1
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Ousalem F, Ngo S, Oïffer T, Omairi-Nasser A, Hamon M, Monlezun L, Boël G. Global regulation via modulation of ribosome pausing by the ABC-F protein EttA. Nat Commun 2024; 15:6314. [PMID: 39060293 PMCID: PMC11282234 DOI: 10.1038/s41467-024-50627-z] [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: 01/26/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
Having multiple rounds of translation of the same mRNA creates dynamic complexities along with opportunities for regulation related to ribosome pausing and stalling at specific sequences. Yet, mechanisms controlling these critical processes and the principles guiding their evolution remain poorly understood. Through genetic, genomic, physiological, and biochemical approaches, we demonstrate that regulating ribosome pausing at specific amino acid sequences can produce ~2-fold changes in protein expression levels which strongly influence cell growth and therefore evolutionary fitness. We demonstrate, both in vivo and in vitro, that the ABC-F protein EttA directly controls the translation of mRNAs coding for a subset of enzymes in the tricarboxylic acid (TCA) cycle and its glyoxylate shunt, which modulates growth in some chemical environments. EttA also modulates expression of specific proteins involved in metabolically related physiological and stress-response pathways. These regulatory activities are mediated by EttA rescuing ribosomes paused at specific patterns of negatively charged residues within the first 30 amino acids of nascent proteins. We thus establish a unique global regulatory paradigm based on sequence-specific modulation of translational pausing.
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Affiliation(s)
- Farès Ousalem
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
- Biomarqueurs et nouvelles cibles thérapeutiques en oncologie, INSERM U981, Université Paris Saclay, Institut de Cancérologie Gustave Roussy, Villejuif Cedex, France
| | - Saravuth Ngo
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
| | - Thomas Oïffer
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
| | - Amin Omairi-Nasser
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
| | - Marion Hamon
- CNRS, Institut de Biologie Physico-Chimique, Plateforme de Protéomique, FR550, Paris, France
| | - Laura Monlezun
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
| | - Grégory Boël
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, Paris, France.
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2
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Hou M, Fan W, Zhong D, Dai X, Wang Q, Liu W, Li S. Ribosome Pausing Negatively Regulates Protein Translation in Maize Seedlings during Dark-to-Light Transitions. Int J Mol Sci 2024; 25:7985. [PMID: 39063227 PMCID: PMC11277263 DOI: 10.3390/ijms25147985] [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: 06/14/2024] [Revised: 07/16/2024] [Accepted: 07/19/2024] [Indexed: 07/28/2024] Open
Abstract
Regulation of translation is a crucial step in gene expression. Developmental signals and environmental stimuli dynamically regulate translation via upstream small open reading frames (uORFs) and ribosome pausing. Recent studies have revealed many plant genes that are specifically regulated by uORF translation following changes in growth conditions, but ribosome-pausing events are less well understood. In this study, we performed ribosome profiling (Ribo-seq) of etiolated maize (Zea mays) seedlings exposed to light for different durations, revealing hundreds of genes specifically regulated at the translation level during the early period of light exposure. We identified over 400 ribosome-pausing events in the dark that were rapidly released after illumination. These results suggested that ribosome pausing negatively regulates translation from specific genes, a conclusion that was supported by a non-targeted proteomics analysis. Importantly, we identified a conserved nucleotide motif downstream of the pausing sites. Our results elucidate the role of ribosome pausing in the control of gene expression in plants; the identification of the cis-element at the pausing sites provides insight into the mechanisms behind translation regulation and potential targets for artificial control of plant translation.
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Affiliation(s)
- Mingming Hou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (M.H.); (W.F.); (Q.W.)
| | - Wei Fan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (M.H.); (W.F.); (Q.W.)
| | - Deyi Zhong
- Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China;
| | - Xing Dai
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China;
| | - Quan Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (M.H.); (W.F.); (Q.W.)
| | - Wanfei Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (M.H.); (W.F.); (Q.W.)
| | - Shengben Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (M.H.); (W.F.); (Q.W.)
- Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China;
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3
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Brischigliaro M, Krüger A, Moran JC, Antonicka H, Ahn A, Shoubridge EA, Rorbach J, Barrientos A. The human mitochondrial translation factor TACO1 alleviates mitoribosome stalling at polyproline stretches. Nucleic Acids Res 2024:gkae645. [PMID: 39036954 DOI: 10.1093/nar/gkae645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 07/04/2024] [Accepted: 07/09/2024] [Indexed: 07/23/2024] Open
Abstract
The prokaryotic translation elongation factor P (EF-P) and the eukaryotic/archaeal counterparts eIF5A/aIF5A are proteins that serve a crucial role in mitigating ribosomal stalling during the translation of specific sequences, notably those containing consecutive proline residues (1,2). Although mitochondrial DNA-encoded proteins synthesized by mitochondrial ribosomes also contain polyproline stretches, an EF-P/eIF5A mitochondrial counterpart remains unidentified. Here, we show that the missing factor is TACO1, a protein causative of a juvenile form of neurodegenerative Leigh's syndrome associated with cytochrome c oxidase deficiency, until now believed to be a translational activator of COX1 mRNA. By using a combination of metabolic labeling, puromycin release and mitoribosome profiling experiments, we show that TACO1 is required for the rapid synthesis of the polyproline-rich COX1 and COX3 cytochrome c oxidase subunits, while its requirement is negligible for other mitochondrial DNA-encoded proteins. In agreement with a role in translation efficiency regulation, we show that TACO1 cooperates with the N-terminal extension of the large ribosomal subunit bL27m to provide stability to the peptidyl-transferase center during elongation. This study illuminates the translation elongation dynamics within human mitochondria, a TACO1-mediated biological mechanism in place to mitigate mitoribosome stalling at polyproline stretches during protein synthesis, and the pathological implications of its malfunction.
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Affiliation(s)
- Michele Brischigliaro
- Department of Neurology, University of Miami Miller School of Medicine, 1600 NW 10th Ave., Miami, FL 33136, USA
| | - Annika Krüger
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Max Planck Institute Biology of Ageing-Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - J Conor Moran
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, 1600 NW 10th Ave., Miami, FL 33136, USA
- The University of Miami Medical Scientist Training Program (MSTP), 1600 NW 10th Ave.,Miami, FL33136, USA
| | - Hana Antonicka
- The Neuro and Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Ahram Ahn
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, 1600 NW 10th Ave., Miami, FL 33136, USA
| | - Eric A Shoubridge
- The Neuro and Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Joanna Rorbach
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Max Planck Institute Biology of Ageing-Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Antoni Barrientos
- Department of Neurology, University of Miami Miller School of Medicine, 1600 NW 10th Ave., Miami, FL 33136, USA
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, 1600 NW 10th Ave., Miami, FL 33136, USA
- The Miami Veterans Affairs (VA) Medical System. 1201 NW 16th St, Miami, FL-33125, USA
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4
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Chen Y, Gavriliuc M, Zeng Y, Xu S, Wang Y. Allosteric Effects of EF-G Domain I Mutations Inducing Ribosome Frameshifting Revealed by Multiplexed Force Spectroscopy. Chembiochem 2024:e202400130. [PMID: 38923096 DOI: 10.1002/cbic.202400130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 06/25/2024] [Accepted: 06/25/2024] [Indexed: 06/28/2024]
Abstract
Ribosome translocation catalyzed by elongation factor G (EF-G) is a critical step in protein synthesis where the ribosome typically moves along the mRNA by three nucleotides at each step. To investigate the mechanism of EF-G catalysis, it is essential to precisely resolve the ribosome motion at both ends of the mRNA, which, to our best knowledge, is only achieved with the magnetic-based force spectroscopy developed by our groups. Here, we introduce a novel multiplexed force spectroscopy technique that, for the first time, offers single-nucleotide resolution for multiple samples. This technique combines multiple acoustic force generators with the smallest atomic magnetometer designed for biological research. Utilizing this technique, we demonstrate that mutating EF-G at the GTP binding pocket results in the ribosome moving only two nucleotides on both ends of the mRNA, thereby compromising ribosome translocation. This finding suggests a direct link between GTP hydrolysis and ribosome translocation. Our results not only provide mechanistic insights into the role of GTP binding pocket but also illuminate how allosteric mutations can manipulate translocation. We anticipate broader applications of our technique in the ribosome field, leveraging its high efficiency and single-nucleotide resolution.
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Affiliation(s)
- Yanjun Chen
- Department of Chemistry, University of Houston, Houston, TX, 77204, USA E-mails
| | - Miriam Gavriliuc
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204, USA
| | - Yi Zeng
- Department of Chemistry, University of Houston, Houston, TX, 77204, USA E-mails
| | - Shoujun Xu
- Department of Chemistry, University of Houston, Houston, TX, 77204, USA E-mails
| | - Yuhong Wang
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204, USA
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5
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Weiss JL, Decker JC, Bolano A, Krahn N. Tuning tRNAs for improved translation. Front Genet 2024; 15:1436860. [PMID: 38983271 PMCID: PMC11231383 DOI: 10.3389/fgene.2024.1436860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 06/06/2024] [Indexed: 07/11/2024] Open
Abstract
Transfer RNAs have been extensively explored as the molecules that translate the genetic code into proteins. At this interface of genetics and biochemistry, tRNAs direct the efficiency of every major step of translation by interacting with a multitude of binding partners. However, due to the variability of tRNA sequences and the abundance of diverse post-transcriptional modifications, a guidebook linking tRNA sequences to specific translational outcomes has yet to be elucidated. Here, we review substantial efforts that have collectively uncovered tRNA engineering principles that can be used as a guide for the tuning of translation fidelity. These principles have allowed for the development of basic research, expansion of the genetic code with non-canonical amino acids, and tRNA therapeutics.
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Affiliation(s)
- Joshua L Weiss
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - J C Decker
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Ariadna Bolano
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Natalie Krahn
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
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6
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Hong HR, Prince CR, Tetreault DD, Wu L, Feaga HA. YfmR is a translation factor that prevents ribosome stalling and cell death in the absence of EF-P. Proc Natl Acad Sci U S A 2024; 121:e2314437121. [PMID: 38349882 PMCID: PMC10895253 DOI: 10.1073/pnas.2314437121] [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: 08/21/2023] [Accepted: 01/09/2024] [Indexed: 02/15/2024] Open
Abstract
Protein synthesis is performed by the ribosome and a host of highly conserved elongation factors. Elongation factor P (EF-P) prevents ribosome stalling at difficult-to-translate sequences, such as polyproline tracts. In bacteria, phenotypes associated with efp deletion range from modest to lethal, suggesting that some species encode an additional translation factor that has similar function to EF-P. Here we identify YfmR as a translation factor that is essential in the absence of EF-P in Bacillus subtilis. YfmR is an ABCF ATPase that is closely related to both Uup and EttA, ABCFs that bind the ribosomal E-site and are conserved in more than 50% of bacterial genomes. We show that YfmR associates with actively translating ribosomes and that depleting YfmR from Δefp cells causes severe ribosome stalling at a polyproline tract in vivo. YfmR depletion from Δefp cells was lethal and caused reduced levels of actively translating ribosomes. Our results therefore identify YfmR as an important translation factor that is essential in B. subtilis in the absence of EF-P.
