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Bellows E, Heatley M, Shah N, Archer N, Giles T, Fray R. Comparative transcriptome reprogramming in oak galls containing asexual or sexual generations of gall wasps. PLANT BIOLOGY (STUTTGART, GERMANY) 2024; 26:798-810. [PMID: 38864838 DOI: 10.1111/plb.13670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 05/07/2024] [Indexed: 06/13/2024]
Abstract
Oak gall wasps have evolved strategies to manipulate the developmental pathways of their host to induce gall formation. This provides shelter and nutrients for the developing larva. Galls are entirely host tissue; however, the initiation, development, and physical appearance are controlled by the inducer. The underlying molecular mechanisms of gall formation, by which one or a small number of cells are reprogrammed and commit to a novel developmental path, are poorly understood. In this study, we sought a deeper insight into the molecular underpinnings of this process. Oak gall wasps have two generations each year, one sexual, and one asexual. Galls formed by these two generations exhibit a markedly different appearance. We sequenced transcriptomes of both the asexual and sexual generations of Neuroterus quercusbaccarum and Neuroterus numismalis. We then deployed Nanopore sequencing to generate long-read sequences to test the hypothesis that gall wasps introduce DNA insertions to determine gall development. We detected potential genome rearrangements but did not uncover any non-host DNA insertions. Transcriptome analysis revealed that transcriptomes of the sexual generations of distinct species of wasp are more similar than inter-generational comparisons from the same species of wasp. Our results highlight the intricate interplay between the host leaves and gall development, suggesting that season and requirements of the gall structure play a larger role than species in controlling gall development and structure.
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Affiliation(s)
- E Bellows
- School of Biosciences, The University of Nottingham, Nottingham, UK
| | - M Heatley
- Advanced Data Analysis Centre, The University of Nottingham, Nottingham, UK
| | - N Shah
- Advanced Data Analysis Centre, The University of Nottingham, Nottingham, UK
| | - N Archer
- School of Veterinary Medicine and Science, The University of Nottingham, Nottingham, UK
| | - T Giles
- Advanced Data Analysis Centre, The University of Nottingham, Nottingham, UK
| | - R Fray
- School of Biosciences, The University of Nottingham, Nottingham, UK
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2
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Rauscher R, Polacek N. Ribosomal RNA expansion segments and their role in ribosome biology. Biochem Soc Trans 2024; 52:1317-1325. [PMID: 38695725 DOI: 10.1042/bst20231106] [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: 01/29/2024] [Revised: 04/15/2024] [Accepted: 04/19/2024] [Indexed: 06/27/2024]
Abstract
Ribosomes are universally conserved cellular machines that catalyze protein biosynthesis. The active sites underly immense evolutionary conservation resulting in virtually identical core structures of ribosomes in all domains of life including organellar ribosomes. However, more peripheral structures of cytosolic ribosomes changed during evolution accommodating new functions and regulatory options. The expansion occurred at the riboprotein level, including more and larger ribosomal proteins and at the RNA level increasing the length of ribosomal RNA. Expansions within the ribosomal RNA occur as clusters at conserved sites that face toward the periphery of the cytosolic ribosome. Recent biochemical and structural work has shed light on how rRNA-specific expansion segments (ESs) recruit factors during translation and how they modulate translation dynamics in the cytosol. Here we focus on recent work on yeast, human and trypanosomal cytosolic ribosomes that explores the role of two specific rRNA ESs within the small and large subunit respectively. While no single regulatory strategy exists, the absence of ESs has consequences for proteomic stability and cellular fitness, rendering them fascinating evolutionary tools for tailored protein biosynthesis.
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Affiliation(s)
- Robert Rauscher
- Department for Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Norbert Polacek
- Department for Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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3
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Rothschild D, Susanto TT, Sui X, Spence JP, Rangan R, Genuth NR, Sinnott-Armstrong N, Wang X, Pritchard JK, Barna M. Diversity of ribosomes at the level of rRNA variation associated with human health and disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.01.30.526360. [PMID: 36778251 PMCID: PMC9915487 DOI: 10.1101/2023.01.30.526360] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Ribosomal DNA and RNA (rDNA and rRNA) sequences are usually discarded from sequencing analyses. But with hundreds of copies of rDNA genes it is unknown whether they possess sequence variations that form different types of ribosomes that affect human physiology and disease. Here, we developed an algorithm for variant-calling between paralog genes (termed RGA) and compared rDNA variations found in short- and long-read sequencing data from the 1,000 Genomes Project (1KGP) and Genome In A Bottle (GIAB). We additionally developed a novel protocol for long-read sequencing full-length rRNA (RIBO-RT) from actively translating ribosomes. Our analyses identified hundreds of rDNA variants, most of which, surprisingly, are short insertion-deletions (indels) and dozens of highly abundant rRNA variants that are incorporated into translationally active ribosomes. To visualize variant ribosomes at the single cell level, we developed an in-situ rRNA sequencing method (SWITCH-seq) which revealed that variants are co-expressed within individual cells. Strikingly, by analyzing rDNA, we found that variants assemble into distinct ribosome subtypes. We discovered that these subtypes acquire different rRNA structures by successfully employing dimethyl sulfate (DMS) probing of full length rRNA. With this atlas we investigated rRNA variation changes across human tissues and cancer types. This revealed tissue-specific rRNA subtype expression in endoderm/ectoderm-derived tissues. In cancer, low abundant rRNA variants can become highly expressed, which suggests the presence of cancer-specific ribosomes. Together, this study identifies and comprehensively characterizes the diversity of ribosomes at the level of rRNA variants which is dominated by indel variants, their chromosomal location and unique structure as well as the association of ribosome variation with tissue-specific biology and cancer.
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Mishra RK, Sharma P, Khaja FT, Uday AB, Hussain T. Cryo-EM structure of wheat ribosome reveals unique features of the plant ribosomes. Structure 2024; 32:562-574.e3. [PMID: 38458197 PMCID: PMC7616111 DOI: 10.1016/j.str.2024.02.006] [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: 08/16/2023] [Revised: 11/16/2023] [Accepted: 02/12/2024] [Indexed: 03/10/2024]
Abstract
Plants being sessile organisms exhibit unique features in ribosomes, which might aid in rapid gene expression and regulation in response to varying environmental conditions. Here, we present high-resolution structures of the 60S and 80S ribosomes from wheat, a monocot staple crop plant (Triticum aestivum). While plant ribosomes have unique plant-specific rRNA modification (Cm1847) in the peptide exit tunnel (PET), the zinc-finger motif in eL34 is absent, and uL4 is extended, making an exclusive interaction network. We note differences in the eL15-helix 11 (25S) interaction, eL6-ES7 assembly, and certain rRNA chemical modifications between monocot and dicot ribosomes. In eukaryotes, we observe highly conserved rRNA modification (Gm75) in 5.8S rRNA and a flipped base (G1506) in PET. These features are likely involved in sensing or stabilizing nascent chain. Finally, we discuss the importance of the universal conservation of three consecutive rRNA modifications in all ribosomes for their interaction with A-site aminoacyl-tRNA.
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Affiliation(s)
- Rishi Kumar Mishra
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru PIN-560012, India
| | - Prafful Sharma
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru PIN-560012, India
| | - Faisal Tarique Khaja
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru PIN-560012, India
| | - Adwaith B Uday
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru PIN-560012, India
| | - Tanweer Hussain
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru PIN-560012, India.
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5
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Rauscher R, Eggers C, Dimitrova-Paternoga L, Shankar V, Rosina A, Cristodero M, Paternoga H, Wilson DN, Leidel SA, Polacek N. Evolving precision: rRNA expansion segment 7S modulates translation velocity and accuracy in eukaryal ribosomes. Nucleic Acids Res 2024; 52:4021-4036. [PMID: 38324474 DOI: 10.1093/nar/gkae067] [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: 08/20/2023] [Revised: 01/16/2024] [Accepted: 01/22/2024] [Indexed: 02/09/2024] Open
Abstract
Ribosome-enhanced translational miscoding of the genetic code causes protein dysfunction and loss of cellular fitness. During evolution, open reading frame length increased, necessitating mechanisms for enhanced translation fidelity. Indeed, eukaryal ribosomes are more accurate than bacterial counterparts, despite their virtually identical, conserved active centers. During the evolution of eukaryotic organisms ribosome expansions at the rRNA and protein level occurred, which potentially increases the options for translation regulation and cotranslational events. Here we tested the hypothesis that ribosomal RNA expansions can modulate the core function of the ribosome, faithful protein synthesis. We demonstrate that a short expansion segment present in all eukaryotes' small subunit, ES7S, is crucial for accurate protein synthesis as its presence adjusts codon-specific velocities and guarantees high levels of cognate tRNA selection. Deletion of ES7S in yeast enhances mistranslation and causes protein destabilization and aggregation, dramatically reducing cellular fitness. Removal of ES7S did not alter ribosome architecture but altered the structural dynamics of inter-subunit bridges thus affecting A-tRNA selection. Exchanging the yeast ES7S sequence with the human ES7S increases accuracy whereas shortening causes the opposite effect. Our study demonstrates that ES7S provided eukaryal ribosomes with higher accuracy without perturbing the structurally conserved decoding center.
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Affiliation(s)
- Robert Rauscher
- Department for Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Cristian Eggers
- Department for Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Lyudmila Dimitrova-Paternoga
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Vaishnavi Shankar
- Department for Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Alessia Rosina
- Department for Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Marina Cristodero
- Department for Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Helge Paternoga
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Sebastian A Leidel
- Department for Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Norbert Polacek
- Department for Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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Parrella P, Elikan AB, Snow JW. Pathogen- and host-directed pharmacologic strategies for control of Vairimorpha (Nosema) spp. infection in honey bees. J Eukaryot Microbiol 2024:e13026. [PMID: 38572630 DOI: 10.1111/jeu.13026] [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: 02/14/2024] [Accepted: 03/07/2024] [Indexed: 04/05/2024]
Abstract
Microsporidia are obligate intracellular parasites of the Fungal Kingdom that cause widespread infections in nature, with important effects on invertebrates involved in food production systems. The two microsporidian species Vairimorpha (Nosema) ceranae (and the less common Vairimorpha (Nosema) apis) can cause individual disease in honey bees and contribute to colony collapse. The efficacy, safety, and availability of fumagillin, the only drug currently approved to treat microsporidia infection in bees, is uncertain. In this review, we will discuss some of the most promising alternative strategies for the mitigation of Vairimorpha spp. with an emphasis on infection by V. ceranae, now the dominant species infecting bees. We will focus on pharmacologic interventions where the mechanism of action is known and examine both pathogen-directed and host-directed approaches. As limiting toxicity to host cells has been especially emphasized in treating bees that are already facing numerous stressors, strategies that disrupt pathogen-specific targets may be especially advantageous. Therefore, efforts to increase the knowledge and tools for facilitating the discovery of such targets and pharmacologic agents directed against them should be prioritized.
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Affiliation(s)
- Parker Parrella
- Department of Biology, Barnard College, New York, New York, USA
| | | | - Jonathan W Snow
- Department of Biology, Barnard College, New York, New York, USA
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7
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Čáp M, Palková Z. Non-Coding RNAs: Regulators of Stress, Ageing, and Developmental Decisions in Yeast? Cells 2024; 13:599. [PMID: 38607038 PMCID: PMC11012152 DOI: 10.3390/cells13070599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/19/2024] [Accepted: 03/27/2024] [Indexed: 04/13/2024] Open
Abstract
Cells must change their properties in order to adapt to a constantly changing environment. Most of the cellular sensing and regulatory mechanisms described so far are based on proteins that serve as sensors, signal transducers, and effectors of signalling pathways, resulting in altered cell physiology. In recent years, however, remarkable examples of the critical role of non-coding RNAs in some of these regulatory pathways have been described in various organisms. In this review, we focus on all classes of non-coding RNAs that play regulatory roles during stress response, starvation, and ageing in different yeast species as well as in structured yeast populations. Such regulation can occur, for example, by modulating the amount and functional state of tRNAs, rRNAs, or snRNAs that are directly involved in the processes of translation and splicing. In addition, long non-coding RNAs and microRNA-like molecules are bona fide regulators of the expression of their target genes. Non-coding RNAs thus represent an additional level of cellular regulation that is gradually being uncovered.
