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Mishra S, Stany B, Das A, Kanagavel D, Vijayan M. A Comprehensive Review of Membrane Transporters and MicroRNA Regulation in Alzheimer's Disease. Mol Neurobiol 2024; 61:8739-8758. [PMID: 38558361 DOI: 10.1007/s12035-024-04135-2] [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: 11/22/2023] [Accepted: 03/15/2024] [Indexed: 04/04/2024]
Abstract
Alzheimer's disease (AD) is a distressing neurodegenerative condition characterized by the accumulation of amyloid-beta (Aβ) plaques and tau tangles within the brain. The interconnectedness between membrane transporters (SLCs) and microRNAs (miRNAs) in AD pathogenesis has gained increasing attention. This review explores the localization, substrates, and functions of SLC transporters in the brain, emphasizing the roles of transporters for glutamate, glucose, nucleosides, and other essential compounds. The examination delves into the significance of SLCs in AD, their potential for drug development, and the intricate realm of miRNAs, encompassing their transcription, processing, functions, and regulation. MiRNAs have emerged as significant players in AD, including those associated with mitochondria and synapses. Furthermore, this review discusses the intriguing nexus of miRNAs targeting SLC transporters and their potential as therapeutic targets in AD. Finally, the review underscores the interaction between SLC transporters and miRNA regulation within the context of Alzheimer's disease, underscoring the need for further research in this area. This comprehensive review aims to shed light on the complex mechanisms underlying the causation of AD and provides insights into potential therapeutic approaches.
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Affiliation(s)
- Shatakshi Mishra
- School of Biosciences and Technology, Department of Biotechnology, VIT University, Vellore, Tamil Nadu, 632014, India
| | - B Stany
- School of Biosciences and Technology, Department of Biotechnology, VIT University, Vellore, Tamil Nadu, 632014, India
| | - Anushka Das
- School of Biosciences and Technology, Department of Biotechnology, VIT University, Vellore, Tamil Nadu, 632014, India
| | - Deepankumar Kanagavel
- School of Biosciences and Technology, Department of Biotechnology, VIT University, Vellore, Tamil Nadu, 632014, India.
| | - Murali Vijayan
- Department of Internal Medicine, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX, 79430, USA.
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2
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Aleksashin NA, Langeberg CJ, Shelke RR, Yin T, Cate JHD. RNA elements required for the high efficiency of West Nile Virus-induced ribosomal frameshifting. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.16.618579. [PMID: 39464146 PMCID: PMC11507841 DOI: 10.1101/2024.10.16.618579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/29/2024]
Abstract
West Nile Virus (WNV), a member of the Flaviviridae family, requires programmed -1 ribosomal frameshifting (PRF) for translation of the viral genome. The efficiency of WNV frameshifting is among the highest observed to date. Despite structural similarities to frameshifting sites in other viruses, it remains unclear why WNV exhibits such a high frameshifting efficiency. Here we employed dual-luciferase reporter assays in multiple human cell lines to probe the RNA requirements for highly efficient frameshifting by the WNV genome. We find that both the sequence and structure of a predicted RNA pseudoknot downstream of the slippery sequence-the codons in the genome on which frameshifting occurs-are required for efficient frameshifting. We also show that multiple proposed RNA secondary structures downstream of the slippery sequence are inconsistent with efficient frameshifting. We mapped the most favorable distance between the slippery site and the pseudoknot essential for optimal frameshifting, and found the base of the pseudoknot structure likely is unfolded prior to frameshifting. Finally, we find that many mutations in the WNV slippery sequence allow efficient frameshifting, but often result in aberrant shifting into other reading frames. Mutations in the slippery sequence also support a model in which frameshifting occurs concurrent with or after translocation of the mRNA and tRNA on the ribosome. These results provide a comprehensive analysis of the molecular determinants of WNV-programmed ribosomal frameshifting and provide a foundation for the development of new antiviral strategies targeting viral gene expression.
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3
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Krawczyk SJ, Leśniczak-Staszak M, Gowin E, Szaflarski W. Mechanistic Insights into Clinically Relevant Ribosome-Targeting Antibiotics. Biomolecules 2024; 14:1263. [PMID: 39456196 PMCID: PMC11505993 DOI: 10.3390/biom14101263] [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: 09/08/2024] [Revised: 10/03/2024] [Accepted: 10/05/2024] [Indexed: 10/28/2024] Open
Abstract
Antibiotics targeting the bacterial ribosome are essential to combating bacterial infections. These antibiotics bind to various sites on the ribosome, inhibiting different stages of protein synthesis. This review provides a comprehensive overview of the mechanisms of action of clinically relevant antibiotics that target the bacterial ribosome, including macrolides, lincosamides, oxazolidinones, aminoglycosides, tetracyclines, and chloramphenicol. The structural and functional details of antibiotic interactions with ribosomal RNA, including specific binding sites, interactions with rRNA nucleotides, and their effects on translation processes, are discussed. Focus is placed on the diversity of these mechanisms and their clinical implications in treating bacterial infections, particularly in the context of emerging resistance. Understanding these mechanisms is crucial for developing novel therapeutic agents capable of overcoming bacterial resistance.
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Affiliation(s)
- Szymon J. Krawczyk
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznań, Poland; (S.J.K.); (M.L.-S.)
| | - Marta Leśniczak-Staszak
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznań, Poland; (S.J.K.); (M.L.-S.)
| | - Ewelina Gowin
- Department of Health Promotion, Poznan University of Medical Sciences, 60-781 Poznań, Poland;
- Department of Immunology, Poznan University of Medical Sciences, 60-806 Poznań, Poland
| | - Witold Szaflarski
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznań, Poland; (S.J.K.); (M.L.-S.)
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4
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Wu X, Xu M, Yang JR, Lu J. Genome-wide impact of codon usage bias on translation optimization in Drosophila melanogaster. Nat Commun 2024; 15:8329. [PMID: 39333102 PMCID: PMC11437122 DOI: 10.1038/s41467-024-52660-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 09/17/2024] [Indexed: 09/29/2024] Open
Abstract
Accuracy and efficiency are fundamental to mRNA translation. Codon usage bias is widespread across species. Despite the long-standing association between optimized codon usage and improved translation, our understanding of its evolutionary basis and functional effects remains limited. Drosophila is widely used to study codon usage bias, but genome-scale experimental data are scarce. Using high-resolution mass spectrometry data from Drosophila melanogaster, we show that optimal codons have lower translation errors than nonoptimal codons after accounting for these biases. Genomic-scale analysis of ribosome profiling data shows that optimal codons are translated more rapidly than nonoptimal codons. Although we find no long-term selection favoring synonymous mutations in D. melanogaster after diverging from D. simulans, we identify signatures of positive selection driving codon optimization in the D. melanogaster population. These findings expand our understanding of the functional consequences of codon optimization and serve as a foundation for future investigations.
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Affiliation(s)
- Xinkai Wu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
| | - Mengze Xu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
| | - Jian-Rong Yang
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China.
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China.
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5
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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; 23:100818. [PMID: 39047911 PMCID: PMC11420639 DOI: 10.1016/j.mcpro.2024.100818] [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: 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 °C, 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 analyzed 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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6
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Schuntermann DB, Jaskolowski M, Reynolds NM, Vargas-Rodriguez O. The central role of transfer RNAs in mistranslation. J Biol Chem 2024; 300:107679. [PMID: 39154912 PMCID: PMC11415595 DOI: 10.1016/j.jbc.2024.107679] [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: 04/25/2024] [Revised: 07/22/2024] [Accepted: 07/23/2024] [Indexed: 08/20/2024] Open
Abstract
Transfer RNAs (tRNA) are essential small non-coding RNAs that enable the translation of genomic information into proteins in all life forms. The principal function of tRNAs is to bring amino acid building blocks to the ribosomes for protein synthesis. In the ribosome, tRNAs interact with messenger RNA (mRNA) to mediate the incorporation of amino acids into a growing polypeptide chain following the rules of the genetic code. Accurate interpretation of the genetic code requires tRNAs to carry amino acids matching their anticodon identity and decode the correct codon on mRNAs. Errors in these steps cause the translation of codons with the wrong amino acids (mistranslation), compromising the accurate flow of information from DNA to proteins. Accumulation of mutant proteins due to mistranslation jeopardizes proteostasis and cellular viability. However, the concept of mistranslation is evolving, with increasing evidence indicating that mistranslation can be used as a mechanism for survival and acclimatization to environmental conditions. In this review, we discuss the central role of tRNAs in modulating translational fidelity through their dynamic and complex interplay with translation factors. We summarize recent discoveries of mistranslating tRNAs and describe the underlying molecular mechanisms and the specific conditions and environments that enable and promote mistranslation.
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Affiliation(s)
- Dominik B Schuntermann
- Department of Biology, Institute of Molecular Biology and Biophysics, Zurich, Switzerland
| | - Mateusz Jaskolowski
- Department of Biology, Institute of Molecular Biology and Biophysics, Zurich, Switzerland
| | - Noah M Reynolds
- School of Integrated Sciences, Sustainability, and Public Health, University of Illinois Springfield, Springfield, Illinois, USA
| | - Oscar Vargas-Rodriguez
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut, USA.
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7
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Zheng ZQ, Zhong CR, Wei CZ, Chen XJ, Chen GM, Nie RC, Chen ZW, Zhang FY, Li YF, Zhou ZW, Chen YM, Liang YL. Hyperactivation of mTOR/eIF4E Signaling Pathway Promotes the Production of Tryptophan-To-Phenylalanine Substitutants in EBV-Positive Gastric Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2402284. [PMID: 38994917 PMCID: PMC11425274 DOI: 10.1002/advs.202402284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 06/26/2024] [Indexed: 07/13/2024]
Abstract
Although messenger RNA translation is tightly regulated to preserve protein synthesis and cellular homeostasis, chronic exposure to interferon-γ (IFN-γ) in several cancers can lead to tryptophan (Trp) shortage via the indoleamine-2,3-dioxygenase (IDO)- kynurenine pathway and therefore promotes the production of aberrant peptides by ribosomal frameshifting and tryptophan-to-phenylalanine (W>F) codon reassignment events (substitutants) specifically at Trp codons. However, the effect of Trp depletion on the generation of aberrant peptides by ribosomal mistranslation in gastric cancer (GC) is still obscure. Here, it is shows that the abundant infiltrating lymphocytes in EBV-positive GC continuously secreted IFN-γ, upregulated IDO1 expression, leading to Trp shortage and the induction of W>F substitutants. Intriguingly, the production of W>F substitutants in EBV-positive GC is linked to antigen presentation and the activation of the mTOR/eIF4E signaling pathway. Inhibiting either the mTOR/eIF4E pathway or EIF4E expression counteracted the production and antigen presentation of W>F substitutants. Thus, the mTOR/eIF4E pathway exposed the vulnerability of gastric cancer by accelerating the production of aberrant peptides and boosting immune activation through W>F substitutant events. This work proposes that EBV-positive GC patients with mTOR/eIF4E hyperactivation may benefit from anti-tumor immunotherapy.
