of E. tarda strain EIB202 using affinity antibody purification combined with LC-MS/MS. A total of 1511 lysine-acetylation sites were identified on 589 proteins, and 2346 lysine-succinylation sites were further identified on 692 proteins of this pathogen. Further bioinformatic analysis showed that both post-translational modifications (PTMs) were enriched in the tricarboxylic acid (TCA) cycle, pyruvate metabolism, biosynthesis, and carbon metabolism. In addition, 948 peptides of 437 proteins had overlapping associations with multiple metabolic pathways. Moreover, both acetylation and succinylation were found in many antimicrobial resistance (AMR) proteins, suggesting their potentially vital roles in antibiotic resistance. In general, our work provides insights into the acetylome and succinylome features responsible for the antibiotic resistance mechanism of E. tarda, and the results may facilitate future investigations into the pathogenesis of this bacterium.
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Affiliation(s)
- Yuying Fu
- School of Safety and Environment, Fujian Chuanzheng Communications College, Fuzhou 350007, China; (Y.F.); (J.L.); (L.L.); (W.J.); (X.W.)
| | - Lishan Zhang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.Z.); (H.S.)
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Huanhuan Song
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.Z.); (H.S.)
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Junyan Liao
- School of Safety and Environment, Fujian Chuanzheng Communications College, Fuzhou 350007, China; (Y.F.); (J.L.); (L.L.); (W.J.); (X.W.)
| | - Li Lin
- School of Safety and Environment, Fujian Chuanzheng Communications College, Fuzhou 350007, China; (Y.F.); (J.L.); (L.L.); (W.J.); (X.W.)
| | - Wenjia Jiang
- School of Safety and Environment, Fujian Chuanzheng Communications College, Fuzhou 350007, China; (Y.F.); (J.L.); (L.L.); (W.J.); (X.W.)
| | - Xiaoyun Wu
- School of Safety and Environment, Fujian Chuanzheng Communications College, Fuzhou 350007, China; (Y.F.); (J.L.); (L.L.); (W.J.); (X.W.)
| | - Guibin Wang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.Z.); (H.S.)
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing 102206, China
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5
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Mathé-Hubert H, Amia R, Martin M, Gaffé J, Schneider D. Evolution of Bacterial Persistence to Antibiotics during a 50,000-Generation Experiment in an Antibiotic-Free Environment. Antibiotics (Basel) 2022; 11:antibiotics11040451. [PMID: 35453204 PMCID: PMC9028194 DOI: 10.3390/antibiotics11040451] [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: 02/25/2022] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 02/05/2023] Open
Abstract
Failure of antibiotic therapies causes > 700,000 deaths yearly and involves both bacterial resistance and persistence. Persistence results in the relapse of infections by producing a tiny fraction of pathogen survivors that stay dormant during antibiotic exposure. From an evolutionary perspective, persistence is either a ‘bet-hedging strategy’ that helps to cope with stochastically changing environments or an unavoidable minimal rate of ‘cellular errors’ that lock the cells in a low activity state. Here, we analyzed the evolution of persistence over 50,000 bacterial generations in a stable environment by improving a published method that estimates the number of persister cells based on the growth of the reviving population. Our results challenged our understanding of the factors underlying persistence evolution. In one case, we observed a substantial decrease in persistence proportion, suggesting that the naturally observed persistence level is not an unavoidable minimal rate of ‘cellular errors’. However, although there was no obvious environmental stochasticity, in 11 of the 12 investigated populations, the persistence level was maintained during 50,000 bacterial generations.