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Affiliation(s)
- Hye-Rim Hong
- Department of Microbiology, Cornell University, Ithaca, NY14853
| | | | | | - Letian Wu
- Department of Microbiology, Cornell University, Ithaca, NY14853
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7
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Vazulka S, Schiavinato M, Tauer C, Wagenknecht M, Cserjan-Puschmann M, Striedner G. RNA-seq reveals multifaceted gene expression response to Fab production in Escherichia coli fed-batch processes with particular focus on ribosome stalling. Microb Cell Fact 2024; 23:14. [PMID: 38183013 PMCID: PMC10768439 DOI: 10.1186/s12934-023-02278-w] [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: 10/12/2023] [Accepted: 12/18/2023] [Indexed: 01/07/2024] Open
Abstract
BACKGROUND Escherichia coli is a cost-effective expression system for production of antibody fragments like Fabs. Various yield improvement strategies have been applied, however, Fabs remain challenging to produce. This study aimed to characterize the gene expression response of commonly used E. coli strains BL21(DE3) and HMS174(DE3) to periplasmic Fab expression using RNA sequencing (RNA-seq). Two Fabs, Fabx and FTN2, fused to a post-translational translocation signal sequence, were produced in carbon-limited fed-batch cultivations. RESULTS Production of Fabx impeded cell growth substantially stronger than FTN2 and yields of both Fabs differed considerably. The most noticeable, common changes in Fab-producing cells suggested by our RNA-seq data concern the cell envelope. The Cpx and Psp stress responses, both connected to inner membrane integrity, were activated, presumably by recombinant protein aggregation and impairment of the Sec translocon. The data additionally suggest changes in lipopolysaccharide synthesis, adjustment of membrane permeability, and peptidoglycan maturation and remodeling. Moreover, all Fab-producing strains showed depletion of Mg2+, indicated by activation of the PhoQP two-component signal transduction system during the early stage and sulfur and phosphate starvation during the later stage of the process. Furthermore, our data revealed ribosome stalling, caused by the Fabx amino acid sequence, as a contributor to low Fabx yields. Increased Fabx yields were obtained by a site-specific amino acid exchange replacing the stalling sequence. Contrary to expectations, cell growth was not impacted by presence or removal of the stalling sequence. Considering ribosome rescue is a conserved mechanism, the substantial differences observed in gene expression between BL21(DE3) and HMS174(DE3) in response to ribosome stalling on the recombinant mRNA were surprising. CONCLUSIONS Through characterization of the gene expression response to Fab production under industrially relevant cultivation conditions, we identified potential cell engineering targets. Thereby, we hope to enable rational approaches to improve cell fitness and Fab yields. Furthermore, we highlight ribosome stalling caused by the amino acid sequence of the recombinant protein as a possible challenge during recombinant protein production.
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Affiliation(s)
- Sophie Vazulka
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Matteo Schiavinato
- Department of Biotechnology, Institute of Computational Biology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Christopher Tauer
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Martin Wagenknecht
- Boehringer Ingelheim RCV, GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, A-1120, Vienna, Austria
| | - Monika Cserjan-Puschmann
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.
| | - Gerald Striedner
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
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8
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Kohl MP, Chane-Woon-Ming B, Bahena-Ceron R, Jaramillo-Ponce J, Antoine L, Herrgott L, Romby P, Marzi S. Ribosome Profiling Methods Adapted to the Study of RNA-Dependent Translation Regulation in Staphylococcus aureus. Methods Mol Biol 2024; 2741:73-100. [PMID: 38217649 DOI: 10.1007/978-1-0716-3565-0_5] [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] [Indexed: 01/15/2024]
Abstract
Noncoding RNAs, including regulatory RNAs (sRNAs), are instrumental in regulating gene expression in pathogenic bacteria, allowing them to adapt to various stresses encountered in their host environments. Staphylococcus aureus is a well-studied model for RNA-mediated regulation of virulence and pathogenicity, with sRNAs playing significant roles in shaping S. aureus interactions with human and animal hosts. By modulating the translation and/or stability of target mRNAs, sRNAs regulate the synthesis of virulence factors and regulatory proteins required for pathogenesis. Moreover, perturbation of the levels of RNA modifications in two other classes of noncoding RNAs, rRNAs, and tRNAs, has been proposed to contribute to stress adaptation. However, the study of how these various factors affect translation regulation has often been restricted to specific genes, using in vivo reporters and/or in vitro translation systems. Genome-wide sequencing approaches offer novel perspectives for studying RNA-dependent regulation. In particular, ribosome profiling methods provide a powerful resource for characterizing the overall landscape of translational regulation, contributing to a better understanding of S. aureus physiopathology. Here, we describe protocols that we have adapted to perform ribosome profiling in S. aureus.
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Affiliation(s)
- Maximilian P Kohl
- Architecture et Réactivité de l'ARN, CNRS 9002, Université de Strasbourg, Strasbourg, France
| | | | - Roberto Bahena-Ceron
- Architecture et Réactivité de l'ARN, CNRS 9002, Université de Strasbourg, Strasbourg, France
| | - Jose Jaramillo-Ponce
- Architecture et Réactivité de l'ARN, CNRS 9002, Université de Strasbourg, Strasbourg, France
| | - Laura Antoine
- Architecture et Réactivité de l'ARN, CNRS 9002, Université de Strasbourg, Strasbourg, France
| | - Lucas Herrgott
- Architecture et Réactivité de l'ARN, CNRS 9002, Université de Strasbourg, Strasbourg, France
| | - Pascale Romby
- Architecture et Réactivité de l'ARN, CNRS 9002, Université de Strasbourg, Strasbourg, France
| | - Stefano Marzi
- Architecture et Réactivité de l'ARN, CNRS 9002, Université de Strasbourg, Strasbourg, France.
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9
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Bryant OJ, Lastovka F, Powell J, Chung BYW. The distinct translational landscapes of gram-negative Salmonella and gram-positive Listeria. Nat Commun 2023; 14:8167. [PMID: 38071303 PMCID: PMC10710512 DOI: 10.1038/s41467-023-43759-1] [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: 06/04/2023] [Accepted: 11/17/2023] [Indexed: 12/18/2023] Open
Abstract
Translational control in pathogenic bacteria is fundamental to gene expression and affects virulence and other infection phenotypes. We used an enhanced ribosome profiling protocol coupled with parallel transcriptomics to capture accurately the global translatome of two evolutionarily distant pathogenic bacteria-the Gram-negative bacterium Salmonella and the Gram-positive bacterium Listeria. We find that the two bacteria use different mechanisms to translationally regulate protein synthesis. In Salmonella, in addition to the expected correlation between translational efficiency and cis-regulatory features such as Shine-Dalgarno (SD) strength and RNA secondary structure around the initiation codon, our data reveal an effect of the 2nd and 3rd codons, where the presence of tandem lysine codons (AAA-AAA) enhances translation in both Salmonella and E. coli. Strikingly, none of these features are seen in efficiently translated Listeria transcripts. Instead, approximately 20% of efficiently translated Listeria genes exhibit 70 S footprints seven nt upstream of the authentic start codon, suggesting that these genes may be subject to a novel translational initiation mechanism. Our results show that SD strength is not a direct hallmark of translational efficiency in all bacteria. Instead, Listeria has evolved additional mechanisms to control gene expression level that are distinct from those utilised by Salmonella and E. coli.
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Affiliation(s)
- Owain J Bryant
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
- Centre for Structural Biology, National Cancer Institute, 21702, Frederick, MD, USA
| | - Filip Lastovka
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - Jessica Powell
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - Betty Y-W Chung
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK.
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10
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Hong HR, Prince CR, Tetreault DD, Wu L, Feaga HA. YfmR is a translation factor that prevents ribosome stalling and cell death in the absence of EF-P. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.04.552005. [PMID: 37577462 PMCID: PMC10418254 DOI: 10.1101/2023.08.04.552005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Protein synthesis is performed by the ribosome and a host of highly conserved elongation factors. Elongation factor P (EF-P) prevents ribosome stalling at difficult-to-translate sequences, particularly polyproline tracts. In bacteria, phenotypes associated with efp deletion range from modest to lethal, suggesting that some species encode an additional translation factor that has similar function to EF-P. Here we identify YfmR as a translation factor that is essential in the absence of EF-P in B. subtilis. YfmR is an ABCF ATPase that is closely related to both Uup and EttA, ABCFs that bind the ribosomal E-site and are conserved in more than 50% of bacterial genomes. We show that YfmR associates with actively translating ribosomes and that depleting YfmR from Δefp cells causes severe ribosome stalling at a polyproline tract in vivo. YfmR depletion from Δefp cells was lethal, and caused reduced levels of actively translating ribosomes. Our results therefore identify YfmR as an important translation factor that is essential in B. subtilis in the absence of EF-P.
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Affiliation(s)
- Hye-Rim Hong
- Department of Microbiology, Cornell University, Ithaca, NY 14853
| | | | | | - Letian Wu
- Department of Microbiology, Cornell University, Ithaca, NY 14853
| | - Heather A. Feaga
- Department of Microbiology, Cornell University, Ithaca, NY 14853
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11
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Bian B, Kumagai T, Saito Y. VeloPro: A pipeline integrating Ribo-seq and AlphaFold deciphers association patterns between translation velocity and protein structure features. IMETA 2023; 2:e148. [PMID: 38868219 PMCID: PMC10989810 DOI: 10.1002/imt2.148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 10/22/2023] [Indexed: 06/14/2024]
Abstract
VeloPro integrates Ribo-seq data and AlphaFold2-predicted 3D protein structure information for characterization of the association patterns between translation velocity and many protein structure features in prokaryotic and eukaryotic organisms across different taxonomical clades such as bacteria, fungi, protozoa, nematode, plants, insect, and mammals. We illustrated that association patterns between translation velocity and protein structure features differ across organisms, partially reflecting their taxonomical relationship.
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Affiliation(s)
- Bian Bian
- Department of Computational Biology and Medical SciencesGraduate School of Frontier Sciences, The University of TokyoKashiwaJapan
- Artificial Intelligence Research CenterNational Institute of Advanced Industrial Science and Technology (AIST)Koto‐kuJapan
| | | | - Yutaka Saito
- Department of Computational Biology and Medical SciencesGraduate School of Frontier Sciences, The University of TokyoKashiwaJapan
- Artificial Intelligence Research CenterNational Institute of Advanced Industrial Science and Technology (AIST)Koto‐kuJapan
- AIST‐Waseda University Computational Bio Big‐Data Open Innovation Laboratory (CBBD‐OIL)Shinjuku‐kuJapan
- Department of Data Science, School of Frontier EngineeringKitasato UniversitySagamiharaJapan
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12
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Daskalova SM, Dedkova LM, Maini R, Talukder P, Bai X, Chowdhury SR, Zhang C, Nangreave RC, Hecht SM. Elongation Factor P Modulates the Incorporation of Structurally Diverse Noncanonical Amino Acids into Escherichia coli Dihydrofolate Reductase. J Am Chem Soc 2023; 145:23600-23608. [PMID: 37871253 PMCID: PMC10762953 DOI: 10.1021/jacs.3c07524] [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] [Indexed: 10/25/2023]
Abstract
The introduction of noncanonical amino acids into proteins and peptides has been of great interest for many years and has facilitated the detailed study of peptide/protein structure and mechanism. In addition to numerous nonproteinogenic α-l-amino acids, bacterial ribosome modification has provided the wherewithal to enable the synthesis of peptides and proteins with a much greater range of structural diversity, as has the use of endogenous bacterial proteins in reconstituted protein synthesizing systems. In a recent report, elongation factor P (EF-P), putatively essential for enabling the incorporation of contiguous proline residues into proteins, was shown to facilitate the introduction of an N-methylated amino acid in addition to proline. This finding prompted us to investigate the properties of this protein factor with a broad variety of structurally diverse amino acid analogues using an optimized suppressor tRNAPro that we designed. While these analogues can generally be incorporated into proteins only in systems containing modified ribosomes specifically selected for their incorporation, we found that EF-P could significantly enhance their incorporation into model protein dihydrofolate reductase using wild-type ribosomes. Plausibly, the increased yields observed in the presence of structurally diverse amino acid analogues may result from the formation of a stabilized ribosomal complex in the presence of EF-P that provides more favorable conditions for peptide bond formation. This finding should enable the facile incorporation of a much broader structural variety of amino acid analogues into proteins and peptides using native ribosomes.