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Affiliation(s)
- Michal Čáp
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, 128 00 Prague, Czech Republic
| | - Zdena Palková
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, 128 00 Prague, Czech Republic
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8
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Klein MA, Wild K, Kišonaitė M, Sinning I. Methionine aminopeptidase 2 and its autoproteolysis product have different binding sites on the ribosome. Nat Commun 2024; 15:716. [PMID: 38267453 PMCID: PMC10808355 DOI: 10.1038/s41467-024-44862-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 01/04/2024] [Indexed: 01/26/2024] Open
Abstract
Excision of the initiator methionine is among the first co-translational processes that occur at the ribosome. While this crucial step in protein maturation is executed by two types of methionine aminopeptidases in eukaryotes (MAP1 and MAP2), additional roles in disease and translational regulation have drawn more attention to MAP2. Here, we report several cryo-EM structures of human and fungal MAP2 at the 80S ribosome. Irrespective of nascent chains, MAP2 can occupy the tunnel exit. On nascent chain displaying ribosomes, the MAP2-80S interaction is highly dynamic and the MAP2-specific N-terminal extension engages in stabilizing interactions with the long rRNA expansion segment ES27L. Loss of this extension by autoproteolytic cleavage impedes interactions at the tunnel, while promoting MAP2 to enter the ribosomal A-site, where it engages with crucial functional centers of translation. These findings reveal that proteolytic remodeling of MAP2 severely affects ribosome binding, and set the stage for targeted functional studies.
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Affiliation(s)
- Marius A Klein
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120, Heidelberg, Germany
| | - Klemens Wild
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120, Heidelberg, Germany
| | - Miglė Kišonaitė
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120, Heidelberg, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120, Heidelberg, Germany.
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9
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Solari CA, Ortolá Martínez MC, Fernandez JM, Bates C, Cueto G, Valacco MP, Morales-Polanco F, Moreno S, Rossi S, Ashe MP, Portela P. Riboproteome remodeling during quiescence exit in Saccharomyces cerevisiae. iScience 2024; 27:108727. [PMID: 38235324 PMCID: PMC10792236 DOI: 10.1016/j.isci.2023.108727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 08/15/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024] Open
Abstract
The quiescent state is the prevalent mode of cellular life in most cells. Saccharomyces cerevisiae is a useful model for studying the molecular basis of the cell cycle, quiescence, and aging. Previous studies indicate that heterogeneous ribosomes show a specialized translation function to adjust the cellular proteome upon a specific stimulus. Using nano LC-MS/MS, we identified 69 of the 79 ribosomal proteins (RPs) that constitute the eukaryotic 80S ribosome during quiescence. Our study shows that the riboproteome is composed of 444 accessory proteins comprising cellular functions such as translation, protein folding, amino acid and glucose metabolism, cellular responses to oxidative stress, and protein degradation. Furthermore, the stoichiometry of both RPs and accessory proteins on ribosome particles is different depending on growth conditions and among monosome and polysome fractions. Deficiency of different RPs resulted in defects of translational capacity, suggesting that ribosome composition can result in changes in translational activity during quiescence.
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Affiliation(s)
- Clara A. Solari
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - María Clara Ortolá Martínez
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - Juan M. Fernandez
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - Christian Bates
- The Michael Smith Building, Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Gerardo Cueto
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Ecología, Genética y Evolución, Instituto IEGEBA (CONICET-UBA), Buenos Aires, Argentina
| | - María Pía Valacco
- CEQUIBIEM- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - Fabián Morales-Polanco
- The Michael Smith Building, Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Silvia Moreno
- CEQUIBIEM- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - Silvia Rossi
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - Mark P. Ashe
- The Michael Smith Building, Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Paula Portela
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
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10
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Susanto TT, Hung V, Levine AG, Kerr CH, Yoo Y, Chen Y, Oses-Prieto JA, Fromm L, Fujii K, Wernig M, Burlingame AL, Ruggero D, Barna M. RAPIDASH: A tag-free enrichment of ribosome-associated proteins reveals compositional dynamics in embryonic tissues and stimulated macrophages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.07.570613. [PMID: 38106052 PMCID: PMC10723405 DOI: 10.1101/2023.12.07.570613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Ribosomes are emerging as direct regulators of gene expression, with ribosome-associated proteins (RAPs) allowing ribosomes to modulate translational control. However, a lack of technologies to enrich RAPs across many sample types has prevented systematic analysis of RAP number, dynamics, and functions. Here, we have developed a label-free methodology called RAPIDASH to enrich ribosomes and RAPs from any sample. We applied RAPIDASH to mouse embryonic tissues and identified hundreds of potential RAPs, including DHX30 and LLPH, two forebrain RAPs important for neurodevelopment. We identified a critical role of LLPH in neural development that is linked to the translation of genes with long coding sequences. Finally, we characterized ribosome composition remodeling during immune activation and observed extensive changes post-stimulation. RAPIDASH has therefore enabled the discovery of RAPs ranging from those with neuroregulatory functions to those activated by immune stimuli, thereby providing critical insights into how ribosomes are remodeled.
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Affiliation(s)
- Teodorus Theo Susanto
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Victoria Hung
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andrew G Levine
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Craig H Kerr
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yongjin Yoo
- Institute for Stem Cell Biology and Regenerative Medicine and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yuxiang Chen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Juan A Oses-Prieto
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Lisa Fromm
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Kotaro Fujii
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marius Wernig
- Institute for Stem Cell Biology and Regenerative Medicine and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Davide Ruggero
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Maria Barna
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
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11
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Zhang L, Braynen J, Fahey A, Chopra K, Cifani P, Tadesse D, Regulski M, Hu F, van Dam HJJ, Xie M, Ware D, Blaby-Haas CE. Two related families of metal transferases, ZNG1 and ZNG2, are involved in acclimation to poor Zn nutrition in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2023; 14:1237722. [PMID: 37965006 PMCID: PMC10642216 DOI: 10.3389/fpls.2023.1237722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 10/02/2023] [Indexed: 11/16/2023]
Abstract
Metal homeostasis has evolved to tightly modulate the availability of metals within the cell, avoiding cytotoxic interactions due to excess and protein inactivity due to deficiency. Even in the presence of homeostatic processes, however, low bioavailability of these essential metal nutrients in soils can negatively impact crop health and yield. While research has largely focused on how plants assimilate metals, acclimation to metal-limited environments requires a suite of strategies that are not necessarily involved in metal transport across membranes. The identification of these mechanisms provides a new opportunity to improve metal-use efficiency and develop plant foodstuffs with increased concentrations of bioavailable metal nutrients. Here, we investigate the function of two distinct subfamilies of the nucleotide-dependent metallochaperones (NMCs), named ZNG1 and ZNG2, that are found in plants, using Arabidopsis thaliana as a reference organism. AtZNG1 (AT1G26520) is an ortholog of human and fungal ZNG1, and like its previously characterized eukaryotic relatives, localizes to the cytosol and physically interacts with methionine aminopeptidase type I (AtMAP1A). Analysis of AtZNG1, AtMAP1A, AtMAP2A, and AtMAP2B transgenic mutants are consistent with the role of Arabidopsis ZNG1 as a Zn transferase for AtMAP1A, as previously described in yeast and zebrafish. Structural modeling reveals a flexible cysteine-rich loop that we hypothesize enables direct transfer of Zn from AtZNG1 to AtMAP1A during GTP hydrolysis. Based on proteomics and transcriptomics, loss of this ancient and conserved mechanism has pleiotropic consequences impacting the expression of hundreds of genes, including those involved in photosynthesis and vesicle transport. Members of the plant-specific family of NMCs, ZNG2A1 (AT1G80480) and ZNG2A2 (AT1G15730), are also required during Zn deficiency, but their target protein(s) remain to be discovered. RNA-seq analyses reveal wide-ranging impacts across the cell when the genes encoding these plastid-localized NMCs are disrupted.
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Affiliation(s)
- Lifang Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Janeen Braynen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Audrey Fahey
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Kriti Chopra
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY, United States
| | - Paolo Cifani
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Dimiru Tadesse
- Biology Department, Brookhaven National Laboratory, Upton, NY, United States
| | - Michael Regulski
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Fangle Hu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Hubertus J. J. van Dam
- Condensed Matter Physics and Materials Science Department, Brookhaven National Laboratory, Upton, NY, United States
| | - Meng Xie
- Biology Department, Brookhaven National Laboratory, Upton, NY, United States
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
- USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY, United States
| | - Crysten E. Blaby-Haas
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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12
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Chojnowski G. DoubleHelix: nucleic acid sequence identification, assignment and validation tool for cryo-EM and crystal structure models. Nucleic Acids Res 2023; 51:8255-8269. [PMID: 37395405 PMCID: PMC10450167 DOI: 10.1093/nar/gkad553] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/29/2023] [Accepted: 06/16/2023] [Indexed: 07/04/2023] Open
Abstract
Sequence assignment is a key step of the model building process in both cryogenic electron microscopy (cryo-EM) and macromolecular crystallography (MX). If the assignment fails, it can result in difficult to identify errors affecting the interpretation of a model. There are many model validation strategies that help experimentalists in this step of protein model building, but they are virtually non-existent for nucleic acids. Here, I present doubleHelix-a comprehensive method for assignment, identification, and validation of nucleic acid sequences in structures determined using cryo-EM and MX. The method combines a neural network classifier of nucleobase identities and a sequence-independent secondary structure assignment approach. I show that the presented method can successfully assist sequence-assignment step in nucleic-acid model building at lower resolutions, where visual map interpretation is very difficult. Moreover, I present examples of sequence assignment errors detected using doubleHelix in cryo-EM and MX structures of ribosomes deposited in the Protein Data Bank, which escaped the scrutiny of available model-validation approaches. The doubleHelix program source code is available under BSD-3 license at https://gitlab.com/gchojnowski/doublehelix.
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Affiliation(s)
- Grzegorz Chojnowski
- European Molecular Biology Laboratory, Hamburg Unit, Notkestraße 85, 22607 Hamburg, Germany
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13
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Höpfler M, Absmeier E, Peak-Chew SY, Vartholomaiou E, Passmore LA, Gasic I, Hegde RS. Mechanism of ribosome-associated mRNA degradation during tubulin autoregulation. Mol Cell 2023; 83:2290-2302.e13. [PMID: 37295431 PMCID: PMC10403363 DOI: 10.1016/j.molcel.2023.05.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 03/28/2023] [Accepted: 05/15/2023] [Indexed: 06/12/2023]
Abstract
Microtubules play crucial roles in cellular architecture, intracellular transport, and mitosis. The availability of free tubulin subunits affects polymerization dynamics and microtubule function. When cells sense excess free tubulin, they trigger degradation of the encoding mRNAs, which requires recognition of the nascent polypeptide by the tubulin-specific ribosome-binding factor TTC5. How TTC5 initiates the decay of tubulin mRNAs is unknown. Here, our biochemical and structural analysis reveals that TTC5 recruits the poorly studied protein SCAPER to the ribosome. SCAPER, in turn, engages the CCR4-NOT deadenylase complex through its CNOT11 subunit to trigger tubulin mRNA decay. SCAPER mutants that cause intellectual disability and retinitis pigmentosa in humans are impaired in CCR4-NOT recruitment, tubulin mRNA degradation, and microtubule-dependent chromosome segregation. Our findings demonstrate how recognition of a nascent polypeptide on the ribosome is physically linked to mRNA decay factors via a relay of protein-protein interactions, providing a paradigm for specificity in cytoplasmic gene regulation.
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Affiliation(s)
- Markus Höpfler
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Eva Absmeier
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Sew-Yeu Peak-Chew
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | - Lori A Passmore
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Ivana Gasic
- Department of Cell Biology, University of Geneva, Geneva, Switzerland
| | - Ramanujan S Hegde
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.