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6
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Josephs-Spaulding J, Krogh TJ, Rettig HC, Lyng M, Chkonia M, Waschina S, Graspeuntner S, Rupp J, Møller-Jensen J, Kaleta C. Recurrent Urinary Tract Infections: Unraveling the Complicated Environment of Uncomplicated rUTIs. Front Cell Infect Microbiol 2021; 11:562525. [PMID: 34368008 PMCID: PMC8340884 DOI: 10.3389/fcimb.2021.562525] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 05/18/2021] [Indexed: 12/14/2022] Open
Abstract
Urinary tract infections (UTIs) are frequent in humans, affecting the upper and lower urinary tract. Present diagnosis relies on the positive culture of uropathogenic bacteria from urine and clinical markers of inflammation of the urinary tract. The bladder is constantly challenged by adverse environmental stimuli which influence urinary tract physiology, contributing to a dysbiotic environment. Simultaneously, pathogens are primed by environmental stressors such as antibiotics, favoring recurrent UTIs (rUTIs), resulting in chronic illness. Due to different confounders for UTI onset, a greater understanding of the fundamental environmental mechanisms and microbial ecology of the human urinary tract is required. Such advancements could promote the tandem translation of bench and computational studies for precision treatments and clinical management of UTIs. Therefore, there is an urgent need to understand the ecological interactions of the human urogenital microbial communities which precede rUTIs. This review aims to outline the mechanistic aspects of rUTI ecology underlying dysbiosis between both the human microbiome and host physiology which predisposes humans to rUTIs. By assessing the applications of next generation and systems level methods, we also recommend novel approaches to elucidate the systemic consequences of rUTIs which requires an integrated approach for successful treatment. To this end, we will provide an outlook towards the so-called 'uncomplicated environment of UTIs', a holistic and systems view that applies ecological principles to define patient-specific UTIs. This perspective illustrates the need to withdraw from traditional reductionist perspectives in infection biology and instead, a move towards a systems-view revolving around patient-specific pathophysiology during UTIs.
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Affiliation(s)
- Jonathan Josephs-Spaulding
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Christian-Albrechts-Universität, Kiel, Germany
| | - Thøger Jensen Krogh
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Hannah Clara Rettig
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Mark Lyng
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Mariam Chkonia
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Silvio Waschina
- Research Group Nutriinformatics, Institute of Human Nutrition and Food Science, Christian-Albrechts-Universität, Kiel, Germany
| | - Simon Graspeuntner
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
| | - Jakob Møller-Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Christian-Albrechts-Universität, Kiel, Germany
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7
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Nombela P, Miguel-López B, Blanco S. The role of m 6A, m 5C and Ψ RNA modifications in cancer: Novel therapeutic opportunities. Mol Cancer 2021; 20:18. [PMID: 33461542 PMCID: PMC7812662 DOI: 10.1186/s12943-020-01263-w] [Citation(s) in RCA: 259] [Impact Index Per Article: 86.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 09/24/2020] [Indexed: 12/12/2022] Open
Abstract
RNA modifications have recently emerged as critical posttranscriptional regulators of gene expression programmes. Significant advances have been made in understanding the functional role of RNA modifications in regulating coding and non-coding RNA processing and function, which in turn thoroughly shape distinct gene expression programmes. They affect diverse biological processes, and the correct deposition of many of these modifications is required for normal development. Alterations of their deposition are implicated in several diseases, including cancer. In this Review, we focus on the occurrence of N6-methyladenosine (m6A), 5-methylcytosine (m5C) and pseudouridine (Ψ) in coding and non-coding RNAs and describe their physiopathological role in cancer. We will highlight the latest insights into the mechanisms of how these posttranscriptional modifications influence tumour development, maintenance, and progression. Finally, we will summarize the latest advances on the development of small molecule inhibitors that target specific writers or erasers to rewind the epitranscriptome of a cancer cell and their therapeutic potential.
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Affiliation(s)
- Paz Nombela
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) - University of Salamanca, 37007, Salamanca, Spain
| | - Borja Miguel-López
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) - University of Salamanca, 37007, Salamanca, Spain
| | - Sandra Blanco
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) - University of Salamanca, 37007, Salamanca, Spain. .,Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain.