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Affiliation(s)
- Zi-Qi Zheng
- Department of Gastric Surgery, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Cheng-Rui Zhong
- Department of General Surgery, Hepatobiliary Pancreatic and Splenic Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510655, P. R. China
| | - Cheng-Zhi Wei
- Department of Gastric Surgery, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Xiao-Jiang Chen
- Department of Gastric Surgery, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Guo-Ming Chen
- Department of Gastric Surgery, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Run-Cong Nie
- Department of Gastric Surgery, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Ze-Wei Chen
- Department of Gastric Surgery, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Fei-Yang Zhang
- Department of Gastric Surgery, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Yuan-Fang Li
- Department of Gastric Surgery, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Zhi-Wei Zhou
- Department of Gastric Surgery, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Yong-Ming Chen
- Department of Gastric Surgery, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Ye-Lin Liang
- Department of Radiology Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
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8
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Dorant Y, Quillien V, Le Luyer J, Ky CL. Comparative transcriptomics identifies genes underlying growth performance of the Pacific black-lipped pearl oyster Pinctada margaritifera. BMC Genomics 2024; 25:717. [PMID: 39049022 PMCID: PMC11270918 DOI: 10.1186/s12864-024-10636-0] [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: 04/04/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND In bivalves, the rate at which organisms grow is a major functional trait underlying many aspects of their commercial production. Growth is a highly polygenic trait, which is typically regulated by many genes with small to moderate effects. Due to its complexity, growth variability in such shellfish remains poorly understood. In this study, we aimed to investigate differential gene expression among spat of the pearl oyster Pinctada margaritifera with distinct growth phenotypes. RESULTS We selected two groups of P. margaritifera spat belonging to the same F2 cohort based on their growth performance at 5.5 months old. Transcriptome profile analysis identified a total of 394 differentially expressed genes between these Fast-growing (F) and Slow-growing (S) phenotypes. According to functional enrichment analysis, S oysters overexpressed genes associated with stress-pathways and regulation of innate immune responses. In contrast, F oysters up-regulated genes associated with cytoskeleton activity, cell proliferation, and apoptosis. Analysis of genome polymorphism identified 16 single nucleotide polymorphisms (SNPs) significantly associated with the growth phenotypes. SNP effect categorization revealed one SNP identified for high effect and annotated for a stop codon gained mutation. Interestingly, this SNP is located within a gene annotated for scavenger receptor class F member 1 (SRF1), which is known to modulate apoptosis. Our analyses also revealed that all F oysters showed up-regulation for this gene and were homozygous for the stop-codon mutation. Conversely, S oysters had a heterozygous genotype and a reduced expression of this gene. CONCLUSIONS Altogether, our findings suggest that differences in growth among the same oyster cohort may be explained by contrasted metabolic allocation between regulatory pathways for growth and the immune system. This study provides a valuable contribution towards our understanding of the molecular components associated with growth performance in the pearl oyster P. margaritifera and bivalves in general.
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Affiliation(s)
- Y Dorant
- Ifremer, ILM, IRD, UPF, UMR 241 SECOPOL, Polynésie française, Taravao, Tahiti, France.
- IHPE, UMR 5244, Université de Montpellier, CNRS, Université de Perpignan Via Domitia, Ifremer, Montpellier, France.
| | - V Quillien
- Ifremer, ILM, IRD, UPF, UMR 241 SECOPOL, Polynésie française, Taravao, Tahiti, France
- Ifremer, Univ Brest, CNRS, IRD, UMR 6539, LEMAR, Plouzane, F-29280, France
| | - J Le Luyer
- Ifremer, ILM, IRD, UPF, UMR 241 SECOPOL, Polynésie française, Taravao, Tahiti, France
- Ifremer, Univ Brest, CNRS, IRD, UMR 6539, LEMAR, Plouzane, F-29280, France
| | - C L Ky
- Ifremer, ILM, IRD, UPF, UMR 241 SECOPOL, Polynésie française, Taravao, Tahiti, France
- IHPE, UMR 5244, Université de Montpellier, CNRS, Université de Perpignan Via Domitia, Ifremer, Montpellier, France
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9
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Jiang D, Kejiou N, Qiu Y, Palazzo AF, Pennell M. Genetic and selective constraints on the optimization of gene product diversity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.17.603951. [PMID: 39091777 PMCID: PMC11291005 DOI: 10.1101/2024.07.17.603951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
RNA and protein expressed from the same gene can have diverse isoforms due to various post-transcriptional and post-translational modifications. For the vast majority of alternative isoforms, It is unknown whether they are adaptive or simply biological noise. As we cannot experimentally probe the function of each isoform, we can ask whether the distribution of isoforms across genes and across species is consistent with expectations from different evolutionary processes. However, there is currently no theoretical framework that can generate such predictions. To address this, we developed a mathematical model where isoform abundances are determined collectively by cis-acting loci, trans-acting factors, gene expression levels, and isoform decay rates to predict isoform abundance distributions across species and genes in the face of mutation, genetic drift, and selection. We found that factors beyond selection, such as effective population size and the number of cis-acting loci, significantly influence evolutionary outcomes. Notably, suboptimal phenotypes are more likely to evolve when the population is small and/or when the number of cis-loci is large. We also explored scenarios where modification processes have both beneficial and detrimental effects, revealing a non-monotonic relationship between effective population size and optimization, demonstrating how opposing selection pressures on cis- and trans-acting loci can constrain the optimization of gene product diversity. As a demonstration of the power of our theory, we compared the expected distribution of A-to-I RNA editing levels in coleoids and found this to be largely consistent with non-adaptive explanations.
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Affiliation(s)
- Daohan Jiang
- Department of Quantitative and Computational Biology, University of Southern California, USA
| | - Nevraj Kejiou
- Department of Biochemistry, University of Toronto, Canada
| | - Yi Qiu
- Department of Biochemistry, University of Toronto, Canada
| | | | - Matt Pennell
- Department of Quantitative and Computational Biology, University of Southern California, USA
- Department of Biological Sciences, University of Southern California, USA
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10
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McShea H, Weibel C, Wehbi S, Goodman P, James JE, Wheeler AL, Masel J. The effectiveness of selection in a species affects the direction of amino acid frequency evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.02.01.526552. [PMID: 38948853 PMCID: PMC11212923 DOI: 10.1101/2023.02.01.526552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Nearly neutral theory predicts that species with higher effective population size (N e ) are better able to purge slightly deleterious mutations. We compare evolution in high-N e vs. low-N e vertebrates to reveal which amino acid frequencies are subject to subtle selective preferences. We take three complementary approaches, two measuring flux and one measuring outcomes. First, we fit non-stationary substitution models of amino acid flux using maximum likelihood, comparing the high-N e clade of rodents and lagomorphs to its low-N e sister clade of primates and colugos. Second, we compare evolutionary outcomes across a wider range of vertebrates, via correlations between amino acid frequencies and N e . Third, we dissect the details of flux in human, chimpanzee, mouse, and rat, as scored by parsimony - this also enables comparison to a historical paper. All three methods agree on which amino acids are preferred under more effective selection. Preferred amino acids tend to be smaller, less costly to synthesize, and to promote intrinsic structural disorder. Parsimony-induced bias in the historical study produces an apparent reduction in structural disorder, perhaps driven by slightly deleterious substitutions. Within highly exchangeable pairs of amino acids, arginine is strongly preferred over lysine, and valine over isoleucine, consistent with more effective selection preferring a marginally larger free energy of folding. These two preferences match differences between thermophiles and mesophilic relatives. These results reveal the biophysical consequences of mutation-selection-drift balance, and demonstrate the utility of nearly neutral theory for understanding protein evolution.
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Affiliation(s)
- Hanon McShea
- Department of Earth System Science, Stanford University
| | - Catherine Weibel
- Department of Ecology & Evolutionary Biology, University of Arizona
- Department of Applied Physics, Stanford University
| | - Sawsan Wehbi
- Graduate Interdisciplinary Program in Genetics, University of Arizona
| | | | - Jennifer E James
- Department of Ecology & Evolutionary Biology, University of Arizona
- Department of Ecology and Genetics, Uppsala University
| | - Andrew L Wheeler
- Graduate Interdisciplinary Program in Genetics, University of Arizona
| | - Joanna Masel
- Department of Ecology & Evolutionary Biology, University of Arizona
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11
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Ha G, Dieterle P, Shen H, Amir A, Needleman DJ. Measuring and modeling the dynamics of mitotic error correction. Proc Natl Acad Sci U S A 2024; 121:e2323009121. [PMID: 38875144 PMCID: PMC11194551 DOI: 10.1073/pnas.2323009121] [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: 01/23/2024] [Accepted: 05/11/2024] [Indexed: 06/16/2024] Open
Abstract
Error correction is central to many biological systems and is critical for protein function and cell health. During mitosis, error correction is required for the faithful inheritance of genetic material. When functioning properly, the mitotic spindle segregates an equal number of chromosomes to daughter cells with high fidelity. Over the course of spindle assembly, many initially erroneous attachments between kinetochores and microtubules are fixed through the process of error correction. Despite the importance of chromosome segregation errors in cancer and other diseases, there is a lack of methods to characterize the dynamics of error correction and how it can go wrong. Here, we present an experimental method and analysis framework to quantify chromosome segregation error correction in human tissue culture cells with live cell confocal imaging, timed premature anaphase, and automated counting of kinetochores after cell division. We find that errors decrease exponentially over time during spindle assembly. A coarse-grained model, in which errors are corrected in a chromosome-autonomous manner at a constant rate, can quantitatively explain both the measured error correction dynamics and the distribution of anaphase onset times. We further validated our model using perturbations that destabilized microtubules and changed the initial configuration of chromosomal attachments. Taken together, this work provides a quantitative framework for understanding the dynamics of mitotic error correction.
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Affiliation(s)
- Gloria Ha
- Department of Systems Biology, Harvard Medical School, Boston, MA02115
| | - Paul Dieterle
- Department of Physics, Harvard University, Cambridge, MA02138
| | - Hao Shen
- Reverie Labs, Cambridge, MA02139
| | - Ariel Amir
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA02138
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Daniel J. Needleman
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA02138
- Center for Computational Biology, Flatiron Institute, New York, NY10010
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12
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Jain V, Cope AL. Examining the Effects of Temperature on the Evolution of Bacterial tRNA Pools. Genome Biol Evol 2024; 16:evae116. [PMID: 38805023 PMCID: PMC11166485 DOI: 10.1093/gbe/evae116] [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: 10/10/2023] [Revised: 05/13/2024] [Accepted: 05/21/2024] [Indexed: 05/29/2024] Open
Abstract
The genetic code consists of 61 codons coding for 20 amino acids. These codons are recognized by transfer RNAs (tRNAs) that bind to specific codons during protein synthesis. All organisms utilize less than all 61 possible anticodons due to base pair wobble: the ability to have a mismatch with a codon at its third nucleotide. Previous studies observed a correlation between the tRNA pool of bacteria and the temperature of their respective environments. However, it is unclear if these patterns represent biological adaptations to maintain the efficiency and accuracy of protein synthesis in different environments. A mechanistic mathematical model of mRNA translation is used to quantify the expected elongation rates and error rate for each codon based on an organism's tRNA pool. A comparative analysis across a range of bacteria that accounts for covariance due to shared ancestry is performed to quantify the impact of environmental temperature on the evolution of the tRNA pool. We find that thermophiles generally have more anticodons represented in their tRNA pool than mesophiles or psychrophiles. Based on our model, this increased diversity is expected to lead to increased missense errors. The implications of this for protein evolution in thermophiles are discussed.