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14
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Gamerdinger M, Jia M, Schloemer R, Rabl L, Jaskolowski M, Khakzar KM, Ulusoy Z, Wallisch A, Jomaa A, Hunaeus G, Scaiola A, Diederichs K, Ban N, Deuerling E. NAC controls cotranslational N-terminal methionine excision in eukaryotes. Science 2023; 380:1238-1243. [PMID: 37347872 DOI: 10.1126/science.adg3297] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 05/18/2023] [Indexed: 06/24/2023]
Abstract
N-terminal methionine excision from newly synthesized proteins, catalyzed cotranslationally by methionine aminopeptidases (METAPs), is an essential and universally conserved process that plays a key role in cell homeostasis and protein biogenesis. However, how METAPs interact with ribosomes and how their cleavage specificity is ensured is unknown. We discovered that in eukaryotes the nascent polypeptide-associated complex (NAC) controls ribosome binding of METAP1. NAC recruits METAP1 using a long, flexible tail and provides a platform for the formation of an active methionine excision complex at the ribosomal tunnel exit. This mode of interaction ensures the efficient excision of methionine from cytosolic proteins, whereas proteins targeted to the endoplasmic reticulum are spared. Our results suggest a broader mechanism for how access of protein biogenesis factors to translating ribosomes is controlled.
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Affiliation(s)
- Martin Gamerdinger
- Department of Biology, Molecular Microbiology, University of Konstanz, 78457 Konstanz, Germany
| | - Min Jia
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Renate Schloemer
- Department of Biology, Molecular Microbiology, University of Konstanz, 78457 Konstanz, Germany
| | - Laurenz Rabl
- Department of Biology, Molecular Microbiology, University of Konstanz, 78457 Konstanz, Germany
| | - Mateusz Jaskolowski
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Katrin M Khakzar
- Department of Biology, Molecular Microbiology, University of Konstanz, 78457 Konstanz, Germany
| | - Zeynel Ulusoy
- Department of Biology, Molecular Microbiology, University of Konstanz, 78457 Konstanz, Germany
| | - Annalena Wallisch
- Department of Biology, Molecular Microbiology, University of Konstanz, 78457 Konstanz, Germany
| | - Ahmad Jomaa
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Gundula Hunaeus
- Department of Biology, Molecular Microbiology, University of Konstanz, 78457 Konstanz, Germany
| | - Alain Scaiola
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Kay Diederichs
- Department of Biology, Molecular Bioinformatics, University of Konstanz, 78457 Konstanz, Germany
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Elke Deuerling
- Department of Biology, Molecular Microbiology, University of Konstanz, 78457 Konstanz, Germany
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15
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McGee JP, Armache JP, Lindner SE. Ribosome heterogeneity and specialization of Plasmodium parasites. PLoS Pathog 2023; 19:e1011267. [PMID: 37053161 PMCID: PMC10101515 DOI: 10.1371/journal.ppat.1011267] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Affiliation(s)
- James P McGee
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, Pennsylvania, United States of America
- Huck Center for Malaria Research, Pennsylvania State University, Pennsylvania, United States of America
| | - Jean-Paul Armache
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, Pennsylvania, United States of America
- Center for Eukaryotic Gene Regulation, Pennsylvania State University, Pennsylvania, United States of America
| | - Scott E Lindner
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, Pennsylvania, United States of America
- Huck Center for Malaria Research, Pennsylvania State University, Pennsylvania, United States of America
- Center for Eukaryotic Gene Regulation, Pennsylvania State University, Pennsylvania, United States of America
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16
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Dove AS, Dzurny DI, Dees WR, Qin N, Nunez Rodriguez CC, Alt LA, Ellward GL, Best JA, Rudawski NG, Fujii K, Czyż DM. Silver nanoparticles enhance the efficacy of aminoglycosides against antibiotic-resistant bacteria. Front Microbiol 2023; 13:1064095. [PMID: 36798870 PMCID: PMC9927651 DOI: 10.3389/fmicb.2022.1064095] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 12/30/2022] [Indexed: 02/04/2023] Open
Abstract
As the threat of antimicrobial-resistant bacteria compromises the safety and efficacy of modern healthcare practices, the search for effective treatments is more urgent than ever. For centuries, silver (Ag) has been known to have antibacterial properties and, over the past two decades, Ag-based nanoparticles have gained traction as potential antimicrobials. The antibacterial efficacy of Ag varies with structure, size, and concentration. In the present study, we examined Ag nanoparticles (AgNPs) for their antimicrobial activity and safety. We compared different commercially-available AgNPs against gram-negative Escherichia coli, Pseudomonas aeruginosa, Acinetobacter baumannii, and gram-positive Staphylococcus aureus methicillin-resistant and susceptible strains. The most effective formula of AgNPs tested had single-digit (μg/mL) minimum inhibitory concentrations against gram-negative multidrug-resistant clinical bacterial isolates with novel and emerging mechanisms of resistance. The mode of killing was assessed in E. coli and was found to be bactericidal, which is consistent with previous studies using other AgNP formulations. We evaluated cytotoxicity by measuring physiological readouts using the Caenorhabditis elegans model and found that motility was affected, but not the lifespan. Furthermore, we found that at their antibacterial concentrations, AgNPs were non-cytotoxic to any of the mammalian cell lines tested, including macrophages, stem cells, and epithelial cells. More interestingly, our experiments revealed synergy with clinically relevant antibiotics. We found that a non-toxic and non-effective concentration of AgNPs reduced the minimum inhibitory concentrations of aminoglycoside by approximately 22-fold. Because both aminoglycosides and Ag are known to target the bacterial ribosome, we tested whether Ag could also target eukaryotic ribosomes. We measured the rate of mistranslation at bactericidal concentration and found no effect, indicating that AgNPs are not proteotoxic to the host at the tested concentrations. Collectively, our results suggest that AgNPs could have a promising clinical application as a potential stand-alone therapy or antibiotic adjuvants.
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Affiliation(s)
- Autumn S. Dove
- Department of Microbiology and Cell Science, College of Agricultural and Life Sciences, University of Florida, Gainesville, FL, United States
| | - Dominika I. Dzurny
- Department of Microbiology and Cell Science, College of Agricultural and Life Sciences, University of Florida, Gainesville, FL, United States
| | - Wren R. Dees
- Department of Microbiology and Cell Science, College of Agricultural and Life Sciences, University of Florida, Gainesville, FL, United States
| | - Nan Qin
- Natural Immunogenics Corporation, Sarasota, FL, United States
| | | | - Lauren A. Alt
- Natural Immunogenics Corporation, Sarasota, FL, United States
| | - Garrett L. Ellward
- Department of Microbiology and Cell Science, College of Agricultural and Life Sciences, University of Florida, Gainesville, FL, United States
| | - Jacob A. Best
- Department of Microbiology and Cell Science, College of Agricultural and Life Sciences, University of Florida, Gainesville, FL, United States
| | - Nicholas G. Rudawski
- Research Service Centers, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, United States
| | - Kotaro Fujii
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL, United States,Center for NeuroGenetics, University of Florida, Gainesville, FL, United States
| | - Daniel M. Czyż
- Department of Microbiology and Cell Science, College of Agricultural and Life Sciences, University of Florida, Gainesville, FL, United States,*Correspondence: Daniel M. Czyż, ✉
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17
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Hariharan N, Ghosh S, Palakodeti D. The story of rRNA expansion segments: Finding functionality amidst diversity. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1732. [PMID: 35429135 DOI: 10.1002/wrna.1732] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 02/24/2022] [Accepted: 03/19/2022] [Indexed: 01/31/2023]
Abstract
Expansion segments (ESs) are multinucleotide insertions present across phyla at specific conserved positions in eukaryotic rRNAs. ESs are generally absent in bacterial rRNAs with some exceptions, while the archaeal rRNAs have microexpansions at regions that coincide with those of eukaryotic ESs. Although there is an increasing prominence of ribosomes, especially the ribosomal proteins, in fine-tuning gene expression through translation regulation, the role of rRNA ESs is relatively underexplored. While rRNAs have been established as the major catalytic hub in ribosome function, the presence of ESs widens their scope as a species-specific regulatory hub of protein synthesis. In this comprehensive review, we have elaborately discussed the current understanding of the functional aspects of rRNA ESs of cytoplasmic eukaryotic ribosomes and discuss their past, present, and future. This article is categorized under: RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems Translation > Ribosome Structure/Function Translation > Regulation.
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Affiliation(s)
- Nivedita Hariharan
- Technologies for the Advancement of Science, Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, India.,The University of Trans-disciplinary Health Sciences and Technology, Bangalore, India
| | - Sumana Ghosh
- Manipal Academy of Higher Education, Manipal, India
| | - Dasaradhi Palakodeti
- Technologies for the Advancement of Science, Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, India
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18
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de Teresa-Trueba I, Goetz SK, Mattausch A, Stojanovska F, Zimmerli CE, Toro-Nahuelpan M, Cheng DWC, Tollervey F, Pape C, Beck M, Diz-Muñoz A, Kreshuk A, Mahamid J, Zaugg JB. Convolutional networks for supervised mining of molecular patterns within cellular context. Nat Methods 2023; 20:284-294. [PMID: 36690741 PMCID: PMC9911354 DOI: 10.1038/s41592-022-01746-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 12/02/2022] [Indexed: 01/24/2023]
Abstract
Cryo-electron tomograms capture a wealth of structural information on the molecular constituents of cells and tissues. We present DeePiCt (deep picker in context), an open-source deep-learning framework for supervised segmentation and macromolecular complex localization in cryo-electron tomography. To train and benchmark DeePiCt on experimental data, we comprehensively annotated 20 tomograms of Schizosaccharomyces pombe for ribosomes, fatty acid synthases, membranes, nuclear pore complexes, organelles, and cytosol. By comparing DeePiCt to state-of-the-art approaches on this dataset, we show its unique ability to identify low-abundance and low-density complexes. We use DeePiCt to study compositionally distinct subpopulations of cellular ribosomes, with emphasis on their contextual association with mitochondria and the endoplasmic reticulum. Finally, applying pre-trained networks to a HeLa cell tomogram demonstrates that DeePiCt achieves high-quality predictions in unseen datasets from different biological species in a matter of minutes. The comprehensively annotated experimental data and pre-trained networks are provided for immediate use by the community.
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Affiliation(s)
- Irene de Teresa-Trueba
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,Present Address: Computer Science and Artificial Intelligence Lab, ENGIE Lab Crigen, Stains, France
| | - Sara K. Goetz
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Alexander Mattausch
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
| | - Frosina Stojanovska
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Christian E. Zimmerli
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.419494.50000 0001 1018 9466Present Address: Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Mauricio Toro-Nahuelpan
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,Present Address: Santiago GmbH & Co. KG, Willich, Germany
| | - Dorothy W. C. Cheng
- grid.7700.00000 0001 2190 4373Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany ,grid.4709.a0000 0004 0495 846XCell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Fergus Tollervey
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Constantin Pape
- grid.4709.a0000 0004 0495 846XCell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.7450.60000 0001 2364 4210Present Address: Institute for Computer Science, Universität Göttingen, Göttingen, Germany
| | - Martin Beck
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.4709.a0000 0004 0495 846XCell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.419494.50000 0001 1018 9466Present Address: Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Alba Diz-Muñoz
- grid.4709.a0000 0004 0495 846XCell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Anna Kreshuk
- grid.4709.a0000 0004 0495 846XCell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany. .,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
| | - Judith B. Zaugg
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.4709.a0000 0004 0495 846XGenome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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19
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Baymukhametov TN, Lyabin DN, Chesnokov YM, Sorokin II, Pechnikova E, Vasiliev A, Afonina Z. Polyribosomes of circular topology are prevalent in mammalian cells. Nucleic Acids Res 2022; 51:908-918. [PMID: 36583341 PMCID: PMC9881139 DOI: 10.1093/nar/gkac1208] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 12/02/2022] [Accepted: 12/06/2022] [Indexed: 12/31/2022] Open
Abstract
Polyribosomes, the groups of ribosomes simultaneously translating a single mRNA molecule, are very common in both, prokaryotic and eukaryotic cells. Even in early EM studies, polyribosomes have been shown to possess various spatial conformations, including a ring-shaped configuration which was considered to be functionally important. However, a recent in situ cryo-ET analysis of predominant regular inter-ribosome contacts did not confirm the abundance of ring-shaped polyribosomes in a cell cytoplasm. To address this discrepancy, here we analyzed the cryo-ET structure of polyribosomes in diluted lysates of HeLa cells. It was shown that the vast majority of the ribosomes were combined into polysomes and were proven to be translationally active. Tomogram analysis revealed that circular polyribosomes are indeed very common in the cytoplasm, but they mostly possess pseudo-regular structures without specific inter-ribosomal contacts. Although the size of polyribosomes varied widely, most circular polysomes were relatively small in size (4-8 ribosomes). Our results confirm the recent data that it is cellular mRNAs with short ORF that most commonly form circular structures providing an enhancement of translation.