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8
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Avcilar-Kucukgoze I, Kashina A. Hijacking tRNAs From Translation: Regulatory Functions of tRNAs in Mammalian Cell Physiology. Front Mol Biosci 2020; 7:610617. [PMID: 33392265 PMCID: PMC7773854 DOI: 10.3389/fmolb.2020.610617] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 11/10/2020] [Indexed: 12/12/2022] Open
Abstract
Transfer tRNAs (tRNAs) are small non-coding RNAs that are highly conserved in all kingdoms of life. Originally discovered as the molecules that deliver amino acids to the growing polypeptide chain during protein synthesis, tRNAs have been believed for a long time to play exclusive role in translation. However, recent studies have identified key roles for tRNAs and tRNA-derived small RNAs in multiple other processes, including regulation of transcription and translation, posttranslational modifications, stress response, and disease. These emerging roles suggest that tRNAs may be central players in the complex machinery of biological regulatory pathways. Here we overview these non-canonical roles of tRNA in normal physiology and disease, focusing largely on eukaryotic and mammalian systems.
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Affiliation(s)
- Irem Avcilar-Kucukgoze
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Anna Kashina
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
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9
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The Boggarts of biology: how non-genetic changes influence the genotype. Curr Genet 2020; 67:65-77. [PMID: 33037901 DOI: 10.1007/s00294-020-01108-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 01/21/2023]
Abstract
The notion that there is a one-one mapping from genotype to phenotype was overturned a long time ago. Along with genotype and environment, 'non-genetic changes' orchestrated by altered RNA and protein molecules also guide the development of phenotype. The idea that there is a route through which changes in phenotype can lead to changes in genotype impinges on several phenomena of molecular, developmental, evolutionary and applied interest. Phenotypic changes that do not alter the underlying DNA sequence have been studied across model systems (eg: DNA and histone modifications, RNA editing, prion formation) and are known to play an important role in short-term adaptation. However, because of their transient nature and unstable inheritance, the role of such changes in long-term evolution has remained controversial. I classify and review three ways in which non-genetic changes can influence genotype and impact cellular fitness across generations, with an emphasis on the enticing idea that they may act as stepping stones for genetic adaptation. I focus on work from microbial systems and attempt to highlight recent experiments and models that bear on this idea. Overall, I review evidence which suggests that non-genetic changes can impact phenotype via their influence on the genotype, and thus play a role in evolutionary change.
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10
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Global mistranslation increases cell survival under stress in Escherichia coli. PLoS Genet 2020; 16:e1008654. [PMID: 32150542 PMCID: PMC7082066 DOI: 10.1371/journal.pgen.1008654] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 03/19/2020] [Accepted: 02/05/2020] [Indexed: 12/23/2022] Open
Abstract
Mistranslation is typically deleterious for cells, although specific mistranslated proteins can confer a short-term benefit in a particular environment. However, given its large overall cost, the prevalence of high global mistranslation rates remains puzzling. Altering basal mistranslation levels of Escherichia coli in several ways, we show that generalized mistranslation enhances early survival under DNA damage, by rapidly activating the SOS response. Mistranslating cells maintain larger populations after exposure to DNA damage, and thus have a higher probability of sampling critical beneficial mutations. Both basal and artificially increased mistranslation increase the number of cells that are phenotypically tolerant and genetically resistant under DNA damage; they also enhance survival at high temperature. In contrast, decreasing the normal basal mistranslation rate reduces cell survival. This wide-ranging stress resistance relies on Lon protease, which is revealed as a key effector that induces the SOS response in addition to alleviating proteotoxic stress. The new links between error-prone protein synthesis, DNA damage, and generalised stress resistance indicate surprising coordination between intracellular stress responses and suggest a novel hypothesis to explain high global mistranslation rates.