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Affiliation(s)
- Vatsal Jain
- Biotechnology High School, Freehold, NJ, USA
| | - Alexander L Cope
- Department of Genetics, Rutgers University, Piscataway, NJ, USA
- Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
- Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, USA
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13
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Michael-Pitschaze T, Cohen N, Ofer D, Hoshen Y, Linial M. Detecting anomalous proteins using deep representations. NAR Genom Bioinform 2024; 6:lqae021. [PMID: 38486884 PMCID: PMC10939404 DOI: 10.1093/nargab/lqae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 11/17/2023] [Accepted: 02/23/2024] [Indexed: 03/17/2024] Open
Abstract
Many advances in biomedicine can be attributed to identifying unusual proteins and genes. Many of these proteins' unique properties were discovered by manual inspection, which is becoming infeasible at the scale of modern protein datasets. Here, we propose to tackle this challenge using anomaly detection methods that automatically identify unexpected properties. We adopt a state-of-the-art anomaly detection paradigm from computer vision, to highlight unusual proteins. We generate meaningful representations without labeled inputs, using pretrained deep neural network models. We apply these protein language models (pLM) to detect anomalies in function, phylogenetic families, and segmentation tasks. We compute protein anomaly scores to highlight human prion-like proteins, distinguish viral proteins from their host proteome, and mark non-classical ion/metal binding proteins and enzymes. Other tasks concern segmentation of protein sequences into folded and unstructured regions. We provide candidates for rare functionality (e.g. prion proteins). Additionally, we show the anomaly score is useful in 3D folding-related segmentation. Our novel method shows improved performance over strong baselines and has objectively high performance across a variety of tasks. We conclude that the combination of pLM and anomaly detection techniques is a valid method for discovering a range of global and local protein characteristics.
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Affiliation(s)
- Tomer Michael-Pitschaze
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Niv Cohen
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dan Ofer
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yedid Hoshen
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Michal Linial
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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14
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Luna Santamaría M, Andersson D, Parris TZ, Helou K, Österlund T, Ståhlberg A. Digital RNA sequencing using unique molecular identifiers enables ultrasensitive RNA mutation analysis. Commun Biol 2024; 7:249. [PMID: 38429519 PMCID: PMC10907754 DOI: 10.1038/s42003-024-05955-7] [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: 05/19/2023] [Accepted: 02/22/2024] [Indexed: 03/03/2024] Open
Abstract
Mutation analysis is typically performed at the DNA level since most technical approaches are developed for DNA analysis. However, some applications, like transcriptional mutagenesis, RNA editing and gene expression analysis, require RNA analysis. Here, we combine reverse transcription and digital DNA sequencing to enable low error digital RNA sequencing. We evaluate yield, reproducibility, dynamic range and error correction rate for seven different reverse transcription conditions using multiplexed assays. The yield, reproducibility and error rate vary substantially between the specific conditions, where the yield differs 9.9-fold between the best and worst performing condition. Next, we show that error rates similar to DNA sequencing can be achieved for RNA using appropriate reverse transcription conditions, enabling detection of mutant allele frequencies <0.1% at RNA level. We also detect mutations at both DNA and RNA levels in tumor tissue using a breast cancer panel. Finally, we demonstrate that digital RNA sequencing can be applied to liquid biopsies, analyzing cell-free gene transcripts. In conclusion, we demonstrate that digital RNA sequencing is suitable for ultrasensitive RNA mutation analysis, enabling several basic research and clinical applications.
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Affiliation(s)
- Manuel Luna Santamaría
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Daniel Andersson
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Toshima Z Parris
- Sahlgrenska Center for Cancer Research, Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Khalil Helou
- Sahlgrenska Center for Cancer Research, Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Tobias Österlund
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
- Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Genetics and Genomics, Gothenburg, Sweden
| | - Anders Ståhlberg
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.
- Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Genetics and Genomics, Gothenburg, Sweden.
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15
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Landerer C, Poehls J, Toth-Petroczy A. Fitness Effects of Phenotypic Mutations at Proteome-Scale Reveal Optimality of Translation Machinery. Mol Biol Evol 2024; 41:msae048. [PMID: 38421032 PMCID: PMC10939442 DOI: 10.1093/molbev/msae048] [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: 09/04/2023] [Revised: 01/30/2024] [Accepted: 02/23/2024] [Indexed: 03/02/2024] Open
Abstract
Errors in protein translation can lead to non-genetic, phenotypic mutations, including amino acid misincorporations. While phenotypic mutations can increase protein diversity, the systematic characterization of their proteome-wide frequencies and their evolutionary impact has been lacking. Here, we developed a mechanistic model of translation errors to investigate how selection acts on protein populations produced by amino acid misincorporations. We fitted the model to empirical observations of misincorporations obtained from over a hundred mass spectrometry datasets of E. coli and S. cerevisiae. We found that on average 20% to 23% of proteins synthesized in the cell are expected to harbor at least one amino acid misincorporation, and that deleterious misincorporations are less likely to occur. Combining misincorporation probabilities and the estimated fitness effects of amino acid substitutions in a population genetics framework, we found 74% of mistranslation events in E. coli and 94% in S. cerevisiae to be neutral. We further show that the set of available synonymous tRNAs is subject to evolutionary pressure, as the presence of missing tRNAs would increase codon-anticodon cross-reactivity and misincorporation error rates. Overall, we find that the translation machinery is likely optimal in E. coli and S. cerevisiae and that both local solutions at the level of codons and a global solution such as the tRNA pool can mitigate the impact of translation errors. We provide a framework to study the evolutionary impact of codon-specific translation errors and a method for their proteome-wide detection across organisms and conditions.
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Affiliation(s)
- Cedric Landerer
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Jonas Poehls
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Agnes Toth-Petroczy
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
- Cluster of Excellence Physics of Life, TU Dresden, 01062 Dresden, Germany
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16
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Springstein BL, Paulo JA, Park H, Henry K, Fleming E, Feder Z, Harper JW, Hochschild A. Systematic analysis of nonprogrammed frameshift suppression in E. coli via translational tiling proteomics. Proc Natl Acad Sci U S A 2024; 121:e2317453121. [PMID: 38289956 PMCID: PMC10861913 DOI: 10.1073/pnas.2317453121] [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: 10/13/2023] [Accepted: 12/20/2023] [Indexed: 02/01/2024] Open
Abstract
The synthesis of proteins as encoded in the genome depends critically on translational fidelity. Nevertheless, errors inevitably occur, and those that result in reading frame shifts are particularly consequential because the resulting polypeptides are typically nonfunctional. Despite the generally maladaptive impact of such errors, the proper decoding of certain mRNAs, including many viral mRNAs, depends on a process known as programmed ribosomal frameshifting. The fact that these programmed events, commonly involving a shift to the -1 frame, occur at specific evolutionarily optimized "slippery" sites has facilitated mechanistic investigation. By contrast, less is known about the scope and nature of error (i.e., nonprogrammed) frameshifting. Here, we examine error frameshifting by monitoring spontaneous frameshift events that suppress the effects of single base pair deletions affecting two unrelated test proteins. To map the precise sites of frameshifting, we developed a targeted mass spectrometry-based method called "translational tiling proteomics" for interrogating the full set of possible -1 slippage events that could produce the observed frameshift suppression. Surprisingly, such events occur at many sites along the transcripts, involving up to one half of the available codons. Only a subset of these resembled canonical "slippery" sites, implicating alternative mechanisms potentially involving noncognate mispairing events. Additionally, the aggregate frequency of these events (ranging from 1 to 10% in our test cases) was higher than we might have anticipated. Our findings point to an unexpected degree of mechanistic diversity among ribosomal frameshifting events and suggest that frameshifted products may contribute more significantly to the proteome than generally assumed.
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Affiliation(s)
| | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, BostonMA02115
| | - Hankum Park
- Department of Cell Biology, Harvard Medical School, BostonMA02115
| | - Kemardo Henry
- Department of Microbiology, Harvard Medical School, BostonMA02115
| | - Eleanor Fleming
- Department of Microbiology, Harvard Medical School, BostonMA02115
| | - Zoë Feder
- Department of Microbiology, Harvard Medical School, BostonMA02115
| | - J. Wade Harper
- Department of Cell Biology, Harvard Medical School, BostonMA02115
| | - Ann Hochschild
- Department of Microbiology, Harvard Medical School, BostonMA02115
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17
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Liu X, Wang B, Chang M, Zhang X, Zou H, Zhang Z, Han G. USP12 regulates ER stress-associated osteogenesis in human periodontal ligament cells under tension stress. Cell Signal 2024; 114:111015. [PMID: 38113977 DOI: 10.1016/j.cellsig.2023.111015] [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: 09/18/2023] [Revised: 11/29/2023] [Accepted: 12/13/2023] [Indexed: 12/21/2023]
Abstract
The bone formation (osteogenesis) of human periodontal ligament cells (hPDLCs) under tension stress is essential for alveolar bone remodeling during orthodontic tooth movement (OTM). Deubiquitinating enzymes (DUBs) remove ubiquitin from target proteins, affecting their function and mediating cell survival and differentiation. However, whether and how DUBs regulate hPDLC function under tension force is poorly understood. In this study, we first investigated the expression of DUBs in hPDLCs under cyclic tension stimulation (CTS). Up-regulation of USP12 was observed in hPDLCs and at the tension side of molar teeth in OTM C57BL6 mice models. Knockdown (KD) of USP12 led to enhanced osteogenesis of hPDLCs under CTS. RNA-seq analysis suggested that the unfolded protein response (UPR) was the prevailing biological process in hPDLCs with USP12 KD, indicating that USP12 depletion triggered endoplasmic reticulum (ER) stress. The three major UPR-related signaling branches, namely PERK/eIF2α/ATF4, IRE1α/XBP1s, and ATF6 axis, were activated in hPDLCs with USP12 KD. By utilizing specific inhibitors, we proved that the PERK/eIF2α/ATF4 axis predominantly mediated the enhanced osteogenesis in hPDLCs with USP12 KD under CTS. In summary, our study demonstrates that USP12 serves as a key regulator for CTS-induced osteogenesis in hPDLCs, suggesting that USP12 upregulation serves as an adaptive mechanism for hPDLCs to alleviate ER stress during OTM.
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Affiliation(s)
- Xiaoyu Liu
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan, China
| | - Beike Wang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan, China; Orthodontic Department Division II, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Maolin Chang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan, China; Orthodontic Department Division II, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Xiaocen Zhang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan, China
| | - Hao Zou
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan, China
| | - Zhen Zhang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan, China; Orthodontic Department Division II, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Guangli Han
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan, China; Orthodontic Department Division II, School & Hospital of Stomatology, Wuhan University, Wuhan, China.
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18
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Wimmer B, Friedrich A, Poeltner K, Edobor G, Mosshammer C, Temaj G, Rathner A, Karl T, Krauss J, von Hagen J, Gerner C, Breitenbach M, Hintner H, Bauer JW, Breitenbach-Koller H. En Route to Targeted Ribosome Editing to Replenish Skin Anchor Protein LAMB3 in Junctional Epidermolysis Bullosa. JID INNOVATIONS 2024; 4:100240. [PMID: 38282649 PMCID: PMC10810840 DOI: 10.1016/j.xjidi.2023.100240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 09/24/2023] [Accepted: 09/25/2023] [Indexed: 01/30/2024] Open
Abstract
Severe junctional epidermolysis bullosa is a rare genetic, postpartum lethal skin disease, predominantly caused by nonsense/premature termination codon (PTC) sequence variants in LAMB3 gene. LAMB3 encodes LAMB3, the β subunit of epidermal-dermal skin anchor laminin 332. Most translational reads of a PTC mRNA deliver truncated, nonfunctional proteins, whereas an endogenous PTC readthrough mechanism produces full-length protein at minimal and insufficient levels. Conventional translational readthrough-inducing drugs amplify endogenous PTC readthrough; however, translational readthrough-inducing drugs are either proteotoxic or nonselective. Ribosome editing is a more selective and less toxic strategy. This technique identified ribosomal protein L35/uL29 (ie, RpL35) and RpL35-ligands repurposable drugs artesunate and atazanavir as molecular tools to increase production levels of full-length LAMB3. To evaluate ligand activity in living cells, we monitored artesunate and atazanavir treatment by dual luciferase reporter assays. Production levels of full-length LAMB3 increased up to 200% upon artesunate treatment, up to 150% upon atazanavir treatment, and up to 170% upon combinatorial treatment of RpL35 ligands at reduced drug dosage, with an unrelated PTC reporter being nonresponsive. Proof of bioactivity of RpL35 ligands in selective increase of full-length LAMB3 provides the basis for an alternative, targeted therapeutic route to replenish LAMB3 in severe junctional epidermolysis bullosa.