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Affiliation(s)
- Sasha M Daskalova
- Biodesign Center for Bioenergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Larisa M Dedkova
- Biodesign Center for Bioenergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Rumit Maini
- Biodesign Center for Bioenergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Poulami Talukder
- Biodesign Center for Bioenergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Xiaoguang Bai
- Biodesign Center for Bioenergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Sandipan Roy Chowdhury
- Biodesign Center for Bioenergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Chao Zhang
- Biodesign Center for Bioenergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Ryan C Nangreave
- Biodesign Center for Bioenergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Sidney M Hecht
- Biodesign Center for Bioenergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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13
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Elias RD, Zhu Y, Su Q, Ghirlando R, Zhang J, Deshmukh L. Reversible phase separation of ESCRT protein ALIX through tyrosine phosphorylation. SCIENCE ADVANCES 2023; 9:eadg3913. [PMID: 37450591 PMCID: PMC10348681 DOI: 10.1126/sciadv.adg3913] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 06/14/2023] [Indexed: 07/18/2023]
Abstract
Cytokinetic abscission, the last step of cell division, is regulated by the ESCRT machinery. In response to mitotic errors, ESCRT proteins, namely, ALIX, CHMP4B, and CHMP4C, accumulate in the cytosolic compartments termed "abscission checkpoint bodies" (ACBs) to delay abscission and prevent tumorigenesis. ALIX contributes to the biogenesis and stability of ACBs via an unknown mechanism. We show that ALIX phase separates into nondynamic condensates in vitro and in vivo, mediated by the amyloidogenic portion of its proline-rich domain. ALIX condensates confined CHMP4 paralogs in vitro. These condensates dissolved and reformed upon reversible tyrosine phosphorylation of ALIX, mediated by Src kinase and PTP1B, and sequestration of CHMP4C altered their Src-mediated dissolution. NMR analysis revealed how ALIX triggers the activation of CHMP4 proteins, which is required for successful abscission. These results implicate ALIX's phase separation in the modulation of ACBs. This study also highlights how posttranslational modifications can control protein phase separation.
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Affiliation(s)
- Ruben D. Elias
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yingqi Zhu
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Qi Su
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jin Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lalit Deshmukh
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
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14
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Choi H, Covert MW. Whole-cell modeling of E. coli confirms that in vitro tRNA aminoacylation measurements are insufficient to support cell growth and predicts a positive feedback mechanism regulating arginine biosynthesis. Nucleic Acids Res 2023; 51:5911-5930. [PMID: 37224536 PMCID: PMC10325894 DOI: 10.1093/nar/gkad435] [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: 02/02/2023] [Revised: 05/04/2023] [Accepted: 05/09/2023] [Indexed: 05/26/2023] Open
Abstract
In Escherichia coli, inconsistencies between in vitro tRNA aminoacylation measurements and in vivo protein synthesis demands were postulated almost 40 years ago, but have proven difficult to confirm. Whole-cell modeling can test whether a cell behaves in a physiologically correct manner when parameterized with in vitro measurements by providing a holistic representation of cellular processes in vivo. Here, a mechanistic model of tRNA aminoacylation, codon-based polypeptide elongation, and N-terminal methionine cleavage was incorporated into a developing whole-cell model of E. coli. Subsequent analysis confirmed the insufficiency of aminoacyl-tRNA synthetase kinetic measurements for cellular proteome maintenance, and estimated aminoacyl-tRNA synthetase kcats that were on average 7.6-fold higher. Simulating cell growth with perturbed kcats demonstrated the global impact of these in vitro measurements on cellular phenotypes. For example, an insufficient kcat for HisRS caused protein synthesis to be less robust to the natural variability in aminoacyl-tRNA synthetase expression in single cells. More surprisingly, insufficient ArgRS activity led to catastrophic impacts on arginine biosynthesis due to underexpressed N-acetylglutamate synthase, where translation depends on repeated CGG codons. Overall, the expanded E. coli model deepens understanding of how translation operates in an in vivo context.
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Affiliation(s)
- Heejo Choi
- Department of Bioengineering, Stanford University, 443 Via Ortega, Stanford, CA 94305, USA
| | - Markus W Covert
- Department of Bioengineering, Stanford University, 443 Via Ortega, Stanford, CA 94305, USA
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15
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Abstract
The universally conserved protein elongation factor P (EF-P) facilitates translation at amino acids that form peptide bonds with low efficiency, particularly polyproline tracts. Despite its wide conservation, it is not essential in most bacteria and its physiological role remains unclear. Here, we show that EF-P affects the process of sporulation initiation in the bacterium Bacillus subtilis. We observe that the lack of EF-P delays expression of sporulation-specific genes. Using ribosome profiling, we observe that expression of spo0A, encoding a transcription factor that functions as the master regulator of sporulation, is lower in a Δefp strain than the wild type. Ectopic expression of Spo0A rescues the sporulation initiation phenotype, indicating that reduced spo0A expression explains the sporulation defect in Δefp cells. Since Spo0A is the earliest sporulation transcription factor, these data suggest that sporulation initiation can be delayed when protein synthesis is impaired. IMPORTANCE Elongation factor P (EF-P) is a universally conserved translation factor that prevents ribosome stalling at amino acids that form peptide bonds with low efficiency, particularly polyproline tracts. Phenotypes associated with EF-P deletion are pleiotropic, and the mechanistic basis underlying many of these phenotypes is unclear. Here, we show that the absence of EF-P affects the ability of B. subtilis to initiate sporulation by preventing normal expression of Spo0A, the key transcriptional regulator of this process. These data illustrate a mechanism that accounts for the sporulation delay and further suggest that cells are capable of sensing translation stress before committing to sporulation.
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16
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Richards J, Belasco JG. Graded impact of obstacle size on scanning by RNase E. Nucleic Acids Res 2023; 51:1364-1374. [PMID: 36620905 PMCID: PMC9943677 DOI: 10.1093/nar/gkac1242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/11/2022] [Accepted: 12/13/2022] [Indexed: 01/10/2023] Open
Abstract
In countless bacterial species, the lifetimes of most mRNAs are controlled by the regulatory endonuclease RNase E, which preferentially degrades RNAs bearing a 5' monophosphate and locates cleavage sites within them by scanning linearly from the 5' terminus along single-stranded regions. Consequently, its rate of cleavage at distal sites is governed by any obstacles that it may encounter along the way, such as bound proteins or ribosomes or base pairing that is coaxial with the path traversed by this enzyme. Here, we report that the protection afforded by such obstacles is dependent on the size and persistence of the structural discontinuities they create, whereas the molecular composition of obstacles to scanning is of comparatively little consequence. Over a broad range of sizes, incrementally larger discontinuities are incrementally more protective, with corresponding effects on mRNA stability. The graded impact of such obstacles suggests possible explanations for why their effect on scanning is not an all-or-none phenomenon dependent simply on whether the size of the resulting discontinuity exceeds the step length of RNase E.
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Affiliation(s)
- Jamie Richards
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA,Department of Microbiology, New York University School of Medicine, 430 E. 29th Street, New York, NY 10016, USA
| | - Joel G Belasco
- To whom correspondence should be addressed. Tel: +1 212 263 5409;
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17
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Zhang D, Li SHJ, King CG, Wingreen NS, Gitai Z, Li Z. Global and gene-specific translational regulation in Escherichia coli across different conditions. PLoS Comput Biol 2022; 18:e1010641. [PMID: 36264977 PMCID: PMC9624429 DOI: 10.1371/journal.pcbi.1010641] [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: 04/27/2022] [Revised: 11/01/2022] [Accepted: 10/06/2022] [Indexed: 11/05/2022] Open
Abstract
How well mRNA transcript levels represent protein abundances has been a controversial issue. Particularly across different environments, correlations between mRNA and protein exhibit remarkable variability from gene to gene. Translational regulation is likely to be one of the key factors contributing to mismatches between mRNA level and protein abundance in bacteria. Here, we quantified genome-wide transcriptome and relative translation efficiency (RTE) under 12 different conditions in Escherichia coli. By quantifying the mRNA-RTE correlation both across genes and across conditions, we uncovered a diversity of gene-specific translational regulations, cooperating with transcriptional regulations, in response to carbon (C), nitrogen (N), and phosphate (P) limitations. Intriguingly, we found that many genes regulating translation are themselves subject to translational regulation, suggesting possible feedbacks. Furthermore, a random forest model suggests that codon usage partially predicts a gene's cross-condition variability in translation efficiency; such cross-condition variability tends to be an inherent quality of a gene, independent of the specific nutrient limitations. These findings broaden the understanding of translational regulation under different environments and provide novel strategies for the control of translation in synthetic biology. In addition, our data offers a resource for future multi-omics studies.
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Affiliation(s)
- Di Zhang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Sophia Hsin-Jung Li
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Institute of Bioengineering, School of Life Sciences, Swiss Federal Institute of Technology Lausanne, Lausanne, Switzerland
- Global Health Institute, School of Life Sciences, Swiss Federal Institute of Technology Lausanne, Lausanne, Switzerland
| | - Christopher G. King
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Ned S. Wingreen
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- * E-mail: (NSW); (ZG); (ZL)
| | - Zemer Gitai
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- * E-mail: (NSW); (ZG); (ZL)
| | - Zhiyuan Li
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- * E-mail: (NSW); (ZG); (ZL)
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18
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Favate JS, Liang S, Cope AL, Yadavalli SS, Shah P. The landscape of transcriptional and translational changes over 22 years of bacterial adaptation. eLife 2022; 11:e81979. [PMID: 36214449 PMCID: PMC9645810 DOI: 10.7554/elife.81979] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/07/2022] [Indexed: 12/31/2022] Open
Abstract
Organisms can adapt to an environment by taking multiple mutational paths. This redundancy at the genetic level, where many mutations have similar phenotypic and fitness effects, can make untangling the molecular mechanisms of complex adaptations difficult. Here, we use the Escherichia coli long-term evolution experiment (LTEE) as a model to address this challenge. To understand how different genomic changes could lead to parallel fitness gains, we characterize the landscape of transcriptional and translational changes across 12 replicate populations evolving in parallel for 50,000 generations. By quantifying absolute changes in mRNA abundances, we show that not only do all evolved lines have more mRNAs but that this increase in mRNA abundance scales with cell size. We also find that despite few shared mutations at the genetic level, clones from replicate populations in the LTEE are remarkably similar in their gene expression patterns at both the transcriptional and translational levels. Furthermore, we show that the majority of the expression changes are due to changes at the transcriptional level with very few translational changes. Finally, we show how mutations in transcriptional regulators lead to consistent and parallel changes in the expression levels of downstream genes. These results deepen our understanding of the molecular mechanisms underlying complex adaptations and provide insights into the repeatability of evolution.
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Affiliation(s)
- John S Favate
- Department of Genetics, Rutgers UniversityPiscatawayUnited States
| | - Shun Liang
- Department of Genetics, Rutgers UniversityPiscatawayUnited States
| | - Alexander L Cope
- Department of Genetics, Rutgers UniversityPiscatawayUnited States
- Robert Wood Johnson Medical School, Rutgers UniversityNew BrunswickUnited States
| | - Srujana S Yadavalli
- Department of Genetics, Rutgers UniversityPiscatawayUnited States
- Waksman Institute, Rutgers UniversityPiscatawayUnited States
| | - Premal Shah
- Department of Genetics, Rutgers UniversityPiscatawayUnited States
- Human Genetics Institute of New Jersey, Rutgers UniversityPiscatawayUnited States
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19
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Flanagan K, Li W, Greenblatt EJ, Dao Duc K. End-to-end pipeline for differential analysis of pausing in ribosome profiling data. STAR Protoc 2022; 3:101605. [PMID: 36035799 PMCID: PMC9405084 DOI: 10.1016/j.xpro.2022.101605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Ribosome profiling is a powerful technique which maps the distribution of ribosomes along mRNAs to analyze translation genome-wide. Ribosome density can be affected by multiple factors, such as changes to translation initiation or elongation rates. We describe the application of a metric for identifying genes rate-limited by these rates by analyzing the relative distribution of ribosome footprints along transcripts. This protocol also details two sample analyses comparing gene translation efficiencies and the distribution of ribosome densities on downloadable datasets. For complete details on the use and execution of this protocol, please refer to Flanagan et al. (2022). Pipeline for measuring translation efficiency using ribosome profiling data Quantification of differential ribosome distributions along mRNAs Determine whether changes are consistent with altered initiation or elongation
Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
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20
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Selective recruitment of stress-responsive mRNAs to ribosomes for translation by acetylated protein S1 during nutrient stress in Escherichia coli. Commun Biol 2022; 5:892. [PMID: 36050442 PMCID: PMC9437053 DOI: 10.1038/s42003-022-03853-4] [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: 12/07/2021] [Accepted: 08/16/2022] [Indexed: 12/02/2022] Open
Abstract
The chemical modification of ribosomes plays an important regulatory role in cellular translation adaptation in response to environmental stresses. Nevertheless, how the modified ribosome reprograms the translation machinery for the preferential expression of the specific mRNAs encoding stress-responsive proteins to stress remains poorly understood. Here, we find that AcP-induced acetylation of K411 and K464 in ribosomal protein S1 during carbon-nitrogen imbalance, which in turn impacts its binding with distinct mRNAs. S1 acetylation shows differential selectivity for recruiting subsets of mRNAs to ribosomes. Using the RNC-Seq method, we find that mimic acetylated S1 prefers transcripts related with the formation of flagella/biofilms, two-component systems, nitrogen assimilation, amino acid degradation, and lipopolysaccharide biosynthesis, whereas inhibits the translation of mRNAs involved in amino acid biosynthesis and most ribosomal proteins. Importantly, further characterization of S1-binding site (SBS) sequences of mRNAs with different translation efficiencies indicated that the presence of a conserved motif allows coordinated regulation of S1 acetylation-driven translation reprogramming for cell survival during nitrogen starvation. These findings expand the repertoire of ribosome heterogeneity to the acetylation level of S1 at specific sites and its role in the ribosome-mediated regulation of gene expression as a cellular response at the translational level to stress. RNA molecular chaperone S1 is acetylated and selectively recruits stress-responsive mRNAs to the ribosome during nitrogen starvation in E. coli, revealing a translation regulation mechanism for nutrient stress adaptation.