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11
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Evans CR, Fan Y, Ling J. Increased mistranslation protects E. coli from protein misfolding stress due to activation of a RpoS-dependent heat shock response. FEBS Lett 2019; 593:3220-3227. [PMID: 31419308 PMCID: PMC6878130 DOI: 10.1002/1873-3468.13578] [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] [Received: 07/10/2019] [Revised: 08/02/2019] [Accepted: 08/08/2019] [Indexed: 01/01/2023]
Abstract
The misincorporation of an incorrect amino acid into a polypeptide during protein synthesis is considered a detrimental phenomenon. A mistranslated protein is often misfolded and degraded or nonfunctional and results in an increased cost to quality control machinery. Despite these costs, errors during protein synthesis are common in bacteria. Here, we report that mistranslation in Escherichia coli increase the protein level of the heat shock sigma factor RpoH and protect cells against heat stress. Surprisingly, this increase in RpoH due to mistranslation is dependent on the presence of the general stress response sigma factor RpoS. This report provides evidence for a protective function of mistranslation and suggests a novel regulatory role of RpoS in the heat shock response.
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Affiliation(s)
- Christopher R Evans
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Yongqiang Fan
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Jiqiang Ling
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
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12
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Advani VM, Ivanov P. Translational Control under Stress: Reshaping the Translatome. Bioessays 2019; 41:e1900009. [PMID: 31026340 PMCID: PMC6541386 DOI: 10.1002/bies.201900009] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/06/2019] [Indexed: 01/01/2023]
Abstract
Adequate reprogramming of cellular metabolism in response to stresses or suboptimal growth conditions involves a myriad of coordinated changes that serve to promote cell survival. As protein synthesis is an energetically expensive process, its regulation under stress is of critical importance. Reprogramming of messenger RNA (mRNA) translation involves well-understood stress-activated kinases that target components of translation initiation machinery, resulting in the robust inhibition of general translation and promotion of the translation of stress-responsive proteins. Translational arrest of mRNAs also results in the accumulation of transcripts in cytoplasmic foci called stress granules. Recent studies focus on the key roles of transfer RNA (tRNA) in stress-induced translational reprogramming. These include stress-specific regulation of tRNA pools, codon-biased translation influenced by tRNA modifications, tRNA miscoding, and tRNA cleavage. In combination, signal transduction pathways and tRNA metabolism changes regulate translation during stress, resulting in adaptation and cell survival. This review examines molecular mechanisms that regulate protein synthesis in response to stress.
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Affiliation(s)
- Vivek M. Advani
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Pavel Ivanov
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- The Broad Institute of Harvard and M.I.T., Cambridge, Massachusetts, United States of America
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13
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Umehara T, Kosono S, Söll D, Tamura K. Lysine Acetylation Regulates Alanyl-tRNA Synthetase Activity in Escherichia coli. Genes (Basel) 2018; 9:genes9100473. [PMID: 30274179 PMCID: PMC6209979 DOI: 10.3390/genes9100473] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 09/09/2018] [Accepted: 09/21/2018] [Indexed: 11/19/2022] Open
Abstract
Protein lysine acetylation is a widely conserved posttranslational modification in all three domains of life. Lysine acetylation frequently occurs in aminoacyl-tRNA synthetases (aaRSs) from many organisms. In this study, we determined the impact of the naturally occurring acetylation at lysine-73 (K73) in Escherichia coli class II alanyl-tRNA synthetase (AlaRS) on its alanylation activity. We prepared an AlaRS K73Ac variant in which Nε-acetyl-l-lysine was incorporated at position 73 using an expanded genetic code system in E. coli. The AlaRS K73Ac variant showed low activity compared to the AlaRS wild type (WT). Nicotinamide treatment or CobB-deletion in an E. coli led to elevated acetylation levels of AlaRS K73Ac and strongly reduced alanylation activities. We assumed that alanylation by AlaRS is affected by K73 acetylation, and the modification is sensitive to CobB deacetylase in vivo. We also showed that E. coli expresses two CobB isoforms (CobB-L and CobB-S) in vivo. CobB-S displayed the deacetylase activity of the AlaRS K73Ac variant in vitro. Our results imply a potential regulatory role for lysine acetylation in controlling the activity of aaRSs and protein synthesis.