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Affiliation(s)
- Bjoern Wimmer
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | - Andreas Friedrich
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | - Katharina Poeltner
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | - Genevieve Edobor
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | - Claudia Mosshammer
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | | | - Adriana Rathner
- Institute of Biochemistry, Johannes Kepler University of Linz, Linz, Austria
| | - Thomas Karl
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | - Jan Krauss
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
- SKM-IP PartGmbB, Munich, Germany
| | - Joerg von Hagen
- Merck KGaA, Gernsheim, Germany
- ryon-Greentech Accelerator, Gernsheim, Germany
| | - Christopher Gerner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Joint Metabolome Facility, University of Vienna, Vienna, Austria
| | - Michael Breitenbach
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | - Helmut Hintner
- Department of Dermatology and Allergology, University Hospital Salzburg, Salzburg, Austria
| | - Johann W. Bauer
- Department of Dermatology and Allergology, University Hospital Salzburg, Salzburg, Austria
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19
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Saleh S, Farabaugh PJ. Posttranscriptional modification to the core of tRNAs modulates translational misreading errors. RNA (NEW YORK, N.Y.) 2023; 30:37-51. [PMID: 37907335 PMCID: PMC10726164 DOI: 10.1261/rna.079797.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 10/09/2023] [Indexed: 11/02/2023]
Abstract
Protein synthesis on the ribosome involves successive rapid recruitment of cognate aminoacyl-tRNAs and rejection of the much more numerous incorrect near- or non-cognates. The principal feature of translation elongation is that at every step, many incorrect aa-tRNAs unsuccessfully enter the A site for each cognate accepted. Normal levels of translational accuracy require that cognate tRNAs have relatively similar acceptance rates by the ribosome. To achieve that, tRNAs evolved to compensate for differences in amino acid properties and codon-anticodon strength that affect acceptance. Part of that response involved tRNA posttranscriptional modifications, which can affect tRNA decoding efficiency, accuracy, and structural stability. The most intensively modified regions of the tRNA are the anticodon loop and structural core of the tRNA. Anticodon loop modifications directly affect codon-anticodon pairing and therefore modulate accuracy. Core modifications have been thought to ensure consistent decoding rates principally by stabilizing tRNA structure to avoid degradation; however, degradation due to instability appears to only be a significant issue above normal growth temperatures. We suspected that the greater role of modification at normal temperatures might be to tune tRNAs to maintain consistent intrinsic rates of acceptance and peptide transfer and that hypomodification by altering these rates might degrade the process of discrimination, leading to increased translational errors. Here, we present evidence that most tRNA core modifications do modulate the frequency of misreading errors, suggesting that the need to maintain accuracy explains their deep evolutionary conservation.
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Affiliation(s)
- Sima Saleh
- Department of Biological Sciences and Program in Molecular and Cell Biology, University of Maryland Baltimore County, Baltimore, Maryland 21250, USA
| | - Philip J Farabaugh
- Department of Biological Sciences and Program in Molecular and Cell Biology, University of Maryland Baltimore County, Baltimore, Maryland 21250, USA
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20
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Katoh T, Suga H. A comprehensive analysis of translational misdecoding pattern and its implication on genetic code evolution. Nucleic Acids Res 2023; 51:10642-10652. [PMID: 37638759 PMCID: PMC10602915 DOI: 10.1093/nar/gkad707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 07/19/2023] [Accepted: 08/19/2023] [Indexed: 08/29/2023] Open
Abstract
The universal genetic code is comprised of 61 sense codons, which are assigned to 20 canonical amino acids. However, the evolutionary basis for the highly conserved mapping between amino acids and their codons remains incompletely understood. A possible selective pressure of evolution would be minimization of deleterious effects caused by misdecoding. Here we comprehensively analyzed the misdecoding pattern of 61 codons against 19 noncognate amino acids where an arbitrary amino acid was omitted, and revealed the following two rules. (i) If the second codon base is U or C, misdecoding is frequently induced by mismatches at the first and/or third base, where any mismatches are widely tolerated; whereas misdecoding with the second-base mismatch is promoted by only U-G or C-A pair formation. (ii) If the second codon base is A or G, misdecoding is promoted by only G-U or U-G pair formation at the first or second position. In addition, evaluation of functional/structural diversities of amino acids revealed that less diverse amino acid sets are assigned at codons that induce more frequent misdecoding, and vice versa, so as to minimize deleterious effects of misdecoding in the modern genetic code.
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Affiliation(s)
- Takayuki Katoh
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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21
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Perriera R, Vitale E, Pibiri I, Carollo PS, Ricci D, Corrao F, Fiduccia I, Melfi R, Zizzo MG, Tutone M, Pace A, Lentini L. Readthrough Approach Using NV Translational Readthrough-Inducing Drugs (TRIDs): A Study of the Possible Off-Target Effects on Natural Termination Codons (NTCs) on TP53 and Housekeeping Gene Expression. Int J Mol Sci 2023; 24:15084. [PMID: 37894764 PMCID: PMC10606485 DOI: 10.3390/ijms242015084] [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: 08/11/2023] [Revised: 09/11/2023] [Accepted: 10/08/2023] [Indexed: 10/29/2023] Open
Abstract
Nonsense mutations cause several genetic diseases such as cystic fibrosis, Duchenne muscular dystrophy, β-thalassemia, and Shwachman-Diamond syndrome. These mutations induce the formation of a premature termination codon (PTC) inside the mRNA sequence, resulting in the synthesis of truncated polypeptides. Nonsense suppression therapy mediated by translational readthrough-inducing drugs (TRIDs) is a promising approach to correct these genetic defects. TRIDs generate a ribosome miscoding of the PTC named "translational readthrough" and restore the synthesis of full-length and potentially functional proteins. The new oxadiazole-core TRIDs NV848, NV914, and NV930 (NV) showed translational readthrough activity in nonsense-related in vitro systems. In this work, the possible off-target effect of NV molecules on natural termination codons (NTCs) was investigated. Two different in vitro approaches were used to assess if the NV molecule treatment induces NTC readthrough: (1) a study of the translational-induced p53 molecular weight and functionality; (2) the evaluation of two housekeeping proteins' (Cys-C and β2M) molecular weights. Our results showed that the treatment with NV848, NV914, or NV930 did not induce any translation alterations in both experimental systems. The data suggested that NV molecules have a specific action for the PTCs and an undetectable effect on the NTCs.
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Affiliation(s)
| | | | - Ivana Pibiri
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy; (R.P.); (E.V.); (P.S.C.); (D.R.); (F.C.); (I.F.); (R.M.); (M.G.Z.); (M.T.); (A.P.)
| | | | | | | | | | | | | | | | | | - Laura Lentini
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy; (R.P.); (E.V.); (P.S.C.); (D.R.); (F.C.); (I.F.); (R.M.); (M.G.Z.); (M.T.); (A.P.)
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22
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Jain V, Cope AL. Determining the effects of temperature on the evolution of bacterial tRNA pools. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.26.559538. [PMID: 37873246 PMCID: PMC10592612 DOI: 10.1101/2023.09.26.559538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The genetic code consists of 61 codon coding for 20 amino acids. These codons are recognized by transfer RNAs (tRNA) that bind to specific codons during protein synthesis. Most organisms utilize less than all 61 possible anticodons due to base pair wobble: the ability to have a mismatch with a codon at its third nucleotide. Previous studies observed a correlation between the tRNA pool of bacteria and the temperature of their respective environments. However, it is unclear if these patterns represent biological adaptations to maintain the efficiency and accuracy of protein synthesis in different environments. A mechanistic mathematical model of mRNA translation is used to quantify the expected elongation rates and error rate for each codon based on an organism's tRNA pool. A comparative analysis across a range of bacteria that accounts for covariance due to shared ancestry is performed to quantify the impact of environmental temperature on the evolution of the tRNA pool. We find that thermophiles generally have more anticodons represented in their tRNA pool than mesophiles or psychrophiles. Based on our model, this increased diversity is expected to lead to increased missense errors. The implications of this for protein evolution in thermophiles are discussed.
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Affiliation(s)
- Vatsal Jain
- Biotechnology High School, Freehold, New Jersey
| | - Alexander L. Cope
- Department of Genetics, Rutgers University, Piscataway, New Jersey
- Human Genetics Institute of New Jersey, Rutgers University, Piscataway, New Jersey
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23
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Inafuku DA, Kirkpatrick KL, Osuagwu O, An Q, Brewster DA, Nakib MZ. Channel capacity of the ribosome. Phys Rev E 2023; 108:044404. [PMID: 37978643 DOI: 10.1103/physreve.108.044404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 08/09/2023] [Indexed: 11/19/2023]
Abstract
Translation is one of the most fundamental processes in the biological cell. Because of the central role that translation plays across all domains of life, the enzyme that carries out this process, the ribosome, is required to process information with high accuracy. This accuracy often approaches values near unity experimentally. In this paper, we model the ribosome as an information channel and demonstrate mathematically that this biological machine has information-processing capabilities that have not been recognized previously. In particular, we calculate bounds on the ribosome's theoretical Shannon capacity and numerically approximate this capacity. Finally, by incorporating estimates on the ribosome's operation time, we show that the ribosome operates at speeds safely below its capacity, allowing the ribosome to process information with an arbitrary degree of error. Our results show that the ribosome achieves a high accuracy in line with purely information-theoretic means.
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Affiliation(s)
- Daniel A Inafuku
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Kay L Kirkpatrick
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Mathematics, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Onyema Osuagwu
- Electrical and Computer Engineering Department, Morgan State University, Baltimore, Maryland 21251, USA
- Cybersecurity Assurance and Policy Center, Morgan State University, Baltimore, Maryland 21251, USA
| | - Qier An
- Department of Physics, University of California, Santa Barbara, Santa Barbara, California 93106, USA
| | - David A Brewster
- Department of Mathematics, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Mayisha Zeb Nakib
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
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24
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Wienecke AN, Barry ML, Pollard DA. Natural variation in codon bias and mRNA folding strength interact synergistically to modify protein expression in Saccharomyces cerevisiae. Genetics 2023; 224:iyad113. [PMID: 37310925 PMCID: PMC10411576 DOI: 10.1093/genetics/iyad113] [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: 04/10/2023] [Revised: 04/10/2023] [Accepted: 05/15/2023] [Indexed: 06/15/2023] Open
Abstract
Codon bias and mRNA folding strength (mF) are hypothesized molecular mechanisms by which polymorphisms in genes modify protein expression. Natural patterns of codon bias and mF across genes as well as effects of altering codon bias and mF suggest that the influence of these 2 mechanisms may vary depending on the specific location of polymorphisms within a transcript. Despite the central role codon bias and mF may play in natural trait variation within populations, systematic studies of how polymorphic codon bias and mF relate to protein expression variation are lacking. To address this need, we analyzed genomic, transcriptomic, and proteomic data for 22 Saccharomyces cerevisiae isolates, estimated protein accumulation for each allele of 1,620 genes as the log of protein molecules per RNA molecule (logPPR), and built linear mixed-effects models associating allelic variation in codon bias and mF with allelic variation in logPPR. We found that codon bias and mF interact synergistically in a positive association with logPPR, and this interaction explains almost all the effects of codon bias and mF. We examined how the locations of polymorphisms within transcripts influence their effects and found that codon bias primarily acts through polymorphisms in domain-encoding and 3' coding sequences, while mF acts most significantly through coding sequences with weaker effects from untranslated regions. Our results present the most comprehensive characterization to date of how polymorphisms in transcripts influence protein expression.