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21
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Sawyer EB, Cortes T. Ribosome profiling enhances understanding of mycobacterial translation. Front Microbiol 2022; 13:976550. [PMID: 35992675 PMCID: PMC9386245 DOI: 10.3389/fmicb.2022.976550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 07/22/2022] [Indexed: 11/21/2022] Open
Abstract
A recent addition to the -omics toolkit, ribosome profiling, enables researchers to gain insight into the process and regulation of translation by mapping fragments of mRNA protected from nuclease digestion by ribosome binding. In this review, we discuss how ribosome profiling applied to mycobacteria has led to discoveries about translational regulation. Using case studies, we show that the traditional view of “canonical” translation mechanisms needs expanding to encompass features of mycobacterial translation that are more widespread than previously recognized. We also discuss the limitations of the method and potential future developments that could yield further insight into the fundamental biology of this important human pathogen.
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Affiliation(s)
- Elizabeth B. Sawyer
- School of Life Sciences, University of Westminster, London, United Kingdom
- *Correspondence: Elizabeth B. Sawyer,
| | - Teresa Cortes
- Pathogen Gene Regulation Unit, Instituto de Biomedicina de Valencia (IBV), CSIC, Valencia, Spain
- Teresa Cortes,
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22
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A Neural Networks Approach for the Analysis of Reproducible Ribo–Seq Profiles. ALGORITHMS 2022. [DOI: 10.3390/a15080274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In recent years, the Ribosome profiling technique (Ribo–seq) has emerged as a powerful method for globally monitoring the translation process in vivo at single nucleotide resolution. Based on deep sequencing of mRNA fragments, Ribo–seq allows to obtain profiles that reflect the time spent by ribosomes in translating each part of an open reading frame. Unfortunately, the profiles produced by this method can vary significantly in different experimental setups, being characterized by a poor reproducibility. To address this problem, we have employed a statistical method for the identification of highly reproducible Ribo–seq profiles, which was tested on a set of E. coli genes. State-of-the-art artificial neural network models have been used to validate the quality of the produced sequences. Moreover, new insights into the dynamics of ribosome translation have been provided through a statistical analysis on the obtained sequences.
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23
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Flanagan K, Baradaran-Heravi A, Yin Q, Dao Duc K, Spradling AC, Greenblatt EJ. FMRP-dependent production of large dosage-sensitive proteins is highly conserved. Genetics 2022; 221:6613139. [PMID: 35731217 PMCID: PMC9339308 DOI: 10.1093/genetics/iyac094] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 06/07/2022] [Indexed: 12/01/2022] Open
Abstract
Mutations in FMR1 are the most common heritable cause of autism spectrum disorder. FMR1 encodes an RNA-binding protein, FMRP, which binds to long, autism-relevant transcripts and is essential for normal neuronal and ovarian development. In contrast to the prevailing model that FMRP acts to block translation elongation, we previously found that FMRP activates the translation initiation of large proteins in Drosophila oocytes. We now provide evidence that FMRP-dependent translation is conserved and occurs in the mammalian brain. Our comparisons of the mammalian cortex and Drosophila oocyte ribosome profiling data show that translation of FMRP-bound mRNAs decreases to a similar magnitude in FMRP-deficient tissues from both species. The steady-state levels of several FMRP targets were reduced in the Fmr1 KO mouse cortex, including a ∼50% reduction of Auts2, a gene implicated in an autosomal dominant autism spectrum disorder. To distinguish between effects on elongation and initiation, we used a novel metric to detect the rate-limiting ribosome stalling. We found no evidence that FMRP target protein production is governed by translation elongation rates. FMRP translational activation of large proteins may be critical for normal human development, as more than 20 FMRP targets including Auts2 are dosage sensitive and are associated with neurodevelopmental disorders caused by haploinsufficiency.
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Affiliation(s)
- Keegan Flanagan
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia, V6T 1Z3 Canada.,Department of Mathematics, University of British Columbia, 1984 Mathematics Road, Vancouver, British Columbia, BC V6T 1Z2
| | - Alireza Baradaran-Heravi
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia, V6T 1Z3 Canada
| | - Qi Yin
- Howard Hughes Medical Institute Research Laboratories, Department of Embryology, Carnegie Institution for Science, 3520 San Martin Dr., Baltimore, Maryland 21218 USA
| | - Khanh Dao Duc
- Department of Mathematics, University of British Columbia, 1984 Mathematics Road, Vancouver, British Columbia, BC V6T 1Z2
| | - Allan C Spradling
- Howard Hughes Medical Institute Research Laboratories, Department of Embryology, Carnegie Institution for Science, 3520 San Martin Dr., Baltimore, Maryland 21218 USA
| | - Ethan J Greenblatt
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia, V6T 1Z3 Canada.,Howard Hughes Medical Institute Research Laboratories, Department of Embryology, Carnegie Institution for Science, 3520 San Martin Dr., Baltimore, Maryland 21218 USA
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24
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Metz JB, Hornstein NJ, Sharma SD, Worley J, Gonzalez C, Sims PA. High-throughput translational profiling with riboPLATE-seq. Sci Rep 2022; 12:5718. [PMID: 35383235 PMCID: PMC8983706 DOI: 10.1038/s41598-022-09638-3] [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: 11/15/2021] [Accepted: 03/18/2022] [Indexed: 11/11/2022] Open
Abstract
Protein synthesis is dysregulated in many diseases, but we lack a systems-level picture of how signaling molecules and RNA binding proteins interact with the translational machinery, largely due to technological limitations. Here we present riboPLATE-seq, a scalable method for generating paired libraries of ribosome-associated and total mRNA. As an extension of the PLATE-seq protocol, riboPLATE-seq utilizes barcoded primers for pooled library preparation, but additionally leverages anti-rRNA ribosome immunoprecipitation on whole polysomes to measure ribosome association (RA). We compare RA to its analogue in ribosome profiling and RNA sequencing, translation efficiency, and demonstrate both the performance of riboPLATE-seq and its utility in detecting translational alterations induced by specific inhibitors of protein kinases.
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Affiliation(s)
- Jordan B Metz
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Medical Scientist Training Program, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Nicholas J Hornstein
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Medical Scientist Training Program, Columbia University Irving Medical Center, New York, NY, 10032, USA
- MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Sohani Das Sharma
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Jeremy Worley
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Christian Gonzalez
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Peter A Sims
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA.
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032, USA.
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25
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Translation stalling proline motifs are enriched in slow-growing, thermophilic, and multicellular bacteria. THE ISME JOURNAL 2022; 16:1065-1073. [PMID: 34824398 DOI: 10.1038/s41396-021-01154-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 12/17/2022]
Abstract
Rapid bacterial growth depends on the speed at which ribosomes can translate mRNA into proteins. mRNAs that encode successive stretches of proline can cause ribosomes to stall, substantially reducing translation speed. Such stalling is especially detrimental for species that must grow and divide rapidly. Here, we focus on di-prolyl motifs (XXPPX) and ask whether their prevalence varies with growth rate. To find out we conducted a broad survey of such motifs in >3000 bacterial genomes across 35 phyla. Indeed, fast-growing species encode fewer motifs than slow-growing species, especially in highly expressed proteins. We also found many di-prolyl motifs within thermophiles, where prolines can help maintain proteome stability. Moreover, bacteria with complex, multicellular lifecycles also encode many di-prolyl motifs. This is especially evident in the slow-growing phylum Myxococcota. Bacteria in this phylum encode many serine-threonine kinases, and many di-prolyl motifs at potential phosphorylation sites within these kinases. Serine-threonine kinases are involved in cell signaling and help regulate developmental processes linked to multicellularity in the Myxococcota. Altogether, our observations suggest that weakened selection on translational rate, whether due to slow or thermophilic growth, may allow di-prolyl motifs to take on new roles in biological processes that are unrelated to translational rate.
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26
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Fiches GN, Wu Z, Zhou D, Biswas A, Li TW, Kong W, Jean M, Santoso NG, Zhu J. Polyamine biosynthesis and eIF5A hypusination are modulated by the DNA tumor virus KSHV and promote KSHV viral infection. PLoS Pathog 2022; 18:e1010503. [PMID: 35486659 PMCID: PMC9094511 DOI: 10.1371/journal.ppat.1010503] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 05/11/2022] [Accepted: 04/05/2022] [Indexed: 12/12/2022] Open
Abstract
Polyamines are critical metabolites involved in various cellular processes and often dysregulated in cancers. Kaposi’s sarcoma-associated Herpesvirus (KSHV), a defined human oncogenic virus, leads to profound alterations of host metabolic landscape to favor development of KSHV-associated malignancies. In our studies, we identified that polyamine biosynthesis and eIF5A hypusination are dynamically regulated by KSHV infection through modulation of key enzymes (ODC1 and DHPS) of these pathways. During KSHV latency, ODC1 and DHPS are upregulated along with increase of hypusinated eIF5A (hyp-eIF5A), while hyp-eIF5A is further induced along with reduction of ODC1 and intracellular polyamines during KSHV lytic reactivation. In return these metabolic pathways are required for both KSHV lytic reactivation and de novo infection. Further analysis unraveled that synthesis of critical KSHV latent and lytic proteins (LANA, RTA) depends on hypusinated-eIF5A. We also demonstrated that KSHV infection can be efficiently and specifically suppressed by inhibitors targeting these pathways. Collectively, our results illustrated that the dynamic and profound interaction of a DNA tumor virus (KSHV) with host polyamine biosynthesis and eIF5A hypusination pathways promote viral propagation, thus defining new therapeutic targets to treat KSHV-associated malignancies. Understanding virus-host interactions is crucial to develop and improve therapies. Kaposi’s sarcoma associated Herpesvirus (KSHV) is a human gamma-herpesvirus which deeply modulates the host metabolism and is associated with various cancers of endothelial and lymphoid origin. Polyamines are critical metabolites often dysregulated in cancers. In this study we demonstrated KSHV dynamically modulates polyamine metabolism to favor eIF5A hypusination and translation of critical KSHV latent and lytic proteins (LANA, RTA). Consequently, we found KSHV lytic switch from latency and de novo infection were dependent on polyamines and hypusination and pharmacological inhibition efficiently and specifically restricted KSHV infection. Our study provides new insights into KSHV alteration of the host metabolism and describe new therapeutic targets to treat KSHV-associated malignancies.