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Affiliation(s)
- Timur N Baymukhametov
- Structural biology department, National Research Center ‘Kurchatov Institute’, Moscow 123182, Russia
| | - Dmitry N Lyabin
- Institute of Protein Research RAS, Pushchino, Moscow Region 142290, Russia
| | - Yury M Chesnokov
- Probe and Electron Microscopy Resource Center, National Research Center ‘Kurchatov Institute’, Moscow 123182, Russia
| | - Ivan I Sorokin
- Institute of Protein Research RAS, Pushchino, Moscow Region 142290, Russia
| | - Evgeniya V Pechnikova
- Probe and Electron Microscopy Resource Center, National Research Center ‘Kurchatov Institute’, Moscow 123182, Russia,Electron Microscopy Laboratory, Shubnikov Institute of Crystallography of Federal Scientific Research Centre ‘Crystallography and Photonics’ RAS, Moscow 119333, Russia
| | - Alexander L Vasiliev
- Probe and Electron Microscopy Resource Center, National Research Center ‘Kurchatov Institute’, Moscow 123182, Russia,Electron Microscopy Laboratory, Shubnikov Institute of Crystallography of Federal Scientific Research Centre ‘Crystallography and Photonics’ RAS, Moscow 119333, Russia
| | - Zhanna A Afonina
- To whom correspondence should be addressed. Tel: +7 985 7232812; Fax: +7 4967 318435;
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20
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Hoffmann PC, Kreysing JP, Khusainov I, Tuijtel MW, Welsch S, Beck M. Structures of the eukaryotic ribosome and its translational states in situ. Nat Commun 2022; 13:7435. [PMID: 36460643 PMCID: PMC9718845 DOI: 10.1038/s41467-022-34997-w] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 11/15/2022] [Indexed: 12/03/2022] Open
Abstract
Ribosomes translate genetic information into primary structure. During translation, various cofactors transiently bind to the ribosome that undergoes prominent conformational and structural changes. Different translational states of ribosomes have been well characterized in vitro. However, to which extent the known translational states are representative of the native situation inside cells has thus far only been addressed in prokaryotes. Here, we apply cryo-electron tomography to cryo-FIB milled Dictyostelium discoideum cells combined with subtomogram averaging and classification. We obtain an in situ structure that is locally resolved up to 3 Angstrom, the distribution of eukaryotic ribosome translational states, and unique arrangement of rRNA expansion segments. Our work demonstrates the use of in situ structural biology techniques for identifying distinct ribosome states within the cellular environment.
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Affiliation(s)
- Patrick C. Hoffmann
- grid.419494.50000 0001 1018 9466Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Jan Philipp Kreysing
- grid.419494.50000 0001 1018 9466Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany ,Department of Molecular Sociology, IMPRS on Cellular Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Iskander Khusainov
- grid.419494.50000 0001 1018 9466Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Maarten W. Tuijtel
- grid.419494.50000 0001 1018 9466Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Sonja Welsch
- grid.419494.50000 0001 1018 9466Central Electron Microscopy Facility, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Martin Beck
- grid.419494.50000 0001 1018 9466Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
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21
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Wang X, Zhu J, Zhang D, Liu G. Ribosomal control in RNA virus-infected cells. Front Microbiol 2022; 13:1026887. [PMID: 36419416 PMCID: PMC9677555 DOI: 10.3389/fmicb.2022.1026887] [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: 08/24/2022] [Accepted: 10/19/2022] [Indexed: 11/09/2022] Open
Abstract
Viruses are strictly intracellular parasites requiring host cellular functions to complete their reproduction cycle involving virus infection of host cell, viral genome replication, viral protein translation, and virion release. Ribosomes are protein synthesis factories in cells, and viruses need to manipulate ribosomes to complete their protein synthesis. Viruses use translation initiation factors through their own RNA structures or cap structures, thereby inducing ribosomes to synthesize viral proteins. Viruses also affect ribosome production and the assembly of mature ribosomes, and regulate the recognition of mRNA by ribosomes, thereby promoting viral protein synthesis and inhibiting the synthesis of host antiviral immune proteins. Here, we review the remarkable mechanisms used by RNA viruses to regulate ribosomes, in particular, the mechanisms by which RNA viruses induce the formation of specific heterogeneous ribosomes required for viral protein translation. This review provides valuable insights into the control of viral infection and diseases from the perspective of viral protein synthesis.
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22
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Biesiada M, Hu MY, Williams LD, Purzycka KJ, Petrov AS. rRNA expansion segment 7 in eukaryotes: from Signature Fold to tentacles. Nucleic Acids Res 2022; 50:10717-10732. [PMID: 36200812 PMCID: PMC9561286 DOI: 10.1093/nar/gkac844] [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: 12/27/2021] [Revised: 09/13/2022] [Accepted: 09/22/2022] [Indexed: 11/14/2022] Open
Abstract
The ribosomal core is universally conserved across the tree of life. However, eukaryotic ribosomes contain diverse rRNA expansion segments (ESs) on their surfaces. Sites of ES insertions are predicted from sites of insertion of micro-ESs in archaea. Expansion segment 7 (ES7) is one of the most diverse regions of the ribosome, emanating from a short stem loop and ranging to over 750 nucleotides in mammals. We present secondary and full-atom 3D structures of ES7 from species spanning eukaryotic diversity. Our results are based on experimental 3D structures, the accretion model of ribosomal evolution, phylogenetic relationships, multiple sequence alignments, RNA folding algorithms and 3D modeling by RNAComposer. ES7 contains a distinct motif, the 'ES7 Signature Fold', which is generally invariant in 2D topology and 3D structure in all eukaryotic ribosomes. We establish a model in which ES7 developed over evolution through a series of elementary and recursive growth events. The data are sufficient to support an atomic-level accretion path for rRNA growth. The non-monophyletic distribution of some ES7 features across the phylogeny suggests acquisition via convergent processes. And finally, illustrating the power of our approach, we constructed the 2D and 3D structure of the entire LSU rRNA of Mus musculus.
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Affiliation(s)
- Marcin Biesiada
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
| | - Michael Y Hu
- Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA 30332, USA.,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Loren Dean Williams
- Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA 30332, USA.,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Katarzyna J Purzycka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
| | - Anton S Petrov
- Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA 30332, USA.,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
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23
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Cottilli P, Itoh Y, Nobe Y, Petrov AS, Lisón P, Taoka M, Amunts A. Cryo-EM structure and rRNA modification sites of a plant ribosome. PLANT COMMUNICATIONS 2022; 3:100342. [PMID: 35643637 PMCID: PMC9483110 DOI: 10.1016/j.xplc.2022.100342] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/07/2022] [Accepted: 05/25/2022] [Indexed: 05/25/2023]
Abstract
Protein synthesis in crop plants contributes to the balance of food and fuel on our planet, which influences human metabolic activity and lifespan. Protein synthesis can be regulated with respect to changing environmental cues via the deposition of chemical modifications into rRNA. Here, we present the structure of a plant ribosome from tomato and a quantitative mass spectrometry analysis of its rRNAs. The study reveals fine features of the ribosomal proteins and 71 plant-specific rRNA modifications, and it re-annotates 30 rRNA residues in the available sequence. At the protein level, isoAsp is found in position 137 of uS11, and a zinc finger previously believed to be universal is missing from eL34, suggesting a lower effect of zinc deficiency on protein synthesis in plants. At the rRNA level, the plant ribosome differs markedly from its human counterpart with respect to the spatial distribution of modifications. Thus, it represents an additional layer of gene expression regulation, highlighting the molecular signature of a plant ribosome. The results provide a reference model of a plant ribosome for structural studies and an accurate marker for molecular ecology.
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Affiliation(s)
- Patrick Cottilli
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165 Solna, Sweden
| | - Yuzuru Itoh
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165 Solna, Sweden
| | - Yuko Nobe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Anton S Petrov
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Purificación Lisón
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València (UPV) - Consejo Superior de Investigaciones Científicas (CSIC), Ciudad Politécnica de la Innovación (CPI), Valencia 46022, Spain
| | - Masato Taoka
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan.
| | - Alexey Amunts
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165 Solna, Sweden.
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24
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Yang CI, Zhu Z, Jones JJ, Lomenick B, Chou TF, Shan SO. System-wide analyses reveal essential roles of N-terminal protein modification in bacterial membrane integrity. iScience 2022; 25:104756. [PMID: 35942092 PMCID: PMC9356101 DOI: 10.1016/j.isci.2022.104756] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/20/2022] [Accepted: 07/07/2022] [Indexed: 11/18/2022] Open
Abstract
The removal of the N-terminal formyl group on nascent proteins by peptide deformylase (PDF) is the most prevalent protein modification in bacteria. PDF is a critical target of antibiotic development; however, its role in bacterial physiology remains a long-standing question. This work used the time-resolved analyses of the Escherichia coli translatome and proteome to investigate the consequences of PDF inhibition. Loss of PDF activity rapidly induces cellular stress responses, especially those associated with protein misfolding and membrane defects, followed by a global down-regulation of metabolic pathways. Rapid membrane hyperpolarization and impaired membrane integrity were observed shortly after PDF inhibition, suggesting that the plasma membrane disruption is the most immediate and primary consequence of formyl group retention on nascent proteins. This work resolves the physiological function of a ubiquitous protein modification and uncovers its crucial role in maintaining the structure and function of the bacterial membrane. PDF inhibition induces membrane defects and metabolic imbalance Deformylation is involved in nascent protein folding Membrane is the earliest and primary target of N-formylation on nascent proteins PDF activity is essential for redox homeostasis in bacteria
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Affiliation(s)
- Chien-I Yang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Zikun Zhu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jeffrey J. Jones
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - Brett Lomenick
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - Tsui-Fen Chou
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - Shu-ou Shan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
- Corresponding author
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25
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Paromomycin Reduces Vairimorpha (Nosema) ceranae Infection in Honey Bees but Perturbs Microbiome Levels and Midgut Cell Function. Microorganisms 2022; 10:microorganisms10061107. [PMID: 35744625 PMCID: PMC9231153 DOI: 10.3390/microorganisms10061107] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 05/23/2022] [Accepted: 05/23/2022] [Indexed: 02/04/2023] Open
Abstract
Paromomycin is a naturally occurring aminoglycoside antibiotic that has effects on both prokaryotic and eukaryotic microbes. However, previous reports have indicated that it has little effect on microsporidia, including Vairimorpha (Nosema) ceranae, in cell culture models. V. ceranae is one of a number of microsporidia species that cause disease in honey bees and substantial efforts to find new treatment strategies for bees that are infected with these pathogens are ongoing. When testing compounds for potential activity against V. ceranae in whole organisms, we found that paromomycin reduces the infection intensity of this parasite. Critically, the necessary doses of paromomycin have high activity against the bacteria of the honey bee microbiome and cause evident stress in bees. Microsporidia have been shown to lack an essential binding site on the ribosome that is known to allow for maximal inhibition by paromomycin. Thus, it is possible that paromomycin impacts parasite levels through non-cell autonomous effects on microsporidia infection levels via effects on the microbiome or midgut cellular function. As paromomycin treatment could cause widespread honey bee health issues in agricultural settings, it does not represent an appropriate anti-microsporidia agent for use in the field.