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Affiliation(s)
- Anastacia N Wienecke
- Biology Department, Western Washington University, Bellingham, WA 98225, USA
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Margaret L Barry
- Biology Department, Western Washington University, Bellingham, WA 98225, USA
| | - Daniel A Pollard
- Biology Department, Western Washington University, Bellingham, WA 98225, USA
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25
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Antoniani F, Cimino M, Mediani L, Vinet J, Verde EM, Secco V, Yamoah A, Tripathi P, Aronica E, Cicardi ME, Trotti D, Sterneckert J, Goswami A, Carra S. Loss of PML nuclear bodies in familial amyotrophic lateral sclerosis-frontotemporal dementia. Cell Death Discov 2023; 9:248. [PMID: 37454169 DOI: 10.1038/s41420-023-01547-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 06/20/2023] [Accepted: 07/04/2023] [Indexed: 07/18/2023] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Dementia (FTD) are two neurodegenerative disorders that share genetic causes and pathogenic mechanisms. The critical genetic players of ALS and FTD are the TARDBP, FUS and C9orf72 genes, whose protein products, TDP-43, FUS and the C9orf72-dipeptide repeat proteins, accumulate in form of cytoplasmic inclusions. The majority of the studies focus on the understanding of how cells control TDP-43 and FUS aggregation in the cytoplasm, overlooking how dysfunctions occurring at the nuclear level may influence the maintenance of protein solubility outside of the nucleus. However, protein quality control (PQC) systems that maintain protein homeostasis comprise a cytoplasmic and a nuclear arm that are interconnected and share key players. It is thus conceivable that impairment of the nuclear arm of the PQC may have a negative impact on the cytoplasmic arm of the PQC, contributing to the formation of the cytoplasmic pathological inclusions. Here we focused on two stress-inducible condensates that act as transient deposition sites for misfolding-prone proteins: Promyelocytic leukemia protein (PML) nuclear bodies (PML-NBs) and cytoplasmic stress granules (SGs). Upon stress, PML-NBs compartmentalize misfolded proteins, including defective ribosomal products (DRiPs), and recruit chaperones and proteasomes to promote their nuclear clearance. SGs transiently sequester aggregation-prone RNA-binding proteins linked to ALS-FTD and mRNAs to attenuate their translation. We report that PML assembly is impaired in the human brain and spinal cord of familial C9orf72 and FUS ALS-FTD cases. We also show that defective PML-NB assembly impairs the compartmentalization of DRiPs in the nucleus, leading to their accumulation inside cytoplasmic SGs, negatively influencing SG dynamics. Although it is currently unclear what causes the decrease of PML-NBs in ALS-FTD, our data highlight the existence of a cross-talk between the cytoplasmic and nuclear PQC systems, whose alteration can contribute to SG accumulation and cytoplasmic protein aggregation in ALS-FTD.
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Affiliation(s)
- Francesco Antoniani
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Marco Cimino
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Laura Mediani
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Jonathan Vinet
- Centro Interdipartimentale Grandi Strumenti (CIGS), University of Modena and Reggio Emilia, Modena, Italy
| | - Enza M Verde
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Valentina Secco
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Alfred Yamoah
- Institute of Neuropathology, RWTH Aachen University Hospital, Aachen, Germany
| | - Priyanka Tripathi
- Institute of Neuropathology, RWTH Aachen University Hospital, Aachen, Germany
| | - Eleonora Aronica
- Amsterdam UMC location University of Amsterdam, Department of (Neuro)Pathology, Amsterdam Neuroscience, Meibergdreef 9, Amsterdam, the Netherlands
| | - Maria E Cicardi
- Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA, USA
| | - Davide Trotti
- Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA, USA
| | - Jared Sterneckert
- Center for Regenerative Therapies TU Dresden, Technische Universität Dresden, Dresden, Germany
- Medical Faculty Carl Gustav Carus of TU Dresden, Dresden, Germany
| | - Anand Goswami
- Institute of Neuropathology, RWTH Aachen University Hospital, Aachen, Germany.
- Department of Neurology, Center for Motor Neuron Biology and Disease, Columbia University, 10032, New York, NY, USA.
- Department of Neurology, Eleanor and Lou Gehrig ALS Center, Columbia University, 10032, New York, NY, USA.
| | - Serena Carra
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy.
- Medical Faculty Carl Gustav Carus of TU Dresden, Dresden, Germany.
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26
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She R, Luo J, Weissman JS. Translational fidelity screens in mammalian cells reveal eIF3 and eIF4G2 as regulators of start codon selectivity. Nucleic Acids Res 2023; 51:6355-6369. [PMID: 37144468 PMCID: PMC10325891 DOI: 10.1093/nar/gkad329] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 04/13/2023] [Accepted: 05/03/2023] [Indexed: 05/06/2023] Open
Abstract
The translation initiation machinery and the ribosome orchestrate a highly dynamic scanning process to distinguish proper start codons from surrounding nucleotide sequences. Here, we performed genome-wide CRISPRi screens in human K562 cells to systematically identify modulators of the frequency of translation initiation at near-cognate start codons. We observed that depletion of any eIF3 core subunit promoted near-cognate start codon usage, though sensitivity thresholds of each subunit to sgRNA-mediated depletion varied considerably. Double sgRNA depletion experiments suggested that enhanced near-cognate usage in eIF3D depleted cells required canonical eIF4E cap-binding and was not driven by eIF2A or eIF2D-dependent leucine tRNA initiation. We further characterized the effects of eIF3D depletion and found that the N-terminus of eIF3D was strictly required for accurate start codon selection, whereas disruption of the cap-binding properties of eIF3D had no effect. Lastly, depletion of eIF3D activated TNFα signaling via NF-κB and the interferon gamma response. Similar transcriptional profiles were observed upon knockdown of eIF1A and eIF4G2, which also promoted near-cognate start codon usage, suggesting that enhanced near-cognate usage could potentially contribute to NF-κB activation. Our study thus provides new avenues to study the mechanisms and consequences of alternative start codon usage.
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Affiliation(s)
- Richard She
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Jingchuan Luo
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
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27
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Cobo I, Paliwal S, Bodas C, Felipe I, Melià-Alomà J, Torres A, Martínez-Villarreal J, Malumbres M, García F, Millán I, Del Pozo N, Park JC, MacDonald RJ, Muñoz J, Méndez R, Real FX. NFIC regulates ribosomal biology and ER stress in pancreatic acinar cells and restrains PDAC initiation. Nat Commun 2023; 14:3761. [PMID: 37353485 PMCID: PMC10290102 DOI: 10.1038/s41467-023-39291-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 06/06/2023] [Indexed: 06/25/2023] Open
Abstract
Pancreatic acinar cells rely on PTF1 and other transcription factors to deploy their transcriptional program. We identify NFIC as a NR5A2 interactor and regulator of acinar differentiation. NFIC binding sites are enriched in NR5A2 ChIP-Sequencing peaks. Nfic knockout mice have a smaller, histologically normal, pancreas with reduced acinar gene expression. NFIC binds and regulates the promoters of acinar genes and those involved in RNA/protein metabolism, and Nfic knockout pancreata show defective ribosomal RNA maturation. NFIC dampens the endoplasmic reticulum stress program through binding to gene promoters and is required for resolution of Tunicamycin-mediated stress. NFIC is down-regulated during caerulein pancreatitis and is required for recovery after damage. Normal human pancreata with low levels of NFIC transcripts display reduced expression of genes down-regulated in Nfic knockout mice. NFIC expression is down-regulated in mouse and human pancreatic ductal adenocarcinoma. Consistently, Nfic knockout mice develop a higher number of mutant Kras-driven pre-neoplastic lesions.
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Affiliation(s)
- Isidoro Cobo
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre-CNIO, Madrid, Spain
- CIBERONC, Madrid, Spain
| | - Sumit Paliwal
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre-CNIO, Madrid, Spain
| | - Cristina Bodas
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre-CNIO, Madrid, Spain
- CIBERONC, Madrid, Spain
| | - Irene Felipe
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre-CNIO, Madrid, Spain
- CIBERONC, Madrid, Spain
| | - Júlia Melià-Alomà
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre-CNIO, Madrid, Spain
- Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Barcelona, Spain
| | - Ariadna Torres
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre-CNIO, Madrid, Spain
- Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Barcelona, Spain
| | | | - Marina Malumbres
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Fernando García
- Proteomics Unit, Spanish National Cancer Research Centre-CNIO, ProteoRed-Instituto de Salud Carlos III, Madrid, Spain
| | - Irene Millán
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre-CNIO, Madrid, Spain
- CIBERONC, Madrid, Spain
| | - Natalia Del Pozo
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre-CNIO, Madrid, Spain
- CIBERONC, Madrid, Spain
| | - Joo-Cheol Park
- Department of Oral Histology-Developmental Biology, School of Dentistry, Seoul National University, Seoul, Korea
| | - Ray J MacDonald
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Javier Muñoz
- Proteomics Unit, Spanish National Cancer Research Centre-CNIO, ProteoRed-Instituto de Salud Carlos III, Madrid, Spain
| | - Raúl Méndez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Francisco X Real
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre-CNIO, Madrid, Spain.
- CIBERONC, Madrid, Spain.
- Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Barcelona, Spain.
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28
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Rodnina MV. Decoding and Recoding of mRNA Sequences by the Ribosome. Annu Rev Biophys 2023; 52:161-182. [PMID: 37159300 DOI: 10.1146/annurev-biophys-101922-072452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Faithful translation of messenger RNA (mRNA) into protein is essential to maintain protein homeostasis in the cell. Spontaneous translation errors are very rare due to stringent selection of cognate aminoacyl transfer RNAs (tRNAs) and the tight control of the mRNA reading frame by the ribosome. Recoding events, such as stop codon readthrough, frameshifting, and translational bypassing, reprogram the ribosome to make intentional mistakes and produce alternative proteins from the same mRNA. The hallmark of recoding is the change of ribosome dynamics. The signals for recoding are built into the mRNA, but their reading depends on the genetic makeup of the cell, resulting in cell-specific changes in expression programs. In this review, I discuss the mechanisms of canonical decoding and tRNA-mRNA translocation; describe alternative pathways leading to recoding; and identify the links among mRNA signals, ribosome dynamics, and recoding.
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Affiliation(s)
- Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany;
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29
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Zhang D, Zhu L, Wang F, Li P, Wang Y, Gao Y. Molecular mechanisms of eukaryotic translation fidelity and their associations with diseases. Int J Biol Macromol 2023; 242:124680. [PMID: 37141965 DOI: 10.1016/j.ijbiomac.2023.124680] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 04/27/2023] [Indexed: 05/06/2023]
Abstract
Converting genetic information into functional proteins is a complex, multi-step process, with each step being tightly regulated to ensure the accuracy of translation, which is critical to cellular health. In recent years, advances in modern biotechnology, especially the development of cryo-electron microscopy and single-molecule techniques, have enabled a clearer understanding of the mechanisms of protein translation fidelity. Although there are many studies on the regulation of protein translation in prokaryotes, and the basic elements of translation are highly conserved in prokaryotes and eukaryotes, there are still great differences in the specific regulatory mechanisms. This review describes how eukaryotic ribosomes and translation factors regulate protein translation and ensure translation accuracy. However, a certain frequency of translation errors does occur in translation, so we describe diseases that arise when the rate of translation errors reaches or exceeds a threshold of cellular tolerance.