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Affiliation(s)
- Guillaume N. Fiches
- Department of Pathology, Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Zhenyu Wu
- Department of Pathology, Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Dawei Zhou
- Department of Pathology, Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Ayan Biswas
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Tai-Wei Li
- Department of Pathology, Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Weili Kong
- Gladstone Institute of Virology and Immunology, University of California, San Francisco, California, United States of America
| | - Maxime Jean
- Department of Neurology, University of Rochester Medical center, Rochester, New York, United States of America
| | - Netty G. Santoso
- Department of Pathology, Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Jian Zhu
- Department of Pathology, Ohio State University College of Medicine, Columbus, Ohio, United States of America
- * E-mail:
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27
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Smith C, Canestrari JG, Wang AJ, Champion MM, Derbyshire KM, Gray TA, Wade JT. Pervasive translation in Mycobacterium tuberculosis. eLife 2022; 11:e73980. [PMID: 35343439 PMCID: PMC9094748 DOI: 10.7554/elife.73980] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
Most bacterial ORFs are identified by automated prediction algorithms. However, these algorithms often fail to identify ORFs lacking canonical features such as a length of >50 codons or the presence of an upstream Shine-Dalgarno sequence. Here, we use ribosome profiling approaches to identify actively translated ORFs in Mycobacterium tuberculosis. Most of the ORFs we identify have not been previously described, indicating that the M. tuberculosis transcriptome is pervasively translated. The newly described ORFs are predominantly short, with many encoding proteins of ≤50 amino acids. Codon usage of the newly discovered ORFs suggests that most have not been subject to purifying selection, and hence are unlikely to contribute to cell fitness. Nevertheless, we identify 90 new ORFs (median length of 52 codons) that bear the hallmarks of purifying selection. Thus, our data suggest that pervasive translation of short ORFs in Mycobacterium tuberculosis serves as a rich source for the evolution of new functional proteins.
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Affiliation(s)
- Carol Smith
- Wadsworth Center, Division of Genetics, New York State Department of HealthAlbanyUnited States
| | - Jill G Canestrari
- Wadsworth Center, Division of Genetics, New York State Department of HealthAlbanyUnited States
| | - Archer J Wang
- Wadsworth Center, Division of Genetics, New York State Department of HealthAlbanyUnited States
| | - Matthew M Champion
- Department of Chemistry and Biochemistry, University of Notre DameNotre DameUnited States
| | - Keith M Derbyshire
- Wadsworth Center, Division of Genetics, New York State Department of HealthAlbanyUnited States
- Department of Biomedical Sciences, School of Public Health, University at AlbanyNew YorkUnited States
| | - Todd A Gray
- Wadsworth Center, Division of Genetics, New York State Department of HealthAlbanyUnited States
- Department of Biomedical Sciences, School of Public Health, University at AlbanyNew YorkUnited States
| | - Joseph T Wade
- Wadsworth Center, Division of Genetics, New York State Department of HealthAlbanyUnited States
- Department of Biomedical Sciences, School of Public Health, University at AlbanyNew YorkUnited States
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28
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Fujita T, Yokoyama T, Shirouzu M, Taguchi H, Ito T, Iwasaki S. The landscape of translational stall sites in bacteria revealed by monosome and disome profiling. RNA (NEW YORK, N.Y.) 2022; 28:290-302. [PMID: 34906996 PMCID: PMC8848927 DOI: 10.1261/rna.078188.120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 11/24/2021] [Indexed: 05/29/2023]
Abstract
Ribosome pauses are associated with various cotranslational events and determine the fate of mRNAs and proteins. Thus, the identification of precise pause sites across the transcriptome is desirable; however, the landscape of ribosome pauses in bacteria remains ambiguous. Here, we harness monosome and disome (or collided ribosome) profiling strategies to survey ribosome pause sites in Escherichia coli Compared to eukaryotes, ribosome collisions in bacteria showed remarkable differences: a low frequency of disomes at stop codons, collisions occurring immediately after 70S assembly on start codons, and shorter queues of ribosomes trailing upstream. The pause sites corresponded with the biochemical validation by integrated nascent chain profiling (iNP) to detect polypeptidyl-tRNA, an elongation intermediate. Moreover, the subset of those sites showed puromycin resistance, presenting slow peptidyl transfer. Among the identified sites, the ribosome pause at Asn586 of ycbZ was validated by biochemical reporter assay, tRNA sequencing (tRNA-seq), and cryo-electron microscopy (cryo-EM) experiments. Our results provide a useful resource for ribosome stalling sites in bacteria.
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Affiliation(s)
- Tomoya Fujita
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198 Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8503, Japan
| | - Takeshi Yokoyama
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama 230-0045, Japan
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8577, Japan
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Hideki Taguchi
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8503, Japan
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Midori-ku, Yokohama 226-8503, Japan
| | - Takuhiro Ito
- Laboratory for Translation Structural Biology, RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198 Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan
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29
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Kreitmeier M, Ardern Z, Abele M, Ludwig C, Scherer S, Neuhaus K. Spotlight on alternative frame coding: Two long overlapping genes in Pseudomonas aeruginosa are translated and under purifying selection. iScience 2022; 25:103844. [PMID: 35198897 PMCID: PMC8850804 DOI: 10.1016/j.isci.2022.103844] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 10/14/2021] [Accepted: 01/27/2022] [Indexed: 12/13/2022] Open
Abstract
The existence of overlapping genes (OLGs) with significant coding overlaps revolutionizes our understanding of genomic complexity. We report two exceptionally long (957 nt and 1536 nt), evolutionarily novel, translated antisense open reading frames (ORFs) embedded within annotated genes in the pathogenic Gram-negative bacterium Pseudomonas aeruginosa. Both OLG pairs show sequence features consistent with being genes and transcriptional signals in RNA sequencing. Translation of both OLGs was confirmed by ribosome profiling and mass spectrometry. Quantitative proteomics of samples taken during different phases of growth revealed regulation of protein abundances, implying biological functionality. Both OLGs are taxonomically restricted, and likely arose by overprinting within the genus. Evidence for purifying selection further supports functionality. The OLGs reported here, designated olg1 and olg2, are the longest yet proposed in prokaryotes and are among the best attested in terms of translation and evolutionary constraint. These results highlight a potentially large unexplored dimension of prokaryotic genomes.
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Affiliation(s)
- Michaela Kreitmeier
- Chair for Microbial Ecology, TUM School of Life Sciences, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Zachary Ardern
- Chair for Microbial Ecology, TUM School of Life Sciences, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Miriam Abele
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technische Universität München, Gregor-Mendel-Strasse 4, 85354 Freising, Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technische Universität München, Gregor-Mendel-Strasse 4, 85354 Freising, Germany
| | - Siegfried Scherer
- Chair for Microbial Ecology, TUM School of Life Sciences, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Klaus Neuhaus
- Core Facility Microbiome, ZIEL – Institute for Food & Health, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
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30
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McDonnell CM, Ghanim M, Mike Southern J, Kelly VP, Connon SJ. De-novo designed β-lysine derivatives can both augment and diminish the proliferation rates of E. coli through the action of Elongation Factor P. Bioorg Med Chem Lett 2022; 59:128545. [PMID: 35032607 DOI: 10.1016/j.bmcl.2022.128545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/06/2022] [Accepted: 01/09/2022] [Indexed: 12/20/2022]
Abstract
An investigation into the effect of modified β -lysines on the growth rates of eubacterial cells is reported. It is shown that the effects observed are due to the post translational modification of Elongation Factor P (EFP) with these compounds catalysed by PoxA. PoxA was found to be remarkably promiscuous, which allowed the activity of a wide range of exogenous β -lysines to be examined. Two chain-elongated β -lysine derivatives which differ in aminoalkyl chain length by only 2 carbon units exhibited opposing biological activities - one promoting growth and the other retarding it. Both compounds were shown to operate through modification of EFP.
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Affiliation(s)
- Ciara M McDonnell
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin 152-160 Pearse Street, Dublin 2, Ireland
| | - Magda Ghanim
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin 152-160 Pearse Street, Dublin 2, Ireland
| | - J Mike Southern
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin 152-160 Pearse Street, Dublin 2, Ireland.
| | - Vincent P Kelly
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin 152-160 Pearse Street, Dublin 2, Ireland.
| | - Stephen J Connon
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin 152-160 Pearse Street, Dublin 2, Ireland.
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31
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Tajima K, Katoh T, Suga H. OUP accepted manuscript. Nucleic Acids Res 2022; 50:2736-2753. [PMID: 35188576 PMCID: PMC8934632 DOI: 10.1093/nar/gkac068] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 01/13/2022] [Accepted: 02/07/2022] [Indexed: 11/13/2022] Open
Abstract
In ribosomal translation, peptidyl transfer occurs between P-site peptidyl-tRNA and A-site aminoacyl-tRNA, followed by translocation of the resulting P-site deacylated-tRNA and A-site peptidyl-tRNA to E and P site, respectively, mediated by EF-G. Here, we report that mistranslocation of P-site peptidyl-tRNA and A-site aminoacyl-tRNA toward E and A site occurs when high concentration of EF-G triggers the migration of two tRNAs prior to completion of peptidyl transfer. Consecutive incorporation of less reactive amino acids, such as Pro and d-Ala, makes peptidyl transfer inefficient and thus induces the mistranslocation event. Consequently, the E-site peptidyl-tRNA drops off from ribosome to give a truncated peptide lacking the C-terminal region. The P-site aminoacyl-tRNA allows for reinitiation of translation upon accommodation of a new aminoacyl-tRNA at A site, leading to synthesis of a truncated peptide lacking the N-terminal region, which we call the ‘reinitiated peptide’. We also revealed that such a drop-off-reinitiation event can be alleviated by EF-P that promotes peptidyl transfer of Pro. Moreover, this event takes place both in vitro and in cell, showing that reinitiated peptides during protein synthesis could be accumulated in this pathway in cells.
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Affiliation(s)
- Kenya Tajima
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | | | - Hiroaki Suga
- To whom correspondence should be addressed. Tel: +81 3 5841 8372; Fax: +81 3 5841 8372;
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32
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Chadani Y, Sugata N, Niwa T, Ito Y, Iwasaki S, Taguchi H. Nascent polypeptide within the exit tunnel stabilizes the ribosome to counteract risky translation. EMBO J 2021; 40:e108299. [PMID: 34672004 PMCID: PMC8634131 DOI: 10.15252/embj.2021108299] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 09/21/2021] [Accepted: 09/29/2021] [Indexed: 01/26/2023] Open
Abstract
Continuous translation elongation, irrespective of amino acid sequences, is a prerequisite for living organisms to produce their proteomes. However, nascent polypeptide products bear an inherent risk of elongation abortion. For example, negatively charged sequences with occasional intermittent prolines, termed intrinsic ribosome destabilization (IRD) sequences, weaken the translating ribosomal complex, causing certain nascent chain sequences to prematurely terminate translation. Here, we show that most potential IRD sequences in the middle of open reading frames remain cryptic and do not interrupt translation, due to two features of the nascent polypeptide. Firstly, the nascent polypeptide itself spans the exit tunnel, and secondly, its bulky amino acid residues occupy the tunnel entrance region, thereby serving as a bridge and protecting the large and small ribosomal subunits from dissociation. Thus, nascent polypeptide products have an inbuilt ability to ensure elongation continuity.
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Affiliation(s)
- Yuhei Chadani
- Cell Biology CenterInstitute of Innovative ResearchTokyo Institute of TechnologyYokohamaJapan
| | - Nobuyuki Sugata
- School of Life Science and TechnologyTokyo Institute of TechnologyYokohamaJapan
| | - Tatsuya Niwa
- Cell Biology CenterInstitute of Innovative ResearchTokyo Institute of TechnologyYokohamaJapan
- School of Life Science and TechnologyTokyo Institute of TechnologyYokohamaJapan
| | - Yosuke Ito
- School of Life Science and TechnologyTokyo Institute of TechnologyYokohamaJapan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry LaboratoryRIKEN Cluster for Pioneering ResearchSaitamaJapan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier SciencesThe University of TokyoKashiwaJapan
| | - Hideki Taguchi
- Cell Biology CenterInstitute of Innovative ResearchTokyo Institute of TechnologyYokohamaJapan
- School of Life Science and TechnologyTokyo Institute of TechnologyYokohamaJapan
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33
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Shirokikh NE. Translation complex stabilization on messenger RNA and footprint profiling to study the RNA responses and dynamics of protein biosynthesis in the cells. Crit Rev Biochem Mol Biol 2021; 57:261-304. [PMID: 34852690 DOI: 10.1080/10409238.2021.2006599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
During protein biosynthesis, ribosomes bind to messenger (m)RNA, locate its protein-coding information, and translate the nucleotide triplets sequentially as codons into the corresponding sequence of amino acids, forming proteins. Non-coding mRNA features, such as 5' and 3' untranslated regions (UTRs), start sites or stop codons of different efficiency, stretches of slower or faster code and nascent polypeptide interactions can alter the translation rates transcript-wise. Most of the homeostatic and signal response pathways of the cells converge on individual mRNA control, as well as alter the global translation output. Among the multitude of approaches to study translational control, one of the most powerful is to infer the locations of translational complexes on mRNA based on the mRNA fragments protected by these complexes from endonucleolytic hydrolysis, or footprints. Translation complex profiling by high-throughput sequencing of the footprints allows to quantify the transcript-wise, as well as global, alterations of translation, and uncover the underlying control mechanisms by attributing footprint locations and sizes to different configurations of the translational complexes. The accuracy of all footprint profiling approaches critically depends on the fidelity of footprint generation and many methods have emerged to preserve certain or multiple configurations of the translational complexes, often in challenging biological material. In this review, a systematic summary of approaches to stabilize translational complexes on mRNA for footprinting is presented and major findings are discussed. Future directions of translation footprint profiling are outlined, focusing on the fidelity and accuracy of inference of the native in vivo translation complex distribution on mRNA.