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26
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Pasquini M, Grosjean N, Hixson KK, Nicora CD, Yee EF, Lipton M, Blaby IK, Haley JD, Blaby-Haas CE. Zng1 is a GTP-dependent zinc transferase needed for activation of methionine aminopeptidase. Cell Rep 2022; 39:110834. [PMID: 35584675 DOI: 10.1016/j.celrep.2022.110834] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 02/28/2022] [Accepted: 04/27/2022] [Indexed: 12/12/2022] Open
Abstract
The evolution of zinc (Zn) as a protein cofactor altered the functional landscape of biology, but dependency on Zn also created an Achilles' heel, necessitating adaptive mechanisms to ensure Zn availability to proteins. A debated strategy is whether metallochaperones exist to prioritize essential Zn-dependent proteins. Here, we present evidence for a conserved family of putative metal transferases in human and fungi, which interact with Zn-dependent methionine aminopeptidase type I (MetAP1/Map1p/Fma1). Deletion of the putative metal transferase in Saccharomyces cerevisiae (ZNG1; formerly YNR029c) leads to defective Map1p function and a Zn-deficiency growth defect. In vitro, Zng1p can transfer Zn2+ or Co2+ to apo-Map1p, but unlike characterized copper chaperones, transfer is dependent on GTP hydrolysis. Proteomics reveal mis-regulation of the Zap1p transcription factor regulon because of loss of ZNG1 and Map1p activity, suggesting that Zng1p is required to avoid a compounding effect of Map1p dysfunction on survival during Zn limitation.
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Affiliation(s)
- Miriam Pasquini
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Nicolas Grosjean
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Kim K Hixson
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Estella F Yee
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Mary Lipton
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Ian K Blaby
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - John D Haley
- Department of Pathology and Biological Mass Spectrometry Facility, Stony Brook University, Stony Brook, NY 11794, USA
| | - Crysten E Blaby-Haas
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA; Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA.
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27
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Fan W, Eklund E, Sherman RM, Liu H, Pitts S, Ford B, Rajeshkumar NV, Laiho M. Widespread genetic heterogeneity of human ribosomal RNA genes. RNA (NEW YORK, N.Y.) 2022; 28:478-492. [PMID: 35110373 PMCID: PMC8925967 DOI: 10.1261/rna.078925.121] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 12/28/2021] [Indexed: 05/28/2023]
Abstract
Polymorphism drives survival under stress and provides adaptability. Genetic polymorphism of ribosomal RNA (rRNA) genes derives from internal repeat variation of this multicopy gene, and from interindividual variation. A considerable amount of rRNA sequence heterogeneity has been proposed but has been challenging to estimate given the scarcity of accurate reference sequences. We identified four rDNA copies on chromosome 21 (GRCh38) with 99% similarity to recently introduced reference sequence KY962518.1. We customized a GATK bioinformatics pipeline using the four rDNA loci, spanning a total 145 kb, for variant calling and used high-coverage whole-genome sequencing (WGS) data from the 1000 Genomes Project to analyze variants in 2504 individuals from 26 populations. We identified a total of 3791 variant positions. The variants positioned nonrandomly on the rRNA gene. Invariant regions included the promoter, early 5' ETS, most of 18S, 5.8S, ITS1, and large areas of the intragenic spacer. A total of 470 variant positions were observed on 28S rRNA. The majority of the 28S rRNA variants were located on highly flexible human-expanded rRNA helical folds ES7L and ES27L, suggesting that these represent positions of diversity and are potentially under continuous evolution. Several variants were validated based on RNA-seq analyses. Population analyses showed remarkable ancestry-linked genetic variance and the presence of both high penetrance and frequent variants in the 5' ETS, ITS2, and 28S regions segregating according to the continental populations. These findings provide a genetic view of rRNA gene array heterogeneity and raise the need to functionally assess how the 28S rRNA variants affect ribosome functions.
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Affiliation(s)
- Wenjun Fan
- Department of Radiation Oncology and Molecular Radiation Sciences, and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Eetu Eklund
- Department of Radiation Oncology and Molecular Radiation Sciences, and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Rachel M Sherman
- Department of Computer Science, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Hester Liu
- Department of Radiation Oncology and Molecular Radiation Sciences, and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Stephanie Pitts
- Department of Radiation Oncology and Molecular Radiation Sciences, and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Brittany Ford
- Drug Research Program, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland
| | - N V Rajeshkumar
- Department of Radiation Oncology and Molecular Radiation Sciences, and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Marikki Laiho
- Department of Radiation Oncology and Molecular Radiation Sciences, and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
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28
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Santos B, Zeng R, Jorge SF, Ferreira-Junior JR, Barrientos A, Barros MH. Functional analyses of mitoribosome 54S subunit devoid of mitochondria-specific protein sequences. Yeast 2022; 39:208-229. [PMID: 34713496 PMCID: PMC8969203 DOI: 10.1002/yea.3678] [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: 02/22/2021] [Revised: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 12/17/2022] Open
Abstract
In Saccharomyces cerevisiae, mitoribosomes are composed of a 54S large subunit (mtLSU) and a 37S small subunit (mtSSU). The two subunits altogether contain 73 mitoribosome proteins (MRPs) and two ribosomal RNAs (rRNAs). Although mitoribosomes preserve some similarities with their bacterial counterparts, they have significantly diverged by acquiring new proteins, protein extensions, and new RNA segments, adapting the mitoribosome to the synthesis of highly hydrophobic membrane proteins. In this study, we investigated the functional relevance of mitochondria-specific protein extensions at the C-terminus (C) or N-terminus (N) present in 19 proteins of the mtLSU. The studied mitochondria-specific extensions consist of long tails and loops extending from globular domains that mainly interact with mitochondria-specific proteins and 21S rRNA moieties extensions. The expression of variants devoid of extensions in uL4 (C), uL5 (N), uL13 (N), uL13 (C), uL16 (C), bL17 (N), bL17 (C), bL21 (24), uL22 (N), uL23 (N), uL23 (C), uL24 (C), bL27 (C), bL28 (N), bL28 (C), uL29 (N), uL29 (C), uL30 (C), bL31 (C), and bL32 (C) did not rescue the mitochondrial protein synthesis capacities and respiratory growth of the respective null mutants. On the contrary, the truncated form of the mitoribosome exit tunnel protein uL24 (N) yields a partially functional mitoribosome. Also, the removal of mitochondria-specific sequences from uL1 (N), uL3 (N), uL16 (N), bL9 (N), bL19 (C), uL29 (C), and bL31 (N) did not affect the mitoribosome function and respiratory growth. The collection of mutants described here provides new means to study and evaluate defective assembly modules in the mitoribosome biogenesis process.
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Affiliation(s)
- Barbara Santos
- Departamento de Microbiologia, Universidade de São Paulo, São Paulo, Brazil
| | - Rui Zeng
- Department of Neurology University of Miami Miller School of Medicine, Miami, USA
| | - Sasa F. Jorge
- Departamento de Microbiologia, Universidade de São Paulo, São Paulo, Brazil
| | | | - Antoni Barrientos
- Department of Neurology University of Miami Miller School of Medicine, Miami, USA
| | - Mario H. Barros
- Departamento de Microbiologia, Universidade de São Paulo, São Paulo, Brazil
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29
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Engineering and functional analysis of yeast with a monotypic 40S ribosome subunit. Proc Natl Acad Sci U S A 2022; 119:2114445119. [PMID: 35105807 PMCID: PMC8833219 DOI: 10.1073/pnas.2114445119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2021] [Indexed: 01/21/2023] Open
Abstract
Ribosomes are not monolithic but dynamic machines composed of heterogeneous ribosomal protein (RP) paralogs with elusive functions. Isolation and characterization of monotypic ribosomes with homogeneous RP paralog compositions represent ideal approaches to understand the role of pervasive RP paralogs in customizing translation abilities but are largely hurdled by the complexity of the cellular ribosome pool (e.g., in Saccharomyces cerevisiae, 59 RP paralog pairs allow >1017 potential RP combinations). Here, we engineered a yeast with monotypic 40S ribosomes, including both defined and homogenous RP paralogs, and further functional studies revealed that duplicated RP paralogs impart robustness and phenotypic plasticity (such as paromomycin tolerance) through both gene dose amplification and paralog-specific regulation, paving a way for the study of monotypic ribosomes. Emerging evidence reveals that ribosomes are not monolithic but dynamic machines with heterogeneous protein compositions that can reshape ribosomal translational abilities and cellular adaptation to environmental changes. Duplications of ribosomal protein (RP) genes are ubiquitous among organisms and are believed to affect cell function through paralog-specific regulation (e.g., by generating heterogeneous ribosomes) and/or gene dose amplification. However, direct evaluations of their impacts on cell function remain elusive due to the highly heterogeneous cellular RP pool. Here, we engineered a yeast with homogeneous 40S RP paralog compositions, designated homo-40S, by deleting the entire set of alternative duplicated genes encoding yeast 40S RP paralogs. Homo-40S displayed mild growth defects along with high sensitivity to the translation inhibitor paromomycin and a significantly increased stop codon readthrough. Moreover, doubling of the remaining RP paralogous genes in homo-40S rescued these phenotypes markedly, although not fully, compared to the wild-type phenotype, indicating that the dose of 40S RP genes together with the heterogeneity of the contents was vital for maintaining normal translational functionalities and growth robustness. Additional experiments revealed that homo-40S improved paromomycin tolerance via acquisition of bypass mutations or evolved to be diploid to generate fast-growing derivatives, highlighting the mutational robustness of engineered yeast to accommodate environmental and genetic changes. In summary, our work demonstrated that duplicated RP paralogs impart robustness and phenotypic plasticity through both gene dose amplification and paralog-specific regulation, paving the way for the direct study of ribosome biology through monotypic ribosomes with a homogeneous composition of specific RP paralogs.
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30
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Jespersen N, Monrroy L, Barandun J. Impact of Genome Reduction in Microsporidia. EXPERIENTIA SUPPLEMENTUM (2012) 2022; 114:1-42. [PMID: 35543997 DOI: 10.1007/978-3-030-93306-7_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Microsporidia represent an evolutionary outlier in the tree of life and occupy the extreme edge of the eukaryotic domain with some of their biological features. Many of these unicellular fungi-like organisms have reduced their genomic content to potentially the lowest limit. With some of the most compacted eukaryotic genomes, microsporidia are excellent model organisms to study reductive evolution and its functional consequences. While the growing number of sequenced microsporidian genomes have elucidated genome composition and organization, a recent increase in complementary post-genomic studies has started to shed light on the impacts of genome reduction in these unique pathogens. This chapter will discuss the biological framework enabling genome minimization and will use one of the most ancient and essential macromolecular complexes, the ribosome, to illustrate the effects of extreme genome reduction on a structural, molecular, and cellular level. We outline how reductive evolution in microsporidia has shaped DNA organization, the composition and function of the ribosome, and the complexity of the ribosome biogenesis process. Studying compacted mechanisms, processes, or macromolecular machines in microsporidia illuminates their unique lifestyle and provides valuable insights for comparative eukaryotic structural biology.
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Affiliation(s)
- Nathan Jespersen
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Science for Life Laboratory, Umeå University, Umeå, Sweden.
| | - Leonardo Monrroy
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Science for Life Laboratory, Umeå University, Umeå, Sweden
| | - Jonas Barandun
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Science for Life Laboratory, Umeå University, Umeå, Sweden.
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31
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tRNA Synthetases Are Recruited to Yeast Ribosomes by rRNA Expansion Segment 7L but Do Not Require Association for Functionality. Noncoding RNA 2021; 7:ncrna7040073. [PMID: 34842814 PMCID: PMC8628890 DOI: 10.3390/ncrna7040073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/16/2021] [Accepted: 11/20/2021] [Indexed: 12/03/2022] Open
Abstract
Protein biosynthesis is essential for any organism, yet how this process is regulated is not fully understood at the molecular level. During evolution, ribosomal RNA expanded in specific regions, referred to as rRNA expansion segments (ES). First functional roles of these expansions have only recently been discovered. Here we address the role of ES7La located in the large ribosomal subunit for factor recruitment to the yeast ribosome and the potential consequences for translation. Truncation of ES7La has only minor effects on ribosome biogenesis, translation efficiency and cell doubling. Using yeast rRNA deletion strains coupled with ribosome-specific mass spectrometry we analyzed the interactome of ribosomes lacking ES7La. Three aminoacyl-tRNA synthetases showed reduced ribosome association. Synthetase activities however remained unaltered suggesting that the pool of aminoacylated tRNAs is unaffected by the ES deletion. These results demonstrated that aminoacylation activities of tRNA synthetases per se do not rely on ribosome association. These findings suggest a role of ribosome-associated aminoacyl-tRNA synthetase beyond their core enzymatic functions.