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Affiliation(s)
- Dejiu Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Lei Zhu
- College of Basic Medical, Qingdao Binhai University, Qingdao, China
| | - Fei Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.
| | - Yanyan Gao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.
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30
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Majumdar S, Emmerich A, Krakovka S, Mandava CS, Svärd SG, Sanyal S. Insights into translocation mechanism and ribosome evolution from cryo-EM structures of translocation intermediates of Giardia intestinalis. Nucleic Acids Res 2023; 51:3436-3451. [PMID: 36912103 PMCID: PMC10123126 DOI: 10.1093/nar/gkad176] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 02/06/2023] [Accepted: 02/24/2023] [Indexed: 03/14/2023] Open
Abstract
Giardia intestinalis is a protozoan parasite that causes diarrhea in humans. Using single-particle cryo-electron microscopy, we have determined high-resolution structures of six naturally populated translocation intermediates, from ribosomes isolated directly from actively growing Giardia cells. The highly compact and uniquely GC-rich Giardia ribosomes possess eukaryotic rRNAs and ribosomal proteins, but retain some bacterial features. The translocation intermediates, with naturally bound tRNAs and eukaryotic elongation factor 2 (eEF2), display characteristic ribosomal intersubunit rotation and small subunit's head swiveling-universal for translocation. In addition, we observe the eukaryote-specific 'subunit rolling' dynamics, albeit with limited features. Finally, the eEF2·GDP state features a uniquely positioned 'leaving phosphate (Pi)' that proposes hitherto unknown molecular events of Pi and eEF2 release from the ribosome at the final stage of translocation. In summary, our study elucidates the mechanism of translocation in the protists and illustrates evolution of the translation machinery from bacteria to eukaryotes from both the structural and mechanistic perspectives.
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Affiliation(s)
- Soneya Majumdar
- Department of Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Andrew Emmerich
- Department of Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Sascha Krakovka
- Department of Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Chandra Sekhar Mandava
- Department of Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Staffan G Svärd
- Department of Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Suparna Sanyal
- Department of Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
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31
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Bednar RM, Karplus PA, Mehl RA. Site-specific dual encoding and labeling of proteins via genetic code expansion. Cell Chem Biol 2023; 30:343-361. [PMID: 36977415 PMCID: PMC10764108 DOI: 10.1016/j.chembiol.2023.03.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 02/10/2023] [Accepted: 03/03/2023] [Indexed: 03/29/2023]
Abstract
The ability to selectively modify proteins at two or more defined locations opens new avenues for manipulating, engineering, and studying living systems. As a chemical biology tool for the site-specific encoding of non-canonical amino acids into proteins in vivo, genetic code expansion (GCE) represents a powerful tool to achieve such modifications with minimal disruption to structure and function through a two-step "dual encoding and labeling" (DEAL) process. In this review, we summarize the state of the field of DEAL using GCE. In doing so, we describe the basic principles of GCE-based DEAL, catalog compatible encoding systems and reactions, explore demonstrated and potential applications, highlight emerging paradigms in DEAL methodologies, and propose novel solutions to current limitations.
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Affiliation(s)
- Riley M Bednar
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences Building, Corvallis, OR 97331-7305, USA; GCE4All Research Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, OR 97331-7305, USA
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences Building, Corvallis, OR 97331-7305, USA; GCE4All Research Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, OR 97331-7305, USA
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences Building, Corvallis, OR 97331-7305, USA; GCE4All Research Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, OR 97331-7305, USA.
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32
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Vasse GF, Russo S, Barcaru A, Oun AAA, Dolga AM, van Rijn P, Kwiatkowski M, Govorukhina N, Bischoff R, Melgert BN. Collagen type I alters the proteomic signature of macrophages in a collagen morphology-dependent manner. Sci Rep 2023; 13:5670. [PMID: 37024614 PMCID: PMC10079972 DOI: 10.1038/s41598-023-32715-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/30/2023] [Indexed: 04/08/2023] Open
Abstract
Idiopathic pulmonary fibrosis is a progressive lung disease that causes scarring and loss of lung function. Macrophages play a key role in fibrosis, but their responses to altered morphological and mechanical properties of the extracellular matrix in fibrosis is relatively unexplored. Our previous work showed functional changes in murine fetal liver-derived alveolar macrophages on fibrous or globular collagen morphologies. In this study, we applied differential proteomics to further investigate molecular mechanisms underlying the observed functional changes. Macrophages cultured on uncoated, fibrous, or globular collagen-coated plastic were analyzed by liquid chromatography-mass spectrometry. The presence of collagen affected expression of 77 proteins, while 142 were differentially expressed between macrophages grown on fibrous or globular collagen. Biological process and pathway enrichment analysis revealed that culturing on any type of collagen induced higher expression of enzymes involved in glycolysis. However, this did not lead to a higher rate of glycolysis, probably because of a concomitant decrease in activity of these enzymes. Our data suggest that macrophages sense collagen morphologies and can respond with changes in expression and activity of metabolism-related proteins. These findings suggest intimate interactions between macrophages and their surroundings that may be important in repair or fibrosis of lung tissue.
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Affiliation(s)
- Gwenda F Vasse
- Biomedical Engineering Department-FB40, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
- University Medical Center Groningen, W.J. Kolff Institute for Biomedical Engineering and Materials Science-FB41, University of Groningen, Groningen, The Netherlands.
- Department of Molecular Pharmacology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands.
- University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands.
| | - Sara Russo
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Andrei Barcaru
- Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Asmaa A A Oun
- Department of Molecular Pharmacology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
- Department of Cell Biochemistry, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, Groningen, The Netherlands
| | - Amalia M Dolga
- Department of Molecular Pharmacology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Patrick van Rijn
- Biomedical Engineering Department-FB40, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- University Medical Center Groningen, W.J. Kolff Institute for Biomedical Engineering and Materials Science-FB41, University of Groningen, Groningen, The Netherlands
| | - Marcel Kwiatkowski
- Functional Proteo-Metabolomics, Department of Biochemistry, University of Innsbruck, Innsbruck, Austria
| | - Natalia Govorukhina
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Rainer Bischoff
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Barbro N Melgert
- Department of Molecular Pharmacology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
- University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands
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33
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Nguyen H, Hoffer E, Fagan C, Maehigashi T, Dunham C. Structural basis for reduced ribosomal A-site fidelity in response to P-site codon-anticodon mismatches. J Biol Chem 2023; 299:104608. [PMID: 36924943 PMCID: PMC10140155 DOI: 10.1016/j.jbc.2023.104608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/10/2023] [Accepted: 03/11/2023] [Indexed: 03/16/2023] Open
Abstract
Rapid and accurate translation is essential in all organisms to produce properly folded and functional proteins. mRNA codons that define the protein coding sequences are decoded by tRNAs on the ribosome in the aminoacyl (A) binding site. The mRNA codon and the tRNA anticodon interaction is extensively monitored by the ribosome to ensure accuracy in tRNA selection. While other polymerases that synthesize DNA and RNA can correct for misincorporations, the ribosome is unable to correct mistakes. Instead, when a misincorporation occurs, the mismatched tRNA-mRNA pair moves to the peptidyl (P) site and from this location, causes a reduction in the fidelity at the A site, triggering post-peptidyl transfer quality control. This reduced fidelity allows for additional incorrect tRNAs to be accepted and for release factor 2 (RF2) to recognize sense codons, leading to hydrolysis of the aberrant peptide. Here, we present crystal structures of the ribosome containing a tRNALys in the P site with a U•U mismatch with the mRNA codon. We find that when the mismatch occurs in the second position of the P-site codon-anticodon interaction, the first nucleotide of the A-site codon flips from the mRNA path to engage highly conserved 16S rRNA nucleotide A1493 in the decoding center. We propose that this mRNA nucleotide mispositioning leads to reduced fidelity at the A site. Further, this state may provide an opportunity for RF2 to initiate premature termination before erroneous nascent chains disrupt the cellular proteome.
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Affiliation(s)
- HaAn Nguyen
- Department of Chemistry, Emory University, Atlanta, GA USA; Emory Antibiotic Resistance Center (ARC), Emory University, Atlanta, GA USA
| | - EricD Hoffer
- Emory Antibiotic Resistance Center (ARC), Emory University, Atlanta, GA USA; Biochemistry, Cell and Developmental Biology Graduate Program, Emory University, Atlanta, GA USA
| | - CrystalE Fagan
- Emory Antibiotic Resistance Center (ARC), Emory University, Atlanta, GA USA; Biochemistry, Cell and Developmental Biology Graduate Program, Emory University, Atlanta, GA USA
| | - Tatsuya Maehigashi
- Department of Chemistry, Emory University, Atlanta, GA USA; Emory Antibiotic Resistance Center (ARC), Emory University, Atlanta, GA USA
| | - ChristineM Dunham
- Department of Chemistry, Emory University, Atlanta, GA USA; Emory Antibiotic Resistance Center (ARC), Emory University, Atlanta, GA USA.
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Raval PK, Ngan WY, Gallie J, Agashe D. The layered costs and benefits of translational redundancy. eLife 2023; 12:81005. [PMID: 36862572 PMCID: PMC9981150 DOI: 10.7554/elife.81005] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 01/25/2023] [Indexed: 03/03/2023] Open
Abstract
The rate and accuracy of translation hinges upon multiple components - including transfer RNA (tRNA) pools, tRNA modifying enzymes, and rRNA molecules - many of which are redundant in terms of gene copy number or function. It has been hypothesized that the redundancy evolves under selection, driven by its impacts on growth rate. However, we lack empirical measurements of the fitness costs and benefits of redundancy, and we have poor a understanding of how this redundancy is organized across components. We manipulated redundancy in multiple translation components of Escherichia coli by deleting 28 tRNA genes, 3 tRNA modifying systems, and 4 rRNA operons in various combinations. We find that redundancy in tRNA pools is beneficial when nutrients are plentiful and costly under nutrient limitation. This nutrient-dependent cost of redundant tRNA genes stems from upper limits to translation capacity and growth rate, and therefore varies as a function of the maximum growth rate attainable in a given nutrient niche. The loss of redundancy in rRNA genes and tRNA modifying enzymes had similar nutrient-dependent fitness consequences. Importantly, these effects are also contingent upon interactions across translation components, indicating a layered hierarchy from copy number of tRNA and rRNA genes to their expression and downstream processing. Overall, our results indicate both positive and negative selection on redundancy in translation components, depending on a species' evolutionary history with feasts and famines.
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Affiliation(s)
- Parth K Raval
- National Centre for Biological Sciences (NCBS-TIFR)BengaluruIndia
| | - Wing Yui Ngan
- Max Plank Institute for Evolutionary BiologyPlönGermany
| | - Jenna Gallie
- Max Plank Institute for Evolutionary BiologyPlönGermany
| | - Deepa Agashe
- National Centre for Biological Sciences (NCBS-TIFR)BengaluruIndia
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35
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Binhi VN. Statistical Amplification of the Effects of Weak Magnetic Fields in Cellular Translation. Cells 2023; 12:724. [PMID: 36899858 PMCID: PMC10000676 DOI: 10.3390/cells12050724] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 03/12/2023] Open
Abstract
We assume that the enzymatic processes of recognition of amino acids and their addition to the synthesized molecule in cellular translation include the formation of intermediate pairs of radicals with spin-correlated electrons. The mathematical model presented describes the changes in the probability of incorrectly synthesized molecules in response to a change in the external weak magnetic field. A relatively high chance of errors has been shown to arise from the statistical enhancement of the low probability of local incorporation errors. This statistical mechanism does not require a long thermal relaxation time of electron spins of about 1 μs-a conjecture often used to match theoretical models of magnetoreception with experiments. The statistical mechanism allows for experimental verification by testing the usual Radical Pair Mechanism properties. In addition, this mechanism localizes the site where magnetic effects originate, the ribosome, which makes it possible to verify it by biochemical methods. This mechanism predicts a random nature of the nonspecific effects caused by weak and hypomagnetic fields and agrees with the diversity of biological responses to a weak magnetic field.