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Affiliation(s)
- Nikolay E Shirokikh
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
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34
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Choe D, Szubin R, Poudel S, Sastry A, Song Y, Lee Y, Cho S, Palsson B, Cho BK. RiboRid: A low cost, advanced, and ultra-efficient method to remove ribosomal RNA for bacterial transcriptomics. PLoS Genet 2021; 17:e1009821. [PMID: 34570751 PMCID: PMC8496792 DOI: 10.1371/journal.pgen.1009821] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 10/07/2021] [Accepted: 09/10/2021] [Indexed: 12/29/2022] Open
Abstract
RNA sequencing techniques have enabled the systematic elucidation of gene expression (RNA-Seq), transcription start sites (differential RNA-Seq), transcript 3′ ends (Term-Seq), and post-transcriptional processes (ribosome profiling). The main challenge of transcriptomic studies is to remove ribosomal RNAs (rRNAs), which comprise more than 90% of the total RNA in a cell. Here, we report a low-cost and robust bacterial rRNA depletion method, RiboRid, based on the enzymatic degradation of rRNA by thermostable RNase H. This method implemented experimental considerations to minimize nonspecific degradation of mRNA and is capable of depleting pre-rRNAs that often comprise a large portion of RNA, even after rRNA depletion. We demonstrated the highly efficient removal of rRNA up to a removal efficiency of 99.99% for various transcriptome studies, including RNA-Seq, Term-Seq, and ribosome profiling, with a cost of approximately $10 per sample. This method is expected to be a robust method for large-scale high-throughput bacterial transcriptomic studies. Removal of ribosomal RNAs, a major constituent (over 90%) of cellular RNA is a critical experimental step for transcriptomic studies that deal with messenger RNAs. In this manuscript, we describe a robust method to subtract ribosomal RNA from various RNA samples. The method is based on the enzymatic degradation of target RNA by short complementary DNA and RNA:DNA duplex specific nuclease. The method comprises carefully designed experimental procedures to minimize experimental bias and unwanted removal of messenger RNAs. We validate the method on various types of transcriptomic studies for seven diverse bacterial species. This method successfully removed ribosomal RNA with over 99% of efficiency and it was comparable to commercial systems even for degraded RNA samples at a fraction of a cost.
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Affiliation(s)
- Donghui Choe
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
- Innovative Biomaterials Research Center, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Richard Szubin
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
| | - Saugat Poudel
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
| | - Anand Sastry
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
| | - Yoseb Song
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Yongjae Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
- Innovative Biomaterials Research Center, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Suhyung Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
- Innovative Biomaterials Research Center, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Bernhard Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
- Department of Pediatrics, University of California San Diego, La Jolla, California, United States of America
- * E-mail: (BP); (B-KC)
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
- Innovative Biomaterials Research Center, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
- * E-mail: (BP); (B-KC)
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35
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Allen GE, Panasenko OO, Villanyi Z, Zagatti M, Weiss B, Pagliazzo L, Huch S, Polte C, Zahoran S, Hughes CS, Pelechano V, Ignatova Z, Collart MA. Not4 and Not5 modulate translation elongation by Rps7A ubiquitination, Rli1 moonlighting, and condensates that exclude eIF5A. Cell Rep 2021; 36:109633. [PMID: 34469733 DOI: 10.1016/j.celrep.2021.109633] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 03/18/2021] [Accepted: 08/09/2021] [Indexed: 12/13/2022] Open
Abstract
In this work, we show that Not4 and Not5 from the Ccr4-Not complex modulate translation elongation dynamics and change ribosome A-site dwelling occupancy in a codon-dependent fashion. These codon-specific changes in not5Δ cells are very robust and independent of codon position within the mRNA, the overall mRNA codon composition, or changes of mRNA expression levels. They inversely correlate with codon-specific changes in cells depleted for eIF5A and positively correlate with those in cells depleted for ribosome-recycling factor Rli1. Not5 resides in punctate loci, co-purifies with ribosomes and Rli1, but not with eIF5A, and limits mRNA solubility. Overexpression of wild-type or non-complementing Rli1 and loss of Rps7A ubiquitination enable Not4 E3 ligase-dependent translation of polyarginine stretches. We propose that Not4 and Not5 modulate translation elongation dynamics to produce a soluble proteome by Rps7A ubiquitination, dynamic condensates that limit mRNA solubility and exclude eIF5A, and a moonlighting function of Rli1.
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Affiliation(s)
- George E Allen
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics Geneva, Faculty of Medicine, University of Geneva, 1211 Geneva 4, Switzerland
| | - Olesya O Panasenko
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics Geneva, Faculty of Medicine, University of Geneva, 1211 Geneva 4, Switzerland
| | - Zoltan Villanyi
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics Geneva, Faculty of Medicine, University of Geneva, 1211 Geneva 4, Switzerland; Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary
| | - Marina Zagatti
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics Geneva, Faculty of Medicine, University of Geneva, 1211 Geneva 4, Switzerland
| | - Benjamin Weiss
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics Geneva, Faculty of Medicine, University of Geneva, 1211 Geneva 4, Switzerland
| | - Lucile Pagliazzo
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics Geneva, Faculty of Medicine, University of Geneva, 1211 Geneva 4, Switzerland
| | - Susanne Huch
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17165 Solna, Sweden
| | - Christine Polte
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany
| | - Szabolcs Zahoran
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics Geneva, Faculty of Medicine, University of Geneva, 1211 Geneva 4, Switzerland; Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary
| | | | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17165 Solna, Sweden
| | - Zoya Ignatova
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany
| | - Martine A Collart
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics Geneva, Faculty of Medicine, University of Geneva, 1211 Geneva 4, Switzerland.
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36
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Comparative ribosome profiling reveals distinct translational landscapes of salt-sensitive and -tolerant rice. BMC Genomics 2021; 22:612. [PMID: 34384368 PMCID: PMC8359061 DOI: 10.1186/s12864-021-07922-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 08/03/2021] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Soil salinization represents a serious threat to global rice production. Although significant research has been conducted to understand salt stress at the genomic, transcriptomic and proteomic levels, few studies have focused on the translatomic responses to this stress. Recent studies have suggested that transcriptional and translational responses to salt stress can often operate independently. RESULTS We sequenced RNA and ribosome-protected fragments (RPFs) from the salt-sensitive rice (O. sativa L.) cultivar 'Nipponbare' (NB) and the salt-tolerant cultivar 'Sea Rice 86' (SR86) under normal and salt stress conditions. A large discordance between salt-induced transcriptomic and translatomic alterations was found in both cultivars, with more translationally regulated genes being observed in SR86 in comparison to NB. A biased ribosome occupancy, wherein RPF depth gradually increased from the 5' ends to the 3' ends of coding regions, was revealed in NB and SR86. This pattern was strengthened by salt stress, particularly in SR86. On the contrary, the strength of ribosome stalling was accelerated in salt-stressed NB but decreased in SR86. CONCLUSIONS This study revealed that translational reprogramming represents an important layer of salt stress responses in rice, and the salt-tolerant cultivar SR86 adopts a more flexible translationally adaptive strategy to cope with salt stress compared to the salt susceptible cultivar NB. The differences in translational dynamics between NB and SR86 may derive from their differing levels of ribosome stalling under salt stress.
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37
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Masuda I, Hwang JY, Christian T, Maharjan S, Mohammad F, Gamper H, Buskirk AR, Hou YM. Loss of N1-methylation of G37 in tRNA induces ribosome stalling and reprograms gene expression. eLife 2021; 10:70619. [PMID: 34382933 PMCID: PMC8384417 DOI: 10.7554/elife.70619] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 08/09/2021] [Indexed: 01/20/2023] Open
Abstract
N1-methylation of G37 is required for a subset of tRNAs to maintain the translational reading-frame. While loss of m1G37 increases ribosomal +1 frameshifting, whether it incurs additional translational defects is unknown. Here, we address this question by applying ribosome profiling to gain a genome-wide view of the effects of m1G37 deficiency on protein synthesis. Using E coli as a model, we show that m1G37 deficiency induces ribosome stalling at codons that are normally translated by m1G37-containing tRNAs. Stalling occurs during decoding of affected codons at the ribosomal A site, indicating a distinct mechanism than that of +1 frameshifting, which occurs after the affected codons leave the A site. Enzyme- and cell-based assays show that m1G37 deficiency reduces tRNA aminoacylation and in some cases peptide-bond formation. We observe changes of gene expression in m1G37 deficiency similar to those in the stringent response that is typically induced by deficiency of amino acids. This work demonstrates a previously unrecognized function of m1G37 that emphasizes its role throughout the entire elongation cycle of protein synthesis, providing new insight into its essentiality for bacterial growth and survival.
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Affiliation(s)
- Isao Masuda
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, United States
| | - Jae-Yeon Hwang
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Thomas Christian
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, United States
| | - Sunita Maharjan
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, United States
| | - Fuad Mohammad
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Howard Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, United States
| | - Allen R Buskirk
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, United States
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38
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Pavlov MY, Ullman G, Ignatova Z, Ehrenberg M. Estimation of peptide elongation times from ribosome profiling spectra. Nucleic Acids Res 2021; 49:5124-5142. [PMID: 33885812 PMCID: PMC8136808 DOI: 10.1093/nar/gkab260] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/25/2021] [Accepted: 04/15/2021] [Indexed: 11/13/2022] Open
Abstract
Ribosome profiling spectra bear rich information on translation control and dynamics. Yet, due to technical biases in library generation, extracting quantitative measures of discrete translation events has remained elusive. Using maximum likelihood statistics and data set from Escherichia coli we develop a robust method for neutralizing technical biases (e.g. base specific RNase preferences in ribosome-protected mRNA fragments (RPF) generation), which allows for correct estimation of translation times at single codon resolution. Furthermore, we validated the method with available datasets from E. coli treated with antibiotic to inhibit isoleucyl-tRNA synthetase, and two datasets from Saccharomyces cerevisiae treated with two RNases with distinct cleavage signatures. We demonstrate that our approach accounts for RNase cleavage preferences and provides bias-corrected translation times estimates. Our approach provides a solution to the long-standing problem of extracting reliable information about peptide elongation times from highly noisy and technically biased ribosome profiling spectra.