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32
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Georgeson J, Schwartz S. The ribosome epitranscriptome: inert-or a platform for functional plasticity? RNA (NEW YORK, N.Y.) 2021; 27:1293-1301. [PMID: 34312287 PMCID: PMC8522695 DOI: 10.1261/rna.078859.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A universal property of all rRNAs explored to date is the prevalence of post-transcriptional ("epitranscriptional") modifications, which expand the chemical and topological properties of the four standard nucleosides. Are these modifications an inert, constitutive part of the ribosome? Or could they, in part, also regulate the structure or function of the ribosome? In this review, we summarize emerging evidence that rRNA modifications are more heterogeneous than previously thought, and that they can also vary from one condition to another, such as in the context of a cellular response or a developmental trajectory. We discuss the implications of these results and key open questions on the path toward connecting such heterogeneity with function.
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Affiliation(s)
- Joseph Georgeson
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
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33
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Streit D, Schleiff E. The Arabidopsis 2'-O-Ribose-Methylation and Pseudouridylation Landscape of rRNA in Comparison to Human and Yeast. FRONTIERS IN PLANT SCIENCE 2021; 12:684626. [PMID: 34381476 PMCID: PMC8351944 DOI: 10.3389/fpls.2021.684626] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/16/2021] [Indexed: 05/25/2023]
Abstract
Eukaryotic ribosome assembly starts in the nucleolus, where the ribosomal DNA (rDNA) is transcribed into the 35S pre-ribosomal RNA (pre-rRNA). More than two-hundred ribosome biogenesis factors (RBFs) and more than two-hundred small nucleolar RNAs (snoRNA) catalyze the processing, folding and modification of the rRNA in Arabidopsis thaliana. The initial pre-ribosomal 90S complex is formed already during transcription by association of ribosomal proteins (RPs) and RBFs. In addition, small nucleolar ribonucleoprotein particles (snoRNPs) composed of snoRNAs and RBFs catalyze the two major rRNA modification types, 2'-O-ribose-methylation and pseudouridylation. Besides these two modifications, rRNAs can also undergo base methylations and acetylation. However, the latter two modifications have not yet been systematically explored in plants. The snoRNAs of these snoRNPs serve as targeting factors to direct modifications to specific rRNA regions by antisense elements. Today, hundreds of different sites of modifications in the rRNA have been described for eukaryotic ribosomes in general. While our understanding of the general process of ribosome biogenesis has advanced rapidly, the diversities appearing during plant ribosome biogenesis is beginning to emerge. Today, more than two-hundred RBFs were identified by bioinformatics or biochemical approaches, including several plant specific factors. Similarly, more than two hundred snoRNA were predicted based on RNA sequencing experiments. Here, we discuss the predicted and verified rRNA modification sites and the corresponding identified snoRNAs on the example of the model plant Arabidopsis thaliana. Our summary uncovers the plant modification sites in comparison to the human and yeast modification sites.
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Affiliation(s)
- Deniz Streit
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt, Germany
| | - Enrico Schleiff
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt, Germany
- Frankfurt Institute for Advanced Studies (FIAS), Frankfurt, Germany
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34
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Gay DM, Lund AH, Jansson MD. Translational control through ribosome heterogeneity and functional specialization. Trends Biochem Sci 2021; 47:66-81. [PMID: 34312084 DOI: 10.1016/j.tibs.2021.07.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/18/2021] [Accepted: 07/01/2021] [Indexed: 12/31/2022]
Abstract
The conceptual origins of ribosome specialization can be traced back to the earliest days of molecular biology. Yet, this field has only recently begun to gather momentum, with numerous studies identifying distinct heterogeneous ribosome populations across multiple species and model systems. It is proposed that some of these compositionally distinct ribosomes may be functionally specialized and able to regulate the translation of specific mRNAs. Identification and functional characterization of specialized ribosomes has the potential to elucidate a novel layer of gene expression control, at the level of translation, where the ribosome itself is a key regulatory player. In this review, we discuss different sources of ribosome heterogeneity, evidence for ribosome specialization, and also the future directions of this exciting field.
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Affiliation(s)
- David M Gay
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Anders H Lund
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
| | - Martin D Jansson
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
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35
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Londei P, Ferreira-Cerca S. Ribosome Biogenesis in Archaea. Front Microbiol 2021; 12:686977. [PMID: 34367089 PMCID: PMC8339473 DOI: 10.3389/fmicb.2021.686977] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 05/14/2021] [Indexed: 12/02/2022] Open
Abstract
Making ribosomes is a major cellular process essential for the maintenance of functional ribosome homeostasis and to ensure appropriate gene expression. Strikingly, although ribosomes are universally conserved ribonucleoprotein complexes decoding the genetic information contained in messenger RNAs into proteins, their biogenesis shows an intriguing degree of variability across the tree of life. In this review, we summarize our knowledge on the least understood ribosome biogenesis pathway: the archaeal one. Furthermore, we highlight some evolutionary conserved and divergent molecular features of making ribosomes across the tree of life.
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Affiliation(s)
- Paola Londei
- Department of Molecular Medicine, University of Rome Sapienza, Rome, Italy
| | - Sébastien Ferreira-Cerca
- Biochemistry III - Regensburg Center for Biochemistry, Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany
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36
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Wang X, Yue Z, Xu F, Wang S, Hu X, Dai J, Zhao G. Coevolution of ribosomal RNA expansion segment 7L and assembly factor Noc2p specializes the ribosome biogenesis pathway between Saccharomyces cerevisiae and Candida albicans. Nucleic Acids Res 2021; 49:4655-4667. [PMID: 33823547 PMCID: PMC8096215 DOI: 10.1093/nar/gkab218] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 03/01/2021] [Accepted: 03/20/2021] [Indexed: 01/20/2023] Open
Abstract
Ribosomes of different species share an evolutionarily conserved core, exhibiting flexible shells formed partially by the addition of species-specific ribosomal RNAs (rRNAs) with largely unexplored functions. In this study, we showed that by swapping the Saccharomyces cerevisiae 25S rRNA genes with non-S. cerevisiae homologs, species-specific rRNA variations caused moderate to severe pre-rRNA processing defects. Specifically, rRNA substitution by the Candida albicans caused severe growth defects and deficient pre-rRNA processing. We observed that such defects could be attributed primarily to variations in expansion segment 7L (ES7L) and could be restored by an assembly factor Noc2p mutant (Noc2p-K384R). We showed that swapping ES7L attenuated the incorporation of Noc2p and other proteins (Erb1p, Rrp1p, Rpl6p and Rpl7p) into pre-ribosomes, and this effect could be compensated for by Noc2p-K384R. Furthermore, replacement of Noc2p with ortholog from C. albicans could also enhance the incorporation of Noc2p and the above proteins into pre-ribosomes and consequently restore normal growth. Taken together, our findings help to elucidate the roles played by the species-specific rRNA variations in ribosomal biogenesis and further provide evidence that coevolution of rRNA expansion segments and cognate assembly factors specialized the ribosome biogenesis pathway, providing further insights into the function and evolution of ribosome.
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Affiliation(s)
- Xiangxiang Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710129, China
| | - Zhiyong Yue
- School of Medicine, Xi'an International University, Xi'an 710077, China
| | - Feifei Xu
- Department of Anesthesiology and Perioperative Medicine, Xijing Hospital, the Fourth Military Medical University, Xi'an 710032, China
| | - Sufang Wang
- School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Xin Hu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710129, China
| | - Junbiao Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Guanghou Zhao
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710129, China
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37
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Loss of m 1acp 3Ψ Ribosomal RNA Modification Is a Major Feature of Cancer. Cell Rep 2021; 31:107611. [PMID: 32375039 DOI: 10.1016/j.celrep.2020.107611] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 02/03/2020] [Accepted: 04/14/2020] [Indexed: 12/22/2022] Open
Abstract
The ribosome is an RNA-protein complex that is essential for translation in all domains of life. The structural and catalytic core of the ribosome is its ribosomal RNA (rRNA). While mutations in ribosomal protein (RP) genes are known drivers of oncogenesis, oncogenic rRNA variants have remained elusive. We identify a cancer-specific single-nucleotide variation in 18S rRNA at nucleotide 1248.U in up to 45.9% of patients with colorectal carcinoma (CRC) and present across >22 cancer types. This is the site of a unique hyper-modified base, 1-methyl-3-α-amino-α-carboxyl-propyl pseudouridine (m1acp3Ψ), a >1-billion-years-conserved RNA modification at the peptidyl decoding site of the ribosome. A subset of CRC tumors we call hypo-m1acp3Ψ shows sub-stoichiometric m1acp3Ψ modification, unlike normal control tissues. An m1acp3Ψ knockout model and hypo-m1acp3Ψ patient tumors share a translational signature characterized by highly abundant ribosomal proteins. Thus, m1acp3Ψ-deficient rRNA forms an uncharacterized class of "onco-ribosome" which may serve as a chemotherapeutic target for treating cancer patients.
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38
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Bhaskar V, Desogus J, Graff-Meyer A, Schenk AD, Cavadini S, Chao JA. Dynamic association of human Ebp1 with the ribosome. RNA (NEW YORK, N.Y.) 2021; 27:411-419. [PMID: 33479117 PMCID: PMC7962488 DOI: 10.1261/rna.077602.120] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 01/02/2021] [Indexed: 05/09/2023]
Abstract
Ribosomes are the macromolecular machines at the heart of protein synthesis; however, their function can be modulated by a variety of additional protein factors that directly interact with them. Here, we report the cryo-EM structure of human Ebp1 (p48 isoform) bound to the human 80S ribosome at 3.3 Å resolution. Ebp1 binds in the vicinity of the peptide exit tunnel on the 80S ribosome, and this binding is enhanced upon puromycin-mediated translational inhibition. The association of Ebp1 with the 80S ribosome centers around its interaction with ribosomal proteins eL19 and uL23 and the 28S rRNA. Further analysis of the Ebp1-ribosome complex suggests that Ebp1 can rotate around its insert domain, which may enable it to assume a wide range of conformations while maintaining its interaction with the ribosome. Structurally, Ebp1 shares homology with the methionine aminopeptidase 2 family of enzymes; therefore, this inherent flexibility may also be conserved.
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Affiliation(s)
- Varun Bhaskar
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Jessica Desogus
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
- University of Basel, CH-4003 Basel, Switzerland
| | | | - Andreas D Schenk
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Simone Cavadini
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Jeffrey A Chao
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
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39
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Leppek K, Byeon GW, Fujii K, Barna M. VELCRO-IP RNA-seq reveals ribosome expansion segment function in translation genome-wide. Cell Rep 2021; 34:108629. [PMID: 33472078 PMCID: PMC8270675 DOI: 10.1016/j.celrep.2020.108629] [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: 09/25/2020] [Revised: 11/07/2020] [Accepted: 12/17/2020] [Indexed: 01/22/2023] Open
Abstract
Roles for ribosomal RNA (rRNA) in gene regulation remain largely unexplored. With hundreds of rDNA units positioned across multiple loci, it is not possible to genetically modify rRNA in mammalian cells, hindering understanding of ribosome function. It remains elusive whether expansion segments (ESs), tentacle-like rRNA extensions that vary in sequence and size across eukaryotic evolution, may have functional roles in translation control. Here, we develop variable expansion segment-ligand chimeric ribosome immunoprecipitation RNA sequencing (VELCRO-IP RNA-seq), a versatile methodology to generate species-adapted ESs and to map specific mRNA regions across the transcriptome that preferentially associate with ESs. Application of VELCRO-IP RNA-seq to a mammalian ES, ES9S, identified a large array of transcripts that are selectively recruited to ribosomes via an ES. We further characterize a set of 5′ UTRs that facilitate cap-independent translation through ES9S-mediated ribosome binding. Thus, we present a technology for studying the enigmatic ESs of the ribosome, revealing their function in gene-specific translation. Leppek et al. develop a pulldown technology employing chimeric yeast ribosomes, VELCRO-IP RNA-seq, to map interactions between ribosomal RNA (rRNA) and mRNAs genome-wide with positional precision. They find that expansion segments (ESs), the extended rRNA tentacles of the ribosome, specifically bind 5′ UTR elements to enable cap-independent translation of select mRNAs.