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Affiliation(s)
- Vladimir N Binhi
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia
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36
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Lant JT, Hasan F, Briggs J, Heinemann IU, O’Donoghue P. Genetic Interaction of tRNA-Dependent Mistranslation with Fused in Sarcoma Protein Aggregates. Genes (Basel) 2023; 14:518. [PMID: 36833445 PMCID: PMC9956149 DOI: 10.3390/genes14020518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
High-fidelity protein synthesis requires properly aminoacylated transfer RNAs (tRNAs), yet diverse cell types, from bacteria to humans, show a surprising ability to tolerate errors in translation resulting from mutations in tRNAs, aminoacyl-tRNA synthetases, and other components of protein synthesis. Recently, we characterized a tRNASerAGA G35A mutant (tRNASerAAA) that occurs in 2% of the human population. The mutant tRNA decodes phenylalanine codons with serine, inhibits protein synthesis, and is defective in protein and aggregate degradation. Here, we used cell culture models to test our hypothesis that tRNA-dependent mistranslation will exacerbate toxicity caused by amyotrophic lateral sclerosis (ALS)-associated protein aggregation. Relative to wild-type tRNA, we found cells expressing tRNASerAAA showed slower but effective aggregation of the fused in sarcoma (FUS) protein. Despite reduced levels in mistranslating cells, wild-type FUS aggregates showed similar toxicity in mistranslating cells and normal cells. The aggregation kinetics of the ALS-causative FUS R521C variant were distinct and more toxic in mistranslating cells, where rapid FUS aggregation caused cells to rupture. We observed synthetic toxicity in neuroblastoma cells co-expressing the mistranslating tRNA mutant and the ALS-causative FUS R521C variant. Our data demonstrate that a naturally occurring human tRNA variant enhances cellular toxicity associated with a known causative allele for neurodegenerative disease.
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Affiliation(s)
- Jeremy T. Lant
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Farah Hasan
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Julia Briggs
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Ilka U. Heinemann
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Patrick O’Donoghue
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
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37
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Le LQ, Zhu K, Su H. Bridging ribosomal synthesis to cell growth through the lens of kinetics. Biophys J 2023; 122:544-553. [PMID: 36564946 PMCID: PMC9941725 DOI: 10.1016/j.bpj.2022.12.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 07/20/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Understanding prokaryotic cell growth requires a multiscale modeling framework from the kinetics perspective. The detailed kinetics pathway of ribosomes exhibits features beyond the scope of the classical Hopfield kinetics model. The complexity of the molecular responses to various nutrient conditions poses additional challenge to elucidate the cell growth. Herein, a kinetics framework is developed to bridge ribosomal synthesis to cell growth. For the ribosomal synthesis kinetics, the competitive binding between cognate and near-cognate tRNAs for ribosomes can be modulated by Mg2+. This results in distinct patterns of the speed - accuracy relation comprising "trade-off" and "competition" regimes. Furthermore, the cell growth rate is optimized by varying the characteristics of ribosomal synthesis through cellular responses to different nutrient conditions. In this scenario, cellular responses to nutrient conditions manifest by two quadratic scaling relations: one for nutrient flux versus cell mass, the other for ribosomal number versus growth rate. Both are in quantitative agreement with experimental measurements.
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Affiliation(s)
- Luan Quang Le
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, Singapore; Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Kaicheng Zhu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Haibin Su
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.
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38
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Kochavi A, Lovecchio D, Faller WJ, Agami R. Proteome diversification by mRNA translation in cancer. Mol Cell 2023; 83:469-480. [PMID: 36521491 DOI: 10.1016/j.molcel.2022.11.014] [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: 09/19/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 12/15/2022]
Abstract
mRNA translation is a highly conserved and tightly controlled mechanism for protein synthesis and is well known to be altered by oncogenes to promote cancer development. This distorted mRNA translation is accompanied by the vulnerability of cancer to inhibitors of key mRNA translation components. Novel studies also suggest that these alternations could be utilized for immunotherapy. Ribosome heterogeneity and alternative responses to nutrient shortages, which aid cancer growth and spread, are proposed to elicit aberrant protein production but may also result in previously unidentified therapeutic targets, such as the presentation of cancer-specific peptides at the surface of cancer cells (neoepitopes). This review will assess the driving forces in tRNA and ribosome function that underlie proteome diversification due to alterations in mRNA translation in cancer cells.
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Affiliation(s)
- Adva Kochavi
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Oncode Institute, the Netherlands
| | - Domenica Lovecchio
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Oncode Institute, the Netherlands
| | - William James Faller
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Reuven Agami
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Oncode Institute, the Netherlands; Erasmus MC, Rotterdam University, Rotterdam, the Netherlands.
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39
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Nguyen HA, Hoffer ED, Fagan CE, Maehigashi T, Dunham CM. Structural basis for reduced ribosomal A-site fidelity in response to P-site codon-anticodon mismatches. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.28.526049. [PMID: 36747737 PMCID: PMC9900946 DOI: 10.1101/2023.01.28.526049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Rapid and accurate translation is essential in all organisms to produce properly folded and functional proteins. mRNA codons that define the protein coding sequences are decoded by tRNAs on the ribosome in the aminoacyl (A) binding site. The mRNA codon and the tRNA anticodon interaction is extensively monitored by the ribosome to ensure accuracy in tRNA selection. While other polymerases that synthesize DNA and RNA can correct for misincorporations, the ribosome is unable to correct mistakes. Instead, when a misincorporation occurs, the mismatched tRNA-mRNA pair moves to the peptidyl (P) site and from this location, causes a reduction in the fidelity at the A site, triggering post-peptidyl transfer quality control. This reduced fidelity allows for additional incorrect tRNAs to be accepted and for release factor 2 (RF2) to recognize sense codons, leading to hydrolysis of the aberrant peptide. Here, we present crystal structures of the ribosome containing a tRNA Lys in the P site with a U•U mismatch with the mRNA codon. We find that when the mismatch occurs in the second position of the P-site codon-anticodon interaction, the first nucleotide of the A-site codon flips from the mRNA path to engage highly conserved 16S rRNA nucleotide A1493 in the decoding center. We propose that this mRNA nucleotide mispositioning leads to reduced fidelity at the A site. Further, this state may provide an opportunity for RF2 to initiate premature termination before erroneous nascent chains disrupt the cellular proteome.
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Affiliation(s)
- Ha An Nguyen
- Department of Chemistry, Emory University, Atlanta, GA USA
- Emory Antibiotic Resistance Center (ARC), Emory University, Atlanta, GA USA
| | - Eric D. Hoffer
- Emory Antibiotic Resistance Center (ARC), Emory University, Atlanta, GA USA
- Biochemistry, Cell and Developmental Biology Graduate Program, Emory University, Atlanta, GA USA
| | - Crystal E. Fagan
- Emory Antibiotic Resistance Center (ARC), Emory University, Atlanta, GA USA
- Biochemistry, Cell and Developmental Biology Graduate Program, Emory University, Atlanta, GA USA
| | - Tatsuya Maehigashi
- Department of Chemistry, Emory University, Atlanta, GA USA
- Emory Antibiotic Resistance Center (ARC), Emory University, Atlanta, GA USA
| | - Christine M. Dunham
- Department of Chemistry, Emory University, Atlanta, GA USA
- Emory Antibiotic Resistance Center (ARC), Emory University, Atlanta, GA USA
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40
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Kiemel K, Gurke M, Paraskevopoulou S, Havenstein K, Weithoff G, Tiedemann R. Variation in heat shock protein 40 kDa relates to divergence in thermotolerance among cryptic rotifer species. Sci Rep 2022; 12:22626. [PMID: 36587065 PMCID: PMC9805463 DOI: 10.1038/s41598-022-27137-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/26/2022] [Indexed: 01/01/2023] Open
Abstract
Genetic divergence and the frequency of hybridization are central for defining species delimitations, especially among cryptic species where morphological differences are merely absent. Rotifers are known for their high cryptic diversity and therefore are ideal model organisms to investigate such patterns. Here, we used the recently resolved Brachionus calyciflorus species complex to investigate whether previously observed between species differences in thermotolerance and gene expression are also reflected in their genomic footprint. We identified a Heat Shock Protein gene (HSP 40 kDa) which exhibits cross species pronounced sequence variation. This gene exhibits species-specific fixed sites, alleles, and sites putatively under positive selection. These sites are located in protein binding regions involved in chaperoning and may therefore reflect adaptive diversification. By comparing three genetic markers (ITS, COI, HSP 40 kDa), we revealed hybridization events between the cryptic species. The low frequency of introgressive haplotypes/alleles suggest a tight, but not fully impermeable boundary between the cryptic species.
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Affiliation(s)
- K. Kiemel
- grid.11348.3f0000 0001 0942 1117Unit of Evolutionary Biology/Systematic Zoology, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht Straße 24-25, 14476 Potsdam, Germany
| | - M. Gurke
- grid.422371.10000 0001 2293 9957Museum für Naturkunde – Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany ,grid.7468.d0000 0001 2248 7639Department of Biology, Humboldt-University, Invalidenstraße 42, 10115 Berlin, Germany
| | - S. Paraskevopoulou
- grid.4514.40000 0001 0930 2361Department of Biology, Lund University, Microbiology Group, Sölvegatan 35, 223 62 Lund, Sweden
| | - K. Havenstein
- grid.11348.3f0000 0001 0942 1117Unit of Evolutionary Biology/Systematic Zoology, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht Straße 24-25, 14476 Potsdam, Germany
| | - G. Weithoff
- grid.11348.3f0000 0001 0942 1117Unit of Ecology and Ecosystem Modelling, Institute for Biochemistry and Biology, University of Potsdam, Am Neuen Palais 10, 14469 Potsdam, Germany
| | - R. Tiedemann
- grid.11348.3f0000 0001 0942 1117Unit of Evolutionary Biology/Systematic Zoology, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht Straße 24-25, 14476 Potsdam, Germany
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41
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Olson AN, Song S, Dinman JD. Deep mutational analysis of elongation factor eEF2 residues implicated in human disease to identify functionally important contacts with the ribosome. J Biol Chem 2022; 299:102771. [PMID: 36470424 PMCID: PMC9830224 DOI: 10.1016/j.jbc.2022.102771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
An emerging body of research is revealing mutations in elongation factor eEF2 that are implicated in both inherited and de novo neurodevelopmental disorders. Previous structural analysis has revealed that most pathogenic amino acid substitutions map to the three main points of contact between eEF2 and critical large subunit rRNA elements of the ribosome, specifically to contacts with Helix 69, Helix 95, also known as the sarcin-ricin loop, and Helix 43 of the GTPase-associated center. In order to further investigate these eEF2-ribosome interactions, we identified a series of yeast eEF2 amino acid residues based on their proximity to these functionally important rRNA elements. Based on this analysis, we constructed mutant strains to sample the full range of amino acid sidechain biochemical properties, including acidic, basic, nonpolar, and deletion (alanine) residues. These were characterized with regard to their effects on cell growth, sensitivity to ribosome-targeting antibiotics, and translational fidelity. We also biophysically characterized one mutant from each of the three main points of contact with the ribosome using CD. Collectively, our findings from these studies identified functionally critical contacts between eEF2 and the ribosome. The library of eEF2 mutants generated in this study may serve as an important resource for biophysical studies of eEF2/ribosome interactions going forward.