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Affiliation(s)
- Takuya Umehara
- Biotechnology Research Center, The University of Tokyo, Tokyo 113-8657, Japan.
- Department of Biological Science and Technology, Tokyo University of Science, Tokyo 125-8585, Japan.
| | - Saori Kosono
- Biotechnology Research Center, The University of Tokyo, Tokyo 113-8657, Japan.
- Center for Sustainable Resource Science, RIKEN, Saitama 351-0198, Japan.
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
- Department of Chemistry, Yale University, New Haven, CT 06520, USA.
| | - Koji Tamura
- Department of Biological Science and Technology, Tokyo University of Science, Tokyo 125-8585, Japan.
- Research Institute for Science and Technology, Tokyo University of Science, Chiba 278-8510, Japan.
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14
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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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15
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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: 277] [Impact Index Per Article: 39.6] [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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16
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Hecht A, Glasgow J, Jaschke PR, Bawazer LA, Munson MS, Cochran JR, Endy D, Salit M. Measurements of translation initiation from all 64 codons in E. coli. Nucleic Acids Res 2017; 45:3615-3626. [PMID: 28334756 PMCID: PMC5397182 DOI: 10.1093/nar/gkx070] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 01/25/2017] [Indexed: 12/21/2022] Open
Abstract
Our understanding of translation underpins our capacity to engineer living systems. The canonical start codon (AUG) and a few near-cognates (GUG, UUG) are considered as the ‘start codons’ for translation initiation in Escherichia coli. Translation is typically not thought to initiate from the 61 remaining codons. Here, we quantified translation initiation of green fluorescent protein and nanoluciferase in E. coli from all 64 triplet codons and across a range of DNA copy number. We detected initiation of protein synthesis above measurement background for 47 codons. Translation from non-canonical start codons ranged from 0.007 to 3% relative to translation from AUG. Translation from 17 non-AUG codons exceeded the highest reported rates of non-cognate codon recognition. Translation initiation from non-canonical start codons may contribute to the synthesis of peptides in both natural and synthetic biological systems.
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Affiliation(s)
- Ariel Hecht
- Joint Initiative for Metrology in Biology, Stanford, CA 94305, USA.,Genome-scale Measurements Group, National Institute of Standards and Technology, Stanford, CA 94305, USA.,Department of Bioengineering, Stanford, CA 94305, USA
| | - Jeff Glasgow
- Joint Initiative for Metrology in Biology, Stanford, CA 94305, USA.,Genome-scale Measurements Group, National Institute of Standards and Technology, Stanford, CA 94305, USA.,Department of Bioengineering, Stanford, CA 94305, USA
| | - Paul R Jaschke
- Department of Bioengineering, Stanford, CA 94305, USA.,Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Lukmaan A Bawazer
- Joint Initiative for Metrology in Biology, Stanford, CA 94305, USA.,Genome-scale Measurements Group, National Institute of Standards and Technology, Stanford, CA 94305, USA.,Department of Bioengineering, Stanford, CA 94305, USA
| | - Matthew S Munson
- Joint Initiative for Metrology in Biology, Stanford, CA 94305, USA.,Genome-scale Measurements Group, National Institute of Standards and Technology, Stanford, CA 94305, USA.,Department of Bioengineering, Stanford, CA 94305, USA
| | - Jennifer R Cochran
- Joint Initiative for Metrology in Biology, Stanford, CA 94305, USA.,Department of Bioengineering, Stanford, CA 94305, USA
| | - Drew Endy
- Joint Initiative for Metrology in Biology, Stanford, CA 94305, USA.,Department of Bioengineering, Stanford, CA 94305, USA
| | - Marc Salit
- Joint Initiative for Metrology in Biology, Stanford, CA 94305, USA.,Genome-scale Measurements Group, National Institute of Standards and Technology, Stanford, CA 94305, USA.,Department of Bioengineering, Stanford, CA 94305, USA
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17
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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: 119] [Impact Index Per Article: 17.0] [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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18