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Affiliation(s)
- Michael Y Pavlov
- Department of Cell and Molecular Biology, Biomedical Center, University of Uppsala, 75237 Uppsala, Sweden
| | - Gustaf Ullman
- Department of Cell and Molecular Biology, Biomedical Center, University of Uppsala, 75237 Uppsala, Sweden
| | - Zoya Ignatova
- Institute for Biochemistry & Molecular Biology, University of Hamburg, 20146 Hamburg, Germany
| | - Måns Ehrenberg
- Department of Cell and Molecular Biology, Biomedical Center, University of Uppsala, 75237 Uppsala, Sweden
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39
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Bartholomäus A, Kolte B, Mustafayeva A, Goebel I, Fuchs S, Benndorf D, Engelmann S, Ignatova Z. smORFer: a modular algorithm to detect small ORFs in prokaryotes. Nucleic Acids Res 2021; 49:e89. [PMID: 34125903 PMCID: PMC8421149 DOI: 10.1093/nar/gkab477] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 04/29/2021] [Accepted: 05/18/2021] [Indexed: 11/15/2022] Open
Abstract
Emerging evidence places small proteins (≤50 amino acids) more centrally in physiological processes. Yet, their functional identification and the systematic genome annotation of their cognate small open-reading frames (smORFs) remains challenging both experimentally and computationally. Ribosome profiling or Ribo-Seq (that is a deep sequencing of ribosome-protected fragments) enables detecting of actively translated open-reading frames (ORFs) and empirical annotation of coding sequences (CDSs) using the in-register translation pattern that is characteristic for genuinely translating ribosomes. Multiple identifiers of ORFs that use the 3-nt periodicity in Ribo-Seq data sets have been successful in eukaryotic smORF annotation. They have difficulties evaluating prokaryotic genomes due to the unique architecture (e.g. polycistronic messages, overlapping ORFs, leaderless translation, non-canonical initiation etc.). Here, we present a new algorithm, smORFer, which performs with high accuracy in prokaryotic organisms in detecting putative smORFs. The unique feature of smORFer is that it uses an integrated approach and considers structural features of the genetic sequence along with in-frame translation and uses Fourier transform to convert these parameters into a measurable score to faithfully select smORFs. The algorithm is executed in a modular way, and dependent on the data available for a particular organism, different modules can be selected for smORF search.
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Affiliation(s)
- Alexander Bartholomäus
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany.,Inst. Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
| | - Baban Kolte
- Inst. Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
| | - Ayten Mustafayeva
- Helmholtz Center for Infection Research, Microbial Proteomics, 38124 Braunschweig, Germany.,Inst. Microbiology, TU Braunschweig, Braunschweig, Germany
| | - Ingrid Goebel
- Inst. Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
| | | | - Dirk Benndorf
- Otto von Guericke University, Bioprocess Engineering, 39106 Magdeburg, Germany.,Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, 39106 Magdeburg, Germany
| | - Susanne Engelmann
- Helmholtz Center for Infection Research, Microbial Proteomics, 38124 Braunschweig, Germany.,Inst. Microbiology, TU Braunschweig, Braunschweig, Germany
| | - Zoya Ignatova
- Inst. Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
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40
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Han P, Shichino Y, Schneider-Poetsch T, Mito M, Hashimoto S, Udagawa T, Kohno K, Yoshida M, Mishima Y, Inada T, Iwasaki S. Genome-wide Survey of Ribosome Collision. Cell Rep 2021; 31:107610. [PMID: 32375038 DOI: 10.1016/j.celrep.2020.107610] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 03/18/2020] [Accepted: 04/13/2020] [Indexed: 12/31/2022] Open
Abstract
Ribosome movement is not always smooth and is rather often impeded. For ribosome pauses, fundamental issues remain to be addressed, including where ribosomes pause on mRNAs, what kind of RNA/amino acid sequence causes this pause, and the physiological significance of this attenuation of protein synthesis. Here, we survey the positions of ribosome collisions caused by ribosome pauses in humans and zebrafish using modified ribosome profiling. Collided ribosomes, i.e., disomes, emerge at various sites: Pro-Pro/Gly/Asp motifs; Arg-X-Lys motifs; stop codons; and 3' untranslated regions. The electrostatic interaction between the charged nascent chain and the ribosome exit tunnel determines the eIF5A-mediated disome rescue at the Pro-Pro sites. In particular, XBP1u, a precursor of endoplasmic reticulum (ER)-stress-responsive transcription factor, shows striking queues of collided ribosomes and thus acts as a degradation substrate by ribosome-associated quality control. Our results provide insight into the causes and consequences of ribosome pause by dissecting collided ribosomes.
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Affiliation(s)
- Peixun Han
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan; RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Yuichi Shichino
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Tilman Schneider-Poetsch
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Mari Mito
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Satoshi Hashimoto
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Tsuyoshi Udagawa
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Kenji Kohno
- Institute for Research Initiatives, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Minoru Yoshida
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yuichiro Mishima
- Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| | - Toshifumi Inada
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Shintaro Iwasaki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan; RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan.
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41
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Luo Z, Hu H, Liu S, Zhang Z, Li Y, Zhou L. Comprehensive analysis of the translatome reveals the relationship between the translational and transcriptional control in high fat diet-induced liver steatosis. RNA Biol 2021; 18:863-874. [PMID: 32967529 PMCID: PMC8081042 DOI: 10.1080/15476286.2020.1827193] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 09/14/2020] [Accepted: 09/18/2020] [Indexed: 12/17/2022] Open
Abstract
Translational regulation plays a critical role in gene expression. However, there are few genome-wide studies on translational regulation in non-alcoholic fatty liver disease (NAFLD), which is a severe non-communicable epidemic worldwide. In this study, we performed RNC-mRNA (mRNAs bound to ribosome-nascent chain complex) sequencing and mRNA sequencing to probe the translation status of high-fat-diet (HFD) induced mouse fatty liver. Generally, in the HFD group compared to the control group, changes of translation ratios and changes in mRNA abundance had a negative correlation. The relative abundance of RNC-mRNAs and mRNAs were positively correlated, yet the former changed more slowly than the latter. However, the rate of change became more balanced when it came to the livers of mice that were fed the HFD plus lycopene, an antioxidant. This indicated relatively independent roles of translational modulation and transcriptional regulation. Furthermore, many genes were differentially regulated at the transcriptional or translational levels, suggesting a new screening strategy for functional genes. In conclusion, our analysis revealed the different and correlated role of translational control with transcriptional regulation in the HFD-induced mouse fatty liver relative to the control, which indicates critical roles of translational control for liver steatosis; thus, adding a new dimension towards a better understanding and improvement of treatment for NAFLD.
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Affiliation(s)
- Zupeng Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, P.R. China
| | - Hailong Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, P.R. China
| | - Siqi Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, P.R. China
| | - Zhiwang Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, P.R. China
| | - Yixing Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, P.R. China
| | - Lei Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, P.R. China
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42
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Li SHJ, Nofal M, Parsons LR, Rabinowitz JD, Gitai Z. Monitoring mammalian mitochondrial translation with MitoRiboSeq. Nat Protoc 2021; 16:2802-2825. [PMID: 33953394 PMCID: PMC8610098 DOI: 10.1038/s41596-021-00517-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 02/05/2021] [Indexed: 02/03/2023]
Abstract
Several essential components of the electron transport chain, the major producer of ATP in mammalian cells, are encoded in the mitochondrial genome. These 13 proteins are translated within mitochondria by 'mitoribosomes'. Defective mitochondrial translation underlies multiple inborn errors of metabolism and has been implicated in pathologies such as aging, metabolic syndrome and cancer. Here, we provide a detailed ribosome profiling protocol optimized to interrogate mitochondrial translation in mammalian cells (MitoRiboSeq), wherein mitoribosome footprints are generated with micrococcal nuclease and mitoribosomes are separated from cytosolic ribosomes and other RNAs by ultracentrifugation in a single straightforward step. We highlight critical steps during library preparation and provide a step-by-step guide to data analysis accompanied by open-source bioinformatic code. Our method outputs mitoribosome footprints at single-codon resolution. Codons with high footprint densities are sites of mitoribosome stalling. We recently applied this approach to demonstrate that defects in mitochondrial serine catabolism or in mitochondrial tRNA methylation cause stalling of mitoribosomes at specific codons. Our method can be applied to study basic mitochondrial biology or to characterize abnormalities in mitochondrial translation in patients with mitochondrial disorders.
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Affiliation(s)
| | - Michel Nofal
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Lance R Parsons
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
| | - Zemer Gitai
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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43
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Krafczyk R, Qi F, Sieber A, Mehler J, Jung K, Frishman D, Lassak J. Proline codon pair selection determines ribosome pausing strength and translation efficiency in bacteria. Commun Biol 2021; 4:589. [PMID: 34002016 PMCID: PMC8129111 DOI: 10.1038/s42003-021-02115-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 04/16/2021] [Indexed: 02/03/2023] Open
Abstract
The speed of mRNA translation depends in part on the amino acid to be incorporated into the nascent chain. Peptide bond formation is especially slow with proline and two adjacent prolines can even cause ribosome stalling. While previous studies focused on how the amino acid context of a Pro-Pro motif determines the stalling strength, we extend this question to the mRNA level. Bioinformatics analysis of the Escherichia coli genome revealed significantly differing codon usage between single and consecutive prolines. We therefore developed a luminescence reporter to detect ribosome pausing in living cells, enabling us to dissect the roles of codon choice and tRNA selection as well as to explain the genome scale observations. Specifically, we found a strong selective pressure against CCC/U-C, a sequon causing ribosomal frameshifting even under wild-type conditions. On the other hand, translation efficiency as positive evolutionary driving force led to an overrepresentation of CCG. This codon is not only translated the fastest, but the corresponding prolyl-tRNA reaches almost saturating levels. By contrast, CCA, for which the cognate prolyl-tRNA amounts are limiting, is used to regulate pausing strength. Thus, codon selection both in discrete positions but especially in proline codon pairs can tune protein copy numbers.
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Affiliation(s)
- Ralph Krafczyk
- grid.5252.00000 0004 1936 973XDepartment of Biology I, Microbiology, Ludwig-Maximilians-Universität München, München, Germany
| | - Fei Qi
- grid.411404.40000 0000 8895 903XInstitute of Genomics, School of Biomedical Sciences, Huaqiao University, Xiamen, China ,grid.6936.a0000000123222966Department of Bioinformatics, Wissenschaftzentrum Weihenstephan, Technische Universität München, Freising, Germany
| | - Alina Sieber
- grid.5252.00000 0004 1936 973XDepartment of Biology I, Microbiology, Ludwig-Maximilians-Universität München, München, Germany
| | - Judith Mehler
- grid.5252.00000 0004 1936 973XDepartment of Biology I, Microbiology, Ludwig-Maximilians-Universität München, München, Germany
| | - Kirsten Jung
- grid.5252.00000 0004 1936 973XDepartment of Biology I, Microbiology, Ludwig-Maximilians-Universität München, München, Germany
| | - Dmitrij Frishman
- grid.6936.a0000000123222966Department of Bioinformatics, Wissenschaftzentrum Weihenstephan, Technische Universität München, Freising, Germany
| | - Jürgen Lassak
- grid.5252.00000 0004 1936 973XDepartment of Biology I, Microbiology, Ludwig-Maximilians-Universität München, München, Germany
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44
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Arella D, Dilucca M, Giansanti A. Codon usage bias and environmental adaptation in microbial organisms. Mol Genet Genomics 2021; 296:751-762. [PMID: 33818631 PMCID: PMC8144148 DOI: 10.1007/s00438-021-01771-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 02/22/2021] [Indexed: 01/01/2023]
Abstract
In each genome, synonymous codons are used with different frequencies; this general phenomenon is known as codon usage bias. It has been previously recognised that codon usage bias could affect the cellular fitness and might be associated with the ecology of microbial organisms. In this exploratory study, we investigated the relationship between codon usage bias, lifestyles (thermophiles vs. mesophiles; pathogenic vs. non-pathogenic; halophilic vs. non-halophilic; aerobic vs. anaerobic and facultative) and habitats (aquatic, terrestrial, host-associated, specialised, multiple) of 615 microbial organisms (544 bacteria and 71 archaea). Principal component analysis revealed that species with given phenotypic traits and living in similar environmental conditions have similar codon preferences, as represented by the relative synonymous codon usage (RSCU) index, and similar spectra of tRNA availability, as gauged by the tRNA gene copy number (tGCN). Moreover, by measuring the average tRNA adaptation index (tAI) for each genome, an index that can be associated with translational efficiency, we observed that organisms able to live in multiple habitats, including facultative organisms, mesophiles and pathogenic bacteria, are characterised by a reduced translational efficiency, consistently with their need to adapt to different environments. Our results show that synonymous codon choices might be under strong translational selection, which modulates the choice of the codons to differently match tRNA availability, depending on the organism's lifestyle needs. To our knowledge, this is the first large-scale study that examines the role of codon bias and translational efficiency in the adaptation of microbial organisms to the environment in which they live.