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Affiliation(s)
- Kathrin Leppek
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Gun Woo Byeon
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Kotaro Fujii
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Maria Barna
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA.
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40
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Metge BJ, Kammerud SC, Pruitt HC, Shevde LA, Samant RS. Hypoxia re-programs 2'-O-Me modifications on ribosomal RNA. iScience 2020; 24:102010. [PMID: 33490918 PMCID: PMC7811136 DOI: 10.1016/j.isci.2020.102010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 12/07/2020] [Accepted: 12/24/2020] [Indexed: 02/07/2023] Open
Abstract
Hypoxia is one of the critical stressors encountered by various cells of the human body under diverse pathophysiologic conditions including cancer and has profound impacts on several metabolic and physiologic processes. Hypoxia prompts internal ribosome entry site (IRES)-mediated translation of key genes, such as VEGF, that are vital for tumor progression. Here, we describe that hypoxia remarkably upregulates RNA Polymerase I activity. We discovered that in hypoxia, rRNA shows a different methylation pattern compared to normoxia. Heterogeneity in ribosomes due to the diversity of ribosomal RNA and protein composition has been postulated to generate “specialized ribosomes” that differentially regulate translation. We find that in hypoxia, a sub-set of differentially methylated ribosomes recognizes the VEGF-C IRES, suggesting that ribosomal heterogeneity allows for altered ribosomal functions in hypoxia. Chronic hypoxia stimulates RNA Pol I activity In hypoxia, a pool of specialized rRNA translates VEGFC IRES Hypoxia changes 2′-O-Me modification - epitranscriptomic marks on rRNA
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Affiliation(s)
- Brandon J Metge
- Department of Pathology, University of Alabama at Birmingham, WTI 320E 1824 6 Avenue South, Birmingham, AL 35233, USA
| | - Sarah C Kammerud
- Department of Pathology, University of Alabama at Birmingham, WTI 320E 1824 6 Avenue South, Birmingham, AL 35233, USA
| | - Hawley C Pruitt
- Department of Pathology, University of Alabama at Birmingham, WTI 320E 1824 6 Avenue South, Birmingham, AL 35233, USA
| | - Lalita A Shevde
- Department of Pathology, University of Alabama at Birmingham, WTI 320E 1824 6 Avenue South, Birmingham, AL 35233, USA.,O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Rajeev S Samant
- Department of Pathology, University of Alabama at Birmingham, WTI 320E 1824 6 Avenue South, Birmingham, AL 35233, USA.,Birmingham VA Medical Center, Birmingham, AL, USA
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41
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Leppek K, Fujii K, Quade N, Susanto TT, Boehringer D, Lenarčič T, Xue S, Genuth NR, Ban N, Barna M. Gene- and Species-Specific Hox mRNA Translation by Ribosome Expansion Segments. Mol Cell 2020; 80:980-995.e13. [PMID: 33202249 PMCID: PMC7769145 DOI: 10.1016/j.molcel.2020.10.023] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 12/24/2022]
Abstract
Ribosomes have been suggested to directly control gene regulation, but regulatory roles for ribosomal RNA (rRNA) remain largely unexplored. Expansion segments (ESs) consist of multitudes of tentacle-like rRNA structures extending from the core ribosome in eukaryotes. ESs are remarkably variable in sequence and size across eukaryotic evolution with largely unknown functions. In characterizing ribosome binding to a regulatory element within a Homeobox (Hox) 5' UTR, we identify a modular stem-loop within this element that binds to a single ES, ES9S. Engineering chimeric, "humanized" yeast ribosomes for ES9S reveals that an evolutionary change in the sequence of ES9S endows species-specific binding of Hoxa9 mRNA to the ribosome. Genome editing to site-specifically disrupt the Hoxa9-ES9S interaction demonstrates the functional importance for such selective mRNA-rRNA binding in translation control. Together, these studies unravel unexpected gene regulation directly mediated by rRNA and how ribosome evolution drives translation of critical developmental regulators.
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Affiliation(s)
- Kathrin Leppek
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Kotaro Fujii
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Nick Quade
- Department of Biology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, ETH Zürich, Zürich 8093, Switzerland
| | - Teodorus Theo Susanto
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Daniel Boehringer
- Department of Biology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, ETH Zürich, Zürich 8093, Switzerland
| | - Tea Lenarčič
- Department of Biology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, ETH Zürich, Zürich 8093, Switzerland
| | - Shifeng Xue
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Naomi R Genuth
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, ETH Zürich, Zürich 8093, Switzerland.
| | - Maria Barna
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA.
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42
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Matzov D, Taoka M, Nobe Y, Yamauchi Y, Halfon Y, Asis N, Zimermann E, Rozenberg H, Bashan A, Bhushan S, Isobe T, Gray MW, Yonath A, Shalev-Benami M. Cryo-EM structure of the highly atypical cytoplasmic ribosome of Euglena gracilis. Nucleic Acids Res 2020; 48:11750-11761. [PMID: 33091122 PMCID: PMC7672448 DOI: 10.1093/nar/gkaa893] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/21/2020] [Accepted: 10/21/2020] [Indexed: 12/11/2022] Open
Abstract
Ribosomal RNA is the central component of the ribosome, mediating its functional and architectural properties. Here, we report the cryo-EM structure of a highly divergent cytoplasmic ribosome from the single-celled eukaryotic alga Euglena gracilis. The Euglena large ribosomal subunit is distinct in that it contains 14 discrete rRNA fragments that are assembled non-covalently into the canonical ribosome structure. The rRNA is substantially enriched in post-transcriptional modifications that are spread far beyond the catalytic RNA core, contributing to the stabilization of this highly fragmented ribosome species. A unique cluster of five adenosine base methylations is found in an expansion segment adjacent to the protein exit tunnel, such that it is positioned for interaction with the nascent peptide. As well as featuring distinctive rRNA expansion segments, the Euglena ribosome contains four novel ribosomal proteins, localized to the ribosome surface, three of which do not have orthologs in other eukaryotes.
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Affiliation(s)
- Donna Matzov
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Masato Taoka
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Yuko Nobe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Yoshio Yamauchi
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Yehuda Halfon
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Nofar Asis
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ella Zimermann
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Haim Rozenberg
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Anat Bashan
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shashi Bhushan
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Toshiaki Isobe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Michael W Gray
- Department of Biochemistry and Molecular Biology and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada B3H 1X5
| | - Ada Yonath
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Moran Shalev-Benami
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
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43
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Ehrenbolger K, Jespersen N, Sharma H, Sokolova YY, Tokarev YS, Vossbrinck CR, Barandun J. Differences in structure and hibernation mechanism highlight diversification of the microsporidian ribosome. PLoS Biol 2020; 18:e3000958. [PMID: 33125369 PMCID: PMC7644102 DOI: 10.1371/journal.pbio.3000958] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 11/05/2020] [Accepted: 10/22/2020] [Indexed: 12/17/2022] Open
Abstract
Assembling and powering ribosomes are energy-intensive processes requiring fine-tuned cellular control mechanisms. In organisms operating under strict nutrient limitations, such as pathogenic microsporidia, conservation of energy via ribosomal hibernation and recycling is critical. The mechanisms by which hibernation is achieved in microsporidia, however, remain poorly understood. Here, we present the cryo–electron microscopy structure of the ribosome from Paranosema locustae spores, bound by the conserved eukaryotic hibernation and recycling factor Lso2. The microsporidian Lso2 homolog adopts a V-shaped conformation to bridge the mRNA decoding site and the large subunit tRNA binding sites, providing a reversible ribosome inactivation mechanism. Although microsporidian ribosomes are highly compacted, the P. locustae ribosome retains several rRNA segments absent in other microsporidia, and represents an intermediate state of rRNA reduction. In one case, the near complete reduction of an expansion segment has resulted in a single bound nucleotide, which may act as an architectural co-factor to stabilize a protein–protein interface. The presented structure highlights the reductive evolution in these emerging pathogens and sheds light on a conserved mechanism for eukaryotic ribosome hibernation. Tiny pathogenic eukaryotes called microsporidia have evolved highly compact ribosomes, smaller than bacterial ribosomes, and employ diverse hibernation factors to facilitate ribosome inactivation and recovery from the latent spore stage, including the conserved eukaryotic hibernation and recycling factor Lso2.
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Affiliation(s)
- Kai Ehrenbolger
- Department of Molecular Biology, Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Science for Life Laboratory, Umeå University, Umeå, Sweden
| | - Nathan Jespersen
- Department of Molecular Biology, Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Science for Life Laboratory, Umeå University, Umeå, Sweden
| | - Himanshu Sharma
- Department of Molecular Biology, Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Science for Life Laboratory, Umeå University, Umeå, Sweden
| | - Yuliya Y. Sokolova
- Department of Microbiology, Immunology, and Tropical Medicine, School of Medicine and Health Sciences, George Washington University, Washington, District of Columbia, United States of America
- Institute of Cytology, St. Petersburg, Russia
| | - Yuri S. Tokarev
- All-Russian Institute of Plant Protection, St. Petersburg, Russia
| | - Charles R. Vossbrinck
- Department of Environmental Science, Connecticut Agricultural Experiment Station, New Haven, Connecticut, United States of America
| | - Jonas Barandun
- Department of Molecular Biology, Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Science for Life Laboratory, Umeå University, Umeå, Sweden
- * E-mail:
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44
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Lauria F, Bernabò P, Tebaldi T, Groen EJN, Perenthaler E, Maniscalco F, Rossi A, Donzel D, Clamer M, Marchioretto M, Omersa N, Orri J, Dalla Serra M, Anderluh G, Quattrone A, Inga A, Gillingwater TH, Viero G. SMN-primed ribosomes modulate the translation of transcripts related to spinal muscular atrophy. Nat Cell Biol 2020; 22:1239-1251. [PMID: 32958857 PMCID: PMC7610479 DOI: 10.1038/s41556-020-00577-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 08/13/2020] [Indexed: 12/20/2022]
Abstract
The contribution of ribosome heterogeneity and ribosome-associated proteins to the molecular control of proteomes in health and disease remains unclear. Here, we demonstrate that survival motor neuron (SMN) protein-the loss of which causes the neuromuscular disease spinal muscular atrophy (SMA)-binds to ribosomes and that this interaction is tissue-dependent. SMN-primed ribosomes are preferentially positioned within the first five codons of a set of mRNAs that are enriched for translational enhancer sequences in the 5' untranslated region (UTR) and rare codons at the beginning of their coding sequence. These SMN-specific mRNAs are associated with neurogenesis, lipid metabolism, ubiquitination, chromatin regulation and translation. Loss of SMN induces ribosome depletion, especially at the beginning of the coding sequence of SMN-specific mRNAs, leading to impairment of proteins that are involved in motor neuron function and stability, including acetylcholinesterase. Thus, SMN plays a crucial role in the regulation of ribosome fluxes along mRNAs encoding proteins that are relevant to SMA pathogenesis.