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Affiliation(s)
- Alexandra N Olson
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Serena Song
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Jonathan D Dinman
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA.
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42
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Altered tRNA dynamics during translocation on slippery mRNA as determinant of spontaneous ribosome frameshifting. Nat Commun 2022; 13:4231. [PMID: 35869111 PMCID: PMC9307594 DOI: 10.1038/s41467-022-31852-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 07/06/2022] [Indexed: 11/08/2022] Open
Abstract
AbstractWhen reading consecutive mRNA codons, ribosomes move by exactly one triplet at a time to synthesize a correct protein. Some mRNA tracks, called slippery sequences, are prone to ribosomal frameshifting, because the same tRNA can read both 0- and –1-frame codon. Using smFRET we show that during EF-G-catalyzed translocation on slippery sequences a fraction of ribosomes spontaneously switches from rapid, accurate translation to a slow, frameshifting-prone translocation mode where the movements of peptidyl- and deacylated tRNA become uncoupled. While deacylated tRNA translocates rapidly, pept-tRNA continues to fluctuate between chimeric and posttranslocation states, which slows down the re-locking of the small ribosomal subunit head domain. After rapid release of deacylated tRNA, pept-tRNA gains unconstrained access to the –1-frame triplet, resulting in slippage followed by recruitment of the –1-frame aa-tRNA into the A site. Our data show how altered choreography of tRNA and ribosome movements reduces the translation fidelity of ribosomes translocating in a slow mode.
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43
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Abstract
Gene-by-environment interactions play a crucial role in horizontal gene transfer by affecting how the transferred genes alter host fitness. However, how the environment modulates the fitness effect of transferred genes has not been tested systematically in an experimental study. We adapted a high-throughput technique for obtaining very precise estimates of bacterial fitness, in order to measure the fitness effects of 44 orthologs transferred from Salmonella Typhimurium to Escherichia coli in six physiologically relevant environments. We found that the fitness effects of individual genes were highly dependent on the environment, while the distributions of fitness effects across genes were not, with all tested environments resulting in distributions of same shape and spread. Furthermore, the extent to which the fitness effects of a gene varied between environments depended on the average fitness effect of that gene across all environments, with nearly neutral and nearly lethal genes having more consistent fitness effects across all environments compared to deleterious genes. Put together, our results reveal the unpredictable nature of how environmental conditions impact the fitness effects of each individual gene. At the same time, distributions of fitness effects across environments exhibit consistent features, pointing to the generalizability of factors that shape horizontal gene transfer of orthologous genes.
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Affiliation(s)
- Hande Acar Kirit
- Veterinary and Ecological Sciences, Institute of Infection, University of Liverpool, Liverpool, Merseyside, United Kingdom
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK
- Department of Anthropology, University of Oklahoma, Norman, OK
| | - Jonathan P Bollback
- Veterinary and Ecological Sciences, Institute of Infection, University of Liverpool, Liverpool, Merseyside, United Kingdom
| | - Mato Lagator
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
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44
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Zhang J, Xu C. Gene product diversity: adaptive or not? Trends Genet 2022; 38:1112-1122. [PMID: 35641344 PMCID: PMC9560964 DOI: 10.1016/j.tig.2022.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/30/2022] [Accepted: 05/03/2022] [Indexed: 01/24/2023]
Abstract
One gene does not equal one RNA or protein. The genomic revolution has revealed numerous different RNA and protein molecules that can be produced from one gene, such as circular RNAs generated by back-splicing, proteins with residues mismatching the genomic encoding because of RNA editing, and proteins extended in the C terminus via stop codon readthrough in translation. Are these diverse products results of exquisite gene regulations or imprecise biological processes? While there are cases where the gene product diversity appears beneficial, genome-scale patterns suggest that much of this diversity arises from nonadaptive, molecular errors. This finding has important implications for studying the functions of diverse gene products and for understanding the fundamental properties and evolution of cellular life.
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Affiliation(s)
- Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Chuan Xu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China
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45
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Borah C, Ali T. Genetic code noise immunity features: Degeneracy and frameshift correction. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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46
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Navarro-Betancourt JR, Cybulsky AV. The IRE1α pathway in glomerular diseases: The unfolded protein response and beyond. FRONTIERS IN MOLECULAR MEDICINE 2022; 2:971247. [PMID: 39086958 PMCID: PMC11285563 DOI: 10.3389/fmmed.2022.971247] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/07/2022] [Indexed: 08/02/2024]
Abstract
Endoplasmic reticulum (ER) function is vital for protein homeostasis ("proteostasis"). Protein misfolding in the ER of podocytes (glomerular visceral epithelial cells) is an important contributor to the pathogenesis of human glomerular diseases. ER protein misfolding causes ER stress and activates a compensatory signaling network called the unfolded protein response (UPR). Disruption of the UPR, in particular deletion of the UPR transducer, inositol-requiring enzyme 1α (IRE1α) in mouse podocytes leads to podocyte injury and albuminuria in aging, and exacerbates injury in glomerulonephritis. The UPR may interact in a coordinated manner with autophagy to relieve protein misfolding and its consequences. Recent studies have identified novel downstream targets of IRE1α, which provide new mechanistic insights into proteostatic pathways. Novel pathways of IRE1α signaling involve reticulophagy, mitochondria, metabolism, vesicular trafficking, microRNAs, and others. Mechanism-based therapies for glomerulopathies are limited, and development of non-invasive ER stress biomarkers, as well as targeting ER stress with pharmacological compounds may represent a therapeutic opportunity for preventing or attenuating progression of chronic kidney disease.
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Affiliation(s)
| | - Andrey V. Cybulsky
- Department of Medicine, McGill University Health Centre Research Institute, McGill University, Montreal, QC, Canada
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47
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Shibai A, Kotani H, Sakata N, Furusawa C, Tsuru S. Purifying selection enduringly acts on the sequence evolution of highly expressed proteins in Escherichia coli. G3 GENES|GENOMES|GENETICS 2022; 12:6694045. [PMID: 36073932 PMCID: PMC9635659 DOI: 10.1093/g3journal/jkac235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/27/2022] [Indexed: 11/17/2022]
Abstract
The evolutionary speed of a protein sequence is constrained by its expression level, with highly expressed proteins evolving relatively slowly. This negative correlation between expression levels and evolutionary rates (known as the E–R anticorrelation) has already been widely observed in past macroevolution between species from bacteria to animals. However, it remains unclear whether this seemingly general law also governs recent evolution, including past and de novo, within a species. However, the advent of genomic sequencing and high-throughput phenotyping, particularly for bacteria, has revealed fundamental gaps between the 2 evolutionary processes and has provided empirical data opposing the possible underlying mechanisms which are widely believed. These conflicts raise questions about the generalization of the E–R anticorrelation and the relevance of plausible mechanisms. To explore the ubiquitous impact of expression levels on molecular evolution and test the relevance of the possible underlying mechanisms, we analyzed the genome sequences of 99 strains of Escherichia coli for evolution within species in nature. We also analyzed genomic mutations accumulated under laboratory conditions as a model of de novo evolution within species. Here, we show that E–R anticorrelation is significant in both past and de novo evolution within species in E. coli. Our data also confirmed ongoing purifying selection on highly expressed genes. Ongoing selection included codon-level purifying selection, supporting the relevance of the underlying mechanisms. However, the impact of codon-level purifying selection on the constraints in evolution within species might be smaller than previously expected from evolution between species.
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Affiliation(s)
- Atsushi Shibai
- Center for Biosystems Dynamics Research (BDR), RIKEN , Osaka 565-0874, Japan
| | - Hazuki Kotani
- Center for Biosystems Dynamics Research (BDR), RIKEN , Osaka 565-0874, Japan
| | - Natsue Sakata
- Center for Biosystems Dynamics Research (BDR), RIKEN , Osaka 565-0874, Japan
| | - Chikara Furusawa
- Center for Biosystems Dynamics Research (BDR), RIKEN , Osaka 565-0874, Japan
- Universal Biology Institute, School of Science, The University of Tokyo , Tokyo 113-0033, Japan
| | - Saburo Tsuru
- Universal Biology Institute, School of Science, The University of Tokyo , Tokyo 113-0033, Japan
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48
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Romero Romero ML, Landerer C, Poehls J, Toth‐Petroczy A. Phenotypic mutations contribute to protein diversity and shape protein evolution. Protein Sci 2022; 31:e4397. [PMID: 36040266 PMCID: PMC9375231 DOI: 10.1002/pro.4397] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/14/2022] [Accepted: 07/04/2022] [Indexed: 11/16/2022]
Abstract
Errors in DNA replication generate genetic mutations, while errors in transcription and translation lead to phenotypic mutations. Phenotypic mutations are orders of magnitude more frequent than genetic ones, yet they are less understood. Here, we review the types of phenotypic mutations, their quantifications, and their role in protein evolution and disease. The diversity generated by phenotypic mutation can facilitate adaptive evolution. Indeed, phenotypic mutations, such as ribosomal frameshift and stop codon readthrough, sometimes serve to regulate protein expression and function. Phenotypic mutations have often been linked to fitness decrease and diseases. Thus, understanding the protein heterogeneity and phenotypic diversity caused by phenotypic mutations will advance our understanding of protein evolution and have implications on human health and diseases.
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Affiliation(s)
- Maria Luisa Romero Romero
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Center for Systems Biology DresdenDresdenGermany
| | - Cedric Landerer
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Center for Systems Biology DresdenDresdenGermany
| | - Jonas Poehls
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Center for Systems Biology DresdenDresdenGermany
| | - Agnes Toth‐Petroczy
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Center for Systems Biology DresdenDresdenGermany
- Cluster of Excellence Physics of LifeTU DresdenDresdenGermany
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49
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Tilk S, Tkachenko S, Curtis C, Petrov DA, McFarland CD. Most cancers carry a substantial deleterious load due to Hill-Robertson interference. eLife 2022; 11:67790. [PMID: 36047771 PMCID: PMC9499534 DOI: 10.7554/elife.67790] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Cancer genomes exhibit surprisingly weak signatures of negative selection1,2. This may be because selective pressures are relaxed or because genome-wide linkage prevents deleterious mutations from being removed (Hill-Robertson interference)3. By stratifying tumors by their genome-wide mutational burden, we observe negative selection (dN/dS ~ 0.56) in low mutational burden tumors, while remaining cancers exhibit dN/dS ratios ~1. This suggests that most tumors do not remove deleterious passengers. To buffer against deleterious passengers, tumors upregulate heat shock pathways as their mutational burden increases. Finally, evolutionary modeling finds that Hill-Robertson interference alone can reproduce patterns of attenuated selection and estimates the total fitness cost of passengers to be 46% per cell on average. Collectively, our findings suggest that the lack of observed negative selection in most tumors is not due to relaxed selective pressures, but rather the inability of selection to remove deleterious mutations in the presence of genome-wide linkage.
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Affiliation(s)
- Susanne Tilk
- Department of Biology, Stanford University, Stanford, United States
| | - Svyatoslav Tkachenko
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, United States
| | - Christina Curtis
- Department of Genetics, Stanford University, Stanford, United States
| | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, United States
| | - Christopher D McFarland
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, United States
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50
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Enfuvirtide biosynthesis in thermostable chaperone-based fusion. BIOTECHNOLOGY REPORTS 2022; 35:e00734. [PMID: 35646620 PMCID: PMC9130503 DOI: 10.1016/j.btre.2022.e00734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 04/13/2022] [Accepted: 04/20/2022] [Indexed: 11/21/2022]
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