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Schwartz MH, Pan T. tRNA Misacylation with Methionine in the Mouse Gut Microbiome in Situ. MICROBIAL ECOLOGY 2017; 74:10-14. [PMID: 28070678 PMCID: PMC5466836 DOI: 10.1007/s00248-016-0928-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 12/28/2016] [Indexed: 06/06/2023]
Abstract
Global protein mistranslation with methionine has been shown to be a conserved biological process that affords distinct functional advantages in all three domains of life. In all instances, methionine mistranslation occurs through a regulated process where low-fidelity forms of methionyl-tRNA synthetase are conditionally induced to mischarge non-methionyl-tRNAs with methionine followed by the utilization of the misacylated tRNAs in translation. In mammals, methionine mistranslation contributes to oxidative stress response; in the hyperthermophilic archaeon Aeropyrum pernix, methionine mistranslation produces proteins that are better adapted to low temperature growth; in E. coli, methionine mistranslation increases resistance to antibiotics and chemical stressors. The phenotypic benefits conferred by tRNA mismethionylation suggest that it should be a widespread adaptational mechanism in diverse bacterial lineages, yet this response has only been described in E. coli. Furthermore, previous microbial investigations on this response have been confined to axenic laboratory cultures. It was unknown whether tRNA mismethionylation was relevant in a natural microbial habitat. Here we show that four abundant gut microbiotal genera belonging to the Firmicutes and Bacteroidetes phyla perform constitutive tRNA misacylation with methionine in the mouse cecum in situ. These results reveal the ubiquity of the tRNA mismethionylation process among bacteria and implicate the potential importance of this response for subsistence and adaptation in natural habitats.
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Affiliation(s)
- Michael H Schwartz
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA.
- Committee on Microbiology, University of Chicago, Chicago, IL, 60637, USA.
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA.
- Committee on Microbiology, University of Chicago, Chicago, IL, 60637, USA.
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19
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Jakubowski H. Homocysteine Editing, Thioester Chemistry, Coenzyme A, and the Origin of Coded Peptide Synthesis †. Life (Basel) 2017; 7:life7010006. [PMID: 28208756 PMCID: PMC5370406 DOI: 10.3390/life7010006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 02/03/2017] [Indexed: 12/22/2022] Open
Abstract
Aminoacyl-tRNA synthetases (AARSs) have evolved “quality control” mechanisms which prevent tRNA aminoacylation with non-protein amino acids, such as homocysteine, homoserine, and ornithine, and thus their access to the Genetic Code. Of the ten AARSs that possess editing function, five edit homocysteine: Class I MetRS, ValRS, IleRS, LeuRS, and Class II LysRS. Studies of their editing function reveal that catalytic modules of these AARSs have a thiol-binding site that confers the ability to catalyze the aminoacylation of coenzyme A, pantetheine, and other thiols. Other AARSs also catalyze aminoacyl-thioester synthesis. Amino acid selectivity of AARSs in the aminoacyl thioesters formation reaction is relaxed, characteristic of primitive amino acid activation systems that may have originated in the Thioester World. With homocysteine and cysteine as thiol substrates, AARSs support peptide bond synthesis. Evolutionary origin of these activities is revealed by genomic comparisons, which show that AARSs are structurally related to proteins involved in coenzyme A/sulfur metabolism and non-coded peptide bond synthesis. These findings suggest that the extant AARSs descended from ancestral forms that were involved in non-coded Thioester-dependent peptide synthesis, functionally similar to the present-day non-ribosomal peptide synthetases.
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Affiliation(s)
- Hieronim Jakubowski
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA.
- Department of Biochemistry and Biotechnology, University of Life Sciences, Poznan 60-632, Poland.
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20
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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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21
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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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