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Affiliation(s)
- Fabio Lauria
- Institute of Biophysics, CNR Unit at Trento, Trento, Italy
| | - Paola Bernabò
- Institute of Biophysics, CNR Unit at Trento, Trento, Italy
| | - Toma Tebaldi
- Department CIBIO, University of Trento, Trento, Italy
- Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Ewout Joan Nicolaas Groen
- Edinburgh Medical School, Biomedical Sciences & Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh, UK
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, Utrecht, the Netherlands
| | - Elena Perenthaler
- Institute of Biophysics, CNR Unit at Trento, Trento, Italy
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Federica Maniscalco
- Institute of Biophysics, CNR Unit at Trento, Trento, Italy
- Department CIBIO, University of Trento, Trento, Italy
| | | | - Deborah Donzel
- Institute of Biophysics, CNR Unit at Trento, Trento, Italy
| | | | | | - Neža Omersa
- National Institute of Chemistry, Ljubljana, Slovenia
| | - Julia Orri
- Institute of Biophysics, CNR Unit at Trento, Trento, Italy
- La Fundació Jesuïtes Educació, Barcelona, Spain
| | | | | | | | - Alberto Inga
- Department CIBIO, University of Trento, Trento, Italy
| | - Thomas Henry Gillingwater
- Edinburgh Medical School, Biomedical Sciences & Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh, UK
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45
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Ghosh A, Shcherbik N. Cooperativity between the Ribosome-Associated Chaperone Ssb/RAC and the Ubiquitin Ligase Ltn1 in Ubiquitination of Nascent Polypeptides. Int J Mol Sci 2020; 21:ijms21186815. [PMID: 32957466 PMCID: PMC7554835 DOI: 10.3390/ijms21186815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 09/12/2020] [Accepted: 09/14/2020] [Indexed: 11/25/2022] Open
Abstract
Eukaryotic cells have evolved multiple mechanisms to detect and eliminate aberrant polypeptides. Co-translational protein surveillance systems play an important role in these mechanisms. These systems include ribosome-associated protein quality control (RQC) that detects aberrant nascent chains stalled on ribosomes and promotes their ubiquitination and degradation by the proteasome, and ribosome-associated chaperone Ssb/RAC, which ensures correct nascent chain folding. Despite the known function of RQC and Ssb/ribosome-associated complex (RAC) in monitoring the quality of newly generated polypeptides, whether they cooperate during initial stages of protein synthesis remains unexplored. Here, we provide evidence that Ssb/RAC and the ubiquitin ligase Ltn1, the major component of RQC, display genetic and functional cooperativity. Overexpression of Ltn1 rescues growth suppression of the yeast strain-bearing deletions of SSB genes during proteotoxic stress. Moreover, Ssb/RAC promotes Ltn1-dependent ubiquitination of nascent chains associated with 80S ribosomal particles but not with translating ribosomes. Consistent with this finding, quantitative western blot analysis revealed lower levels of Ltn1 associated with 80S ribosomes and with free 60S ribosomal subunits in the absence of Ssb/RAC. We propose a mechanism in which Ssb/RAC facilitates recruitment of Ltn1 to ribosomes, likely by detecting aberrations in nascent chains and leading to their ubiquitination and degradation.
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46
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Luo EC, Nathanson JL, Tan FE, Schwartz JL, Schmok JC, Shankar A, Markmiller S, Yee BA, Sathe S, Pratt GA, Scaletta DB, Ha Y, Hill DE, Aigner S, Yeo GW. Large-scale tethered function assays identify factors that regulate mRNA stability and translation. Nat Struct Mol Biol 2020; 27:989-1000. [PMID: 32807991 DOI: 10.1038/s41594-020-0477-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 07/02/2020] [Indexed: 02/07/2023]
Abstract
The molecular functions of the majority of RNA-binding proteins (RBPs) remain unclear, highlighting a major bottleneck to a full understanding of gene expression regulation. Here, we develop a plasmid resource of 690 human RBPs that we subject to luciferase-based 3'-untranslated-region tethered function assays to pinpoint RBPs that regulate RNA stability or translation. Enhanced UV-cross-linking and immunoprecipitation of these RBPs identifies thousands of endogenous mRNA targets that respond to changes in RBP level, recapitulating effects observed in tethered function assays. Among these RBPs, the ubiquitin-associated protein 2-like (UBAP2L) protein interacts with RNA via its RGG domain and cross-links to mRNA and rRNA. Fusion of UBAP2L to RNA-targeting CRISPR-Cas9 demonstrates programmable translational enhancement. Polysome profiling indicates that UBAP2L promotes translation of target mRNAs, particularly global regulators of translation. Our tethering survey allows rapid assignment of the molecular activity of proteins, such as UBAP2L, to specific steps of mRNA metabolism.
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Affiliation(s)
- En-Ching Luo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.,Stem Cell Program, University of California, San Diego, La Jolla, CA, USA.,Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jason L Nathanson
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.,Stem Cell Program, University of California, San Diego, La Jolla, CA, USA.,Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Frederick E Tan
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.,Stem Cell Program, University of California, San Diego, La Jolla, CA, USA.,Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Joshua L Schwartz
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.,Stem Cell Program, University of California, San Diego, La Jolla, CA, USA.,Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jonathan C Schmok
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.,Stem Cell Program, University of California, San Diego, La Jolla, CA, USA.,Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Archana Shankar
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.,Stem Cell Program, University of California, San Diego, La Jolla, CA, USA.,Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Sebastian Markmiller
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.,Stem Cell Program, University of California, San Diego, La Jolla, CA, USA.,Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Brian A Yee
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.,Stem Cell Program, University of California, San Diego, La Jolla, CA, USA.,Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Shashank Sathe
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.,Stem Cell Program, University of California, San Diego, La Jolla, CA, USA.,Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Gabriel A Pratt
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.,Stem Cell Program, University of California, San Diego, La Jolla, CA, USA.,Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Duy B Scaletta
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.,Stem Cell Program, University of California, San Diego, La Jolla, CA, USA.,Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Yuanchi Ha
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.,Stem Cell Program, University of California, San Diego, La Jolla, CA, USA.,Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - David E Hill
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
| | - Stefan Aigner
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.,Stem Cell Program, University of California, San Diego, La Jolla, CA, USA.,Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA. .,Stem Cell Program, University of California, San Diego, La Jolla, CA, USA. .,Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA.
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47
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Li D, Wang J. Ribosome heterogeneity in stem cells and development. J Cell Biol 2020; 219:e202001108. [PMID: 32330234 PMCID: PMC7265316 DOI: 10.1083/jcb.202001108] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/03/2020] [Accepted: 04/06/2020] [Indexed: 02/08/2023] Open
Abstract
Translation control is critical to regulate protein expression. By directly adjusting protein levels, cells can quickly respond to dynamic transitions during stem cell differentiation and embryonic development. Ribosomes are multisubunit cellular assemblies that mediate translation. Previously seen as invariant machines with the same composition of components in all conditions, recent studies indicate that ribosomes are heterogeneous and that different ribosome types can preferentially translate specific subsets of mRNAs. Such heterogeneity and specialized translation functions are very important in stem cells and development, as they allow cells to quickly respond to stimuli through direct changes of protein abundance. In this review, we discuss ribosome heterogeneity that arises from multiple features of rRNAs, including rRNA variants and rRNA modifications, and ribosomal proteins, including their stoichiometry, compositions, paralogues, and posttranslational modifications. We also discuss alterations of ribosome-associated proteins (RAPs), with a particular focus on their consequent specialized translational control in stem cells and development.
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Affiliation(s)
- Dan Li
- Department of Cell, Developmental and Regenerative Biology, The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jianlong Wang
- Department of Cell, Developmental and Regenerative Biology, The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY
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48
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Shankar V, Rauscher R, Reuther J, Gharib WH, Koch M, Polacek N. rRNA expansion segment 27Lb modulates the factor recruitment capacity of the yeast ribosome and shapes the proteome. Nucleic Acids Res 2020; 48:3244-3256. [PMID: 31960048 PMCID: PMC7102955 DOI: 10.1093/nar/gkaa003] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 12/30/2019] [Accepted: 01/03/2020] [Indexed: 12/14/2022] Open
Abstract
Fine-tuned regulation of protein biosynthesis is crucial for cellular fitness and became even more vital when cellular and organismal complexity increased during the course of evolution. In order to cope with this augmented demand for translation control, eukaryal ribosomes have gained extensions both at the ribosomal protein and rRNA levels. Here we analyze the functional role of ES27L, an rRNA expansion segment in the large ribosomal subunit of Saccharomyces cerevisiae. Deletion of the b-arm of this expansion segment, called ES27Lb, did not hamper growth during optimal conditions, thus demonstrating that this 25S rRNA segment is not inherently crucial for ribosome functioning. However, reductive stress results in retarded growth and rendered unique protein sets prone to aggregation. Lack of ES27Lb negatively affects ribosome-association of known co-translational N-terminal processing enzymes which in turn contributes to the observed protein aggregation. Likely as a compensatory response to these challenges, the truncated ribosomes showed re-adjusted translation of specific sets of mRNAs and thus fine-tune the translatome in order to re-establish proteostasis. Our study gives comprehensive insight into how a highly conserved eukaryal rRNA expansion segment defines ribosomal integrity, co-translational protein maturation events and consequently cellular fitness.
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Affiliation(s)
- Vaishnavi Shankar
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Robert Rauscher
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Julia Reuther
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Walid H Gharib
- Interfaculty Bioinformatics Unit, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
| | - Miriam Koch
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Norbert Polacek
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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49
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Ghosh A, Williams LD, Pestov DG, Shcherbik N. Proteotoxic stress promotes entrapment of ribosomes and misfolded proteins in a shared cytosolic compartment. Nucleic Acids Res 2020; 48:3888-3905. [PMID: 32030400 PMCID: PMC7144922 DOI: 10.1093/nar/gkaa068] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 01/03/2020] [Accepted: 01/21/2020] [Indexed: 11/23/2022] Open
Abstract
Cells continuously monitor protein synthesis to prevent accumulation of aberrant polypeptides. Insufficient capacity of cellular degradative systems, chaperone shortage or high levels of mistranslation by ribosomes can result in proteotoxic stress and endanger proteostasis. One of the least explored reasons for mistranslation is the incorrect functioning of the ribosome itself. To understand how cells deal with ribosome malfunction, we introduced mutations in the Expansion Segment 7 (ES7L) of 25S rRNA that allowed the formation of mature, translationally active ribosomes but induced proteotoxic stress and compromised cell viability. The ES7L-mutated ribosomes escaped nonfunctional rRNA Decay (NRD) and remained stable. Remarkably, ES7L-mutated ribosomes showed increased segregation into cytoplasmic foci containing soluble misfolded proteins. This ribosome entrapment pathway, termed TRAP (Translational Relocalization with Aberrant Polypeptides), was generalizable beyond the ES7L mutation, as wild-type ribosomes also showed increased relocalization into the same compartments in cells exposed to proteotoxic stressors. We propose that during TRAP, assembled ribosomes associated with misfolded nascent chains move into cytoplasmic compartments enriched in factors that facilitate protein quality control. In addition, TRAP may help to keep translation at its peak efficiency by preventing malfunctioning ribosomes from active duty in translation.
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Affiliation(s)
- Arnab Ghosh
- Department for Cell Biology and Neuroscience, Rowan University, School of Osteopathic Medicine, 2 Medical Center Drive, Stratford, NJ 08084, USA
| | - Loren Dean Williams
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 315 Ferst Drive NW, Atlanta, GA 30332, USA
| | - Dimitri G Pestov
- Department for Cell Biology and Neuroscience, Rowan University, School of Osteopathic Medicine, 2 Medical Center Drive, Stratford, NJ 08084, USA
| | - Natalia Shcherbik
- Department for Cell Biology and Neuroscience, Rowan University, School of Osteopathic Medicine, 2 Medical Center Drive, Stratford, NJ 08084, USA
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50
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Ghulam MM, Catala M, Abou Elela S. Differential expression of duplicated ribosomal protein genes modifies ribosome composition in response to stress. Nucleic Acids Res 2020; 48:1954-1968. [PMID: 31863578 PMCID: PMC7038994 DOI: 10.1093/nar/gkz1183] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/25/2019] [Accepted: 12/09/2019] [Indexed: 01/08/2023] Open
Abstract
In Saccharomyces cerevisiae, most ribosomal proteins are synthesized from duplicated genes, increasing the potential for ribosome heterogeneity. However, the contribution of these duplicated genes to ribosome production and the mechanism determining their relative expression remain unclear. Here we demonstrate that in most cases, one of the two gene copies generate the bulk of the active ribosomes under normal growth conditions, while the other copy is favored only under stress. To understand the origin of these differences in paralog expression and their contribution to ribosome heterogeneity we used RNA polymerase II ChIP-Seq, RNA-seq, polyribosome association and peptide-based mass-spectrometry to compare their transcription potential, splicing, mRNA abundance, translation potential, protein abundance and incorporation into ribosomes. In normal conditions a post-transcriptional expression hierarchy of the duplicated ribosomal protein genes is the product of the efficient splicing, high stability and efficient translation of the major paralog mRNA. Exposure of the cell to stress modifies the expression ratio of the paralogs by repressing the expression of the major paralog and thus increasing the number of ribosomes carrying the minor paralog. Together the data indicate that duplicated ribosomal protein genes underlie a modular network permitting the modification of ribosome composition in response to changing growth conditions.
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Affiliation(s)
- Mustafa Malik Ghulam
- Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Mathieu Catala
- Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Sherif Abou Elela
- Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
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