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Affiliation(s)
- Davide Arella
- Department of Physics, Sapienza University of Rome, 00185, Rome, Italy.
| | - Maddalena Dilucca
- Department of Physics, Sapienza University of Rome, 001885, Rome, Italy
| | - Andrea Giansanti
- Department of Physics, Sapienza University of Rome, 00185, Rome, Italy
- INFN, Roma1 Unit, 00185, Rome, Italy
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45
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Pinheiro B, Scheidler CM, Kielkowski P, Schmid M, Forné I, Ye S, Reiling N, Takano E, Imhof A, Sieber SA, Schneider S, Jung K. Structure and Function of an Elongation Factor P Subfamily in Actinobacteria. Cell Rep 2021; 30:4332-4342.e5. [PMID: 32234471 DOI: 10.1016/j.celrep.2020.03.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 02/06/2020] [Accepted: 03/02/2020] [Indexed: 12/28/2022] Open
Abstract
Translation of consecutive proline motifs causes ribosome stalling and requires rescue via the action of a specific translation elongation factor, EF-P in bacteria and archaeal/eukaryotic a/eIF5A. In Eukarya, Archaea, and all bacteria investigated so far, the functionality of this translation elongation factor depends on specific and rather unusual post-translational modifications. The phylum Actinobacteria, which includes the genera Corynebacterium, Mycobacterium, and Streptomyces, is of both medical and economic significance. Here, we report that EF-P is required in these bacteria in particular for the translation of proteins involved in amino acid and secondary metabolite production. Notably, EF-P of Actinobacteria species does not need any post-translational modification for activation. While the function and overall 3D structure of this EF-P type is conserved, the loop containing the conserved lysine is flanked by two essential prolines that rigidify it. Actinobacteria's EF-P represents a unique subfamily that works without any modification.
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Affiliation(s)
- Bruno Pinheiro
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | | | - Pavel Kielkowski
- Department of Chemistry, Technische Universität München, Garching, Germany
| | - Marina Schmid
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Ignasi Forné
- Biomedical Center Munich, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Suhui Ye
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, University of Manchester, Manchester, UK
| | - Norbert Reiling
- RG Microbial Interface Biology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Eriko Takano
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, University of Manchester, Manchester, UK
| | - Axel Imhof
- Biomedical Center Munich, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Stephan A Sieber
- Department of Chemistry, Technische Universität München, Garching, Germany
| | - Sabine Schneider
- Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
| | - Kirsten Jung
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany.
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46
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Tian T, Li S, Lang P, Zhao D, Zeng J. Full-length ribosome density prediction by a multi-input and multi-output model. PLoS Comput Biol 2021; 17:e1008842. [PMID: 33770074 PMCID: PMC8026034 DOI: 10.1371/journal.pcbi.1008842] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 04/07/2021] [Accepted: 03/01/2021] [Indexed: 11/29/2022] Open
Abstract
Translation elongation is regulated by a series of complicated mechanisms in both prokaryotes and eukaryotes. Although recent advance in ribosome profiling techniques has enabled one to capture the genome-wide ribosome footprints along transcripts at codon resolution, the regulatory codes of elongation dynamics are still not fully understood. Most of the existing computational approaches for modeling translation elongation from ribosome profiling data mainly focus on local contextual patterns, while ignoring the continuity of the elongation process and relations between ribosome densities of remote codons. Modeling the translation elongation process in full-length coding sequence (CDS) level has not been studied to the best of our knowledge. In this paper, we developed a deep learning based approach with a multi-input and multi-output framework, named RiboMIMO, for modeling the ribosome density distributions of full-length mRNA CDS regions. Through considering the underlying correlations in translation efficiency among neighboring and remote codons and extracting hidden features from the input full-length coding sequence, RiboMIMO can greatly outperform the state-of-the-art baseline approaches and accurately predict the ribosome density distributions along the whole mRNA CDS regions. In addition, RiboMIMO explores the contributions of individual input codons to the predictions of output ribosome densities, which thus can help reveal important biological factors influencing the translation elongation process. The analyses, based on our interpretable metric named codon impact score, not only identified several patterns consistent with the previously-published literatures, but also for the first time (to the best of our knowledge) revealed that the codons located at a long distance from the ribosomal A site may also have an association on the translation elongation rate. This finding of long-range impact on translation elongation velocity may shed new light on the regulatory mechanisms of protein synthesis. Overall, these results indicated that RiboMIMO can provide a useful tool for studying the regulation of translation elongation in the range of full-length CDS. Translation elongation is a process in which amino acids are linked into proteins by ribosomes in cells. Translation elongation rates along the mRNAs are not constant, and are regulated by a series of mechanisms, such as codon rarity and mRNA stability. In this study, we modeled the translation elongation process at a full-length coding sequence level and developed a deep learning based approach to predict the translation elongation rates from mRNA sequences, through extracting the regulatory codes of elongation rates from the contextual sequences. The analyses, based on our interpretable metric named codon impact score, for the first time (to the best of our knowledge), revealed that in addition to the neighboring codons of the ribosomal A sites, the remote codons may also have an important impact on the translation elongation rates. This new finding may stimulate additional experiments and shed light on the regulatory mechanisms of protein synthesis.
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Affiliation(s)
- Tingzhong Tian
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China
| | - Shuya Li
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China
| | - Peng Lang
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China
| | - Dan Zhao
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China
- * E-mail: (DZ); (JZ)
| | - Jianyang Zeng
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
- * E-mail: (DZ); (JZ)
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47
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Shao D, Ahmed N, Soni N, O'Brien EP. RiboA: a web application to identify ribosome A-site locations in ribosome profiling data. BMC Bioinformatics 2021; 22:156. [PMID: 33765913 PMCID: PMC7992832 DOI: 10.1186/s12859-021-04068-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 03/10/2021] [Indexed: 12/12/2022] Open
Abstract
Background Translation is a fundamental process in gene expression. Ribosome profiling is a method that enables the study of transcriptome-wide translation. A fundamental, technical challenge in analyzing Ribo-Seq data is identifying the A-site location on ribosome-protected mRNA fragments. Identification of the A-site is essential as it is at this location on the ribosome where a codon is translated into an amino acid. Incorrect assignment of a read to the A-site can lead to lower signal-to-noise ratio and loss of correlations necessary to understand the molecular factors influencing translation. Therefore, an easy-to-use and accurate analysis tool is needed to accurately identify the A-site locations. Results We present RiboA, a web application that identifies the most accurate A-site location on a ribosome-protected mRNA fragment and generates the A-site read density profiles. It uses an Integer Programming method that reflects the biological fact that the A-site of actively translating ribosomes is generally located between the second codon and stop codon of a transcript, and utilizes a wide range of mRNA fragment sizes in and around the coding sequence (CDS). The web application is containerized with Docker, and it can be easily ported across platforms. Conclusions The Integer Programming method that RiboA utilizes is the most accurate in identifying the A-site on Ribo-Seq mRNA fragments compared to other methods. RiboA makes it easier for the community to use this method via a user-friendly and portable web application. In addition, RiboA supports reproducible analyses by tracking all the input datasets and parameters, and it provides enhanced visualization to facilitate scientific exploration. RiboA is available as a web service at https://a-site.vmhost.psu.edu/. The code is publicly available at https://github.com/obrien-lab/aip_web_docker under the MIT license.
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Affiliation(s)
- Danying Shao
- Institute for Computational and Data Sciences, Pennsylvania State University, University Park, USA
| | - Nabeel Ahmed
- Department of Chemistry, Pennsylvania State University, University Park, USA
| | - Nishant Soni
- Department of Chemistry, Pennsylvania State University, University Park, USA
| | - Edward P O'Brien
- Institute for Computational and Data Sciences, Pennsylvania State University, University Park, USA. .,Department of Chemistry, Pennsylvania State University, University Park, USA.
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48
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Sakiyama K, Shimokawa-Chiba N, Fujiwara K, Chiba S. Search for translation arrest peptides encoded upstream of genes for components of protein localization pathways. Nucleic Acids Res 2021; 49:1550-1566. [PMID: 33503266 PMCID: PMC7897499 DOI: 10.1093/nar/gkab024] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 01/05/2021] [Accepted: 01/08/2021] [Indexed: 02/06/2023] Open
Abstract
Regulatory nascent peptides participate in the regulation of cellular functions by the mechanisms involving regulated translation arrest. A class of them in bacteria, called monitoring substrates, feedback-regulates the expression of a specific component of protein localization machinery. Three monitoring substrates, SecM, MifM and VemP have previously been identified. Here, we attempt at identifying additional arrest peptides in bacteria. Our bioinformatic searches over more than 400 bacterial genomic sequences for proteins that have the common characteristic features shared by the known monitoring substrates and subsequent in vitro and in vivo characterization of the highlighted sequences allowed the identification of three arrest peptides termed ApcA, ApdA and ApdP. ApcA and ApdA homologs are conserved among a subset of actinobacteria, whereas ApdP has homologs in a subset of α-proteobacteria. We demonstrate that these arrest peptides, in their ribosome-tethered nascent states, inhibit peptidyl transfer. The elongation arrest occurs at a specific codon near the 3′ end of the coding region, in a manner depending on the amino acid sequence of the nascent chain. Interestingly, the arrest sequences of ApcA, ApdA and ApdP share a sequence R-A-P-G/P that is essential for the elongation arrest.
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Affiliation(s)
- Karen Sakiyama
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto 603-8555, Japan
| | - Naomi Shimokawa-Chiba
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto 603-8555, Japan.,Institute for Protein Dynamics, Kyoto Sangyo University, Japan
| | - Keigo Fujiwara
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto 603-8555, Japan.,Institute for Protein Dynamics, Kyoto Sangyo University, Japan
| | - Shinobu Chiba
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto 603-8555, Japan.,Institute for Protein Dynamics, Kyoto Sangyo University, Japan
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49
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Sawyer EB, Phelan JE, Clark TG, Cortes T. A snapshot of translation in Mycobacterium tuberculosis during exponential growth and nutrient starvation revealed by ribosome profiling. Cell Rep 2021; 34:108695. [PMID: 33535039 PMCID: PMC7856553 DOI: 10.1016/j.celrep.2021.108695] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/20/2020] [Accepted: 01/05/2021] [Indexed: 12/15/2022] Open
Abstract
Mycobacterium tuberculosis, which causes tuberculosis, can undergo prolonged periods of non-replicating persistence in the host. The mechanisms underlying this are not fully understood, but translational regulation is thought to play a role. A large proportion of mRNA transcripts expressed in M. tuberculosis lack canonical bacterial translation initiation signals, but little is known about the implications of this for fine-tuning of translation. Here, we perform ribosome profiling to characterize the translational landscape of M. tuberculosis under conditions of exponential growth and nutrient starvation. Our data reveal robust, widespread translation of non-canonical transcripts and point toward different translation initiation mechanisms compared to canonical Shine-Dalgarno transcripts. During nutrient starvation, patterns of ribosome recruitment vary, suggesting that regulation of translation in this pathogen is more complex than originally thought. Our data represent a rich resource for others seeking to understand translational regulation in bacterial pathogens.
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Affiliation(s)
- Elizabeth B Sawyer
- TB Centre and Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Jody E Phelan
- TB Centre and Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Taane G Clark
- TB Centre and Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK; Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Teresa Cortes
- TB Centre and Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK.
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50
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Samatova E, Daberger J, Liutkute M, Rodnina MV. Translational Control by Ribosome Pausing in Bacteria: How a Non-uniform Pace of Translation Affects Protein Production and Folding. Front Microbiol 2021; 11:619430. [PMID: 33505387 PMCID: PMC7829197 DOI: 10.3389/fmicb.2020.619430] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/11/2020] [Indexed: 11/23/2022] Open
Abstract
Protein homeostasis of bacterial cells is maintained by coordinated processes of protein production, folding, and degradation. Translational efficiency of a given mRNA depends on how often the ribosomes initiate synthesis of a new polypeptide and how quickly they read the coding sequence to produce a full-length protein. The pace of ribosomes along the mRNA is not uniform: periods of rapid synthesis are separated by pauses. Here, we summarize recent evidence on how ribosome pausing affects translational efficiency and protein folding. We discuss the factors that slow down translation elongation and affect the quality of the newly synthesized protein. Ribosome pausing emerges as important factor contributing to the regulatory programs that ensure the quality of the proteome and integrate the cellular and environmental cues into regulatory circuits of the cell.
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Affiliation(s)
- Ekaterina Samatova
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Jan Daberger
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Marija Liutkute
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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